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Is it ok to keep primers at 4 degrees?

Is it ok to keep primers at 4 degrees?


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I reconstitute my primers in nuclease free water ( no sterilised) this morning and I forgot them at 4 degrees, acording to the instructions, they should be storage at -20 after the reconstitution. I am wondering if it will affect to have them overnight at 4 degrees, just for one day.


There is absolutely no problem here. Primers will degrade only very slowly at 4 degrees and even at room temperature leaving them out overnight would not degrade them enough to be of practical consequence. In fact, if you're using them today it's probably better to have stored them at 4 degrees than -20 because repeated freeze/thaw cycles will also degrade primers.


In my experience this is not a problem. I keep my working stocks at 4°C until they are finished to avoid freeze-thaw cycles and better convenience and they work all the time. I also dissolve my primers in pure water, not in TE.

Long-term storage of stocks should be done at -20.


Ammo Storage Best Practices - Do's and Don'ts

If you buy ammo then you also need to be prepared to purchase the proper storage for it. While ammunition is typically built to endure most environments, there are proper precautions to take to keep your ammo in the best condition and ready to use when you need it most.

It is best to store your ammo indoors in a dry place where the temperature remains consistent all year round. You will also want to store your ammo in a safe and secure place, especially in terms of long-term storage.

Below are some of the do’s and don'ts of storing your ammunition.


Biochemistry. 5th edition.

So far, we have met many of the key players in DNA replication. Here, we ask, Where on the DNA molecule does replication begin, and how is the double helix manipulated to allow the simultaneous use of the two strands as templates? In E. coli, DNA replication starts at a unique site within the entire 4.8 × 10 6 bp genome. This origin of replication, called the oriC locus, is a 245-bp region that has several unusual features (Figure 27.25). The oriC locus contains four repeats of a sequence that together act as a binding site for an initiation protein called dnaA. In addition, the locus contains a tandem array of 13-bp sequences that are rich in A-T base pairs.

Figure 27.25

Origin of Replication in E. coli. OriC has a length of 245 bp. It contains a tandem array of three nearly identical 13-nucleotide sequences (green) and four binding sites (yellow) for the dnaA protein. The relative orientations of the four dnaA sites (more. )

The binding of the dnaA protein to the four sites initiates an intricate sequence of steps leading to the unwinding of the template DNA and the synthesis of a primer. Additional proteins join dnaA in this process. The dnaB protein is a helicase that utilizes ATP hydrolysis to unwind the duplex. The single-stranded regions are trapped by a single-stranded binding protein (SSB). The result of this process is the generation of a structure called the prepriming complex, which makes single-stranded DNA accessible for other enzymes to begin synthesis of the complementary strands.


Basic Concepts of DNA Biochemistry

The molecular structure of every protein present in living organisms is encoded by DNA. The backbone of DNA consists of sugar (deoxyribose) residues linked together by phosphodiester bonds. A phosphate moiety links the 3' carbon of one sugar to the 5' carbon of the next sugar group. Each sugar has a base attached-either a purine (adenine, A guanine, G) or a pyrimidine (thymine, T cytosine, C). Together, the base and sugar are called a nucleoside. In a DNA molecule, two strands of nucleotides wind together in an antiparallel fashion (one strand in the 5' to 3' direction and one strand 3' to 5') to form a double helix. Every adenine binds pairs via two hydrogen bonds to thymine, whereas cytosine pairs to guanine with three hydrogen bonds (Figure 1). During replication, hydrogen bonds between A-T and C-G are broken base by base, and DNA polymerase catalyzes the addition of a complementary strand to each single-stranded DNA molecule. This enzyme requires a primer (a short strand of complementary DNA) to initiate replication. DNA polymerase requires that a deoxyribonucleotide pair with the template strand to be recognized therefore, the template strand determines which base pair is added. Because each of the new DNA strands contain one of the original strands and a newly synthesized strand, DNA replication is said to be semi-conservative. Although hydrogen bonds are, individually, relatively weak, each DNA molecule contains so many base pairs that, under physiologic conditions (other than during replication), complementary DNA strands never spontaneously separate. In the laboratory, however, base pair interactions can be disrupted with strong alkali or with temperatures near 100 degrees Celsius, a process called denaturation. Annealing occurs when the temperature is decreased and DNA base pairs recombine specifically to form the original double helix. DNA molecules are packaged into compact structures by small proteins called histones. Histones contain a high proportion of positively charged amino acids, which helps in tightly packaging the negatively charged DNA double helix. Histones are unique to eukaryotes and highly abundant, with approximately 60 million molecules per cell. Histones and nuclear DNA in eukaryotes are collectively referred to as chromatin.

Figure 1. Identical double helices are formed by DNA replication. (Reprinted with permission: Watson J, Gilman M, Witkowski J, Zoller M: Recombinant DNA. New York, W. H. Freeman and Co., 1992, p. 22.)

Figure 1. Identical double helices are formed by DNA replication. (Reprinted with permission: Watson J, Gilman M, Witkowski J, Zoller M: Recombinant DNA. New York, W. H. Freeman and Co., 1992, p. 22.)

Although most DNA is found in the nucleus, mitochondria contain a separate set of double-stranded DNA. All mitochondrial DNA is maternally inherited and mutates at a rate 10 times greater than nuclear DNA. Although mitochondrial DNA represents only 4% of all DNA in human cells, high mutation rates and the maternal inheritance pattern make this DNA source important in phylogenetic studies.

RNA and Transcription

Whereas DNA encodes genetic information, RNA is the intermediate molecule required for the synthesis of proteins from DNA. RNA differs from DNA by the following: 1) ribose (instead of deoxyribose) in the sugar backbone, 2) the base uracil replaces thymine, and 3) RNA is single stranded, as opposed to double-stranded DNA. Three types of RNA are involved in protein synthesis-messenger RNA (mRNA), ribosomal RNA (rRNA) and transfer RNA (tRNA). Before proteins can be synthesized, genetic information contained in DNA must be transferred to complementary bases in mRNA, a process called transcription. Transcription occurs in the nucleus, with mRNA produced by the enzyme RNA polymerase. Theoretically, any region of the DNA double helix can be copied into two different RNA molecules-one from each DNA strand, with the RNA produced identical in nucleotide sequence to the opposite, nontemplate DNA strand. However, a promoter, a specific DNA sequence found approximately 25-200 base pairs proximal to the 5' transcription initiation site, determines which of the two strands will be replicated by orienting RNA polymerase in a specific direction. Only DNA encoding proteins necessary for a cell's structure and function at that moment undergo transcription.

Before being transported to the cytoplasm, mRNA undergoes modification. A methylated guanine is added to the 5' end, a process known as capping, which is important for efficient translation in the cytoplasm. Multiple adenine bases are attached to the 3' end to form a poly-A "tail" that is thought to aid in the transport of mRNA from the nucleus to the cytoplasm. Further modification includes splicing, where introns (areas within the coding region of the gene that do not code for protein) are excised by enzymes called spliceosomes, and the remaining exons (areas of DNA that code for protein) are joined together. The final "mature" mRNA is then ready to be transferred to the cytoplasm.

Gene Regulation

Although a wide variety of cell types (from lymphocytes to neurons) are present in multicellular organism, DNA contained in all cells remains constant, although different proteins are produced in different cells, depending on its function. Control of gene expression may be regulated at a variety of steps, including the following: 1) transcriptional control (how and when a gene is transcribed), 2) RNA processing control (how a primary RNA transcript is spliced), 3) RNA transport control (which mRNA is moved from the nucleus to the cytoplasm), 4) translational control (which RNA is translated), 5) mRNA degradation control (which RNA remains stable in the cytoplasm vs. being degraded), and 6) protein activity control (selectively activating or inactivating proteins after they are made). For most cells, the majority of regulation occurs at the transcriptional level, thereby precluding the production of unnecessary RNA intermediates or proteins. Transcriptional regulation occurs when specific DNA sequences are recognized by gene regulatory proteins. Gene regulatory proteins recognize a specific sequence of the DNA helix and modulate which of the thousands of genes in a cell will be transcribed. For example, gene regulated proteins can bind to specific DNA sequences known as enhancers, which are distant from the promoter region and which activate transcription. When an enhancer is bound by a gene regulatory protein, the DNA between the enhancer and promoter loops out and allows the enhancer to interact directly with the RNA polymerase. After DNA is transcribed into mRNA, the cell can then splice the transcript in various ways and produce different polypeptide chains from the same gene-this is known as alternative RNA splicing. These and other methods of regulation of gene expression provide the basis of cell differentiation in both structure and function.

The Genetic Code

The genetic code enables the "message" of DNA (via RNA) to be translated into a specific protein. This process takes place in the cytoplasm. Proteins contain a specific sequence of amino acids that form three-dimensional structures according to the chemical composition of the individual amino acids. The order of amino acids for a given protein is determined by the sequence of nucleotides in mRNA. Three sequential mRNA nucleotides, known as a codon, encode each amino acid. Transfer RNA (tRNA) functions as an adapter between mRNA and protein. The tRNA molecule contains a region that decodes the mRNA (called an anticodon loop, which contains base pairs complementary to the three bases read in mRNA), and another region carrying the corresponding amino acid. Therefore, each codon in mRNA ultimately corresponds to a specific amino acid in the resulting peptide/protein (Table 1). This relation is known as the genetic code and is universal for all living organisms, strongly suggesting that all cells have descended from a single line of primitive cells. Because RNA is constructed from four types of nucleotides, 64 combinations of 3 nucleotides are possible. Three of these sequences identify termination of a polypeptide chain and are called stop codons. The remaining 61 codons specify 20 amino acids, so most amino acids are represented by several different codons. The genetic code is, therefore, said to be degenerate. Degeneracy implies that either there is more than one tRNA for each amino acid or that a single tRNA molecule can base pair with more than one codon both of these situations occur. Some tRNA molecules only require accurate base pairing of the first two nucleotides and tolerate a mismatch of the third. This is known as "wobble" base pairing and conserves tRNA molecules, because only 31 different kinds of tRNA molecules (instead of 61) are required to match all 20 amino acids.

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Protein Synthesis and Modification

Protein synthesis begins with ribosomes attaching to mRNA and moving along the molecule in a 5' to 3' direction. Ribosomes are responsible for bringing mRNA codons into position, where they can be recognized by tRNA. The process of the "message" of RNA producing specific proteins is known as translation. During translation, as additional amino acids are aligned and added, the enzyme peptidyl transferase forms peptide bonds between neighboring amino acids. Translation ends when a stop codon is identified and the newly formed protein is released. Proteins frequently undergo posttranslational modification, including glycosylation (the attachment of sugar groups on sections of proteins exposed to the extracellular matrix), palmitoylation (the attachment of fatty acid moieties to help anchor proteins in the membrane), and myristylation (the addition of myristic acid to N-terminal glycine). These (and other) modifications enable the protein to function more effectively.


Contents

Although the first microsatellite was characterised in 1984 at the University of Leicester by Weller, Jeffreys and colleagues as a polymorphic GGAT repeat in the human myoglobin gene, the term "microsatellite" was introduced later, in 1989, by Litt and Luty. [1] The name "satellite" DNA refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA. [6] The increasing availability of DNA amplification by PCR at the beginning of the 1990s triggered a large number of studies using the amplification of microsatellites as genetic markers for forensic medicine, for paternity testing, and for positional cloning to find the gene underlying a trait or disease. Prominent early applications include the identifications by microsatellite genotyping of the eight-year-old skeletal remains of a British murder victim (Hagelberg et al. 1991), and of the Auschwitz concentration camp doctor Josef Mengele who escaped to South America following World War II (Jeffreys et al. 1992). [1]

A microsatellite is a tract of tandemly repeated (i.e. adjacent) DNA motifs that range in length from one to six or up to ten nucleotides (the exact definition and delineation to the longer minisatellites varies from author to author), [1] [2] and are typically repeated 5–50 times. For example, the sequence TATATATATA is a dinucleotide microsatellite, and GTCGTCGTCGTCGTC is a trinucleotide microsatellite (with A being Adenine, G Guanine, C Cytosine, and T Thymine). Repeat units of four and five nucleotides are referred to as tetra- and pentanucleotide motifs, respectively. Most eukaryotes have microsatellites, with the notable exception of some yeast species. Microsatellites are distributed throughout the genome. [7] [1] [8] The human genome for example contains 50,000–100,000 dinucleotide microsatellites, and lesser numbers of tri-, tetra- and pentanucleotide microsatellites. [9] Many are located in non-coding parts of the human genome and therefore do not produce proteins, but they can also be located in regulatory regions and coding regions.

Microsatellites in non-coding regions may not have any specific function, and therefore might not be selected against this allows them to accumulate mutations unhindered over the generations and gives rise to variability that can be used for DNA fingerprinting and identification purposes. Other microsatellites are located in regulatory flanking or intronic regions of genes, or directly in codons of genes – microsatellite mutations in such cases can lead to phenotypic changes and diseases, notably in triplet expansion diseases such as fragile X syndrome and Huntington's disease. [10]

The telomeres at the ends of the chromosomes, thought to be involved in ageing/senescence, consist of repetitive DNA, with the hexanucleotide repeat motif TTAGGG in vertebrates. They are thus classified as minisatellites. Similarly, insects have shorter repeat motifs in their telomeres that could arguably be considered microsatellites.

Unlike point mutations, which affect only a single nucleotide, microsatellite mutations lead to the gain or loss of an entire repeat unit, and sometimes two or more repeats simultaneously. Thus, the mutation rate at microsatellite loci is expected to differ from other mutation rates, such as base substitution rates. The actual cause of mutations in microsatellites is debated.

One proposed cause of such length changes is replication slippage, caused by mismatches between DNA strands while being replicated during meiosis. [11] DNA polymerase, the enzyme responsible for reading DNA during replication, can slip while moving along the template strand and continue at the wrong nucleotide. DNA polymerase slippage is more likely to occur when a repetitive sequence (such as CGCGCG) is replicated. Because microsatellites consist of such repetitive sequences, DNA polymerase may make errors at a higher rate in these sequence regions. Several studies have found evidence that slippage is the cause of microsatellite mutations. [12] [13] Typically, slippage in each microsatellite occurs about once per 1,000 generations. [14] Thus, slippage changes in repetitive DNA are three orders of magnitude more common than point mutations in other parts of the genome. [15] Most slippage results in a change of just one repeat unit, and slippage rates vary for different allele lengths and repeat unit sizes, [3] and within different species. [16] If there is a large size difference between individual alleles, then there may be increased instability during recombination at meiosis. [15]

Another possible cause of microsatellite mutations are point mutations, where only one nucleotide is incorrectly copied during replication. A study comparing human and primate genomes found that most changes in repeat number in short microsatellites appear due to point mutations rather than slippage. [17]

Microsatellite mutation rates Edit

Microsatellite mutation rates vary with base position relative to the microsatellite, repeat type, and base identity. [17] Mutation rate rises specifically with repeat number, peaking around six to eight repeats and then decreasing again. [17] Increased heterozygosity in a population will also increase microsatellite mutation rates, [18] especially when there is a large length difference between alleles. This is likely due to homologous chromosomes with arms of unequal lengths causing instability during meiosis. [19]

Direct estimates of microsatellite mutation rates have been made in numerous organisms, from insects to humans. In the desert locust Schistocerca gregaria, the microsatellite mutation rate was estimated at 2.1 x 10 −4 per generation per locus. [20] The microsatellite mutation rate in human male germ lines is five to six times higher than in female germ lines and ranges from 0 to 7 x 10 −3 per locus per gamete per generation. [3] In the nematode Pristionchus pacificus, the estimated microsatellite mutation rate ranges from 8.9 × 10 −5 to 7.5 × 10 −4 per locus per generation. [21]

Many microsatellites are located in non-coding DNA and are biologically silent. Others are located in regulatory or even coding DNA – microsatellite mutations in such cases can lead to phenotypic changes and diseases. A genome-wide study estimates that microsatellite variation contributes 10–15% of heritable gene expression variation in humans. [22]

Effects on proteins Edit

In mammals, 20% to 40% of proteins contain repeating sequences of amino acids encoded by short sequence repeats. [23] Most of the short sequence repeats within protein-coding portions of the genome have a repeating unit of three nucleotides, since that length will not cause frame-shifts when mutating. [24] Each trinucleotide repeating sequence is transcribed into a repeating series of the same amino acid. In yeasts, the most common repeated amino acids are glutamine, glutamic acid, asparagine, aspartic acid and serine.

Mutations in these repeating segments can affect the physical and chemical properties of proteins, with the potential for producing gradual and predictable changes in protein action. [25] For example, length changes in tandemly repeating regions in the Runx2 gene lead to differences in facial length in domesticated dogs (Canis familiaris), with an association between longer sequence lengths and longer faces. [26] This association also applies to a wider range of Carnivora species. [27] Length changes in polyalanine tracts within the HoxA13 gene are linked to Hand-Foot-Genital Syndrome, a developmental disorder in humans. [28] Length changes in other triplet repeats are linked to more than 40 neurological diseases in humans, notably triplet expansion diseases such as fragile X syndrome and Huntington's disease. [10] Evolutionary changes from replication slippage also occur in simpler organisms. For example, microsatellite length changes are common within surface membrane proteins in yeast, providing rapid evolution in cell properties. [29] Specifically, length changes in the FLO1 gene control the level of adhesion to substrates. [30] Short sequence repeats also provide rapid evolutionary change to surface proteins in pathenogenic bacteria this may allow them to keep up with immunological changes in their hosts. [31] Length changes in short sequence repeats in a fungus (Neurospora crassa) control the duration of its circadian clock cycles. [32]

Effects on gene regulation Edit

Length changes of microsatellites within promoters and other cis-regulatory regions can change gene expression quickly, between generations. The human genome contains many (>16,000) short sequence repeats in regulatory regions, which provide ‘tuning knobs’ on the expression of many genes. [22] [33]

Length changes in bacterial SSRs can affect fimbriae formation in Haemophilus influenzae, by altering promoter spacing. [31] Dinucleotide microsatellites are linked to abundant variation in cis-regulatory control regions in the human genome. [33] Microsatellites in control regions of the Vasopressin 1a receptor gene in voles influence their social behavior, and level of monogamy. [34]

In Ewing's sarcoma (a type of painful bone cancer in young humans), a point mutation has created an extended GGAA microsatellite which binds a transcription factor, which in turn activates the EGR2 gene which drives the cancer. [35] In addition, other GGAA microsatellites may influence the expression of genes that contribute to the clinical outcome of Ewing sarcoma patients. [36]

Effects within introns Edit

Microsatellites within introns also influence phenotype, through means that are not currently understood. For example, a GAA triplet expansion in the first intron of the X25 gene appears to interfere with transcription, and causes Friedreich Ataxia. [37] Tandem repeats in the first intron of the Asparagine synthetase gene are linked to acute lymphoblastic leukaemia. [38] A repeat polymorphism in the fourth intron of the NOS3 gene is linked to hypertension in a Tunisian population. [39] Reduced repeat lengths in the EGFR gene are linked with osteosarcomas. [40]

An archaic form of splicing preserved in Zebrafish is known to use microsatellite sequences within intronic mRNA for the removal of introns in the absence of U2AF2 and other splicing machinery. It is theorized that these sequences form highly stable cloverleaf configurations that bring the 3' and 5' intron splice sites into close proximity, effectively replacing the spliceosome. This method of RNA splicing is believed to have diverged from human evolution at the formation of tetrapods and to represent an artifact of an RNA world. [41]

Effects within transposons Edit

Almost 50% of the human genome is contained in various types of transposable elements (also called transposons, or ‘jumping genes’), and many of them contain repetitive DNA. [42] It is probable that short sequence repeats in those locations are also involved in the regulation of gene expression. [43]

Microsatellites are used for assessing chromosomal DNA deletions in cancer diagnosis. Microsatellites are widely used for DNA profiling, also known as "genetic fingerprinting", of crime stains (in forensics) and of tissues (in transplant patients). They are also widely used in kinship analysis (most commonly in paternity testing). Also, microsatellites are used for mapping locations within the genome, specifically in genetic linkage analysis to locate a gene or a mutation responsible for a given trait or disease. As a special case of mapping, they can be used for studies of gene duplication or deletion. Researchers use microsatellites in population genetics and in species conservation projects. Plant geneticists have proposed the use of microsatellites for marker assisted selection of desirable traits in plant breeding.

Cancer diagnosis Edit

In tumour cells, whose controls on replication are damaged, microsatellites may be gained or lost at an especially high frequency during each round of mitosis. Hence a tumour cell line might show a different genetic fingerprint from that of the host tissue, and, especially in colorectal cancer, might present with loss of heterozygosity. Microsatellites have therefore been routinely used in cancer diagnosis to assess tumour progression. [44] [45] [46]

Forensic and medical fingerprinting Edit

Microsatellite analysis became popular in the field of forensics in the 1990s. [47] It is used for the genetic fingerprinting of individuals where it permits forensic identification (typically matching a crime stain to a victim or perpetrator). It is also used to follow up bone marrow transplant patients. [48]

The microsatellites in use today for forensic analysis are all tetra- or penta-nucleotide repeats, as these give a high degree of error-free data while being short enough to survive degradation in non-ideal conditions. Even shorter repeat sequences would tend to suffer from artifacts such as PCR stutter and preferential amplification, while longer repeat sequences would suffer more highly from environmental degradation and would amplify less well by PCR. [49] Another forensic consideration is that the person's medical privacy must be respected, so that forensic STRs are chosen which are non-coding, do not influence gene regulation, and are not usually trinucleotide STRs which could be involved in triplet expansion diseases such as Huntington's disease. Forensic STR profiles are stored in DNA databanks such as the UK National DNA Database (NDNAD), the American CODIS or the Australian NCIDD.

Kinship analysis (paternity testing) Edit

Autosomal microsatellites are widely used for DNA profiling in kinship analysis (most commonly in paternity testing). [50] Paternally inherited Y-STRs (microsatellites on the Y chromosome) are often used in genealogical DNA testing.

Genetic linkage analysis Edit

During the 1990s and the first several years of this millennium, microsatellites were the workhorse genetic markers for genome-wide scans to locate any gene responsible for a given phenotype or disease, using segregation observations across generations of a sampled pedigree. Although the rise of higher throughput and cost-effective single-nucleotide polymorphism (SNP) platforms led to the era of the SNP for genome scans, microsatellites remain highly informative measures of genomic variation for linkage and association studies. Their continued advantage lies in their greater allelic diversity than biallelic SNPs, thus microsatellites can differentiate alleles within a SNP-defined linkage disequilibrium block of interest. Thus, microsatellites have successfully led to discoveries of type 2 diabetes (TCF7L2) and prostate cancer genes (the 8q21 region). [2] [51]

Population genetics Edit

Microsatellites were popularized in population genetics during the 1990s because as PCR became ubiquitous in laboratories researchers were able to design primers and amplify sets of microsatellites at low cost. Their uses are wide-ranging. [53] A microsatellite with a neutral evolutionary history makes it applicable for measuring or inferring bottlenecks, [54] local adaptation, [55] the allelic fixation index (FST), [56] population size, [57] and gene flow. [58] As next generation sequencing becomes more affordable the use of microsatellites has decreased, however they remain a crucial tool in the field. [59]

Plant breeding Edit

Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker (morphological, biochemical or DNA/RNA variation) linked to a trait of interest (e.g. productivity, disease resistance, stress tolerance, and quality), rather than on the trait itself. Microsatellites have been proposed to be used as such markers to assist plant breeding. [60]

Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with homopolymeric tracts. Therefore, microsatellites are normally analysed by conventional PCR amplification and amplicon size determination, sometimes followed by Sanger DNA sequencing.

In forensics, the analysis is performed by extracting nuclear DNA from the cells of a sample of interest, then amplifying specific polymorphic regions of the extracted DNA by means of the polymerase chain reaction. Once these sequences have been amplified, they are resolved either through gel electrophoresis or capillary electrophoresis, which will allow the analyst to determine how many repeats of the microsatellites sequence in question there are. If the DNA was resolved by gel electrophoresis, the DNA can be visualized either by silver staining (low sensitivity, safe, inexpensive), or an intercalating dye such as ethidium bromide (fairly sensitive, moderate health risks, inexpensive), or as most modern forensics labs use, fluorescent dyes (highly sensitive, safe, expensive). [61] Instruments built to resolve microsatellite fragments by capillary electrophoresis also use fluorescent dyes. [61] Forensic profiles are stored in major databanks. The British data base for microsatellite loci identification was originally based on the British SGM+ system [62] [63] using 10 loci and a sex marker. The Americans [64] increased this number to 13 loci. [65] The Australian database is called the NCIDD, and since 2013 it has been using 18 core markers for DNA profiling. [47]

Amplification Edit

Microsatellites can be amplified for identification by the polymerase chain reaction (PCR) process, using the unique sequences of flanking regions as primers. DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow annealing of primers and the extension of nucleotide sequences through the microsatellite. This process results in production of enough DNA to be visible on agarose or polyacrylamide gels only small amounts of DNA are needed for amplification because in this way thermocycling creates an exponential increase in the replicated segment. [66] With the abundance of PCR technology, primers that flank microsatellite loci are simple and quick to use, but the development of correctly functioning primers is often a tedious and costly process.

Design of microsatellite primers Edit

If searching for microsatellite markers in specific regions of a genome, for example within a particular intron, primers can be designed manually. This involves searching the genomic DNA sequence for microsatellite repeats, which can be done by eye or by using automated tools such as repeat masker. Once the potentially useful microsatellites are determined, the flanking sequences can be used to design oligonucleotide primers which will amplify the specific microsatellite repeat in a PCR reaction.

Random microsatellite primers can be developed by cloning random segments of DNA from the focal species. These random segments are inserted into a plasmid or bacteriophage vector, which is in turn implanted into Escherichia coli bacteria. Colonies are then developed, and screened with fluorescently–labelled oligonucleotide sequences that will hybridize to a microsatellite repeat, if present on the DNA segment. If positive clones can be obtained from this procedure, the DNA is sequenced and PCR primers are chosen from sequences flanking such regions to determine a specific locus. This process involves significant trial and error on the part of researchers, as microsatellite repeat sequences must be predicted and primers that are randomly isolated may not display significant polymorphism. [15] [67] Microsatellite loci are widely distributed throughout the genome and can be isolated from semi-degraded DNA of older specimens, as all that is needed is a suitable substrate for amplification through PCR.

More recent techniques involve using oligonucleotide sequences consisting of repeats complementary to repeats in the microsatellite to "enrich" the DNA extracted (Microsatellite enrichment). The oligonucleotide probe hybridizes with the repeat in the microsatellite, and the probe/microsatellite complex is then pulled out of solution. The enriched DNA is then cloned as normal, but the proportion of successes will now be much higher, drastically reducing the time required to develop the regions for use. However, which probes to use can be a trial and error process in itself. [68]

ISSR-PCR Edit

ISSR (for inter-simple sequence repeat) is a general term for a genome region between microsatellite loci. The complementary sequences to two neighboring microsatellites are used as PCR primers the variable region between them gets amplified. The limited length of amplification cycles during PCR prevents excessive replication of overly long contiguous DNA sequences, so the result will be a mix of a variety of amplified DNA strands which are generally short but vary much in length.

Sequences amplified by ISSR-PCR can be used for DNA fingerprinting. Since an ISSR may be a conserved or nonconserved region, this technique is not useful for distinguishing individuals, but rather for phylogeography analyses or maybe delimiting species sequence diversity is lower than in SSR-PCR, but still higher than in actual gene sequences. In addition, microsatellite sequencing and ISSR sequencing are mutually assisting, as one produces primers for the other.

Limitations Edit

Repetitive DNA is not easily analysed by next generation DNA sequencing methods, which struggle with homopolymeric tracts. [69] Therefore, microsatellites are normally analysed by conventional PCR amplification and amplicon size determination. The use of PCR means that microsatellite length analysis is prone to PCR limitations like any other PCR-amplified DNA locus. A particular concern is the occurrence of ‘null alleles’:


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Kimchi fermentation

Fermentation of Kimchi depends on your room temperature, and the saltiness of your kimchi.

Mostly, it will take a few days to ferment your kimchi at room temperature. However if you live in a warm country, it may take only 1 day because your room temperature will be higher.

Another factor that affects your kimchi fermentation will be how salty your kimchi is. If your kimchi is made very salty, it will take longer. My grandmother used to add more salt for her winter kimchi that she had to feed all family during winter time (3-4 months).

Hi maangchi, thank you for your reply!

I do live in a warm country but I have them stored in a cool dark place in airtight containers. I made two, one is destined to be eaten raw or with rice and the other one to make Kimchi jjigae.

Hi, I just made my kimchi yesterday for the first time in my life. In Asia, we can just get it from the supermarket easily. Now I live oversea and craving it, I had to make my own. But I have a question, I made it yesterday, and left it in my kitchken then went to sleep, next morning, I found out my husband put the container in the fridge. I tasted the kimchi, it is SALTY! Like very salty compares to the ones I bought from store. Is it suppose to be like that? Or should I take it out again? What should I do? Or Should I just let it sit for a bit longer?

Plz answer my question, I hope I didn’t ruined the whole kimchi.

Your kimchi must be made very salty. Did you follow the recipe on my website tightly? Check the comments under my kimchi recipe. You will read so many good tips for making kimchi.

I live in California and I’ve been having trouble trying to find those clay pots that you can store kimchi in. do you happen to know of a website in english that sells it or where i can buy one?

Thanks for the reply. As I just found your lovely website today so didn’t have much time to read all of the comments and your replies. Actually I did not follow your recipe. I watched this video from youtube and decided to make it yesterday. Maybe I just didn’t follow the video properly.

I surfed online today to see if there is any way to save my kimchi. Then I found here :D

Anyways, I just checked the comments and found the answer I wanted. I will try to put water in my kimchi container.

I also found I made other mistake, I didn’t put sugar in it XD

hopefully my next kimchi will turn out perfect.

Chiao,
I’m copying and pasting my answer related to salty kimchi that I made for someone else.
“If you already made kimchi and it’s too salty, add more radish to the kimchi. Just cut a few radishes into disks and insert them into the salty kimchi. That’s my way to dilute”

Good luck in making your next batch of kimchi!

I normally put my kimchi jars in the basement (about 65 degrees) for 3 days, but this last time I decided to try 5 days to see what would happen. I’m so happy I did! I opened them today and they were bubbling like crazy! I think this latest batch tastes a lot better than ones I left for only 3 days, and now I’m thinking I might want to leave them sit for 10 days next time.

My recommendation is to just experiment. Try 3 days, 5 days, 7 days, whatever. From what I understand, the longer it ferments, the more sour it tastes. I like the sour flavor, but if you don’t like it that sour, then don’t let it go past 3 days. Also, don’t worry about it going bad. If it does goes bad, you WILL know it when you first smell it. If that happens, throw it away, and next time add some shrimp paste and/or fish sauce to aid the fermentation process. Good luck!!

Hi,Maangchi,can I ask you a question about kimchi,pls?

I sucessfully made raddish kimchi according to your reciept, now the raddish is almost finished, leaving a lot of kimchi juice in my container. I want to make more this weekend, can I put the salt-soaked raddish into the leftover juice instead of making fresh paste? (the juice smells too nice to pour into sink…)

give me a shout when you got a second, thanks a million!

dont throw away the juice, but dont put the raddish into the juice either, since it is already fermented and won’t probably ferment any more.

use the juice to marinade meat or make soups. or use it as a condiment for ramyon or something. its orange/yellow gold.

If the kimchi is too salty, you suggested adding discs of radish in with the kimchi. Does this radish need to be put in salted water or does it just have to be peeled and cut and placed right into the kimchi container?

does it just have to be peeled and cut and placed right into the kimchi container?

Yes, insert the radish disks right into the kimchi.

dorkielala – I know you asked two years ago, but if you are still reading you can find onngi (the clay pots) on http://english.gmarket.co.kr – they sell everything you can’t get outside of Korea and have been very reliable for me – I have bought a sinseollo pan from there, dasik molds, yukgwa molds, and a set of brass royal chopstick/spoon sets – all arrived in NZ in perfect condition and well wrapped.

Do you think adding a teaspoon or two of live yoghurt to kimchi would accelerate the fermentation?

I just made a batch of “emergency kimchi”, but I used Huy Fong Foods’ Chili-Garlic sauce instead of doing it from scratch, and I’m guessing it’s pasteurized. I don’t know if that will make a difference in the fermentation, but I’m thinking maybe I could add a spoon of yogurt to be on the safe side.

They both use varieties of Lactobacillus, albeit different ones, so maybe it would work? What do you think?

PS: Unfortunately, I can’t find any “live” sauerkraut or kimchi at the store, because they’re also pasteurized.

Absolutely do not add yoghurt!It has dairy proteins which would give very undesirable flavors. Kimchi will ferment naturally. You have to give it time. You need to plan ahead and have patience.

As for the finding “live” kimchi, you wouldn’t be able to use kimchi as a “starter” like you do with sourdough. Simply follow the directions that Maangchi has given, and the kimchi will ferment on its own.

As for the Hoy Fong Chili Garlic paste, that is a chinese product, with totally different types of peppers, flavors and ingredients. Don’t know what you will get, but I don’t think it will taste like kimchi. Kimchi was developed over hundreds of years using specific types of ingredients. Yes, there are hundreds of variations, and lots of substitutions, but I rather think this might not work.

But please do update everyone with how it turns out.

@Ashimi: Huy Fong Foods is Vietnamese, but I get your point.

Regardless, you’re right about giving it time: I just checked and it’s starting to smell like kimchi :)

Maanchi, i need help, what if I do not have radish and my kimchi is too salty, what can I use as a substitute to radish?

Hi Maangchi, my name is Kelly, my hometown in Vietnam, and I am going to make Kimchi when I get home. I will back home this summer as you know, Vietnam is a hot country specially will hotter in summer. So, do I need to put kimchi box into the refrigerator after i mixed or just left it (the kimchi box) outside (I mean cold place). Also, I have one more question, If I can’t find out the sweet rice flour (chapssal garu) in Vietnam, so what flour can I replace it (sweet rice flour)? I was think buy in here and bring it back, but I think I will have problems if I am carrying it because the police officer will think I am bringing drug :)) it hard for me to bring it back to Vietnam :(.

Hope to see your response soon. Thank you, and have a nice day

@kelly hi i am from malaysia, i think the weather of our country is almost the same! >< i put my kimchi in indoors for 3 days with the fermentation process.. after that u can straight put it into the refrigirator already.. I also cant find the sweet rice flour in the place i live so i used the substitution which is recommended by maachi, the plain flour! Yup, the flour which is used to make noodle and cake! XP

@austintexican: I know you asked this question almost a year ago, but thought I could help if you’re still wondering about using yogurt. You can strain the yogurt by lining a fine mesh strainer with cheesecloth or a few layers of paper towels, pouring in regular yogurt (not Greek yogurt, as it has already been strained), then setting the strainer over a bowl in your fridge. After several hours or overnight, the whey will strain out of the yogurt and be collected in the bottom of the bowl and the strained yogurt will remain in the lined strainer. You can put the yogurt aside to use as a healthier alternative for sour cream, in smoothies or to use as you would for Greek yogurt, and the whey that strained out can be used to speed up lactofermented veggies, like kimchi! This can be used in kimchi that you want to make with less salt, since you will only need to ferment it for 1 or 2 days. By using whey, you are adding lactobacilli directly into your fresh kimchi, so less salt is necsessary, since the salt acts to inhibit “bad” bacteria while the lactobacteria are growing over the first few days in traditional kimchi (kimchi made without a starter).

If you do use the whey starter, be sure to taste your kimchi daily to be sure it isn’t getting too sour for your liking too fast. When it reaches the right sourness for your liking, put it in the fridge. When I make kimchi the traditional way, using just veggies, salt and spices, I ferment at room temp for 5 days. When I use whey, it is 2 days, max.

As another poster said you don’t want to add the actual yogurt to your kimchi, because it will spoil and ruin your batch. But the whey is fine to add, and works wonders when you need “quick” kimchi!

If you need any more info using whey as a starter for lactofermented veggies of any kind, you can look up “Nourishing Traditions” recipes online or get the Nourish traditions cookbook by Sally Fallon. Lots of good fermented recipes, and she gives the correct amount of whey to use in your recipes (it isn’t much — maybe a tablespoon in a big batch of kimchi? I can’t remember the exact amount off the top of my head, but you can find it if you google it).

i made kimchi 3 days ago. i packed it into old glass pasta sauce jars and screwed the lid on tightly. i left 2 jars in a dark cupboard in my kitchen, and put the remaining jars in the fridge to ferment more slowly. i unscrewed the lids of the 2 jars left out only once, just to let some of the gases out (but i didn’t open the lid all the way), then screwed them back on. after 2 days, i put the 2 jars into the fridge. today (day 3), i decided to taste some to see how it is doing. well, it is very sour (more than expected after just 3 days?) and tastes kind of carbonated or “fizzy”! the cabbage is also a bit softer than i am used to with store bought kimchi. did i do something wrong? is it still safe to eat? is there a way to get rid of the fizziness (i don’t like it like that).

also, when making kimchi, after packing the kimchi into jars, i found that there wasn’t much kimchi juice (the sauce was more like a paste). i added a bit of brine (salt + water mixed in with the little remaining kimchi juice in the bowl) to cover the kimchi because ir ead that a few other places online (and also, i was worried about the kimchi being exposed to air an going bad in the jar). after a day, i noticed lots of bubbles and the brine seemed to get less liquidy? is this all normal too?

helenhelen it sounds to me like your kimchi is fermenting perfectly. When it’s fizzy that means everything is going well.

I am so glad for your #1 success, you deserve it!!

Anyway, I’m confused about whether or not to use fish sauce and/or squid as an igredient as I’m making large batches and I want it to last as long as possible……….

Is it best not to use fish/animal products if I want maximum life on my kim chee. / Do the salty fish products speed or slow fermentation time?

If so, are there other ingredients I should us to substitute for best flavor.

I made my first batch of spicy baechu kimchi. It is delicious, but it is VERY SALTY! I used a Korean sea salt to salt the cabbage, and I let it sit overnight in the refrigerator, so it was 24 hours before I rinsed it. I am thinking this is probably why. Is there a rule about how long cabbage should be salted or what kind of salt should be used?

I have the same problem as Dan but in my case it was because I bungled the instructions and put way too much salt. I’ve been trying to troubleshoot this first kimchi batch of mine ever since. I followed Maangchi’s recommendation to add more veg, but because I had no more radish I julienned a carrot and a red apple and mixed it in. It helped a bit, but then I had too little juice. I tried to push the veggies down under the liquid but I had too little liquid…

Thank goodness for this thread. I saw Maangchi’s advice not to add water which I was VERY tempted to do. Then I saw Emaline904’s experiment with whey and a light bulb went off!!

I know not many people out there make water kefir, but just in case you do, and land in the same pickle as me, pour it in! It is fermented and full of great lactobacillus so unless it has strange reactions with the salt, it should boost the fermentation process.

I just added about half a quart of water kefir a few hours ago. I shall add an update later on how my experiment turned out.

I messed around with the recipe too much this time. Not a smart thing for a first-timer to do. Will adhere to instructions strictly next time.


What is the best temperature and humidity for gun storage

Moisture inside a gun safe can make gun rusty. This is why you should keep your gun at a safe place, a non-temperature-controlled storage (like the shed or the garage) that is not subject to temperature changes between night and day. There are various dehumidifying products available on the market. This is made of silica gel, a material that absorbs moisture from the air. Whenever you choose to store the gun, be sure to keep a dehumidifying system around.


Minor

The biology minor requires 16 credits of biology courses. Students must take any two of the three biology core lectures with their associated laboratories, plus electives.

Master of Science

The Department of Biology offers both thesis and non-thesis Master of Science degree programs. Both programs require a minimum of 30 semester hours of courses at the 300 level or higher. A minimum of 18 semester hours of formal course work is required for the thesis degree, and a minimum of 27 semester hours of formal course work for the non-thesis degree. The remaining credits may be research credits ( BIOL 601 Research and BIOL 651 Thesis M.S. ). The Entrepreneurial Biotechnology (EB) is a two-year Plan A professional Master of Science degree in Biology. The EB program includes four required courses, an internship, and electives to make up the 30 semester hours. The thesis is based on a real entrepreneurial project with an existing company or your own startup (the internship).

Plan A (Thesis)

The Plan A Master of Science degree in biology is a thesis graduate degree program. The purpose of the program is to provide advanced exposure to biology for interested professionals, to provide additional training for those wishing to resume or change careers, or to provide additional preparation in biology for students interested in pursuing professional studies in the health sciences. Students are required to write and defend a Master of Science thesis.

Program of Study

All candidates must complete a total of 30 credit hours in course work at the 300 level or higher within 5 years of matriculation into the graduate program. At least 18 of these credit hours must be must be at the 400 level or above. Further, at least 15 credit hours must be in courses offered by the biology department. The remaining course work may include courses offered by any department within the University, subject to an advisor’s approval and School of Graduate Studies regulations. Candidates are limited to 3 credit hours of BIOL 601 Research , but may take up to 9 credit hours of BIOL 651 Thesis M.S. According to rules of the School of Graduate Studies, once a candidate registers for BIOL 651, the registration must continue for a minimum of 1 credit per semester until completion of the degree program. Students who are uncertain about completing requirements for a Plan A Master of Science degree should consult the regulations for the Plan B Master of Science degree. These two master's degrees have different regulations concerning use of BIOL 601. A candidate may wish to use BIOL 599 Advanced Independent Study for Graduate Students the letter grade assigned will reflect the evaluation by the entire Advisory Committee.

Plan A (Thesis) Entrepreneurial Biotechnology

The Entrepreneurial Biotechnology (EB) students study state-of-the-art biotechnology, practical business, and technology innovation while working on a real-world entrepreneurial project with an existing company or their own startup. The EB helps to connect students with mentors, advisors, partners, funding sources and job opportunities. EB prepares students to work in diverse research or technology-centered environments. The Entrepreneurial Biotechnology Program (EB) requires students to write a thesis in order to graduate with a Master of Science in Biology, Entrepreneurship Track. The thesis must be based on a project of significant time investment on the part of the student and must be grounded in the real world (i.e., not simply an academic exercise). Thus, each student is required to work as an intern, employee, or entrepreneur, typically with a start-up, existing company, early-stage investment firm, or affiliate of a research organization. The duration must be at least one year, with one semester reserved for full-time work outside of the classroom (usually the fourth and final semester). Under this requirement, international students will be permitted no more than one semester of full-time curricular practical training (CPT).

Plan B (Non-thesis)

The Plan B Master of Science degree in biology is a non-thesis graduate degree program. The purpose of the program is to provide advanced exposure to biology for interested professionals, to provide additional training for those wishing to resume or change careers, or to provide additional preparation in biology for students interested in pursuing professional studies in the health sciences. Students are not required to write a Master of Science thesis, but the program does require passing a comprehensive oral examination.

Program of Study

All candidates must complete a total of 30 credit hours in course work at the 300 level or higher. At least 18 of these credit hours must be at the 400 levels or above. Further, at least 15 credit hours must be in courses offered by the Biology Department. At least one course must be taken in each of the following areas of biology: cell and molecular biology (including chemical biology), organismal biology, and population biology. The remaining course work may include courses offered by any department within the University, subject to the advisor’s approval and School of Graduate Studies regulations. Candidates are limited to a total of 6 credit hours of independent study (up to 3 credits of BIOL 599 Advanced Independent Study for Graduate Students and up to 3 credits of BIOL 601 Research ). BIOL 599 requires completion of a Course Proposal Form (available in the Biology Departmental Office) and approval by the advisor. In the case of enrollment in BIOL 599, the letter grade assigned will reflect the evaluation by a two-person committee recruited by the student and advisor.

Doctor of Philosophy

The degree of Doctor of Philosophy is awarded in recognition of in-depth knowledge in a major field and comprehensive understanding of related subjects together with a demonstration of ability to perform independent investigation and to communicate the results of such investigation in an acceptable dissertation.

Students entering with a bachelor’s degree will satisfactorily complete a minimum of 36 credit hours (which may include independent study/research taken as BIOL 601 Research ), tutorials, and seminars. For students entering with an approved master’s degree, completion of at least 18 semester hours of course work is required. A minimum of 18 semester hours of dissertation research ( BIOL 701 Dissertation Ph.D. ) is required for all doctoral students.

Teaching experience is an integral part of the graduate training. Students are involved in supervised laboratory teaching in selected undergraduate courses taking into account both the specialized areas of interest of the student and his or her broader professional development. The normal teaching requirement consists of four semesters.

Courses

BIOL𧅰. Biology's Survival Guide to College: How stress impacts a student's ability to thrive. 3 Units.

Stress can test the limit of an individual's ability to maintain balance, thrive and survive. This non-majors biology course explores how cells, organs and organ systems work together to maintain homeostasis. Equipped with knowledge of how the body functions, students will explore how common stressors experienced by college students (sleep deprivation, lack of relaxation, poor diet, and others) can test the limits of maintaining homeostasis. Understanding the body's stress response and how stress impacts well-being will enable students to make informed decisions about how to promote balance in their own life.

BIOL𧅲. Principles of Biology. 3 Units.

A one-semester course in biology designed for the non-major. A primary objective of this course is to demonstrate how biological principles impact an individual's daily life. BIOL𧅲 introduces students to the molecules of life, cell structure and function, respiration and photosynthesis, molecular genetics, heredity and human genetics, evolution, diversity of life, and ecology. Minimal background is required however, some exposure to biology and chemistry at the high school level is helpful. This course is not open to students with credit for BIOL𧇖 or BIOL 250. This course does not count toward any Biology degree.

BIOL𧅴. Introduction to Human Anatomy and Physiology I. 3 Units.

This is the first course in a two-semester sequence that covers human anatomy and physiology for the non-major. BIOL𧅴 covers homeostasis, cell structure and function, membrane transport, tissue types and the integumentary, skeletal, muscular and nervous systems. This course is not open to students with credit for BIOL𧇘, BIOL𧉔, or BIOL𧉚. This course does not count toward any Biology degree. Prereq or Coreq: (Undergraduate Student and BIOL𧅲) or Requisites Not Met Permission.

BIOL𧅵. Introduction to Human Anatomy and Physiology II. 3 Units.

This is the second course in a two-semester sequence that covers human anatomy and physiology for the non-major. BIOL𧅵 covers the endocrine, circulatory, respiratory, digestive, lymphatic, urinary systems including acid-base regulation, and reproductive systems. This course is not open to students with credit for BIOL𧇘, BIOL𧉔, or BIOL𧉚. This course does not count toward any Biology degree. Prereq: (Undergraduate Student and BIOL𧅲 and BIOL𧅴) or Requisites Not Met Permission.

BIOL𧇖. Genes, Evolution and Ecology. 3 Units.

First in a series of three courses required of the Biology major. Topics include: biological molecules (focus on DNA and RNA) mitotic and meiotic cell cycles, gene expression, genetics, population genetics, evolution, biological diversity and ecology. Prereq or Coreq: (Undergraduate Student and CHEM𧅩 or CHEM𧅯) or Requisites Not Met permission.

BIOL𧇖L. Genes, Evolution and Ecology Lab. 1 Unit.

First in a series of three laboratory courses required of the Biology major. Topics include: biological molecules (with a focus on DNA and RNA) basics of cell structure (with a focus on malaria research) molecular genetics, biotechnology population genetics and evolution, ecology. Assignments will be in the form of a scientific journal submission. Prereq or Coreq: (Undergraduate Student and BIOL𧇖) or Requisites Not Met permission.

BIOL𧇗. Cells and Proteins. 3 Units.

Second in a series of three courses required of the Biology major. Topics include: biological molecules (focus on proteins, carbohydrates, and lipids) cell structure (focus on membranes, energy conversion organelles and cytoskeleton) protein structure-function enzyme kinetics, cellular energetics, and cell communication and motility strategies. Requirements to enroll: 1) Undergraduate degree seeking student AND 2) Previous enrollment in BIOL𧇖 and (CHEM𧅩 or CHEM𧅯) AND Previous or concurrent enrollment in CHEM𧅪 or ENGR𧆑 OR Requisites Not Met permission.

BIOL𧇗L. Cells and Proteins Laboratory. 1 Unit.

Second in a series of three laboratory courses required of the Biology major. Topics to include: protein structure-function, enzymes kinetics cell structure cellular energetics, respiration and photosynthesis. In addition, membrane structure and transport will be covered. Laboratory and discussion sessions offered in alternate weeks. Prereq: (Undergraduate Student and BIOL𧇖L and Prereq or Coreq: BIOL𧇗) or Requisites Not Met permission.

BIOL𧇘. Development and Physiology. 3 Units.

This is the final class in the series of three courses required of the Biology major. As with the two previous courses, BIOL𧇖 and 215, this course is designed to provide an overview of fundamental biological processes. It will examine the complexity of interactions controlling reproduction, development and physiological function in animals. The Developmental Biology section will review topics such as gametogenesis, fertilization, cleavage, gastrulation, the genetic control of development, stem cells and cloning. Main topics included in the Physiology portion consist of: homeostasis, the function of neurons and nervous systems the major organ systems and processes involved in circulation, excretion, osmoregulation, gas exchange, feeding, digestion, temperature regulation, endocrine function and the immunologic response. There are two instructional modes for this course: lecture mode and hybrid mode. In the lecture mode students attend class for their instruction. In the hybrid mode students watch online lectures from the course instructor and attend one discussion section with the course instructor each week. The online content prepares students for the discussion. Which mode is offered varies depending on the term. Students are made aware of what mode is offered at the time of registration. The total student effort and course content is identical for both instructional modes. Either instructional mode fulfills the BIOL𧇘 requirement for the BA and BS in Biology. Prereq: (Undergraduate Student and BIOL𧇖) or Requisites Not Met permission.

BIOL𧇘L. Development and Physiology Lab. 1 Unit.

Third in a series of three laboratory courses required of the Biology major. Students will conduct laboratory experiments designed to provide hands-on, empirical laboratory experience in order to better understand the complex interactions governing the basic physiology and development of organisms. Laboratories and discussion sessions offered in alternate weeks. Prereq: (Undergraduate Student and BIOL𧇖L and Prereq or Coreq: BIOL𧇘) or Requisites Not Met permission.

BIOL𧇟. Vertebrate Biology. 3 Units.

A survey of vertebrates from jawless fishes to mammals. Functional morphology, physiology, behavior and ecology as they relate to the groups' relationships with their environment. Evolution of organ systems. Two lectures and one laboratory per week. The laboratory will involve a study of the detailed anatomy of the shark and cat used as representative vertebrates. Students are expected to spend at least three hours of unscheduled laboratory each week. This course fulfills a laboratory requirement for the biology major. Prereq: Undergraduate Student or Requisites Not Met permission.

BIOL𧇡. Evolution. 3 Units.

Multidisciplinary study of the course and processes of organic evolution provides a broad understanding of the evolution of structural and functional diversity, the relationships among organisms and their environments, and the phylogenetic relationships among major groups of organisms. Topics include the genetic basis of micro- and macro-evolutionary change, the concept of adaptation, natural selection, population dynamics, theories of species formation, principles of phylogenetic inference, biogeography, evolutionary rates, evolutionary convergence, homology, Darwinian medicine, and conceptual and philosophic issues in evolutionary theory. Offered as ANTH𧇡, BIOL𧇡, EEPS𧇡, HSTY𧇡, and PHIL𧇡.

BIOL𧇰. Personalized Medicine. 3 Units.

The emphasis of clinical practice is slowly shifting from one-disease and one-treatment-fits-all to more personalized care based on molecular markers of disease risk, disease subtype, drug effectiveness, and adverse drug reactions. This course, designed for non-biology majors, will introduce how the developments in gene sequencing, genetic markers, and stem cells can be applied for predictive testing and personalized therapies. Core concepts to be covered include the principles of genetics including the inheritance of traits determined by single genes and by multiple genes, the assignment of risk to particular genetic constitutions, and the nature and use of stem cells. The emergence of private companies as resources for the performance of the tests, and how the general public will be able to interpret their own data (with or without the access to genetic counselors), will also be covered. The course will include hands-on laboratory experiences of DNA manipulation and detection using the polymerase chain reaction and gel electrophoresis. The ethical, legal, and social issues associated with personal genetic testing will also be covered. This course does not count towards any Biology degree, nor towards the Biology minor. Prereq: Undergraduate Student or Requisites Not Met permission

BIOL𧈬. Dynamics of Biological Systems: A Quantitative Introduction to Biology. 3 Units.

This course will introduce students to dynamic biological phenomena, from the molecular to the population level, and models of these dynamical phenomena. It will describe a biological system, discuss how to model its dynamics, and experimentally evaluate the resulting models. Topics will include molecular dynamics of biological molecules, kinetics of cell metabolism and the cell cycle, biophysics of excitability, scaling laws for biological systems, biomechanics, and population dynamics. Mathematical tools for the analysis of dynamic biological processes will also be presented. Students will manipulate and analyze simulations of biological processes, and learn to formulate and analyze their own models. This course satisfies a laboratory requirement for the biology major. Offered as BIOL𧈬 and EBME𧈬.

BIOL𧈭. Biotechnology Laboratory: Genes and Genetic Engineering. 3 Units.

Laboratory training in recombinant DNA techniques. Basic microbiology, growth, and manipulation of bacteriophage, bacteria and yeast. Students isolate and characterize DNA, construct recombinant DNA molecules, and reintroduce them into eukaryotic cells (yeast, plant, animal) to assess their viability and function. Two laboratories per week. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies an additional laboratory requirement of the B.S. in Biology. Offered as BIOL𧈭 and BIOL𧊑. Prereq: Undergraduate Student and BIOL𧇗 or Requisites Not Met permission.

BIOL𧈮. Human Learning and the Brain. 3 Units.

This course focuses on the question, "How does my brain learn and how can its learning best be facilitated?" Each student is required to develop a comprehensive theory about personal learning. These theories will take the form of a major paper which will be expanded and modified throughout the semester. Readings and class discussions will focus on the following topics: learning and education systems, major structures of the brain and their role in learning, neuronal wiring of the brain and how learning changes it, the emotional brain and its essential role in learning, language and the brain, the role of images in learning, memory and learning (and related pathologies, such as PTSD). Students are expected to incorporate information on these topics into their personal theory of learning. In so doing, students are expected to articulate meaningful questions, skillfully employ research and apply their own knowledge to address such questions, produce clear, precise academic prose to explicate their ideas, and provide relevant and constructive criticism during class discussions. Offered as BIOL𧈮 and COGS𧉂. Counts as SAGES Departmental Seminar. Prereq: Undergraduate Student or Requisites Not Met Permission.

BIOL𧈯. From Blackbox to Toolbox: How Molecular Biology Moves Forward. 3 Units.

The pioneers of modern biology knew very little about the internal workings of the cell, and they had access to only a very limited set of very low-resolution tools. Yet clean experimental design and careful analysis let them ask and answer fundamental biological questions and enabled the development of better tools to use the next time around. In just seven decades, biologists have built a toolbox that offers astonishing precision and power, but the logic of biological experimentation hasn't changed. In this course, we will study that underlying logic, and what it lets us do. We will read key papers spanning the development of modern biology, from the most basic working-out of the Central Dogma to recent advances. We will pay particular attention to how well the authors used the tools available, and how successfully they accounted for their shortcomings--if indeed they did. The emphasis of the course will be on classroom discussion. In lieu of exams, students will (1) write brief responses to weekly in-class prompts for understanding, (2) write in-depth proposals for a molecular biology research project, and (3) present their proposals orally to the class. These assignments are designed to check that students are keeping up with weekly discussions and synthesizing what they have learned into a deeper understanding of how we develop questions and construct arguments in biological research. This course is offered as a SAGES departmental seminar and fulfills the Cell and Molecular breadth requirement of the B.A. and B.S. in Biology. Counts as SAGES Departmental Seminar. Prereq: Undergraduate Student and BIOL𧇗 or Requisites Not Met permission.

BIOL𧈰. Fitting Models to Data: Maximum Likelihood Methods and Model Selection. 3 Units.

This course will introduce students to maximum likelihood methods for fitting models to data and to ways of deciding which model is best supported by the data (model selection). Along the way, students will learn some basic tenets of probability and develop competency in R, a commonly used statistical package. Examples will be drawn from ecology, epidemiology, and potentially other areas of biology. The second half of the course is devoted to in-class projects, and students are encouraged to bring their own data. Offered as BIOL𧈰 and BIOL𧊔. Prereq: (Undergraduate Student and MATH𧅹 and MATH𧅺) or (Undergraduate Student and MATH𧅽 and MATH𧅾) or Requisites Not Met permission.

BIOL𧈱. Herpetology. 3 Units.

Amphibians and reptiles exhibit tremendous diversity in development, physiology, anatomy, behavior and ecology. As a result, amphibians and reptiles have served as model organisms for research in many different fields of biology. This course will cover many aspects of amphibian and reptile biology, including anatomy, evolution, geographical distribution, physiological adaptations to their environment, reproductive strategies, moisture-, temperature-, and food-relations, sensory mechanisms, predator-prey relationships, communication (vocal, chemical, behavioral), population biology, and the effects of venomous snake bite. The graduate version of the course requires a research project and term paper. This course satisfies the Organismal breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧈱 and BIOL𧊕. Prereq: Undergraduate Student and BIOL𧇖 or Requisites Not Met permission.

BIOL𧈱L. Herpetology Lab. 2 Units.

This course will combine field and laboratory sessions to investigate the diversity and biology of reptiles and amphibians. Topics covered will include identification and classification, field research techniques, experimental design and statistical analysis, safe handling of live individuals and working with museum specimens. Laboratory sessions will include trips to the Squire Valleevue Farm, and may also include trips at the Cleveland Museum of Natural History and the Cleveland Metroparks Zoo. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies an additional laboratory requirement of the B.S. in Biology. Prereq or Coreq: BIOL𧈱.

BIOL𧈲. Mathematical Analysis of Biological Models. 3 Units.

This course focuses on the mathematical methods used to analyze biological models, with examples drawn largely from ecology but also from epidemiology, developmental biology, and other areas. Mathematical topics include equilibrium and stability in discrete and continuous time, some aspects of transient dynamics, and reaction-diffusion equations (steady state, diffusive instabilities, and traveling waves). Biological topics include several "classic" models, such as the Lotka-Volterra model, the Ricker model, and Michaelis-Menten/type II/saturating responses. The emphasis is on approximations that lead to analytic solutions, not numerical analysis. An important aspect of this course is translating between verbal and mathematical descriptions: the goal is not just to solve mathematical problems but to extract biological meaning from the answers we find. Offered as BIOL𧈲 and MATH𧉸. Prereq: Undergraduate Student and (BIOL𧈬 or MATH𧇠 or MATH𧇤) or Requisites Not Met permission.

BIOL𧈳. Evolutionary Biology of the Invertebrates. 3 Units.

Important events in the evolution of invertebrate life, as well as structure, function, and phylogeny of major invertebrate groups.

BIOL𧈵. Biology Field Studies. 3 Units.

Intensive investigation of living organisms in a natural environment. Location of the field site may vary with each course offering, and may be either domestic or international. Topics covered include logistics, biodiversity, and current ecological, environmental, and social issues surrounding the specific ecosystem being studied. Time at the field site will be spent listening to resident lecturers, receiving guided tours, observing and identifying wild organisms in their natural habitat, and conducting a research project. The undergraduate version requires students to plan and conduct a group research project and present results independently. The graduate version requires students to plan, conduct, and present an independent research project. Instructor consent required to register. This course will fulfill a laboratory requirement of the B.A. in Biology. This course will fulfill an additional laboratory requirement of the B.S. in Biology. Course may be repeated for credit up to two times if traveling to a new destination. Offered as BIOL𧈵 and BIOL𧊙. Prereq: BIOL𧇘.

BIOL𧈶. Field Studies in Evolutionary Ecology. 3 Units.

The field of Evolutionary Ecology examines how the interactions between organisms and their environments evolve. In this field-based course, students will conduct a variety of experimental and observational field studies aimed at addressing key concepts in Evolutionary Ecology. Students will gain experience in study design and data collection in natural populations, data analysis, and the writing and presentation of scientific results. This course satisfies a laboratory requirement of a B.A. in Biology. This course satisfies an additional laboratory requirement of a B.S. in Biology. Prereq: BIOL𧇖.

BIOL𧈷A. Survey of Bioinformatics: Technologies in Bioinformatics. 1 Unit.

SYBB𧈷A/411A is a 5-week course that introduces students to the high-throughput technologies used to collect data for bioinformatics research in the fields of genomics, proteomics, and metabolomics. In particular, we will focus on mass spectrometer-based proteomics, DNA and RNA sequencing, genotyping, protein microarrays, and mass spectrometry-based metabolomics. This is a lecture-based course that relies heavily on out-of-class readings. Graduate students will be expected to write a report and give an oral presentation at the end of the course. SYBB𧈷A/411A is part of the SYBB survey series which is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB𧈷A/411A), to data integration (SYBB𧈷B/411B), to research applications (SYBB𧈷C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming skills. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB𧊛A. Offered as SYBB𧈷A, BIOL𧈷A and SYBB𧊛A. Prereq: BIOL𧇖 and BIOL𧇗. Coreq: BIOL𧈷B and BIOL𧈷C.

BIOL𧈷B. Survey of Bioinformatics: Data Integration in Bioinformatics. 1 Unit.

SYBB𧈷B/411B is a five week course that surveys the conceptual models and tools used to analyze and interpret data collected by high-throughput technologies, providing an entry points for students new to the field of bioinformatics. The knowledge structures that we will cover include: biomedical ontologies, signaling pathways, and interaction networks. We will also cover tools for genome exploration and analysis. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB𧈷A/411A), to data integration (SYBB𧈷B/411B), to research applications (SYBB𧈷C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB𧊛A. Offered as SYBB𧈷B, BIOL𧈷B, and SYBB𧊛B. Prereq: BIOL𧇖 and BIOL𧇗. Coreq: BIOL𧈷A and BIOL𧈷C.

BIOL𧈷C. Survey of Bioinformatics: Translational Bioinformatics. 1 Unit.

SYBB𧈷C/411C is a longitudinal course that introduces students to the latest applications of bioinformatics, with a focus on translational research. Topics include: `omic drug discovery, pharmacogenomics, microbiome analysis, and genomic medicine. The focus of this course is on illustrating how bioinformatic technologies can be paired with data integration tools for various applications in medicine. The course is organized as a weekly journal club, with instructors leading the discussion of recent literature in the field of bioinformatics. Students will be expected to complete readings beforehand students will also work in teams to write weekly reports reviewing journal articles in the field. The SYBB survey series is composed of the following course sequence: (1) Technologies in Bioinformatics, (2) Data Integration in Bioinformatics, (3) Translational Bioinformatics, and (4) Programming for Bioinformatics. Each standalone section of this course series introduces students to an aspect of a bioinformatics project - from data collection (SYBB𧈷A/411A), to data integration (SYBB𧈷B/411B), to research applications (SYBB𧈷C/411C), with a fourth module (SYBB 311D/411D) introducing basic programming. Graduate students have the option of enrolling in all four courses or choosing the individual modules most relevant to their background and goals with the exception of SYBB 411D, which must be taken with SYBB𧊛A. Offered as SYBB𧈷C, BIOL𧈷C and SYBB𧊛C. Prereq: BIOL𧇖 and BIOL𧇗. Coreq: BIOL𧈷A and BIOL𧈷B.

BIOL𧈸. Introductory Plant Biology. 3 Units.

This course will provide an overview of plant biology. Topics covered will include: (1) Plant structure, function and development from the cellular level to the whole plant (2) plant diversity, evolution of the bacteria, fungi, algae, bryophytes and vascular plants (3) adaptations to their environment, plant-animal interactions, and human uses of plants. Prereq: (Undergraduate student and BIOL𧇗) or Requisites Not Met permission.

BIOL𧈺. Taming the Tree of Life: Phylogenetic Comparative Methods-from Concept to Practical Application. 3 Units.

"Nothing in biology makes sense except in the light of evolution" -- Dobzhansky Biologists have long been fascinated by the diversity of life. Why are there so many species? Why are some of them similar and others divergent? How has evolution shaped ecological interactions, such as disease-host dynamics? The "tree of life" describes phylogenetic hypotheses for evolutionary history among species, and modern phylogenetic comparative methods allow us to incorporate the tree of life into statistical analyses. This course will introduce phylogenetic comparative methods, why they are needed to answer many biological questions, how they are conducted, and how they can be used to evaluate hypotheses. These methods can be used for any group of organisms, from humans and their diseases, to plants, animals, or fungi. These methods also can be used to address a broad suite of questions in biology, including biomedical, ecological, evolutionary, developmental, and neuromechanical questions. For example, issues of public health can be more deeply addressed using these tools. Students may bring their own data sets, or may use existing data sets, and will develop an independent research project using these tools. Undergraduates will present a poster at a public poster fair, as part of the requirements for the SAGES capstone. No prior experience with the R statistics language is necessary for this course. BIOL314 fulfills the requirements for an undergraduate capstone in biology. Offered as BIOL𧈺 and BIOL𧊞. Counts as SAGES Senior Capstone. Prereq: (Undergraduate student with at least Junior standing and BIOL𧇖) or Requisite Not Met permission.

BIOL𧈻. Quantitative Biology Laboratory. 3 Units.

This course will apply a range of quantitative techniques to explore structure-function relations in biological systems. Using a case study approach, students will explore causes of impairments of normal function, will assemble diverse sets of information into a database format for the analysis of causes of impairment, will analyze the data with appropriate statistical and other quantitative tools, and be able to communicate their results to both technical and non-technical audiences. The course has one lecture and one lab per week. Students will be required to maintain a journal of course activities and demonstrate mastery of quantitative tools and statistical techniques. Graduate students will have a final project that applies these techniques to a problem of their choice. Offered as BIOL𧈻 and BIOL𧊟. Prereq: (Undergraduate Student and BIOL𧇖) or Requisites Not Met permission.

BIOL𧈼. Fundamental Immunology. 4 Units.

Introductory immunology providing an overview of the immune system, including activation, effector mechanisms, and regulation. Topics include antigen-antibody reactions, immunologically important cell surface receptors, cell-cell interactions, cell-mediated immunity, innate versus adaptive immunity, cytokines, and basic molecular biology and signal transduction in B and T lymphocytes, and immunopathology. Three weekly lectures emphasize experimental findings leading to the concepts of modern immunology. An additional recitation hour is required to integrate the core material with experimental data and known immune mediated diseases. Five mandatory 90 minute group problem sets per semester will be administered outside of lecture and recitation meeting times. Graduate students will be graded separately from undergraduates, and 22 percent of the grade will be based on a critical analysis of a recently published, landmark scientific article. Offered as BIOL𧈼, BIOL𧊠, CLBY𧊠, PATH𧈼 and PATH𧊠. Prereq: BIOL𧇗 and 215L.

BIOL𧈾. Introductory Entomology. 4 Units.

The goal of this course is to discover that, for the most part, insects are not aliens from another planet. Class meetings will alternate with some structured as lectures, while others are laboratory exercises. Sometimes we will meet at the Cleveland Museum of Natural History, or in the field to collect and observe insects. The 50 minute discussion meeting once a week will serve to address questions from both lectures and lab exercises. The students will be required to make a small but comprehensive insect collection. Early in the semester we will focus on collecting the insects, and later, when insects are gone for the winter, we will work to identify the specimens collected earlier. Students will be graded based on exams, class participation and their insect collections. This course satisfies either the Organismal breadth requirement of the B.A. and B.S. in Biology, or the laboratory requirement of the B.A. in Biology, or an additional laboratory requirement of the B.S. in Biology. Offered as BIOL𧈾 and BIOL𧊢. Prereq: (Undergraduate Student and BIOL𧇖 and BIOL𧇗 and BIOL𧇘) or Requisites Not Met permission.

BIOL𧈿. Applied Probability and Stochastic Processes for Biology. 3 Units.

Applications of probability and stochastic processes to biological systems. Mathematical topics will include: introduction to discrete and continuous probability spaces (including numerical generation of pseudo random samples from specified probability distributions), Markov processes in discrete and continuous time with discrete and continuous sample spaces, point processes including homogeneous and inhomogeneous Poisson processes and Markov chains on graphs, and diffusion processes including Brownian motion and the Ornstein-Uhlenbeck process. Biological topics will be determined by the interests of the students and the instructor. Likely topics include: stochastic ion channels, molecular motors and stochastic ratchets, actin and tubulin polymerization, random walk models for neural spike trains, bacterial chemotaxis, signaling and genetic regulatory networks, and stochastic predator-prey dynamics. The emphasis will be on practical simulation and analysis of stochastic phenomena in biological systems. Numerical methods will be developed using a combination of MATLAB, the R statistical package, MCell, and/or URDME, at the discretion of the instructor. Student projects will comprise a major part of the course. Offered as BIOL𧈿, ECSE𧈿, MATH𧈿, SYBB𧈿, BIOL𧊣, EBME𧊣, MATH𧊣, PHOL𧊣, and SYBB𧊣. Prereq: MATH𧇠 or MATH𧇟 and BIOL𧈬 or BIOL𧈲 and MATH𧇉 or MATH𧈳 or consent of instructor.

BIOL𧉁. Design and Analysis of Biological Experiments. 3 Units.

In this laboratory course, students will learn how to use a computer programming language (MATLAB) to design, execute, and analyze biological experiments. The course will begin with basic programming and continue to data output and acquisition, image analysis, and statistics. Students who are interested in carrying out research projects in any lab setting are encouraged to take this course and use the skills acquired to better organize and analyze their experiments. No prior programming knowledge is assumed. This course satisfies a laboratory requirement of the B.A. in biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in biology. Students will complete a final project on a topic of their choice graduate students will be required to give an oral presentation of this project. Offered as BIOL𧉁 and BIOL𧊥. Counts for CAS Quantitative Reasoning Requirement. Prereq: Undergraduate Student and BIOL𧇘 or Requisites Not Met permission.

BIOL𧉂. Sensory Biology. 3 Units.

The task of a sensory system is to collect, process, store, and transmit information about the environment. How do sensory systems convert information from the environment into neural information in an animal's brain? This course will explore the ecology, physiology, and behavior of the senses across the animal kingdom. We will cover introductory neurobiology and principles of sensory system organization before delving more deeply into vision, olfaction, audition, mechanosensation, and multi-modal sensory integration. For each sensory modality, we will consider how the sensory system operates and how its operation affects the animal's behavior and ecology. We will also explore the evolution of sensory systems and their specialization for specific behavioral tasks. Students will finish the course with a research project on a topic of their choice graduate students will present this project to the class. Offered as BIOL𧉂 and BIOL𧊦. Prereq: (Undergraduate Student and BIOL𧇘) or Requisites Not Met permission.

BIOL𧉄. Introduction to Stem Cell Biology. 3 Units.

This discussion-based course will introduce students to the exciting field of stem cell research. Students will first analyze basic concepts of stem cell biology, including stem cell niche, cell quiescence, asymmetric cell division, cell proliferation and differentiation, and signaling pathways involved in these processes. This first part of the course will focus on invertebrate genetic models for the study of stem cells. In the second part of the course, students will search for primary research papers on vertebrate and human stem cells, and application of stem cell research in regenerative medicine and cancer. Finally, students will have the opportunity to discuss about ethical controversies in the field. Students will rotate in weekly presentations, and will write two papers during the semester. Students will improve skills on searching and reading primary research papers, gain presentation skills, and further their knowledge in related subjects in the fields of cell biology, genetics and developmental biology. This course may be used as a cell/molecular subject area elective for the B.A. and B.S. Biology degrees. Offered as BIOL𧉄 and BIOL𧊨. Prereq: Undergraduate Student and (BIOL𧉅 or BIOL𧉆 or BIOL𧉪) or Requisites Not Met permission.

BIOL𧉅. Cell Biology. 3 Units.

This course will emphasize an understanding of the structure and function of eukaryotic cells from a molecular viewpoint. We will explore cell activities by answering the questions: What are the critical components of specific cellular processes and how are they regulated? An important part of this course will be appreciation of the experimental evidence that supports our current understanding of cell function. To achieve this aim, we will highlight a variety of experimental techniques currently used in research, and students will read papers from the primary literature to supplement the text. Topics will include cell structure, protein structure and function, internal organization of the eukaryotic cell, membrane structure and function, protein sorting, organelle biogenesis, and cytoskeleton structure and function. The course will also cover the life cycles of cells, their interactions with each other and their environment, intracellular signaling and cell death mechanisms. After establishing a detailed understanding of cell biology, we will explore how normal cellular processes go awry, leading to diseases such as cancer. This course fulfills the Cell and Molecular breadth requirement of the B.A. and B.S. in Biology. Prereq: (Undergraduate Student and BIOL𧇗) or Requisites Not Met permission.

BIOL𧉆. Genetics. 3 Units.

Transmission genetics, nature of mutation, microbial genetics, somatic cell genetics, recombinant DNA techniques and their application to genetics, human genome mapping, plant breeding, transgenic plants and animals, uniparental inheritance, evolution, and quantitative genetics. Offered as BIOL𧉆 and BIOL𧊪. Prereq: (Undergraduate student and BIOL𧇖) or Requisites Not Met permission

BIOL𧉇. Functional Genomics. 3 Units.

In this course, students will learn how to access and use genomics data to address questions in cell biology, development and evolution. The genome of Drosophila melanogaster will serve as a basis for exploring genome structure and learning how to use a variety of available software to identify similar genes in different species, predict protein sequence and functional domains, design primers for PCR, analyze cis-regulatory sequences, access microarray and RNAseq databases, among others. Classes will be in the format of short lectures, short oral presentations made by students and hands-on experimentation using computers. Discussions will be centered in primary research papers that used these tools to address specific biological questions. A final project will consist of a research project formulated by a group of 2-3 students to test a hypothesis formulated by the students using the bioinformatics tools learned in the course. Graduate students will be required to make additional presentations of research papers. They also will have additional questions in exams and a distinct page requirement on written assignments. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in Biology. Offered as BIOL𧉇 and BIOL𧊫. Prereq: Undergraduate Student and (BIOL𧇖L and BIOL𧉆) or Requisites Not Met permission.

BIOL𧉈. Plant Genomics and Proteomics. 3 Units.

The development of molecular tools has impacted agriculture as much as human health. The application of new techniques to improve food crops, including the development of genetically modified crops, has also become controversial. This course covers the nature of the plant genome and the role of sequenced-based methods in the identification of the genes. The application of the whole suite of modern molecular tools to understand plant growth and development, with specific examples related agronomically important responses to biotic and abiotic stresses, is included. The impact of the enormous amounts of data generated by these methods and their storage and analysis (bioinformatics) is also considered. Finally, the impact on both the developed and developing world of the generation and release of genetically modified food crops will be covered. Recommended preparation: BIOL𧉆. Offered as BIOL𧉈 and BIOL𧊬. Prereq: Undergraduate Student or Requisites Not Met permission.

BIOL𧉉. Genome Dynamics. 3 Units.

We will examine how the physical architecture of the genome facilitates a dynamic genome ecosystem. Topics will be selected from current research in the field, including: how the three dimensional architecture of chromosomes within the nucleus impacts information storage and retrieval, how biochemical phase separation impacts nucleic acid storage (including RNA), how structural features of chromosomes are critical for function, genome engineering approaches, and the clinical implications of mutations in the 3D nuclear architecture. Course materials will come from the primary research literature, supplemented with appropriate background material. This course fulfills the cell and molecular biology breadth requirement of the BA and BS in Biology. Counts as a SAGES Departmental Seminar. Offered as BIOL𧉉 and BIOL𧊭. Counts as SAGES Departmental Seminar. Prereq: Undergraduate Student and BIOL𧉆 or Requisites Not Met permission.

BIOL𧉍. The Human Microbiome. 3 Units.

This departmental seminar is designed to reveal how the abundant community of human-associated microorganisms influence human development, physiology, immunity and nutrition. Using a survey of current literature, this discussion-based course will emphasize an understanding of the complexity and dynamics of human/microbiome interactions and the influence of environment, genetics and individual life histories on the microbiome and human health. Grades will be based on participation, written assignments, exams, an oral presentation and a final paper. This class is offered as a SAGES Departmental Seminar and fulfills an Organismal breadth requirement of the BA and BS in Biology. Counts as SAGES Departmental Seminar. Prereq: (Undergraduate Student and BIOL𧇖 and BIOL𧇘) or Requisites Not Met Permission.

BIOL𧉐. Aquatic Biology. 3 Units.

Physical, chemical, and biological dynamics of lake ecosystems. Factors governing the distribution, abundance, and diversity of freshwater organisms. This course satisfies the Population Biology/Ecology breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧉐 and BIOL𧊴. Prereq: Undergraduate Student and BIOL𧇖 or Requisites Not Met permission.

BIOL𧉒. Ichthyology. 4 Units.

Biology of fishes. Students will develop fundamental understanding of the evolutionary history and systematics of fishes to provide a context within which they can address aspects of biology including anatomy, physiology (e.g., in species that change sex osmoregulation in freshwater vs. saltwater), and behavior (e.g., visual, auditory, chemical, electric communication social structures), ecology, and evolution (e.g., speciation). We will explore the biodiversity of fishes around the world, with emphasis on Ohio species, by examining preserved specimens, observing captive living specimens, and observing, capturing, and identifying wild fishes in their natural habitats. Practical applications will be emphasized, such as aquaculture, fisheries management, and biomedical research. Course will conclude with an analysis of the current global fisheries crisis that has resulted from human activities. There will be many field trips and networking with the Cleveland Metroparks Zoo, the Cleveland Museum of Natural History, and local, state, and federal government agencies. Some classes meet at the Cleveland Museum of Natural History. This course satisfies a laboratory requirement of the B.A. and B.S. in biology. The graduate version of the course requires a research project and term paper. Offered as BIOL𧉒 and BIOL𧊶. Prereq: (Undergraduate Student and BIOL𧇘) or Requisites Not Met permission.

BIOL𧉓. Aquatic Biology Laboratory. 2 Units.

The physical, chemical, and biological limnology of freshwater ecosystems will be investigated. Emphasis will be on identification of the organisms inhabiting these systems and their ecological interactions with each other. This course will combine both field and laboratory analysis to characterize and compare the major components of these ponds. Students will have the opportunity to design and conduct individual projects. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies an additional laboratory requirement of the B.S. in Biology. Prereq or Coreq: Undergraduate Student and BIOL𧉐 or Requisites Not Met permission.

BIOL𧉔. Human Physiology. 3 Units.

This course will provide functional correlates to the students' previous knowledge of human anatomy. Building upon the basic principles covered in BIOL𧇘 and BIOL𧉚, the physiology of organs and organ systems of humans, including the musculoskeletal, nervous, cardiovascular, lymphatic, immune, respiratory, digestive, excretory, reproductive, and endocrine systems, will be studied at an advanced level. The contribution of each system to homeostasis will be emphasized. Prereq: (Undergraduate Student and BIOL𧉚 and BIOL𧇗 and BIOL𧇘) or Requisites Not Met permission.

BIOL𧉕. Basic Biology of Blood and Blood Diseases. 3 Units.

This course incorporates biology, physiology, biochemistry, and pathology to understand how one of the most important tissues in the human body functions: blood. The course will investigate the normal flow of traffic in the body, as well as some of the biological diseases that hinder this flow. It will focus on understanding the basic and fundamental principles as it relates to biological and disease processes of blood. The course will apply scientific reasoning and critical thinking in investigating these processes. Additionally, it will explore the basic understanding of how scientific research in the area of hematology and oncology is conducted and how we apply laboratory discoveries towards treating blood-related disorders. Our focus will center upon examining the molecular mechanisms associated with bone marrow and several blood disorders. Specifically, we will study cancer (leukemia and lymphoma), anemia (sickle cell disease), blood coagulation (hemophilia and thrombosis), and atherosclerosis. Upon completion of this course, students will have gained the knowledge to apply basic biological concepts to larger, complex pathological diseases. This course fulfills the Cell & Molecular Breadth Requirement of the BA and BS in Biology. Prereq: Undergraduate Student and BIOL𧇖 or Requisites Not Met permission.

BIOL𧉖. Parasitology. 3 Units.

This course will introduce students to classical and current parasitology. Students will discuss basic principles of parasitology, parasite life cycles, host-parasite interaction, therapeutic and control programs, epidemiology, and ecological and societal considerations. The course will explore diverse classes of parasitic organisms with emphasis on protozoan and helminthic diseases and the parasites' molecular biology. Group discussion and selected reading will facilitate further integrative learning and appreciation for parasite biology. This course counts as an elective in the cell/molecular biology subject area for the Biology B.A. and B.S. degrees. Offered as BIOL𧉖 and BIOL𧊺. Prereq: (Undergraduate Student and BIOL𧇖, BIOL𧇗, BIOL𧇘 and BIOL𧉆) or Requisites Not Met permission.

BIOL𧉗. Microbiology. 3 Units.

The physiology, genetics, biochemistry, and diversity of microorganisms. The subject will be approached both as a basic biological science that studies the molecular and biochemical processes of cells and viruses, and as an applied science that examines the involvement of microorganisms in human disease as well as in workings of ecosystems, plant symbioses, and industrial processes. The course is divided into four major areas: bacteria, viruses, medical microbiology, and environmental and applied microbiology. Offered as BIOL𧉗 and BIOL𧊻. Prereq: (Undergraduate Student and BIOL𧇗) or Requisites Not Met permission.

BIOL𧉘. Laboratory for Microbiology. 3 Units.

Practical microbiology, with an emphasis on bacteria as encountered in a variety of situations. Sterile techniques, principles of identification, staining and microscopy, growth and nutritional characteristics, genetics, enumeration methods, epidemiology, immunological techniques (including ELISA and T cell identification), antibiotics and antibiotic resistance, chemical diagnostic tests, sampling the human environment, and commercial applications. One three hour lab plus one lecture per week. Prereq or Coreq: (Undergraduate Student and BIOL𧉗) or Requisites Not Met permission.

BIOL𧉙. Mammal Diversity and Evolution. 4 Units.

This course focuses on the anatomical and taxonomic diversity of mammals in an evolutionary context. The emphasis is on living (extant) mammals, but extinct mammals are also discussed. By the end of the course, students will be able to: (1) describe the key anatomical and physiological features of mammals (2) name all orders and most families of living mammals (3) identify a mammal skull to order and family (4) understand how to create and interpret a phylogenetic tree (5) appreciate major historical patterns in mammal diversity and biogeography as revealed by the fossil record (6) read and critique a scientific article dealing with mammal evolution. One weekend field trip to Cleveland Metroparks Zoo additional individual and group visits to the Cleveland Museum of Natural History. This course satisfies a laboratory requirement for the biology major. Recommended preparation: BIOL𧇟 Vertebrate Biology, BIOL𧇡 Evolution, or BIOL𧉚 Human Anatomy. Offered as ANAT𧊽 and BIOL𧉙. Prereq: BIOL𧇖.

BIOL𧉚. Human Anatomy. 3 Units.

Gross anatomy of the human body. Two lectures and one laboratory demonstration per week. Prereq: (Undergraduate Student and BIOL𧇘) or Requisites Not Met permission.

BIOL𧉟. Principles of Ecology. 3 Units.

This lecture course explores spatial and temporal relationships involving organisms and the environment at individual, population, and community levels. An underlying theme of the course will be neo-Darwinian evolution through natural selection with an emphasis on organismal adaptations to abiotic and biotic environments. Studies and models will illustrate ecological principles, and there will be some emphasis on the applicability of these principles to ecosystem conservation. This course satisfies the Population Biology/Ecology breadth requirement of the B.A. and B.S. in Biology. Students taking the graduate level course will prepare a grant proposal in which hypotheses will be based on some aspect of ecological theory. Offered as BIOL𧉟 and BIOL𧋃. Prereq: Undergraduate Student and BIOL𧇖 or Requisites Not Met permission.

BIOL𧉟L. Principles of Ecology Laboratory. 2 Units.

Students in this laboratory course will conduct a variety of ecological investigations that are designed to examine relationships involving organisms and the environment at individual, population, and community levels. Descriptive and hypothesis-driven investigations will take place at Case Western Reserve University's Squire Valleevue Farm, in both field and greenhouse settings. The course is designed to explore as well as test a variety of ecological paradigms. Students taking the graduate level course will prepare a grant proposal in which hypotheses will be based on a select number of lab investigations. This course satisfies a laboratory requirement for biology majors. Offered as BIOL𧉟L and BIOL𧋃L. Prereq or Coreq: Undergraduate Student and BIOL𧉟 or Requisites Not Met permission.

BIOL𧉠. Ecology and Evolution of Infectious Diseases. 3 Units.

This course explores the effects of infectious diseases on populations of hosts, including humans and other animals. We will use computer models to study how infectious diseases enter and spread through populations, and how factors like physiological and behavioral differences among host individuals, host and pathogen evolution, and the environment affect this spread. Our emphasis will be on understanding and applying quantitative models for studying disease spread and informing policy in public health and conservation. To that end, computer labs are the central component of the course. This course satisfies a laboratory requirement of the B.A. in biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in biology. Offered as BIOL𧉠 and BIOL𧋄. Prereq: (Undergraduate Student and BIOL𧇖 and (MATH𧅹 or MATH𧅽) and (MATH𧅺 or MATH𧅾)) or Requisites Not Met permission

BIOL𧉡. Ecophysiology of Global Change. 3 Units.

Global change is an emerging threat to human health and economic stability. Rapid changes in climate, land use, and prevalence of non-native species generate novel conditions outside the range of typical conditions under which organisms evolved. Already we are witnessing the global redistribution of plants and animals, changes in the timing of critical life cycle events, and in some cases local extinction of populations. This course explores the impacts of global change on biological systems at levels from individuals to ecosystems among animals, plants and microbes across ecological to evolutionary timescales and from local to global spatial scales. Throughout, physiology is emphasized as a core driver of biological responses to global change. Traditional lectures will be accompanied by discussions of primary literature articles. The laboratory component will involve the development of an independent project at the University Farm, and dissemination of results through traditional (e.g. written paper) and new (e.g. podcast) media. This class will fulfill a laboratory requirement of the B.A. in Biology. This class will fulfill an additional laboratory requirement of the B.S. in Biology. Offered as BIOL𧉡 and BIOL𧋅. Prereq: (Undergraduate Student and BIOL𧇖. Prereq or Coreq: BIOL𧇘) or Requisites Not Met Permission.

BIOL𧉥. Backyard Behavior Capstone. 3 Units.

Interesting animal behavior is all around us. We need not go into a laboratory to observe it, but laboratory tools can help to understand the behaviors that we encounter every day. We interact with animals in our homes, in forests and wilderness areas and even in our own backyards. As pet dogs or cats interact with wild squirrels and birds, they provide insights regarding predation, neuromechanics, and mating behaviors, just to list a few concepts. This course takes advantage of the rich behavior that exists around us to provide a capstone experience for students who have an interest in animal behavior. The course will be open to 10 senior Biology majors who have emphasized the animal behavior and neurobiology courses offered by the Biology department. Each student will have taken at least one advanced course in Animal Behavior, Neurobiology, or Neuroethology. Entry into the course will be by permit, and permits will be issued only after an interview in which each student demonstrates to the instructor a deep interest in animal behavior and underlying neural control systems. Through classroom discussion, viewing of behaviorally-based video shows, and field trips, each student will choose one behavior to investigate in detail over the course of the semester. In order to move beyond casual observation to in-depth analysis, video cameras will be available to the students, as well as computer based motion analysis systems. The class will meet as a group twice weekly. During this formal classroom period, students will discuss behaviors in general and , as the course progresses, the specific topics that each student is investigating. They will present journal articles that are relevant to their topics, a prospectus on their intended study, and ultimately describe their projects outside of class time and will present a poster at a public poster fair. Counts as SAGES Senior Capstone. Prereq: BIOL𧈱 or BIOL𧈾 or BIOL𧉦 or BIOL𧉵 or BIOL𧉶.

BIOL𧉦. Animal Behavior. 4 Units.

Ultimately the success or failure (i.e., life or death) of any individual animal is determined by its behavior. The ability to locate and capture food, avoid being food, acquiring and defending territory, and successfully passing your genes to the next generation, are all dependent on complex interactions between an animal's design, environment and behavior. This course will be an integrative approach emphasizing experimental studies of animal behavior. You will be introduced to state-of-the-art approaches to the study of animal behavior, including neural and hormonal mechanisms, genetic and developmental mechanisms and ecological and evolutionary approaches. We will learn to critique examples of current scientific papers, and learn how to conduct observations and experiments with real animals. We will feature guest appearances by the Curator of Research from the Cleveland MetroParks Zoo and visits to working animal behavior research labs here at CWRU. Group discussions and writing will be emphasized. This course satisfies a laboratory requirement for biology majors. Offered as BIOL𧉦 and BIOL𧋊. Prereq: (Undergraduate Student and BIOL𧇖, BIOL𧇗 and BIOL𧇘) or Requisites Not Met permission.

BIOL𧉪. Principles of Developmental Biology. 3 Units.

The descriptive and experimental aspects of animal development. Gametogenesis, fertilization, cleavage, morphogenesis, induction, differentiation, organogenesis, growth, and regeneration. Students taking the graduate-level course will prepare an NIH-format research proposal as the required term paper. Offered as BIOL𧉪, BIOL𧋎 and ANAT𧋎. Prereq: Undergraduate Student and (BIOL𧇘 or (EBME𧇉 and EBME𧇊)) or Requisites Not Met Permission.

BIOL𧉬. Research Methods in Evolutionary Biology. 3 Units.

The process of evolution explains not only how the present diversity of life on earth has formed, but also provides insights into current pressing issues today, including the spread of antibiotic resistance, the causes of geographic variation in genetic diseases, and explanations for modern patterns of extinction risk. Students in Research Methods in Evolutionary Biology will be introduced to several of the major research approaches of evolutionary biology, including methods of measuring natural selection on the phenotypic and genotypic levels, quantifying the rate of evolution, reconstructing evolutionary relationships, and assessing the factors that affect rates of speciation and extinction. The course will consist of a combination of interactive lectures, in-class problem solving and data analysis, and the discussion of peer-reviewed scientific papers. Grades are based on participation in class, discussions and written summaries of published papers, in-class presentations, and two writing assignments. Offered as BIOL𧉬 and BIOL𧋐. Counts as SAGES Departmental Seminar. Prereq: (Undergraduate Student and BIOL𧇖) or Requisites Not Met Permission.

BIOL𧉭. Evo-Devo:Evolution of Body Plans and Pathologies. 3 Units.

This discussion-based course offers a detailed introduction to Evolutionary Developmental Biology. The field seeks to explain evolutionary events through the mechanisms of Developmental Biology and Medical Genetics. The course is structured into different modules. First we will look at the developmental genetic mechanisms that can cause variation and medical pathologies. Then we focus on how alterations of these mechanisms can generate novel structural changes. We will then examine a few areas of active debate, where Evo-Devo is attempting to solve major problems in evolutionary biology and congenital birth defects. We will conclude with two writing assignments. Students will be required to present, read, and discuss primary literature in each module. This course is offered as a SAGES Departmental Seminar and fulfills a Cell and Molecular breadth requirement of the BA and BS in Biology. Offered as BIOL𧉭 and BIOL𧋑. Counts as SAGES Departmental Seminar. Prereq: Undergraduate Student and (BIOL𧇡 or BIOL𧉆 or BIOL𧉪) or Requisites Not Met permission.

BIOL𧉰. Topics in Evolutionary Biology. 3 Units.

The focus for this course on a special topic of interest in evolutionary biology will vary from one offering to the next. Examples of possible topics include theories of speciation, the evolution of language, the evolution of sex, evolution and biodiversity, molecular evolution. ANAT/ANTH/EEPS/PHIL/PHOL𧋓/BIOL𧋔 will require a longer, more sophisticated term paper, and additional class presentation. Offered as ANTH𧉯, BIOL𧉰, EEPS𧉯, PHIL𧉯, ANAT𧋓, ANTH𧋓, BIOL𧋔, EEPS𧋓, PHIL𧋓 and PHOL𧋓. Prereq: BIOL𧇡 or equivalent.

BIOL𧉵. Introduction to Neurobiology. 3 Units.

How nervous systems control behavior. Biophysical, biochemical and molecular biological properties of nerve cells, their organization into circuitry, and their function within networks. Emphasis on quantitative methods for modeling neurons and networks, and on critical analysis of the contemporary technical literature in the neurosciences. Term paper required for graduate students. This course satisfies a lab requirement for the B.A. in Biology, and a Quantitative Laboratory requirements for the B.S. in Biology. Offered as BIOL𧉵, BIOL𧋙, and NEUR𧋙.

BIOL𧉶. Neurobiology of Behavior. 3 Units.

In this course, students will examine how neurobiologists interested in animal behavior study the linkage between neural circuitry and complex behavior. Various vertebrate and invertebrate systems will be considered. Several exercises will be used in this endeavor. Although some lectures will provide background and context on specific neural systems, the emphasis of the course will be on classroom discussion of specific journal articles. In addition, students will each complete a project in which they will observe some animal behavior and generate both behavioral and neurobiological hypotheses related to it. In lieu of examinations, students will complete three written assignments, including a theoretical grant proposal, a one-page Specific Aims paper related to the project, and a final project paper. These assignments are designed to give each student experience in writing biologically-relevant documents. Classroom discussions will help students understand the content and format of each type document. They will also present their projects orally to the entire class. Offered as BIOL𧉶, BIOL𧋚 and NEUR𧋚. Counts as SAGES Departmental Seminar.

BIOL𧉹. Biorobotics Team Research. 3 Units.

Many exciting research opportunities cross disciplinary lines. To participate in such projects, researchers must operate in multi-disciplinary teams. The Biorobotics Team Research course offers a unique capstone opportunity for undergraduate students to utilize skills they developed during their undergraduate experience while acquiring new teaming skills. A group of eight students form a research team under the direction of two faculty leaders. Team members are chosen from appropriate majors through interviews with the faculty. They will research a biological mechanism or principle and develop a robotic device that captures the actions of that mechanism. Although each student will cooperate on the team, they each have a specific role, and must develop a final paper that describes the research generated on their aspect of the project. Students meet for one class period per week and two 2-hour lab periods. Initially students brainstorm ideas and identify the project to be pursued. They then acquire biological data and generate robotic designs. Both are further developed during team meetings and reports. Final oral reports and a demonstration of the robotic device occur in week 15. Offered as BIOL𧉹, EMAE𧉹, BIOL𧋓, and EMAE𧋝. Counts as SAGES Senior Capstone.

BIOL𧉺. Computational Neuroscience. 3 Units.

Computer simulations and mathematical analysis of neurons and neural circuits, and the computational properties of nervous systems. Students are taught a range of models for neurons and neural circuits, and are asked to implement and explore the computational and dynamic properties of these models. The course introduces students to dynamical systems theory for the analysis of neurons and neural learning, models of brain systems, and their relationship to artificial and neural networks. Term project required. Students enrolled in MATH𧋞 will make arrangements with the instructor to attend additional lectures and complete additional assignments addressing mathematical topics related to the course. Recommended preparation: MATH𧇟 and MATH𧇠 or BIOL𧈬 and BIOL𧈲. Offered as BIOL𧉺, COGS𧉺, MATH𧉺, BIOL𧋞, CSDS𧋞, EBME𧋞, ECSE𧋞, MATH𧋞 and NEUR𧋞.

BIOL𧉻. Transformative Animal Models in Modern Biology. 3 Units.

Animal models are extremely important in the study of biology and in modern medicine. They allow us to determine fundamental biological mechanisms and cellular and molecular causes of disease. There is logic to how each animal model has found its place in the menagerie of accepted animal models. Certain animal models allow us to test particular hypotheses that may not be possible to address in other animals. Moreover, some animal models are more relevant than others to studying a particular human disease. This seminar-based course will focus on animal models that either are effective at modeling human disease, approach relevant neurobiological questions, or play a role in translational medicine. The course will focus on mammalian and non-mammalian animal models that are important to biomedical research, including the primate, mouse, zebrafish, and roundworm. Comparisons between popular animal models will be made. This course satisfies the Organismal breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧉻 and BIOL𧋟. Counts as SAGES Departmental Seminar. Prereq: Undergraduate student and (BIOL𧉆 or BIOL𧉵) or Requisites Not Met permission.

BIOL𧊀. Reading and Writing Like an Ecologist. 3 Units.

Students usually learn from textbooks, but scientists communicate with each other through journal articles. The purpose of this class is to help you learn to read and write like an ecologist. We will spend our time reading and discussing journal articles about three or four issues in ecology, including papers from both empirical and theoretical perspectives. In addition to the science, we'll talk about strategies for how to keep reading when you encounter something you don't understand and what makes a paper well or poorly written. At the end of each section, you will synthesize your ideas into a review article. Your initial paper will be submitted to me as hypothetical journal editor. I will send your paper out for review to two fellow classmates, and I'll send their comments back to you along with brief comments of my own. As all scientists know, it is virtually unheard of for a journal to accept a paper for publication without revisions. After this peer review, you will revise your papers and resubmit them to me. Your grade will be based on your participation in class discussions, your papers (both drafts) and your work as a reviewer for other students. This course satisfies the Population Biology/Ecology breadth requirement of the B.A. and B.S. in Biology. Counts as SAGES Departmental Seminar. Prereq: Undergraduate Student and BIOL𧇖 or Requisites Not Met permission.

BIOL𧊁. Seminar on Biological Processes in Learning and Cognition. 3 Units.

Students will read and discuss research papers on a range of topics relevant to the biological processes that lead to cognition and learning in humans. Sample topics are: cellular and molecular mechanisms of memory visual sensory detection of images, movement, and color role of slow neurotransmitters in synaptic plasticity cortical distribution of cognitive functions such as working memory, decision making, and image analysis functions of emotion-structures and their role in cognition brain structures and mechanisms involved in language creation others. Some papers will be assigned and others will be selected by students. Discussions will focus on the methods used, the experimental results, and the interpretations of significance. Students will work in groups on a semester project to be presented near the end of the semester. Counts as SAGES Senior Capstone. Prereq: Undergraduate Student and BIOL𧈮 or Requisites Not Met permission.

BIOL𧊄. Undergraduate Research. 1 - 3 Units.

Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. Only 3 credit-hours may count towards the biology majors or minor. Offered as BIOL𧊄 and SYBB𧊄.

BIOL𧊄S. Undergraduate Research - SAGES Capstone. 3 Units.

Guided laboratory research under the sponsorship of a biology faculty member. May be carried out within the biology department or in associated departments. May be taken only one semester during the student's academic career. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. A public presentation is required. Offered as BIOL𧊄S and SYBB𧊄S. Counts as SAGES Senior Capstone.

BIOL𧊅. Selected Topics. 1 - 3 Units.

Individual library research projects completed under the guidance of a biology sponsor. May be carried out within the biology department or in associated departments. Appropriate forms must be secured in the biology department office. A written report must be approved by the biology sponsor and submitted to the chairman of the biology department before credit is granted. Only 3 credit-hours may count towards the biology majors or minor.

BIOL𧊅S. Selected Topics in Biology--SAGES Capstone. 3 Units.

Individual library research projects under the guidance of a biology sponsor. A major paper must be submitted and approved before credit is awarded. A public presentation is required. Counts as SAGES Senior Capstone.

BIOL𧊆. Advanced Undergraduate Research. 1 - 3 Units.

Offered on a credit only basis. Students may carry out research in biology or related departments, but a biology sponsor is required. Does not count toward the 30 hours required for a major in biology, but may be counted toward the total number of hours required for graduation. A written report must be submitted to the chairman's office and approved before credit is granted. Prereq: BIOL𧊄 or BIOL𧊄S

BIOL𧊌. Undergraduate Research in Evolutionary Biology. 3 Units.

Students propose and conduct guided research on an aspect of evolutionary biology. The research will be sponsored and supervised by a member of the CASE faculty or other qualified professional. A written report must be submitted to the Evolutionary Biology Steering Committee before credit is granted. Offered as ANTH𧊌, BIOL𧊌, EEPS𧊌, and PHIL𧊌.

BIOL𧊍. Molecular Phylogenetics. 4 Units.

This course is designed to teach the theory and practice of molecular based phylogenetics with attention to evolutionary analysis through lecture, readings, discussion, and a quantitative laboratory section. A comprehensive overview of the history of systematics and morphology based phylogenetics will help familiarize students with the theory, methods, and character analysis frameworks used in current genetic based approaches. A laboratory section of the course will provide working knowledge in designing and carrying out an original phylogenetics project beginning with data procurement to writing a research manuscript. Through readings and discussions of research articles as well as presented content, the relevant course material will be utilized in practice by students analyzing their project data sets. The semester-long research project will take students through the process of building a data set, aligning sequences, reconstructing phylogenies, conducting evolutionary analyses, and interpreting and writing results as a scientific manuscript. In addition, students will orally present their research proposal as well as the final research project. Undergraduate students will work in teams of two on the research project component of the course and independently throughout the other course components (discussions). Graduate students will work independently and have an extra assignment. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in Biology. Offered as: BIOL𧊍 and BIOL𧋱. Prereq: Undergraduate Student and BIOL𧇖 and (BIOL𧇡 or BIOL𧉬) or Requisites Not Met permission.

BIOL𧊎. Modern Human Biological Variation. 3 Units.

The objectives of this course are to provide students with an introduction to human biological variation and to understand the variation within an evolutionary framework through lecture, readings, discussion, and labs. We will examine the patterns of morphological and genetic variation in modern human populations and discuss the evolutionary explanations for the observed patterns. In order to do this, we will first build a solid foundation in the scientific method, population genetics, and evolutionary theory before exploring the adaptive significance of the observed variation. A major component of the class will be the discussion of the social and health implications of these patterns of biological variation, particularly in the construction and application of the concept of race and its use in medicine. There are three units to the course. Unit 1 focuses on the fundamentals to understanding biological variation, we will cover basic population genetics, evolution, and the human fossil record. Unit 2 concentrates on surveying modern human biological variation, examining both morphological and genetic traits, and why these variations exist. Unit 3 examines how race is constructed using population-based biological differences, its validity, and the implications for health and medicine. This course fulfills the Population and Ecology breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧊎 and BIOL𧋲. Prereq: Undergraduate Student and BIOL𧇖 or Requisites Not Met permission.

BIOL𧊑. Biotechnology Laboratory: Genes and Genetic Engineering. 3 Units.

Laboratory training in recombinant DNA techniques. Basic microbiology, growth, and manipulation of bacteriophage, bacteria and yeast. Students isolate and characterize DNA, construct recombinant DNA molecules, and reintroduce them into eukaryotic cells (yeast, plant, animal) to assess their viability and function. Two laboratories per week. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies an additional laboratory requirement of the B.S. in Biology. Offered as BIOL𧈭 and BIOL𧊑.

BIOL𧊒. Principles of Neural Science. 3 Units.

Lecture/discussion course covering concepts in cell and molecular neuroscience, principles of systems neuroscience as demonstrated in the somatosensory system, and fundamentals of the development of the nervous system. This course will prepare students for upper level Neuroscience courses and is also suitable for students in other programs who desire an understanding of neurosciences. Recommended preparation: CBIO 453. Offered as BIOL𧊒 and NEUR𧊒.

BIOL𧊔. Fitting Models to Data: Maximum Likelihood Methods and Model Selection. 3 Units.

This course will introduce students to maximum likelihood methods for fitting models to data and to ways of deciding which model is best supported by the data (model selection). Along the way, students will learn some basic tenets of probability and develop competency in R, a commonly used statistical package. Examples will be drawn from ecology, epidemiology, and potentially other areas of biology. The second half of the course is devoted to in-class projects, and students are encouraged to bring their own data. Offered as BIOL𧈰 and BIOL𧊔. Prereq: MATH𧅹 and MATH𧅺 OR MATH𧅽 and MATH𧅾 or consent of instructor.

BIOL𧊕. Herpetology. 3 Units.

Amphibians and reptiles exhibit tremendous diversity in development, physiology, anatomy, behavior and ecology. As a result, amphibians and reptiles have served as model organisms for research in many different fields of biology. This course will cover many aspects of amphibian and reptile biology, including anatomy, evolution, geographical distribution, physiological adaptations to their environment, reproductive strategies, moisture-, temperature-, and food-relations, sensory mechanisms, predator-prey relationships, communication (vocal, chemical, behavioral), population biology, and the effects of venomous snake bite. The graduate version of the course requires a research project and term paper. This course satisfies the Organismal breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧈱 and BIOL𧊕.

BIOL𧊙. Biology Field Studies. 3 Units.

Intensive investigation of living organisms in a natural environment. Location of the field site may vary with each course offering, and may be either domestic or international. Topics covered include logistics, biodiversity, and current ecological, environmental, and social issues surrounding the specific ecosystem being studied. Time at the field site will be spent listening to resident lecturers, receiving guided tours, observing and identifying wild organisms in their natural habitat, and conducting a research project. The undergraduate version requires students to plan and conduct a group research project and present results independently. The graduate version requires students to plan, conduct, and present an independent research project. Instructor consent required to register. This course will fulfill a laboratory requirement of the B.A. in Biology. This course will fulfill an additional laboratory requirement of the B.S. in Biology. Course may be repeated for credit up to two times if traveling to a new destination. Offered as BIOL𧈵 and BIOL𧊙. Prereq: Graduate Standing.

BIOL𧊞. Taming the Tree of Life: Phylogenetic Comparative Methods-from Concept to Practical Application. 3 Units.

"Nothing in biology makes sense except in the light of evolution" -- Dobzhansky Biologists have long been fascinated by the diversity of life. Why are there so many species? Why are some of them similar and others divergent? How has evolution shaped ecological interactions, such as disease-host dynamics? The "tree of life" describes phylogenetic hypotheses for evolutionary history among species, and modern phylogenetic comparative methods allow us to incorporate the tree of life into statistical analyses. This course will introduce phylogenetic comparative methods, why they are needed to answer many biological questions, how they are conducted, and how they can be used to evaluate hypotheses. These methods can be used for any group of organisms, from humans and their diseases, to plants, animals, or fungi. These methods also can be used to address a broad suite of questions in biology, including biomedical, ecological, evolutionary, developmental, and neuromechanical questions. For example, issues of public health can be more deeply addressed using these tools. Students may bring their own data sets, or may use existing data sets, and will develop an independent research project using these tools. Undergraduates will present a poster at a public poster fair, as part of the requirements for the SAGES capstone. No prior experience with the R statistics language is necessary for this course. BIOL314 fulfills the requirements for an undergraduate capstone in biology. Offered as BIOL𧈺 and BIOL𧊞. Counts as SAGES Senior Capstone.

BIOL𧊟. Quantitative Biology Laboratory. 3 Units.

This course will apply a range of quantitative techniques to explore structure-function relations in biological systems. Using a case study approach, students will explore causes of impairments of normal function, will assemble diverse sets of information into a database format for the analysis of causes of impairment, will analyze the data with appropriate statistical and other quantitative tools, and be able to communicate their results to both technical and non-technical audiences. The course has one lecture and one lab per week. Students will be required to maintain a journal of course activities and demonstrate mastery of quantitative tools and statistical techniques. Graduate students will have a final project that applies these techniques to a problem of their choice. Offered as BIOL𧈻 and BIOL𧊟.

BIOL𧊠. Fundamental Immunology. 4 Units.

Introductory immunology providing an overview of the immune system, including activation, effector mechanisms, and regulation. Topics include antigen-antibody reactions, immunologically important cell surface receptors, cell-cell interactions, cell-mediated immunity, innate versus adaptive immunity, cytokines, and basic molecular biology and signal transduction in B and T lymphocytes, and immunopathology. Three weekly lectures emphasize experimental findings leading to the concepts of modern immunology. An additional recitation hour is required to integrate the core material with experimental data and known immune mediated diseases. Five mandatory 90 minute group problem sets per semester will be administered outside of lecture and recitation meeting times. Graduate students will be graded separately from undergraduates, and 22 percent of the grade will be based on a critical analysis of a recently published, landmark scientific article. Offered as BIOL𧈼, BIOL𧊠, CLBY𧊠, PATH𧈼 and PATH𧊠. Prereq: Graduate standing.

BIOL𧊡. Cytokines: Function, Structure, and Signaling. 3 Units.

Regulation of immune responses and differentiation of leukocytes is modulated by proteins (cytokines) secreted and/or expressed by both immune and non-immune cells. Course examines the function, expression, gene organization, structure, receptors, and intracellular signaling of cytokines. Topic include regulatory and inflammatory cytokines, colony stimulating factors, chemokines, cytokine and cytokine receptor gene families, intracellular signaling through STAT proteins and tyrosine phosphorylation, clinical potential, and genetic defects. Lecture format using texts, scientific reviews and research articles. Recommended preparation: PATH𧊠 or equivalent. Offered as BIOL𧊡, CLBY𧊡, and PATH𧊡.

BIOL𧊢. Introductory Entomology. 4 Units.

The goal of this course is to discover that, for the most part, insects are not aliens from another planet. Class meetings will alternate with some structured as lectures, while others are laboratory exercises. Sometimes we will meet at the Cleveland Museum of Natural History, or in the field to collect and observe insects. The 50 minute discussion meeting once a week will serve to address questions from both lectures and lab exercises. The students will be required to make a small but comprehensive insect collection. Early in the semester we will focus on collecting the insects, and later, when insects are gone for the winter, we will work to identify the specimens collected earlier. Students will be graded based on exams, class participation and their insect collections. This course satisfies either the Organismal breadth requirement of the B.A. and B.S. in Biology, or the laboratory requirement of the B.A. in Biology, or an additional laboratory requirement of the B.S. in Biology. Offered as BIOL𧈾 and BIOL𧊢. Prereq: BIOL𧇖, and BIOL𧇗, and BIOL𧇘.

BIOL𧊣. Applied Probability and Stochastic Processes for Biology. 3 Units.

Applications of probability and stochastic processes to biological systems. Mathematical topics will include: introduction to discrete and continuous probability spaces (including numerical generation of pseudo random samples from specified probability distributions), Markov processes in discrete and continuous time with discrete and continuous sample spaces, point processes including homogeneous and inhomogeneous Poisson processes and Markov chains on graphs, and diffusion processes including Brownian motion and the Ornstein-Uhlenbeck process. Biological topics will be determined by the interests of the students and the instructor. Likely topics include: stochastic ion channels, molecular motors and stochastic ratchets, actin and tubulin polymerization, random walk models for neural spike trains, bacterial chemotaxis, signaling and genetic regulatory networks, and stochastic predator-prey dynamics. The emphasis will be on practical simulation and analysis of stochastic phenomena in biological systems. Numerical methods will be developed using a combination of MATLAB, the R statistical package, MCell, and/or URDME, at the discretion of the instructor. Student projects will comprise a major part of the course. Offered as BIOL𧈿, ECSE𧈿, MATH𧈿, SYBB𧈿, BIOL𧊣, EBME𧊣, MATH𧊣, PHOL𧊣, and SYBB𧊣.

BIOL𧊥. Design and Analysis of Biological Experiments. 3 Units.

In this laboratory course, students will learn how to use a computer programming language (MATLAB) to design, execute, and analyze biological experiments. The course will begin with basic programming and continue to data output and acquisition, image analysis, and statistics. Students who are interested in carrying out research projects in any lab setting are encouraged to take this course and use the skills acquired to better organize and analyze their experiments. No prior programming knowledge is assumed. This course satisfies a laboratory requirement of the B.A. in biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in biology. Students will complete a final project on a topic of their choice graduate students will be required to give an oral presentation of this project. Offered as BIOL𧉁 and BIOL𧊥. Counts for CAS Quantitative Reasoning Requirement. Prereq: Graduate standing.

BIOL𧊦. Sensory Biology. 3 Units.

The task of a sensory system is to collect, process, store, and transmit information about the environment. How do sensory systems convert information from the environment into neural information in an animal's brain? This course will explore the ecology, physiology, and behavior of the senses across the animal kingdom. We will cover introductory neurobiology and principles of sensory system organization before delving more deeply into vision, olfaction, audition, mechanosensation, and multi-modal sensory integration. For each sensory modality, we will consider how the sensory system operates and how its operation affects the animal's behavior and ecology. We will also explore the evolution of sensory systems and their specialization for specific behavioral tasks. Students will finish the course with a research project on a topic of their choice graduate students will present this project to the class. Offered as BIOL𧉂 and BIOL𧊦. Prereq: Graduate standing.

BIOL𧊨. Introduction to Stem Cell Biology. 3 Units.

This discussion-based course will introduce students to the exciting field of stem cell research. Students will first analyze basic concepts of stem cell biology, including stem cell niche, cell quiescence, asymmetric cell division, cell proliferation and differentiation, and signaling pathways involved in these processes. This first part of the course will focus on invertebrate genetic models for the study of stem cells. In the second part of the course, students will search for primary research papers on vertebrate and human stem cells, and application of stem cell research in regenerative medicine and cancer. Finally, students will have the opportunity to discuss about ethical controversies in the field. Students will rotate in weekly presentations, and will write two papers during the semester. Students will improve skills on searching and reading primary research papers, gain presentation skills, and further their knowledge in related subjects in the fields of cell biology, genetics and developmental biology. This course may be used as a cell/molecular subject area elective for the B.A. and B.S. Biology degrees. Offered as BIOL𧉄 and BIOL𧊨. Prereq: Graduate standing.

BIOL𧊪. Genetics. 3 Units.

Transmission genetics, nature of mutation, microbial genetics, somatic cell genetics, recombinant DNA techniques and their application to genetics, human genome mapping, plant breeding, transgenic plants and animals, uniparental inheritance, evolution, and quantitative genetics. Offered as BIOL𧉆 and BIOL𧊪.

BIOL𧊫. Functional Genomics. 3 Units.

In this course, students will learn how to access and use genomics data to address questions in cell biology, development and evolution. The genome of Drosophila melanogaster will serve as a basis for exploring genome structure and learning how to use a variety of available software to identify similar genes in different species, predict protein sequence and functional domains, design primers for PCR, analyze cis-regulatory sequences, access microarray and RNAseq databases, among others. Classes will be in the format of short lectures, short oral presentations made by students and hands-on experimentation using computers. Discussions will be centered in primary research papers that used these tools to address specific biological questions. A final project will consist of a research project formulated by a group of 2-3 students to test a hypothesis formulated by the students using the bioinformatics tools learned in the course. Graduate students will be required to make additional presentations of research papers. They also will have additional questions in exams and a distinct page requirement on written assignments. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in Biology. Offered as BIOL𧉇 and BIOL𧊫. Prereq: Graduate standing.

BIOL𧊬. Plant Genomics and Proteomics. 3 Units.

The development of molecular tools has impacted agriculture as much as human health. The application of new techniques to improve food crops, including the development of genetically modified crops, has also become controversial. This course covers the nature of the plant genome and the role of sequenced-based methods in the identification of the genes. The application of the whole suite of modern molecular tools to understand plant growth and development, with specific examples related agronomically important responses to biotic and abiotic stresses, is included. The impact of the enormous amounts of data generated by these methods and their storage and analysis (bioinformatics) is also considered. Finally, the impact on both the developed and developing world of the generation and release of genetically modified food crops will be covered. Recommended preparation: BIOL𧉆. Offered as BIOL𧉈 and BIOL𧊬.

BIOL𧊭. Genome Dynamics. 3 Units.

We will examine how the physical architecture of the genome facilitates a dynamic genome ecosystem. Topics will be selected from current research in the field, including: how the three dimensional architecture of chromosomes within the nucleus impacts information storage and retrieval, how biochemical phase separation impacts nucleic acid storage (including RNA), how structural features of chromosomes are critical for function, genome engineering approaches, and the clinical implications of mutations in the 3D nuclear architecture. Course materials will come from the primary research literature, supplemented with appropriate background material. This course fulfills the cell and molecular biology breadth requirement of the BA and BS in Biology. Counts as a SAGES Departmental Seminar. Offered as BIOL𧉉 and BIOL𧊭. Counts as SAGES Departmental Seminar.

BIOL𧊯. Statistical Methods I. 3 Units.

Application of statistical techniques with particular emphasis on problems in the biomedical sciences. Basic probability theory, random variables, and distribution functions. Point and interval estimation, regression, and correlation. Problems whose solution involves using packaged statistical programs. First part of year-long sequence. Offered as ANAT𧊯, BIOL𧊯, CRSP𧊯, PQHS𧊯 and MPHP𧊯.

BIOL𧊰. Statistical Methods II. 3 Units.

Methods of analysis of variance, regression and analysis of quantitative data. Emphasis on computer solution of problems drawn from the biomedical sciences. Design of experiments, power of tests, and adequacy of models. Offered as BIOL𧊰, PQHS𧊰, CRSP𧊰 and MPHP𧊰. Prereq: PQHS/EPBI 431 or equivalent.

BIOL𧊴. Aquatic Biology. 3 Units.

Physical, chemical, and biological dynamics of lake ecosystems. Factors governing the distribution, abundance, and diversity of freshwater organisms. This course satisfies the Population Biology/Ecology breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧉐 and BIOL𧊴.

BIOL𧊶. Ichthyology. 4 Units.

Biology of fishes. Students will develop fundamental understanding of the evolutionary history and systematics of fishes to provide a context within which they can address aspects of biology including anatomy, physiology (e.g., in species that change sex osmoregulation in freshwater vs. saltwater), and behavior (e.g., visual, auditory, chemical, electric communication social structures), ecology, and evolution (e.g., speciation). We will explore the biodiversity of fishes around the world, with emphasis on Ohio species, by examining preserved specimens, observing captive living specimens, and observing, capturing, and identifying wild fishes in their natural habitats. Practical applications will be emphasized, such as aquaculture, fisheries management, and biomedical research. Course will conclude with an analysis of the current global fisheries crisis that has resulted from human activities. There will be many field trips and networking with the Cleveland Metroparks Zoo, the Cleveland Museum of Natural History, and local, state, and federal government agencies. Some classes meet at the Cleveland Museum of Natural History. This course satisfies a laboratory requirement of the B.A. and B.S. in biology. The graduate version of the course requires a research project and term paper. Offered as BIOL𧉒 and BIOL𧊶. Prereq: Graduate Standing.

BIOL𧊺. Parasitology. 3 Units.

This course will introduce students to classical and current parasitology. Students will discuss basic principles of parasitology, parasite life cycles, host-parasite interaction, therapeutic and control programs, epidemiology, and ecological and societal considerations. The course will explore diverse classes of parasitic organisms with emphasis on protozoan and helminthic diseases and the parasites' molecular biology. Group discussion and selected reading will facilitate further integrative learning and appreciation for parasite biology. This course counts as an elective in the cell/molecular biology subject area for the Biology B.A. and B.S. degrees. Offered as BIOL𧉖 and BIOL𧊺. Prereq Graduate standing and consent of instructor.

BIOL𧊻. Microbiology. 3 Units.

The physiology, genetics, biochemistry, and diversity of microorganisms. The subject will be approached both as a basic biological science that studies the molecular and biochemical processes of cells and viruses, and as an applied science that examines the involvement of microorganisms in human disease as well as in workings of ecosystems, plant symbioses, and industrial processes. The course is divided into four major areas: bacteria, viruses, medical microbiology, and environmental and applied microbiology. Offered as BIOL𧉗 and BIOL𧊻.

BIOL𧋃. Principles of Ecology. 3 Units.

This lecture course explores spatial and temporal relationships involving organisms and the environment at individual, population, and community levels. An underlying theme of the course will be neo-Darwinian evolution through natural selection with an emphasis on organismal adaptations to abiotic and biotic environments. Studies and models will illustrate ecological principles, and there will be some emphasis on the applicability of these principles to ecosystem conservation. This course satisfies the Population Biology/Ecology breadth requirement of the B.A. and B.S. in Biology. Students taking the graduate level course will prepare a grant proposal in which hypotheses will be based on some aspect of ecological theory. Offered as BIOL𧉟 and BIOL𧋃.

BIOL𧋃L. Principles of Ecology Laboratory. 2 Units.

Students in this laboratory course will conduct a variety of ecological investigations that are designed to examine relationships involving organisms and the environment at individual, population, and community levels. Descriptive and hypothesis-driven investigations will take place at Case Western Reserve University's Squire Valleevue Farm, in both field and greenhouse settings. The course is designed to explore as well as test a variety of ecological paradigms. Students taking the graduate level course will prepare a grant proposal in which hypotheses will be based on a select number of lab investigations. This course satisfies a laboratory requirement for biology majors. Offered as BIOL𧉟L and BIOL𧋃L.

BIOL𧋄. Ecology and Evolution of Infectious Diseases. 3 Units.

This course explores the effects of infectious diseases on populations of hosts, including humans and other animals. We will use computer models to study how infectious diseases enter and spread through populations, and how factors like physiological and behavioral differences among host individuals, host and pathogen evolution, and the environment affect this spread. Our emphasis will be on understanding and applying quantitative models for studying disease spread and informing policy in public health and conservation. To that end, computer labs are the central component of the course. This course satisfies a laboratory requirement of the B.A. in biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in biology. Offered as BIOL𧉠 and BIOL𧋄. Prereq: Graduate standing.

BIOL𧋅. Ecophysiology of Global Change. 3 Units.

Global change is an emerging threat to human health and economic stability. Rapid changes in climate, land use, and prevalence of non-native species generate novel conditions outside the range of typical conditions under which organisms evolved. Already we are witnessing the global redistribution of plants and animals, changes in the timing of critical life cycle events, and in some cases local extinction of populations. This course explores the impacts of global change on biological systems at levels from individuals to ecosystems among animals, plants and microbes across ecological to evolutionary timescales and from local to global spatial scales. Throughout, physiology is emphasized as a core driver of biological responses to global change. Traditional lectures will be accompanied by discussions of primary literature articles. The laboratory component will involve the development of an independent project at the University Farm, and dissemination of results through traditional (e.g. written paper) and new (e.g. podcast) media. This class will fulfill a laboratory requirement of the B.A. in Biology. This class will fulfill an additional laboratory requirement of the B.S. in Biology. Offered as BIOL𧉡 and BIOL𧋅. Prereq: Graduate Standing.

BIOL𧋉. Conversations on Protein Structure and Function. 2 Units.

The goal of this course is to supplement the short and basic presentation of Proteins in C3MB by lectures and discussions for students with backgrounds in physical-chemical sciences or students who already have a good basic background in protein science. The course presents an overview of Protein structure/function. Following an introduction to the principles of protein structure, the physical basis of protein folding and stability, and a brief overview of structural and bioinformatics approaches to protein analysis is presented. Typically two lecture/discussion style presentations are followed by a student lead journal club on recent high profile papers. The way the Journal club is done is that one student presents a paper (background and figures in powerpoint slides) while presentation of the main figures is shared between the class. Papers and Figures will be assigned by instructor. Typically two papers will be presented per session. Offered as PHOL𧋈 and BIOL𧋉.

BIOL𧋊. Animal Behavior. 4 Units.

Ultimately the success or failure (i.e., life or death) of any individual animal is determined by its behavior. The ability to locate and capture food, avoid being food, acquiring and defending territory, and successfully passing your genes to the next generation, are all dependent on complex interactions between an animal's design, environment and behavior. This course will be an integrative approach emphasizing experimental studies of animal behavior. You will be introduced to state-of-the-art approaches to the study of animal behavior, including neural and hormonal mechanisms, genetic and developmental mechanisms and ecological and evolutionary approaches. We will learn to critique examples of current scientific papers, and learn how to conduct observations and experiments with real animals. We will feature guest appearances by the Curator of Research from the Cleveland MetroParks Zoo and visits to working animal behavior research labs here at CWRU. Group discussions and writing will be emphasized. This course satisfies a laboratory requirement for biology majors. Offered as BIOL𧉦 and BIOL𧋊.

BIOL𧋎. Principles of Developmental Biology. 3 Units.

The descriptive and experimental aspects of animal development. Gametogenesis, fertilization, cleavage, morphogenesis, induction, differentiation, organogenesis, growth, and regeneration. Students taking the graduate-level course will prepare an NIH-format research proposal as the required term paper. Offered as BIOL𧉪, BIOL𧋎 and ANAT𧋎.

BIOL𧋐. Research Methods in Evolutionary Biology. 3 Units.

The process of evolution explains not only how the present diversity of life on earth has formed, but also provides insights into current pressing issues today, including the spread of antibiotic resistance, the causes of geographic variation in genetic diseases, and explanations for modern patterns of extinction risk. Students in Research Methods in Evolutionary Biology will be introduced to several of the major research approaches of evolutionary biology, including methods of measuring natural selection on the phenotypic and genotypic levels, quantifying the rate of evolution, reconstructing evolutionary relationships, and assessing the factors that affect rates of speciation and extinction. The course will consist of a combination of interactive lectures, in-class problem solving and data analysis, and the discussion of peer-reviewed scientific papers. Grades are based on participation in class, discussions and written summaries of published papers, in-class presentations, and two writing assignments. Offered as BIOL𧉬 and BIOL𧋐. Counts as SAGES Departmental Seminar. Prereq: BIOL𧇖, BIOL𧇘, BIOL 251.

BIOL𧋑. Evo-Devo:Evolution of Body Plans and Pathologies. 3 Units.

This discussion-based course offers a detailed introduction to Evolutionary Developmental Biology. The field seeks to explain evolutionary events through the mechanisms of Developmental Biology and Medical Genetics. The course is structured into different modules. First we will look at the developmental genetic mechanisms that can cause variation and medical pathologies. Then we focus on how alterations of these mechanisms can generate novel structural changes. We will then examine a few areas of active debate, where Evo-Devo is attempting to solve major problems in evolutionary biology and congenital birth defects. We will conclude with two writing assignments. Students will be required to present, read, and discuss primary literature in each module. This course is offered as a SAGES Departmental Seminar and fulfills a Cell and Molecular breadth requirement of the BA and BS in Biology. Offered as BIOL𧉭 and BIOL𧋑. Counts as SAGES Departmental Seminar.

BIOL𧋓. Biorobotics Team Research. 3 Units.

Many exciting research opportunities cross disciplinary lines. To participate in such projects, researchers must operate in multi-disciplinary teams. The Biorobotics Team Research course offers a unique capstone opportunity for undergraduate students to utilize skills they developed during their undergraduate experience while acquiring new teaming skills. A group of eight students form a research team under the direction of two faculty leaders. Team members are chosen from appropriate majors through interviews with the faculty. They will research a biological mechanism or principle and develop a robotic device that captures the actions of that mechanism. Although each student will cooperate on the team, they each have a specific role, and must develop a final paper that describes the research generated on their aspect of the project. Students meet for one class period per week and two 2-hour lab periods. Initially students brainstorm ideas and identify the project to be pursued. They then acquire biological data and generate robotic designs. Both are further developed during team meetings and reports. Final oral reports and a demonstration of the robotic device occur in week 15. Offered as BIOL𧉹, EMAE𧉹, BIOL𧋓, and EMAE𧋝. Counts as SAGES Senior Capstone.

BIOL𧋔. Topics in Evolutionary Biology. 3 Units.

The focus for this course on a special topic of interest in evolutionary biology will vary from one offering to the next. Examples of possible topics include theories of speciation, the evolution of language, the evolution of sex, evolution and biodiversity, molecular evolution. ANAT/ANTH/EEPS/PHIL/PHOL𧋓/BIOL𧋔 will require a longer, more sophisticated term paper, and additional class presentation. Offered as ANTH𧉯, BIOL𧉰, EEPS𧉯, PHIL𧉯, ANAT𧋓, ANTH𧋓, BIOL𧋔, EEPS𧋓, PHIL𧋓 and PHOL𧋓.

BIOL𧋗. Foundations of Advanced Ecology. 3 Units.

Advanced ecology, including discussion of the classic literature, in-depth study of key terms and concepts, applications of these foundational ideas to the modern literature, and current and future directions in the field. Intended for graduate students who have already taken undergraduate ecology (BIOL𧉟/451 or equivalent). Prereq: Graduate standing.

BIOL𧋘. Foundations of Advanced Evolution. 3 Units.

Advanced evolutionary biology, including discussion of the classic literature, in-depth study of key terms and concepts, applications of these foundational ideas to the modern literature, and current and future directions in the field. Intended for graduate students who have already taken undergraduate evolution. Prereq: Graduate standing.

BIOL𧋙. Introduction to Neurobiology. 3 Units.

How nervous systems control behavior. Biophysical, biochemical and molecular biological properties of nerve cells, their organization into circuitry, and their function within networks. Emphasis on quantitative methods for modeling neurons and networks, and on critical analysis of the contemporary technical literature in the neurosciences. Term paper required for graduate students. This course satisfies a lab requirement for the B.A. in Biology, and a Quantitative Laboratory requirements for the B.S. in Biology. Offered as BIOL𧉵, BIOL𧋙, and NEUR𧋙.

BIOL𧋚. Neurobiology of Behavior. 3 Units.

In this course, students will examine how neurobiologists interested in animal behavior study the linkage between neural circuitry and complex behavior. Various vertebrate and invertebrate systems will be considered. Several exercises will be used in this endeavor. Although some lectures will provide background and context on specific neural systems, the emphasis of the course will be on classroom discussion of specific journal articles. In addition, students will each complete a project in which they will observe some animal behavior and generate both behavioral and neurobiological hypotheses related to it. In lieu of examinations, students will complete three written assignments, including a theoretical grant proposal, a one-page Specific Aims paper related to the project, and a final project paper. These assignments are designed to give each student experience in writing biologically-relevant documents. Classroom discussions will help students understand the content and format of each type document. They will also present their projects orally to the entire class. Offered as BIOL𧉶, BIOL𧋚 and NEUR𧋚. Counts as SAGES Departmental Seminar.

BIOL𧋞. Computational Neuroscience. 3 Units.

Computer simulations and mathematical analysis of neurons and neural circuits, and the computational properties of nervous systems. Students are taught a range of models for neurons and neural circuits, and are asked to implement and explore the computational and dynamic properties of these models. The course introduces students to dynamical systems theory for the analysis of neurons and neural learning, models of brain systems, and their relationship to artificial and neural networks. Term project required. Students enrolled in MATH𧋞 will make arrangements with the instructor to attend additional lectures and complete additional assignments addressing mathematical topics related to the course. Recommended preparation: MATH𧇟 and MATH𧇠 or BIOL𧈬 and BIOL𧈲. Offered as BIOL𧉺, COGS𧉺, MATH𧉺, BIOL𧋞, CSDS𧋞, EBME𧋞, ECSE𧋞, MATH𧋞 and NEUR𧋞.

BIOL𧋟. Transformative Animal Models in Modern Biology. 3 Units.

Animal models are extremely important in the study of biology and in modern medicine. They allow us to determine fundamental biological mechanisms and cellular and molecular causes of disease. There is logic to how each animal model has found its place in the menagerie of accepted animal models. Certain animal models allow us to test particular hypotheses that may not be possible to address in other animals. Moreover, some animal models are more relevant than others to studying a particular human disease. This seminar-based course will focus on animal models that either are effective at modeling human disease, approach relevant neurobiological questions, or play a role in translational medicine. The course will focus on mammalian and non-mammalian animal models that are important to biomedical research, including the primate, mouse, zebrafish, and roundworm. Comparisons between popular animal models will be made. This course satisfies the Organismal breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧉻 and BIOL𧋟. Counts as SAGES Departmental Seminar. Prereq: Graduate Standing.

BIOL𧋠. Physiology of Organ Systems. 4 Units.

Our intent is to expand the course from the current 3 hours per week (1.5 hour on Monday and Wednesday) to 4 hours per week (1.5 hours on Monday and Wednesday plus 1 hour on Friday). Muscle structure and Function, Myasthenia gravis and Sarcopenia Central Nervous System, (Synaptic Transmission, Sensory System, Autonomic Nervous System, CNS circuits, Motor System, Neurodegenerative Diseases, Paraplegia and Nerve Compression) Cardiovascular Physiology (Regulation of Pressure and flow Circulation, Cardiac Cycle, Electrophysiology, Cardiac Function, Control of Cardiovascular function, Hypertension) Hemorragy, Cardiac Hypertrophy and Fibrillation Respiration Physiology (Gas Transport and Exchange, Control of Breathing, Acid/base regulation, Cor Pulmonaris and Cystic Fibrosis, Sleeping apnea and Emphysema) Renal Physiology (Glomerular Filtration, Tubular Function/transport, Glomerulonephritis, Tubulopaties) Gastro-Intestinal Physiology (Gastric motility, gastric function, pancreas and bile function, digestion and absorption, Liver Physiology Pancreatitis, Liver Disease and cirrhosis) Endocrine Physiology (Thyroid, Adrenal glands, endocrine pancreas, Parathyroid, calcium sensing receptor, Cushing and diabetes, Reproductive hormones, eclampsia) Integrative Physiology (Response to exercise, fasting and feeding, aging). For all the classes, the students will receive a series of learning objectives by the instructor to help the students address and focus their attention to the key aspects of the organ physiology (and physiopathology). The evaluation of the students will continue to be based upon the students' participation in class (60% of the grade) complemented by a mid-term and a final exam (each one accounting for 20% of the final grade). Offered as BIOL𧋠 and PHOL𧋠.

BIOL𧋫. Contemporary Biology and Biotechnology for Innovation I. 3 Units.

The first half of a two-semester sequence providing an understanding of biology as a basis for successfully launching new high-tech ventures. The course will examine physical limitations to present technologies and the use of biology to identify potential opportunities for new venture creation. The course will provide experience in using biology in both identification of incremental improvements and as the basis for alternative technologies. Case studies will be used to illustrate recent commercially successful (and unsuccessful) biotechnology-based venture creation and will illustrate characteristics for success.

BIOL𧋬. Contemporary Biology and Biotechnology for Innovation II. 3 Units.

Continuation of BIOL𧋫 with an emphasis on current and prospective opportunities for Biotechnology Entrepreneurship. Longer term opportunities for Biotechnology Entrepreneurship in emerging areas including (but not limited to) applications of DNA sequence information in medicine and agriculture energy and the environment biologically-inspired robots. Recommended preparation: BIOL𧋫 or consent of department.

BIOL𧋭. Feasibility and Technology Analysis. 3 Units.

This course provides the tools scientists need to determine whether a technology is ready for commercialization. These tools include (but are not limited to): financial analysis, market analysis, industry analysis, technology analysis, intellectual property protection, the entrepreneurial process and culture, an introduction to entrepreneurial strategy and new venture financing. Deliverables will include a technology feasibility analysis on a possible application in the student's scientific area. Offered as BIOL𧋭, CHEM𧋭, and PHYS𧋭.

BIOL𧋯. Introduction to Graduate School in the Biological Sciences. 1 Unit.

This course will help incoming Biology MS and Ph.D. students navigate their way through graduate school and participate in the scientific process. Students in the Biology graduate program will be strongly encouraged to take this course in their first year. This will be a skill-based course that will become part of their academic toolbox. In addition, there will be sessions to offer general tips for life in graduate school. Prereq: Graduate Standing.

BIOL𧋱. Molecular Phylogenetics. 4 Units.

This course is designed to teach the theory and practice of molecular based phylogenetics with attention to evolutionary analysis through lecture, readings, discussion, and a quantitative laboratory section. A comprehensive overview of the history of systematics and morphology based phylogenetics will help familiarize students with the theory, methods, and character analysis frameworks used in current genetic based approaches. A laboratory section of the course will provide working knowledge in designing and carrying out an original phylogenetics project beginning with data procurement to writing a research manuscript. Through readings and discussions of research articles as well as presented content, the relevant course material will be utilized in practice by students analyzing their project data sets. The semester-long research project will take students through the process of building a data set, aligning sequences, reconstructing phylogenies, conducting evolutionary analyses, and interpreting and writing results as a scientific manuscript. In addition, students will orally present their research proposal as well as the final research project. Undergraduate students will work in teams of two on the research project component of the course and independently throughout the other course components (discussions). Graduate students will work independently and have an extra assignment. This course satisfies a laboratory requirement of the B.A. in Biology. This course satisfies a laboratory or quantitative laboratory requirement of the B.S. in Biology. Offered as: BIOL𧊍 and BIOL𧋱. Prereq: Graduate Standing.

BIOL𧋲. Modern Human Biological Variation. 3 Units.

The objectives of this course are to provide students with an introduction to human biological variation and to understand the variation within an evolutionary framework through lecture, readings, discussion, and labs. We will examine the patterns of morphological and genetic variation in modern human populations and discuss the evolutionary explanations for the observed patterns. In order to do this, we will first build a solid foundation in the scientific method, population genetics, and evolutionary theory before exploring the adaptive significance of the observed variation. A major component of the class will be the discussion of the social and health implications of these patterns of biological variation, particularly in the construction and application of the concept of race and its use in medicine. There are three units to the course. Unit 1 focuses on the fundamentals to understanding biological variation, we will cover basic population genetics, evolution, and the human fossil record. Unit 2 concentrates on surveying modern human biological variation, examining both morphological and genetic traits, and why these variations exist. Unit 3 examines how race is constructed using population-based biological differences, its validity, and the implications for health and medicine. This course fulfills the Population and Ecology breadth requirement of the B.A. and B.S. in Biology. Offered as BIOL𧊎 and BIOL𧋲. Prereq: Graduate Standing.

BIOL𧌥. Mathematical Life Sciences Seminar. 1 - 3 Units.

Continuing seminar on areas of current interest in the applications of mathematics to the life sciences. Allows graduate and advanced undergraduate students to become involved in research. Topics will reflect interests and expertise of the faculty and may include topics in mathematical biology, computational neuroscience, mathematical modeling of biological systems, models of infectious diseases, computational cell biology, mathematical ecology and mathematical biomedicine broadly construed. May be taken more than once for credit.

BIOL𧍗. Advanced Independent Study for Graduate Students. 1 - 3 Units.

Independent study of advanced topics in biology under the supervision of a biology faculty member. Registration requires submission of a proposal for a project or study and approval of the department.