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Comparative leg sizes

Comparative leg sizes


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When I was a child, my father showed me the classic essay "On Being the Right Size", J. B. S. Haldane. It talks (among other things) about how large animals need stockier legs to support their weight. I weigh about the same per leg as a 350 lb deer, but my legs are closer in diameter to those of a 1500 lb horse. Why?


There is an interesting relationship between the length of an animals femur, the thickness and the mass of the thickness. A point that should be taken into account is that bones can different densities and so might be able to support varying amounts. The muscle in you leg also does nothing for the support of you weight it is (basically) all in the bone. Really looking purely at the leg won't tell you much you need to strip back the tissue and get you measurements straight from that. Given the different gate strategies of various animals this can lead to differing levels of muscle surrounding the leg and could be confounding your answer.

Walter Lewin a professor of physics at MIT did a lecture series where in the first lecture he went off on one about the relative sizes and thickness of animal femurs and it is really interesting (http://www.youtube.com/watch?v=PmJV8CHIqFc - between 11 minutes and 22 minutes). The short answer was that the ratio between the thickness and the length stays similar relative to the length.


Comparative morphology of the prothoracic leg in heliconian butterflies: Tracing size allometry, podite fusions and losses in ontogeny and phylogeny

Prothoracic legs of heliconian butterflies (Nymphalidae, Heliconiinae, Heliconiini) are reduced in size compared to mesothoracic and metathoracic legs. They have no apparent function in males, but are used by females for drumming on host plants, a behavior related to oviposition site selection. Here, taking into account all recognized lineages of heliconian butterflies, we described their tarsi using optical and scanning electron microscopy and searched for podite fusions and losses, and analyzed allometry at the static, ontogenetic and phylogenetic levels. Female tarsi were similar, club-shaped, showing from four to five tarsomeres, each bearing sensilla chaetica and trichodea. Male tarsi were cylindrical, formed from five (early diverging lineages) to one (descendant lineages) either partially or totally fused tarsomeres, all deprived of sensilla. Pretarsi were reduced in both sexes, in some species being either vestigial or absent. Tarsal lengths were smaller for males in almost all species. An abrupt decrease in size was detected for the prothoracic legs during molting to the last larval instar at both histological and morphometric levels. In both sexes, most allometric coefficients found at the population level for the prothoracic legs were negative compared to the mesothoracic leg and also to wings. Prothoracic tarsi decreased proportionally in size over evolutionary time the largest and smallest values being found for nodes of the oldest and youngest lineages, respectively. Our results demonstrate that evolution of the prothoracic leg in heliconian butterflies has been based on losses and fusions of podites, in association with negative size allometry at static, ontogenetic and phylogenetic levels. These processes have been more pronounced in males. Our study provided further support to the hypothesis that evolution of these leg structures is driven by females, by changing their use from walking to drumming during oviposition site selection. In males the leg would have been selected against due to absence of function and thus progressively reduced in size, in association with podites fusions and lost.

Keywords: Allometric growth Drumming behavior Evolutionary losses Heliconian butterflies Host plant selection Insect legs.


Scaling functions to body size: theories and facts

FIG1`Why do small animals live faster and shorter?' `What sets the pace of life?' These are questions that have interested biologists for more than 150 years, leading to debates between theorists and experimentalists that continue today. As early as 1839, Sarrus and Rameaux (1839) realized that metabolic power cannot increase with the third power of the linear dimension or body mass, but is limited by the capacity to get rid of heathence, for organisms to stay in energy balance, metabolism can only vary in proportion to their surface area. Rubner(1883) found in fact that metabolic rate in dogs was in proportion to body surface area and proposed that it should scale with body mass raised to the power of 2/3. Obtaining estimates of basal metabolic rate (BMR) on a large number of species small and large, Kleiber (1932)experimentally found a (close to) 3/4 exponent to describe the relationship between BMR and body mass rather than the 2/3 exponent predicted from Rubner's`law'. Kleiber's `law' has been confirmed by many studies since(Schmidt-Nielsen, 1984), even though it continues to be contested.

Knut Schmidt-Nielsen on a field trip to the Masai Mara in Kenya in 1977 with C. Richard Taylor from Harvard University and Ewald R. Weibel from the University of Berne and their collaborators working on the scaling of metabolic rate in African mammals.

This Special Issue is dedicated to Knut Schmidt-Nielsen - pioneer,mentor, friend

Knut Schmidt-Nielsen on a field trip to the Masai Mara in Kenya in 1977 with C. Richard Taylor from Harvard University and Ewald R. Weibel from the University of Berne and their collaborators working on the scaling of metabolic rate in African mammals.

This Special Issue is dedicated to Knut Schmidt-Nielsen - pioneer,mentor, friend

In contrast to Rubner's surface law, Kleiber's 3/4 exponent is enigmatic,with no obvious relation to body design. A quest for explaining such an important allometric relationship fostered new theories. McMahon(1975) developed the concept of elastic similarity, stating that the likelihood of elastic failure of support structures should be kept similar in animals of all sizes. The result of this analysis indicates that legs of smaller animals can be more slender than legs of large animals. Considering elastic similarity and that the power costs of muscle work are proportional to muscle cross-sectional area, the 3/4 scaling of MR is obtained, and thus scaling theory and the experimental evidence can be brought in line. Using an entirely different intellectual approach, West et al. (1997) have more recently invoked the fractal nature of the (energy) distributing vascular network in animals, to arrive at the 3/4 scaling exponent from first principles. A similar approach, also yielding a 3/4 scaling exponent but using fewer assumptions, has been proposed by Banvar et al.(1999). Bejan's `constructal theory' (Bejan, 2000, and p. 1677) also explains a 3/4 scaling exponent by considering that flow architectures can be deduced by a single law of maximization of access for currents.

So where do we stand today? This review volume tries to answer this question by having scientists from different areas present their theories or their experimental data. By contrasting theories with data the debate becomes transparent and the reader must make his choice - a meeting that preceded this volume was certainly spiked with numerous and heated debates, with no resolution of the conflicts. There was only one consensus that could be reached by all attending: `there is scaling' - but `how' and`why'?

On the question of principles, there are two fundamentally different approaches on which the papers presented here are based. (1) Experimentalists explore the fascinating range of variations that occur in nature, one case being the modulation of the basic blueprint of animals to accommodate the same functions in bodies of varying size, from 2 g to 5 tons in mammals whereas(2) the theorists seek explanations from first principles for empirically established relationships, for example the scaling of metabolic rate with body size. Ideally the predictions of theory should be supported by evidence, but here the crux is that life conditions are not always simple. For example, it is important to realize that the metabolic rate of an animal will depend on many factors and can easily vary by factors of 10 or more, depending on the level of activity. Even though the 3/4 power law predicts that the mass-specific basal metabolic rate of a mouse of 20 g is five times greater than that of a 500 kg racehorse, when these two animals run as hard as they can their maximal metabolic rate per gram body mass is nearly the same. The conditions under which measurements are made must therefore be clearly defined, and the theories must account for this variation in metabolic scope. Theory and experiments must, in the end, converge.

What ultimately determines the scaling of a function with body size? An answer to this can only be found by developing mechanistic theories based on an understanding of the underlying functional principles and processes. For the case of metabolic rate, two powerful `models' or `theories' are presented in this issue (West et al., p. 1575 and Bejan, p. 1677), which both predict that metabolism should scale with the 3/4 power of body mass Mb on the basis of the design properties of the vascular system. For a biologist it seems hard to accept a priori that the rate of energy utilization in animals should be dictated by its `fuel delivery' system: he would think of animals as systems driven by demand rather than supply of energy. The vasculature is highly malleable and molecular mechanisms have been discovered that can adjust the supply to the demand of the tissues. But maybe it is simply not as simple. A possible solution to the problem of supply vs demand control of metabolism is offered by the proposition of `multi-level regulation of metabolic scaling' by Suarez and Darveau (p. 1627). They consider that supply and demand systems have co-evolved and that observed metabolic scaling is the consequence of the contribution of various steps (in an allometric cascade model) controlling both supply and demand processes relevant in setting the rate energy utilization in animals (Darveau et al.,2002). The problem here, however, is that such a model is hard to reduce to first principles and that power law scaling does not follow directly from the theory. And furthermore, if the sequential steps are all co-adjusted to an integral performance level it will be hard if not impossible to sort out primary and secondary effects.

The second caveat with modeling BMR to the 3/4 power is that BMR is only one, and quite artificial, state of living for an animal as it reflects the absolute minimum of energy needs. But energy supply must be able to accommodate a large range of different functional or metabolic states. Which of these has the strongest evolutionary effect? Maybe it would be better to consider the scaling of field metabolic rate (FMR) - the average metabolic rate effectively expended by animals over longer time periods going about their daily business of surviving (see Nagy, 1999, and p. 1621). The upper well-defined end point of the metabolic scope, maximal metabolic rate(MMR) achieved by animals running under conditions of maximal aerobic energy flow (Weibel et al., 2004Weibel and Hoppeler, p. 1635), is also a candidate to be considered and analyzed in terms of the `scaling laws', because it is a state that may be highly pertinent for survival and hence for selection in evolution. Looking at the three contributions in this issue of JEB dealing with BMR, FMR and MMR, we can find no convincing evidence for a general 3/4 power scaling of metabolic rate in any of these conditions. White and Seymour (2000, and p. 1611) argue that the observed 3/4 power scaling of BMR is an artifact of the inclusion of large herbivores in the published BMR datasets, as these animals take very long time periods to become post-absorptive because of fermentation of food stuffs and hence inflate the scaling exponent. They report the `true' exponent for BMR to be 0.686, closer to the 2/3 power suggested by Rubner. For FMR,Nagy (p. 1621) reports scaling exponents ranging from <0.6 to >0.9 in 229 species of mammals, birds and reptiles. For mammals weighing 7 g to 500 kg, the scaling exponent for MMR is found to be 0.872, which is identical to the scaling of mitochondrial volume in the musculature of these animals(Weibel and Hoppeler, p. 1635). Considering all these conditions, is it then possible to find a simple universal scaling law for metabolic rate that is supported, or at least not refuted, by the experimental data?

In all this we must bear in mind that observed overall metabolic rate is the reflection of a multitude of functions of the whole body, from cell activity to locomotor performance, from the circulation of blood to digestion,respiration or reproduction, and much more. We have therefore included in this volume a number of contributions that extend beyond metabolism, in order to give a broader overview of current issues in scaling as seen by prominent comparative biologists short resumes of these are covered in `Inside JEB'. All these functions take place in a well-integrated system whereby some functions run in parallel while others are in series. Can such a system be simple and reducible to first principles? Or can complexity theory make a complex system simple? These questions provide food for further reflection that we hope will be fostered by the set of papers collected here.


2 thoughts on &ldquo Size Matters &rdquo

Fascinating! But very sad about Tusko the elephant. What a tragic story.

I really like what JBS Haldane has to say about this topic:
“The most obvious differences between different animals are differences of size, but for some reason the zoologists have paid singularly little attention to them. In a large textbook of zoology before me I find no indication that the eagle is larger than the sparrow, or the hippopotamus bigger than the hare, though some grudging admissions are made in the case of the mouse and the whale. But yet it is easy to show that a hare could not be as large as a hippopotamus, or a whale as small as a herring. For every type of animal there is a most convenient size, and a large change in size inevitably carries with it a change of form.”


Discussion

Genome assembly

The genomes of four chromosomal races of the viatica species group that we assembled here with 2.94–3.27 Gb assembly sizes are the third largest assembled insect genomes so far, with the largest being the two locust grasshoppers L. migratoria and Schistocerca gregaria with 6.5 and 8.6 Gb assembly sizes, respectively [55, 56]. We believe that genome size estimates based on k-mer analysis better represent the genome size of these grasshoppers than the genome assembly sizes because highly repetitive sequences (e.g., centromeres, telomeres, satDNAs, non-recombining part of sex chromosomes) are likely collapsed during the assembly process [66, 67, 78, 79]. However, the two different k-mer approaches yielded quite different estimates between the chromosomal races (3.30–3.82 Gb by Supernova, and 5.42–6.32 Gb by findGSE), the reasons for which remain unclear. The large differences in contig size (contig N50 29.11–35.69 kb) of the assembled genomes of the viatica species group, L. migratoria (contig N50 10.78 kb) [55] and S. gregaria (contig N50 12.03 kb) [56] are probably due to the difference in the DNA library preparation and sequencing methods. The L. migratoria genome is based on Illumina short reads (2 × 45–150 bp paired-end) with multiple insert-size libraries (i.e., four paired-end libraries ranging from 170 to 800 bp and five mate-pair libraries ranging from 2 to 40 kb) while we used linked reads (150 bp paired-end Illumina short reads with barcode information from long input DNA molecules), and the S. gregaria assembly used paired-end and mate-pair Illumina short reads and PacBio long reads. The scaffold N50 (158 kb) of the S. gregaria genome assembly (8.6 Gb) is smaller than the scaffold N50 (326 kb) of L. migratoria and the scaffold N50 (317 kb) that we obtained in the P24X0 race. In addition, the S. gregaria genome assembly is even more fragmented than the L. migratoria as indicated by the BUSCO scores (see [56]), indicating that assembling such large grasshopper genomes is challenging even using the combination of technologies above. Although the smaller genome assemblies of the viatica species group were more contiguous than the assembly of L. migratoria, they still contained missing and fragmented genes. This may be due to 1) large numbers of repetitive non-coding DNAs, 2) intron gigantism, 3) errors during the assembly process, 4) true missing genes, 5) failure in identifying any significant matches, and/or 6) failure in the gene prediction step to produce even a partial gene model that might have been recognized as a fragmented BUSCO match [65]. Among these, we suspect that intron gigantism and repetitive elements might be the main reasons for assembly fragmentation because the length of introns, intergenic regions, and repetitive elements in grasshoppers is much larger than that of D. melanogaster [55, 56], for example.

TE dynamics and genome evolution

Approximately 66 to 72% of the genome assembly of the viatica species group corresponds to TEs. These are even larger than the 60 to 62% reported for the genome assemblies of L. migratoria [55] and S. gregaria [56] respectively, likely owing to the combination of methodological approaches to annotate TEs that we used. Given the deep divergence of Eumastacoidea and Acridoidea (

197 million years ago [38]), the two Orthopteran superfamilies to which the viatica species group and the locusts grasshoppers belong, respectively, these findings suggest that large repeatomes are widespread in grasshoppers. The S. gregaria genome assembly has 18,815 annotated genes, and the L. migratoria genome assembly has a similar number of annotated genes (17,307) to those recently reported in two cricket species with genome assembly sizes of 1.6 Gb (TE content 40% [80]), indicating the absence of partial or whole genome duplication events in these orthopteran lineages. Additionally, there was no evidence for such large-scale genome duplication events in the viatica species group because only 3–5% of BUSCO genes were duplicated. Therefore, the large genome sizes in these grasshoppers are likely due to the expansion of TEs, which has been correlated with genome size evolution across the Tree of Life [2, 81]. Indeed, we found massive recent amplification in hundreds of Mb (between 314 and 464 Mb) of the TE groups per genome assembly, an amount that is notably larger than the estimated genome size of many other insects [54, 81]. The recent amplification mainly occurred in eight TE superfamilies (DNA/DNA, DNA/P, DNA/Sola, DNA/hAT, DNA/TcMar, Helitron, LINE/L2, LTR/LTR, LTR/Gypsy and SINE/tRNA) with largest variation for LTR/Gypsy and DNA/TcMar, indicating that the recent amplifications of TE superfamilies have widely shaped the TE landscape in the genomes of the chromosomal races. We thus suggest that the massive proliferation of TEs combined with a slow deletion rate might contribute to the genomic gigantism in grasshoppers, as proposed for other large eukaryotic genomes [81]. In this regard, it is worth mentioning that our estimation of massive recent proliferation of TEs (314–464 Mb per assembly) is likely underestimated because low-divergence TEs are generally underrepresented in genome assemblies [66, 67].

Recently active TEs are permissively transcribed in gonads

We restricted our analysis to transcripts that originated from recent TEs (i.e., K2P < 5%) because these are likely to be a relevant source of transcriptional and transpositional activity. Our results demonstrated that recently active TE superfamilies from all five major TE groups (LINE/SINE/DNA/Helitron/LTR) are transcribed, suggesting that at least some of the transcribed TEs are capable of (retro)transposition. Recent TE expression tended to be differentially expressed in gonads compared to somatic tissues, similar to that reported in mammalian lineages [82]. This indicates that TEs are likely transcribed and might transpose themselves more frequently in gonads, transmitting new TE insertions to the next generation. The grasshopper ovaries and testes showed uneven expression of recent TEs, suggesting that substantial TE transcriptional variation likely exists across sexes. The expression variation of recent TEs between reproductive and somatic tissues is puzzling especially because we used somatic body parts that contained multiple types of somatic tissues, and studies on vertebrates showed that there is great variability in TE expression levels across somatic tissues [83]. TE transcription also varies temporally with gonad development which explains the transcriptome complexity of gonads as a whole in animals [82, 84]. We speculate that the expression variation might result from either global epigenetic reprograming during gametogenesis or the many more cell types/stages present in gonads than in individual somatic tissues of these grasshoppers. Alternatively, TE control might be tighter in somatic tissues, such that tight repression of TEs is important for the host and more feasible in somatic tissues (no global epigenetic reprogramming). It remains to be investigated if higher transcriptional activities of all five major TE groups, particularly in reproductive tissues, is associated with higher TE repressive mechanism activation (piwi/piRNA pathway [85,86,87]) to prevent the potentially deleterious effects of TE (retro) transposition in the host during global epigenetic reprogramming [85,86,87,88]. To further address this, expression analyses of genes involved in the piwi/piRNA pathway will be needed together with small RNA sequencing data.

The chromosomal races of V. viatica species group share a common collection of satDNAs which mostly experienced quantitative changes during evolution

By performing a high-quality annotation of repeats, we uncovered the largest collection of satDNA families (129) ever reported for grasshopper genomes. We propose that the 102 satDNA families shared among all four chromosomal races (Additional file 1: Table S6 and S8) represent the “library” present in the viatica ancestor. The 27 satDNA families that were not shared between all the four races either emerged after the divergence of the viatica ancestor or were lost in one or more races. This implies that the essential step in the evolution of a satDNA family might either be the acquisition of biological functions or the accumulation of sufficiently many copies to be maintained in the “library” over long evolutionary periods. How the novel satDNA families emerged remains unclear in the viatica species group, although unequal crossing over, intra-strand homologous recombination, gene conversion, rolling-circle replication, and transposition are possible mechanisms [11, 14,15,16, 18, 20, 22]. After satDNA emergence, it is logical to assume that satDNA families stochastically expand or disappear and are only maintained in the long term if they acquire a function, such as in centromeres or heterochromatin formation. To test for satDNA functionality and to determine whether satDNAs were independently acquired or lost, additional data (e.g. chromosome in situ hybridization and ChIP-seq) is needed including races/species from the other morabine grasshoppers and under a robust phylogenetic hypothesis.

In line with the satDNA library hypothesis [28, 29], 50 of the 102 satDNA families shared among all four chromosomal races experienced quantitative changes in copy number, and these happened over different K2P bins of divergence (see Fig. 6b-d), suggesting parallel amplification of satDNAs in some races or contraction/deterioration in others. The changes in copy number likely occurred by unequal crossing over, which is the mechanism that can yield changes in TR abundance, either as gains (amplifications) or losses (contractions) [89]. The large number of satDNA families in these chromosomal races is puzzling. The non-coding satDNAs have been traditionally viewed as mostly useless material capable of accumulating primarily in heterochromatin [11,12,13, 32, 34] until they become a too heavy load for the host genome (reviewed in [50]). It will be interesting to test whether the differential amplification of satDNAs is correlated with the amount of heterochromatin or involved in the conversion of a euchromatic chromosome into a heterochromatic one, particularly in neo-Y chromosomes which have been shown to be a trap for satDNAs in grasshoppers and crickets (see [33, 34, 90]). On the other hand, it has been suggested that differential expression of satDNAs as satRNAs can cause genomic incompatibilities in hybrids because satRNAs play critical roles in kinetochore assembly (i.e., by binding to specific centromeric proteins like CENP-A and CENP-C) [30, 31, 50, 51], heterochromatin formation [49, 52, 53] and function during cell division via siRNAs and piRNA pathways in Schizosaccharomyces pombe, Drosophila, nematodes, humans [49,50,51,52,53, 91]. The satDNA families identified here are thus a set of candidates for future studies on which satDNAs are located in centromeres and which are involved in heterochromatin formation of grasshoppers.


Materials and methods

The protein sequences of the 127 completely sequenced eubacterial genomes at the time this paper was submitted for publication were retrieved from the Genome division, Entrez retrieval system of the National Center for Biotechnology Information (NCBI [39]). Table 1 shows a list with all the genomes used, with their genome size and accession numbers. To detect potentially homologous genes we started by carrying out an all-against-all BLASTP [40] search of every protein sequence in one genome against every protein sequence in all the other genomes. We then recorded the best reciprocal hit for each protein sequence with an E-value lower than 10 -5 and sequence identity higher than 50% over more than 60% of the length. To validate the results, we performed some representative comparisons by studying the distribution of the ratio of bit score to the maximal bit score [41]. This method would separate probable homology from random similarity. We obtained almost identical results, with only a reduced set of the respective homologous genes being different in the two lists. For example, out of 3,026 homolog pairs between E. coli K12 and S. typhimurium detected by the reciprocal hit method, only one pair was found to differ with the bit score method. In addition, only three genes were detected with the reciprocal best-hit method that were not selected as homologs using the bit score method (using a cut-off value of 0.4). Finally, the bit-score ratio method identified 165 additional homologs that were not selected using reciprocal best-hits because they did not satisfy the length and/or sequence-identity requirements. Therefore, the list of homologous genes obtained by reciprocal best-hits was used for all the analyses.

To detect potential paralogous genes, we carried out an all-against-all BLASTP [40] search of every protein sequence in a genome against every protein sequence in the same genome. We define paralogs as protein sequences satisfying an E-value threshold of 10 -5 in BLASTP [40] search and having at least 30% sequence identity over more than 60% of their lengths [3].

When comparing paralogs between two species, a gene family was created for each homologous gene detected in both genomes. This gave rise to some redundant families but ensured that the comparison between species was done between equivalent gene families. To describe the functional assignment of paralogous genes, extended gene families were created [3] that contained all genes that were interrelated by hits among any of their members. This is based on the transitive nature of sequence homology [34] and is supported by the findings on well-studied genomes of species with a relatively well-known metabolism. In these cases, extended gene families seem to be formed by genes involved in similar functions [4]. To minimize the incorporation of multidomain proteins in a family together with unrelated members [2], length cut-offs were kept at 60%. The assignment of a function to a gene was based on the Clusters of Orthologous Groups (COGs) classification [42].


Data availability

Raw sequencing data used in this study can be found in the NCBI database under the following Bioproject accession numbers: PRJNA603155 (genome sequencing dataset of Harukei-3 melon), PRJNA624817 (genome sequencing dataset of seven melon accessions), PRJNA603146 (ONT cDNA RNA-seq), PRJNA603129 (ONT direct RNA-seq), PRJNA603204 (tissue-wide RNA-seq of Harukei-3 melon), or PRJNA603202 (leaf RNA-seq in the greenhouse). Genome assembly and annotation of Harukei-3 melon (ver. 1.41 genome reference) is available on Melonet-DB (https://melonet-db.dna.affrc.go.jp/ap/dnl).


Teachers in any context could use this lesson. It is meant to be an investigation into homologous structures. The lesson is intended for middle school through high school but could easily be adapted for the younger age levels as well. This lesson would work for any class size. It is intended to be completed in one class (50 minutes) session. The only materials necessary would be colored pencils/markers/or crayons and copies of the bone structure of a bird and a human. This activity could be easily adapted into many different settings and difficulty levels.

This lesson can be introduced before, during, or after lessons on evolution and/or adaptation. Materials are simple – copies of the labeled bone structure of a bird and a human, and coloring materials. Consult your school's anatomy teacher or the internet or even your own textbook for examples. Students will be given the copies of the labeled bone structures and asked to color each similar bone type the same color (femur of both organisms orange, for example). Color does not matter, as long as the structures on each organism are the same color. Any different structures can be left blank (talons, for example). This will assist them to note differences later. After coloring, students can them make a list of the similarities and differences in the bone structures of each organism. A Venn diagram would be a good guide for comparison. Guide them particularly to the foot and ankle region of the bird, which "stands up" vs. on a human which lays flat. Guide students to take off their shoes if necessary to feel their own foot bones and have them lift their ankles off the floor while they are seated in a chair to observe how this positioning is similar to how a bird "perches" or stands. After students note the similarities and differences, guide them to circle and label the "common" part on each such as the "hip," "knee," "ankle," "foot" and "toes" of each. They should note the differences in the length of each but the similarities of how they bend (birds "knees" do NOT bend backwards – it is most often their "ankle" people think is the knee). Have students feel their own patella and direct them to the bird's patella. For closure, students can be challenged to "walk" like a bird. To do this, they can lift their ankles off the floor and walk on the ball of their feet and their bent toes. The teacher can ask how a bird's toes differ from a humans (much longer) and ask why they think this might be (to grasp a tree branch or food for example). This activity can easily be extended into discussions about anatomy and physiology (form and function), evolutionary tracks of prehistoric animals like dinosaurs, and even just bird identification, for example. In the case of comparing and contrasting to dinosaurs, it would be necessary to have illustrations of the bone structures of these as well. It could also be extended to other animals as well.


Results

Performance metrics

All described tools have been tested with regard to their assembly time, memory and CPU utilization.

Time requirements

Massive differences between the different tools were observed in terms of the run time for the assembly. Apart from tool-specific differences, input data and number of threads used had a huge impact on the time requirement. The observed run times varied from a few minutes to several hours (Fig. 1).

Computation time depending on number of threads and size of input data. The boxplots show the differences in demand of CPU time for different number of threads and input data size for the seven different assemblers

Some assemblies failed to finish within our time limit of 48 h. On average, the longest time to generate an assembly was taken by IOGA and Fast-Plast followed by ORG.Asm and GetOrganelle . The most time efficient tool was chloroExtractor , which was a little faster than NOVOPlasty and Chloroplast assembly protocol .

Not all tested tools were able to benefit from having access to multiple threads. Both NOVOPlasty and ORG.Asm required almost the same time independent of being allowed to utilize 1, 2, 4, or 8 threads. In contrast, Chloroplast assembly protocol , chloroExtractor , GetOrganelle , and Fast-Plast all profited from multi-threading settings (Figs. 1 and 2 and Additional file 1: Tables S4 to S6).

Performance metrics. Boxplots depicting the demand of CPU and RAM and disk space needed depending on the assembler, input data size and number of threads

Memory and CPU usage

The peak and mean CPU usage as well as peak memory and disk usage were recorded for all assemblers based on the same input data set and number of threads (Fig. 2 and Additional file 1: Tables S4 to S6). In general, the size of the input data influenced the peak memory usage with the exception of chloroExtractor and IOGA . Those two assemblers showed a memory usage pattern, which was less influenced by the size of the data. The number of allowed threads had only a limited impact on the peak memory usage. All programs profited from a higher number of threads, if the size of the input data was increased concerning their memory and CPU usage footprint. In contrast, the disk usage was independent of the size of the input data and the number of threads for all assemblers.

Qualitative

On average, the user experience in terms of installation and running the analyses was evaluated as GOOD for all tools (Table 1).

However, we discovered the following slight problems:

Two minor dependencies were missing in the GetOrganelle installation instructions and there were no test data available [36]. Additionally, an issue occurred when running it on one particular A. thaliana data set. This was resolved after contact with the authors via GitHub [37].

The Fast-Plast installation instructions were missing some dependencies [38]. Like GetOrganelle , Fast-Plast does not offer a test data set or a tutorial, except for some example commands [36].

The ORG.Asm installation instructions did not work. We found some issues, which were probably related to the requirement of Python 3.7 [39]. A tutorial including sample data was available, but following the instructions resulted in a segmentation fault (Table 2). We found a workaround for this bug and contacted the authors [40].

The main critique point of NOVOPlasty was the lack of test data and instructions. This was fixed by the authors after we contacted them [41]. Additionally, NOVOPlasty uses a custom license, where an OSI approved license would be preferable.

The chloroExtractor does come with test data and a short tutorial. However, it is currently not possible to evaluate the results of the test run as the expected results are not available [42].

The IOGA installation instructions were missing many dependencies [43]. There was also no test data or tutorial available and no license assigned to it [44]. After contacting the authors, the AGPL-3.0 license was added [45], as well as a note in the description explaining that IOGA is no longer maintained.

Installation instructions for Chloroplast assembly protocol were also missing some dependencies. The list was updated after we contacted the authors [46]. This tool does come with an extensive tutorial and test data, but the expected outcome is not provided.

Quantitative

For a quantitative evaluation, we tested the capacity of all programs to assemble chloroplasts based on different input data. Input data were either generated from existing chloroplast genomes or downloaded from sequencing repositories.

Simulated data

The different simulated data were all based on the A. thaliana chloroplast and core genome sequence. Some general trends could be observed: a ratio of 1:10 genome to chloroplast reads contains too few chloroplastic reads for most tools (except Fast-Plast and GetOrganelle ). A good performance for all tools was observed at a ratio of 1:100. Increasing the ratio further had no additional benefit, even if pure chloroplast reads were used (Fig. 3). Using 250 bp paired read compared to 150 bp paired reads did not produce improved results (Fig. 3). In the case of Fast-Plast , the performance was even worse with the longer read length as more than a single copy of the chloroplast genome was returned.

Score of assemblies on simulated data. Results of assemblies from simulated data sets. Color scale of the tiles represents the score

Overall, GetOrganelle and Fast-Plast were the most successful tools on the simulated data while Chloroplast assembly protocol and IOGA were unable to successfully assemble any chloroplasts out of the 16 different data sets.

Real data sets

To evaluate the performance on real data, we used publicly available short read data from NCBI’s SRA with existing reference chloroplasts. We observed considerable differences for the tested assemblers, if we compared the generated alignments against the reference chloroplasts (Fig. 4). The highest scores were achieved by GetOrganelle with a median of 99.8 and 210 circular assemblies out of a total of 360 assemblies that resulted in an output (Table 3). The performance of GetOrganelle was followed by Fast-Plast , NOVOPlasty , IOGA , and ORG.Asm . Fast-Plast outperformed NOVOPlasty and ORG.Asm in terms of score, producing twice as many 113 perfectly assembled chloroplast genomes ( NOVOPlasty produced 58 and ORG.Asm 46 circular genomes). IOGA and Chloroplast assembly protocol were both unable to assemble a circular, single-contig genome (Table 3, Fig. 5).

Results of scoring of the seven assemblers. The boxplots and swarplots depict the results of the scoring algorithm we used. For the different assemblers. The whiskers of boxplots indicate the 1.5 x interquartile range

Upset plot [47] comparing success of assemblers on the real data sets. The plot shows the intersection of success (score>99) between assemblers. For 69 data sets, only GetOrganelle was able to obtain a complete chloroplast. Forty-three were successful with both GetOrganelle and Fast-Plast and so on

Consistency

Consistency was tested by re-running assemblies using the real data and comparison of the two assemblies (Fig. 6). chloroExtractor was the only tool able to reproduce the same scores in all runs (Fig. 6). GetOrganelle , ORG.Asm , Chloroplast assembly protocol , and IOGA generated some assemblies that were unsuccessful in one run, but produced an output in the other attempt. For these assemblers, the scores were virtually identical if both runs were successful (Table 4). Both Fast-Plast and NOVOPlasty show only minor changes for the successful assemblies, leading to arrow-shaped scatter plots (Fig. 6). chloroExtractor appears to be the most robust assembler, showing no deviations between the two runs.

Scores between two repeated runs for consistency testing. The scatter plots depicts the scores of the 1. runs x-axis versus the scores of the 2. run y-axis of the data sets that were selected for re-evaluation

Novel

Finally, the assembly of chloroplasts for species without a published chloroplast was performed with the different tools (Fig. 7). In total, 49 out of 105 chloroplasts (46.7%) with no reference sequence in CpBase were successfully assembled (Fig. 8).

Success for chloroplast assembly shows no taxonomic bias. Success of assemblers on real data sets on tree derived from NCBI taxonomy [51]. Plot was prepared using [52]

Upset plot [47] comparing success of assemblers on the novel data sets. The plot shows the intersection of success (single contig, length≥130kbp,ir≥17kbp) between assemblers. For 15 data sets, only GetOrganelle was able to obtain a complete chloroplast. Ten were successful with GetOrganelle , Fast-Plast , NOVOPlasty , ORG.Asm , and so on

Almost half (44.9%) of the successful assembled chloroplasts were assembled by three or more different tools, while the remaining ones were only successfully generated by one or two different assemblers. Here, GetOrganelle showed the best performance and produced 15 distinct chloroplast genomes. For the assemblies obtained from multiple assemblers, we kept the GetOrganelle assemblies, after visually inspecting all assemblies using AliTV [48].

For three assemblies, that were obtained by different assemblers, but not by GetOrganelle , we kept one assembly obtained by NOVOPlasty and two from Fast-Plast . All resulting 49 sequences have been annotated with GeSeq [49]. The median number of distinct genes annotated were 80 for coding sequences, 4 for rRNA, and 27 for tRNA (Table 5, Fig. 10). All sequences were stored in our repository [50]. To avoid multi submissions of the same sequence to Genbank, all 49 sequences have been inspected against Genbank database via BLAST. Finally, 20 sequences were uploaded to NCBI TPA:inferential (Additional file 1: Table S1) as novel chloroplast genomes. Moreover, a search for the species name unveiled that 7 of the 20 sequences are used as ornamental plant, in folk medicine, or as crop plant.


Biology (BIOL)

This is the preliminary (or launch) version of the 2021-2022 VCU Bulletin. This edition includes all programs and courses approved by the publication deadline however we may receive notification of additional program approvals after the launch. The final edition and full PDF version will include these updates and will be available in August prior to the beginning of the fall semester.

BIOL 101. Biological Concepts. 3 Hours.

Semester course 3 lecture hours. 3 credits. A topical approach to basic biological principles. Topics include molecular aspects of cells, bioenergetics, photosynthesis, cellular respiration, cellular and organismal reproduction, genetics and evolution, and ecology. Not applicable for credit toward the major in biology.

BIOL 103. Global Environmental Biology. 4 Hours.

Semester course 3 lecture and 2 laboratory hours (delivered mostly online). 4 credits. Online presentations, assignments, debates and exams require students to understand situations and ideas that involve scientific, social and economic concepts associated with Earth’s environment. Laboratory exercises reinforce major course concepts. Integrates aspects of biology, chemistry, geology, physics and sociology. Topics include ecology, evolution, natural resources, air and water resources, energy and recycling, population biology, and sustainable global societies. Not applicable as a prerequisite for any biology course at the 200 level or above, nor for credit toward the B.S. in Biology.

BIOL 151. Introduction to Biological Sciences I. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: MATH 141, MATH 151, MATH 200, MATH 201 or a satisfactory score on the math placement exam and CHEM 100 with a minimum grade of B, CHEM 101 with a minimum grade of C or a satisfactory score on the chemistry placement exam. Introduction to core biological concepts including cell structure, cellular metabolism, cell division, DNA replication, gene expression and genetics. Designed for biology majors.

BIOL 152. Introduction to Biological Sciences II. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and CHEM 101, both with a minimum grade of C. Focuses on evolutionary principles, the role of natural selection in the evolution of life forms, taxonomy and phylogenies, biological diversity in the context of form and function of organisms, and and basic principles of ecology. Designed for biology majors.

BIOL 200. Quantitative Biology. 3 Hours.

Semester course 3 lecture hours (delivered online or hybrid). 3 credits. Prerequisites: BIOL 151 and BIOZ 151 with minimum grades of C and MATH 151, MATH 200, MATH 201, STAT 210 or satisfactory score on the VCU Mathematics Placement Test within a one-year period immediately preceding the beginning of the course. Enrollment is restricted to biology majors and biology minors. An introduction to the application of the scientific method, experimental design and quantitative aspects of biology.

BIOL 201. Human Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 101, 151, or 152, or BIOL/ENVS 103. Fundamentals of human biology, including the structure, function and disorders of human body systems, principles of human genetics and inheritance, human evolution, and the interaction of humans with the environment. Not applicable for credit toward the B.S. in Biology.

BIOL 205. Basic Human Anatomy. 4 Hours.

Semester course 3 lecture and 3 laboratory hours (plus online component). 4 credits. Prerequisites: BIOL 101 and BIOZ 101, BIOL 151 and BIOZ 151, or BIOL 152 and BIOZ 152, each with a minimum grade of C. Enrollment is restricted to students majoring in communication arts, health and physical education, health, physical education and exercise science pre-health majors in clinical laboratory sciences, clinical radiation sciences, dental hygiene and nursing students enrolled in the health sciences certificate program and students in the advising tracks for pre-occupational therapy, pre-physician assistant, pre-pharmacy and pre-physical therapy. Additionally, students in the pre-dentistry and pre-nursing accelerated advising tracks must speak with a pre-professional health adviser prior to enrolling in the class. Human specimens, models and interactive software are used to study human body structures emphasis is on the skeleto-muscular aspects. Not applicable for credit toward the B.S. in Biology.

BIOL 209. Medical Microbiology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 101 and BIOZ 101, BIOL 151 and BIOZ 151, or BIOL 152 and BIOZ 152, each with a minimum grade of C. General principles of microbiology and immunology to provide a thorough understanding of the host-microbe relationship in disease. Not applicable for credit toward the B.S. in Biology.

BIOL 217. Principles of Nutrition. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 101, 151 or 152 with a minimum grade of C, or BIOL/ENVS 103 with a minimum grade of C. An introduction to basic principles of nutrition and their application in promoting growth and maintaining health throughout the life cycle. Not applicable for credit toward the B.S. in Biology.

BIOL 284. Laboratory Assistant Experience. 0 Hours.

Semester course 0 hours. 0 credits. Enrollment is restricted to students with permission of the departmental chair and limited to students for whom a laboratory supervisor has agreed to mentor their laboratory assistantship. Helps facilitate student involvement in research laboratories within the Department of Biology. Students will assist with components of the laboratory’s operation and gain experience working in a laboratory setting. Students will gain hands-on experience in performing tasks related to specific research areas based on the laboratory in which they are accepted to work. Graded as pass/fail.

BIOL 291. Topics in Biology. 1-4 Hours.

Semester course variable hours. Variable credit. Prerequisites: BIOL 151, 152 and BIOZ 151, 152, with minimum grades of C. A study of a selected topic in biology. See the Schedule of Classes for specific topics to be offered each semester and prerequisites.

BIOL 300. Cellular and Molecular Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and 152 BIOZ 151 or LFSC/BNFO 251 BIOZ 152 or LFSC/BNFO 252 CHEM 101 and CHEZ 101, all with a minimum grade of C BIOL 200, MATH 200, MATH 201, STAT 210, STAT 212 or STAT 314. Biology majors must have completed BIOL 200. Pre- or corequisites: CHEM 102 and CHEZ 102. A study of the molecular biology of the cell as it relates to gene expression, cell signaling, and cell growth and differentiation.

BIOL 303. Microbiology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C. The morphological, biochemical, taxonomic, genetic and evolutionary characteristics of microorganisms with a primary focus on bacteria. Focuses on the structural, mechanical and biochemical adaptations employed by microorganisms in their interactions with host cells and substrates.

BIOL 304. Biology Skills. 2 Hours.

Semester course 1 lecture hour (delivered online) and 3 laboratory hours. 2 credits. Prerequisites: BIOL 151 and BIOZ 151 and permission of instructor. This course provides a hands-on experience in laboratory techniques, emphasizes the development of library and informational fluency skills, and uses current biological and/or biomedical research topics to aid in development of critical-thinking and problem-solving skills.

BIOL 307. Aquatic Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 317, CHEM 102 and CHEZ 102, with minimum grades of C. The physical, chemical and especially the biological aspects of freshwater ecosystems.

BIOL 308. Vertebrate Histology. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisite: BIOL 300 with a minimum grade of C. Microanatomy of vertebrate cells, tissues and organs and the relationship of structure to function. Laboratory work involves an in-depth study of vertebrate microanatomy at the light microscope level as well as an introduction to techniques used for the preparation of materials for histological study.

BIOL 309. Entomology. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisites: BIOL 151, 152 and BIOZ 151, 152, with minimum grades of C. A field-based course that focuses on insect diversification, identification, natural history and basic biology.

BIOL 310. Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and 152 BIOZ 151 or LFSC/BNFO 251 BIOZ 152 or LFSC/BNFO 252 BIOL 300 CHEM 101 and CHEZ 101, each with a minimum grade of C and BIOL 200, MATH 200, MATH 201, STAT 210, STAT 212 or STAT 314. Biology majors must have completed BIOL 200. Pre- or corequisites: CHEM 102 and CHEZ 102. The basic principles of molecular and applied genetics of plants, animals and microorganisms.

BIOL 312. Invertebrate Zoology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151, 152 and BIOZ 151, 152, with minimum grades of C. A survey of the invertebrate animals with emphasis on environmental interactions. A weekend trip to a marine environment is required.

BIOL 313. Vertebrate Natural History. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151, 152 and BIOZ 151, 152, with minimum grades of C. The natural history of vertebrates with emphasis on the species native to Virginia.

BIOL 314. Animal Reproduction. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL and BIOZ 151, BIOL and BIOZ 152, and BIOL 300, each with a minimum grade of C. Introduction to basic reproductive anatomy and physiology. Examination of the basic factors that affect reproductive performance and how these factors are used to regulate the reproductive processes of domestic animals and humans.

BIOL 317. Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and 152 BIOZ 151 or LFSC/BNFO 251 BIOZ 152 or LFSC/BNFO 252 CHEM 101 and CHEZ 101, all with a minimum grade of C BIOL 200, MATH 200, MATH 201, STAT 210, STAT 212 or STAT 314. Biology majors must have completed BIOL 200. An introduction to the basic principles of ecology, including interactions among organisms and influences of the physical environment.

BIOL 318. Evolution. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and 152 BIOZ 151 or LFSC/BNFO 251 BIOZ 152 or LFSC/BNFO 252 CHEM 101 and CHEZ 101, all with a minimum grade of C BIOL 200, MATH 200, MATH 201, STAT 210, STAT 212 or STAT 314. Biology majors must have completed BIOL 200. An exploration of the theoretical and empirical foundations of evolutionary biology with a focus on the processes driving evolutionary change across all of life.

BIOL 320. Biology of the Seed Plant. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisites: BIOL and BIOZ 151 and BIOL and BIOZ 152, each with a minimum grade of C. The physiology, structure and adaptation of seed plants.

BIOL 321. Plant Development. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 and 310, each with a minimum grade of C. A survey of the developmental changes that take place during the life cycle of lower and higher plants. Emphasis is placed on the control factors that are involved in regulating the ordered changes which take place during development.

BIOL 322. Economic Botany. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and 152 and BIOZ 151 and 152, or equivalents, with minimum grades of C. This class focuses on plant morphology, anatomy, phytochemistry, growth and reproduction through an examination of the biology of economically and culturally important plants, including crops used for foods and beverages, medicines and drugs, fibers, and timber.

BIOL 324. Medicinal Botany. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and BIOZ 151 BIOL 152 and BIOZ 152 and BIOL 300, all with a minimum grade of C. Topics include plant anatomy, morphology and reproduction traditional plant medicine such as Ayurveda and traditional Chinese medicine plant defense systems and secondary metabolites and plant-derived drugs for various illnesses/ailments including cancer, arthritis, depression and diabetes.

BIOL 325. Fungal Biology. 3 Hours.

Semester course 2 lecture and 3 laboratory hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C. The basic biology of fungi, including growth, structure, genetics, diversity, the commercial uses of fungi and their importance as model organisms. Also discusses the interactions between fungi and plants and fungi and humans.

BIOL 332. Environmental Pollution. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: eight credits in biology. The study of pollution in the environment with emphasis on the procedures for detection and abatement. Crosslisted as: ENVS 330.

BIOL 333. Evolution of the Angiosperms. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151,152 and BIOZ 151, 152, all with minimum grade of C. Application of evolutionary concepts to flowering plants. Topics include speciation concepts, evolution of vegetative and sexual characteristics and an overview of angiosperm diversity to the level of family.

BIOL 335. Global Change Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151, BIOL 152, BIOZ 151 and BIOZ 152, all with minimum grade of C. Examines how humans influence biological systems and explores what can be done to adapt to or to mitigate future global change, emphasizing anthropogenic climate change.

BIOL 340. Development and Stem Cells. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 and CHEM 102, each with a minimum grade of C. Basic principles of developmental biology and stem cells of vertebrates, pinpointing the underlying cellular and molecular mechanisms that guide development and stem cell biology. Significant emphasis on medical aspects of development such as human birth defects, cloning, properties of stem cells and their medical uses, and careers in developmental and stem cell biology.

BIOL 341. Human Evolution. 4 Hours.

Semester course 3 lecture and 2 laboratory hours. 4 credits. Prerequisite: UNIV 200 or HONR 200 with a minimum grade of C. Introduces the range of human diversity as well as a broad understanding of evolution and evolutionary biology, particularly as it applies to hominid evolution. Specific topics include basic genetics, primatology, paleontology and the hominin fossil record. Crosslisted as: ANTH 301.

BIOL 351. Introduction to Bioinformatics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BNFO 201 and BNFO 300 or permission of instructor. The course will present a practical and theoretical introduction to the tools and techniques needed to obtain and interpret a variety of genome-related data types. The course will include several bioinformatic methods underlying nucleotide and protein sequence alignment, statistical methods for data visualization in R, the types of experimental results commonly encountered in bioinformatics data analysis and the public databases where these data can be accessed. Crosslisted as: BNFO 301.

BIOL 391. Topics in Biology. 1-4 Hours.

Semester course 1-4 lecture hours. 1-4 credits. Prerequisites: BIOL 152 and BIOZ 152 and BIOL 300, BIOL 310, BIOL 317 or BIOL 318, each with a minimum grade of C. A study of a selected topic in biology. See the Schedule of Classes for specific topics to be offered each semester and prerequisites.

BIOL 392. Introduction to Research. 2 Hours.

Semester course 1 lecture and 1 demonstration hour. 2 credits. Prerequisite: BIOL 300, BIOL 310, BIOL 317 or BIOL 318 with a minimum grade of C. An introduction to the scientific process, including the mechanics of problem definition, information gathering and experimental design. Experimentation is discussed in context with methods of data collection and analysis. Aims are to prepare the student for future research experiences and to have the student write detailed research proposals.

BIOL 395. Directed Study. 1-2 Hours.

Semester course 1-2 independent study hours. 1-2 credits. Prerequisites: BIOZ 151 and BIOZ 152 with minimum grades of C, permission of the Department of Biology and research mentor. A maximum of two credits may be earned between BIOL 395 and BIOZ 395 maximum total of six credits for all research and internship courses (BIOL 395, BIOL 451, BIOL 453, BIOL 492, BIOL 493, BIOL 495 and/or BIOZ 395) may be applied to the the 40 credits of biology required for the major. Additional credits from these courses may be applied to upper-level and open elective credits toward the degree. Mentors are not limited to faculty members within the Department of Biology, but the context of the research study must be applicable to the biological sciences as determined by the department. Studies should include directed readings, directed experimentation or advanced guided inquiry — all under the direct supervision of a faculty member. A minimum of three hours of supervised activity per week per credit hour is required. This course may not apply as a laboratory experience. Graded as pass/fail.

BIOL 401. Applied and Environmental Microbiology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: 300 and 317, each with a minimum grade of C. The biology and chemical activities of microorganisms (bacteria, algae, virus and fungi) of industrial, pharmaceutical and agricultural importance.

BIOL 402. Comparative Vertebrate Anatomy. 5 Hours.

Semester course 3 lecture and 4 laboratory hours. 5 credits. Prerequisites: BIOL 300 and BIOL 318, each with a minimum grade of C. The evolution of vertebrate forms as demonstrated by anatomical studies of selected vertebrate types.

BIOL 403. Primatology. 4 Hours.

Semester course 3 lecture and 2 laboratory hours. 4 credits. Prerequisite: ANTH 210 or ANTH 301/BIOL 341. Primatology investigates the taxonomic relationships among primates through comparative anatomy, comparative behavior and comparative biochemistry. Study of primate evolution, demography, subsistence, reproduction, social organization, communication systems and ecology. Crosslisted as: ANTH 403.

BIOL 411. Physiology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 and CHEM 301, each with a minimum grade of C. Focuses on the characterization and understanding of the function and mechanisms of major physiological systems, primarily using human physiology as a model. Emphasis is placed on understanding how different physiological systems work together to maintain homeostasis and predicting the consequences of damaging or deleting system components that can occur in diseases and injuries.

BIOL 413. Parasitology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C. The epidemiology and pathological effects of eukaryotic parasites, including parasite life cycles and host-parasite relationships.

BIOL 415. Mangrove Avian Field Ecology. 4 Hours.

Semester course two weeks abroad in Panama (or other tropical location with mangrove forests) followed by class meetings two days per week throughout most of spring semester. 4 credits. Prerequisite: BIOL 317. An immersive study of tropical ecology with a focus on bird ecology and conservation of mangrove ecosystems through a unique blend of rigorous science and community engagement. Two weeks of study abroad, including engagement with local conservation organizations and participation in education outreach with local schools, followed by discussion, data analysis and presentation of progress and research in a public symposium on campus.

BIOL 416. Ornithology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 317 with a minimum grade of C. Provides an integrative study of birds, including avian evolution and diversity, general anatomy and physiology, behavior, and ecology.

BIOL 417. Mammalogy. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisites: BIOL 218 and 317 with minimum grades of C. Study of the characteristics, adaptive radiation and distribution of mammals, with emphasis on North American forms.

BIOL 420. Yeast and Fermentation. 3 Hours.

Semester course 2 lecture and 3 laboratory hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C. Corequisites: BIOL 303 and BIOL 310. Addresses the basic biology of yeast used in brewing beer and briefly in wine production. Topics will include yeast properties such as growth, structure, genetics, biodiversity and natural habitats. The process of wine and beer production will be discussed. Laboratory sessions include basic microbiology techniques, yeast isolations and characterization using DNA and biochemical methods, as well as the study of factors that affect fermentation. At the end of the course the students will give a presentation on other fermentation products of their interest such as vinegar, bread, etc., providing an expanded version of this important process.

BIOL 422. Forest Ecology. 4 Hours.

Semester course 3 lecture hours and 3 laboratory hours. 4 credits. Prerequisite: BIOL 317 with a minimum grade of C. Covers the fundamentals of forest ecology, with a particular emphasis on Virginia’s diverse forest ecosystems. Students gain an understanding of the principal controls on forest structure, growth and distribution and relate these principles to sustainable forest management.

BIOL 423. Plant Physiology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151 and BIOZ 151 BIOL 152 and BIOZ 152 and BIOL 300 or equivalents, all with minimum grades of C. Physiology of higher plants at molecular, cellular and organism level. Topics include transport processes, metabolism, growth, stress responses and plant-soil interactions.

BIOL 425. Field Botany. 3 Hours. Play course video for Field Botany

Semester course 2 lecture hours and 3 laboratory hours.(60 percent online, 40 percent field/laboratory) 3 credits. Prerequisites: BIOL 310 and BIOL 317, both with minimum grades of C. Online lectures, discussions, reflections and assessments in conjunction with field experience. Explores the effects of environmental conditions on plant morphology and adaptations, with emphasis on plant anatomy, plant physiology and ecology.

BIOL 430. Invasion Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151, BIOL 152, BIOZ 151, BIOZ 152 and BIOL 317, all with minimum grade of C. A comprehensive view of the ecology and impacts of invasive species. Integrates the effects of historical human demography, ecological disturbance, natural history, species interactions, barriers to invasion, invasive species management and impacts on natural communities and ecosystems.

BIOL 431. Introduction to Marine Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 317, CHEM 102 and CHEZ 102, with minimum grades of C. An introduction to physical, chemical and geological oceanography and a more detailed treatment of the organisms and ecological processes involved in the pelagic and benthic environments of the world's oceans and estuaries.

BIOL 435. Herpetology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 317 with a minimum grade of C. The evolution, ecology, structure, taxonomy and behavior of reptiles and amphibians.

BIOL 438. Forensic Molecular Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 310 with a minimum grade of C. Provides an understanding of molecular biology testing methodologies as applied to analysis of forensic samples. Current topics in forensic DNA analysis will include quality assurance, DNA databanking, contemporary research and population genetics. Crosslisted as: FRSC 438.

BIOL 440. Developmental Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 and 310, each with a minimum grade of C. Basic principles of developmental biology focused on vertebrate model organisms with an emphasis on the underlying cellular and molecular mechanisms that guide development.

BIOL 445. Neurobiology and Behavior. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisite: BIOL 317 with a minimum grade of C. The study of animal behavior stressing ecological, evolutionary and neurobiological approaches.

BIOL 448. Neuroscience. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C. Pre- or corequisite: BIOL 310. An examination of the basic structure of the nervous system, nervous system operation on a cellular and molecular level and the formation of the nervous system during development.

BIOL 450. Biology of Cancer I. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 with a minimum grade of C or PHIS 309. An examination of the cellular, molecular and clinical aspects of cancer development, progression and treatment.

BIOL 451. Biology of Cancer II. 4 Hours.

Semester course 1 lecture and 12 laboratory hours. 4 credits. Prerequisites: BIOL 450 and instructor's permission. A maximum total of six credits for all research and internship courses (BIOL 395, BIOL 451, BIOL 453, BIOL 492, BIOL 493, BIOL 495 and/or BIOZ 395) may be applied to the the 40 credits of biology required for the major. Additional credits from these courses may be applied to upper-level and open elective credits toward the degree. An examination of the cellular, molecular and clinical aspects of cancer development, progression and treatment.

BIOL 452. Biology of Drugs. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C. Explores how drugs modulate biological signaling pathways to study, cure, enhance and intoxicate organisms. An introduction to basic pharmacology that largely focuses on human pathways and diseases. Topics include major drug classes (cardiovascular, gastrointestinal, etc.) and drugs of abuse (alcohol, marijuana, etc.).

BIOL 453. Cancer Biology Thesis. 4 Hours.

Semester course 1 recitation and 12 laboratory hours. 4 credits. Prerequisite: BIOL 451. A maximum total of six credits for all research and internship courses (BIOL 395, BIOL 451, BIOL 453, BIOL 492, BIOL 493, BIOL 495 and/or BIOZ 395) may be applied to the the 40 credits of biology required for the major. Additional credits from these courses may be applied to upper-level and open elective credits toward the degree. Enrollment is restricted to students with permission of the instructor and research mentor. Students will benefit from invaluable learning opportunities in cancer research including hands-on learning, direct mentorship from a VCU faculty member, scientific writing skills, time and research project management, and exposure to and training in various laboratory techniques. In addition, students will gain experience in preparation of a cancer research proposal and thesis.

BIOL 455. Immunology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 300 with a minimum grade of C or PHIS 309. A comprehensive introduction to the immune system of higher animals, emphasizing the molecular and cellular basis for antibody-medicated immunity.

BIOL 459. Infectious Disease Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 151, BIOL 152, BIOZ 151, BIOZ 152 and BIOL 317, all with minimum grade of C. A comprehensive and up-to-date overview of the causes and consequences of infectious disease at levels from individual organisms to global scale. Examines the history of infectious disease ecology in human and nonhuman populations. Students learn about the roles of transmission and coevolution in infectious disease ecology and how population models are used to inform management of epidemics and emerging infectious diseases.

BIOL 460. Human Evolutionary Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 318 or BIOL 341 with a minimum grade of C. The origin and genetic history of modern humans, our historic colonization and migration, the utility of the Human Genome Project, our differences from other primates, adaptation to our environment and disease, and the ethical implications of genetic research in our society.

BIOL 475. Biology Capstone Seminar: ____. 1-3 Hours.

Semester course 1-3 seminar hours. 1-3 credits. Prerequisites: BIOL 300, BIOL 310, BIOL 317 and BIOL 318, each with a minimum grade of C. Enrollment is restricted to biology majors with senior standing. Students read assigned topical papers before class, prepare critical analyses, discuss and debate selected positions. See Schedule of Classes for specific topics.

BIOL 477. Biology Capstone Experience. 0 Hours.

Semester course variable hours. 0 credits. Prerequisites: BIOL 300, BIOL 310, BIOL 317 and BIOL 318, each with a minimum grade of C and 90 hours of undergraduate course work. The following courses qualify as a capstone experience if taken concurrently with this course: BIOL 492, BIOL 493, BIOL 495, BIOL 497 or other courses, including topics courses, which include the core competencies required for a capstone experience and are approved by the chair of the Department of Biology. Graded as pass/fail.

BIOL 480. Animal-Plant Interactions. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 317 or BIOL 318 with a minimum grade of C, or permission of the instructor. Ecological and evolutionary consequences of interactions among animals and plants.

BIOL 482. Preceptor Experience. 0 Hours.

Semester course 0 hours. 0 credits. Enrollment is restricted to students who have completed the relevant course for which they will be a teaching assistant with a minimum grade of B and who have a minimum cumulative GPA of 3.0. Permission of instructor and departmental chair also required prior to registration. Teaching assistants will enhance their knowledge of course content and develop skills that are natural to an instructional role, an understanding of the learning process within a discipline and the ability to explain the importance and value of course content to a novice audience. Graded as pass/fail.

BIOL 484. Research Assistant Experience. 0 Hours.

Semester course 0 hours. 0 credits. Enrollment is restricted to students with permission of the departmental chair and limited to students for whom a research supervisor has agreed to be a mentor. Helps facilitate student involvement in research laboratories within the Department of Biology. Students will gain hands-on experience including data collection and analysis, learning field and/or laboratory techniques, and/or mastering experimental procedures, all under the direct supervision of a faculty member. Graded as pass/fail.

BIOL 489. Communicating Research. 1 Hour.

Semester course 1 lecture hour. 1 credit. Prerequisite: Completion of the Biocore with minimum grades of C. Corequisite: BIOL 495, senior standing. An opportunity for students to develop skills necessary for effective communication of their research in writing. Includes a variety of seminar discussions and activities including preparation of figures for publication and the crafting of a research paper with correct usage of the primary literature. Students will use this as an opportunity to aid the writing of their thesis for BIOL 495.

BIOL 490. Presenting Research. 1 Hour.

Semester course 1 credit. Prerequisite: Completion of the Biocore with minimum grades of C. Pre- or corequisites: BIOL 492 or 495, and senior standing. Opportunity for students to develop skills necessary for effective oral presentation of their research work. Includes a variety of seminar discussions and activities such as preparation of visual materials and statistical analysis of data. Students will make several oral presentations directly related to their specific BIOL 492 or 495 projects.

BIOL 491. Topics in Biology. 1-4 Hours.

Semester course variable hours. Variable credit. Prerequisite: BIOL 300. A study of a selected topic in biology. See the Schedule of Classes for specific topics to be offered each semester and prerequisites.

BIOL 492. Independent Study. 1-4 Hours.

Semester course 1-4 independent study hours. 1-4 credits. Prerequisites: BIOZ 151 and BIOZ 152, each with a minimum grade of C and permission of the chair of the Department of Biology. May be repeated for credit. A maximum total of six credits for all research and internship courses (BIOL 395, BIOL 451, BIOL 453, BIOL 492, BIOL 493, BIOL 495 and/or BIOZ 395) may be applied to the 40 credits of biology required for the major. Additional credits from these courses may be applied to upper-level and open elective credits toward the degree. A minimum of two credits is required for the course to count as a laboratory experience. Projects should include data collection and analysis, learning field and/or laboratory techniques, and/or mastering experimental procedures, all under the direct supervision of a faculty member. A minimum of three hours of supervised activity per week per credit hour is required. A final report must be submitted at the completion of the project.

BIOL 493. Biology Internship. 1-3 Hours.

Semester course 1-3 field experience hours. 1-3 credits. Prerequisites: BIOL 310 or 317 with minimum grades of C and permission of the chair of the Department of Biology and of the agency, company or organization in which internship will be held. May be repeated for credit. Students may take a maximum of three credits per semester maximum total of six credits for all research and internship courses (BIOL 395, BIOL 451, BIOL 453, BIOL 492, BIOL 493, BIOL 495 and/or BIOZ 395) may be applied to the 40 credits of biology required for the major. Additional credits from these courses may be applied to upper-level and open elective credits toward the degree. One credit is awarded for each 100 hours of work experience in professional biology setting. Internship designed to provide laboratory or field experience in an off-campus professional biology setting. A final report must be submitted upon completion of the internship. Graded as pass/fail.

BIOL 495. Research and Thesis. 1-4 Hours.

Semester course 1-4 research hours. 1-4 credits. Prerequisites: BIOL 392, permission of the supervising faculty member and a research proposal acceptable to the departmental chair. Corequisite: BIOL 489 or BIOL 490. May be repeated for a maximum of eight credits. Students may take a maximum of four credits per semester maximum total of six credits for all research and internship courses (BIOL 395, BIOL 451, BIOL 453, BIOL 492, BIOL 493, BIOL 495 and/or BIOZ 395) may be applied to the 40 credits of biology required for the major. Additional credits from these courses may be applied to upper-level and open elective credits toward the degree. A minimum of two credits is required for the course to count as a laboratory experience. A minimum of four credits is required for honors in biology. Activities include field and/or laboratory research under the direct supervision of a faculty mentor. A minimum of three hours of supervised activity per week per credit hour is required. Research projects must include experimental design and analysis of data. This course must be taken for two consecutive semesters starting in the fall. A written thesis of substantial quality is required upon completion of the research.

BIOL 496. Biology Preceptorship: ____. 2 Hours.

Semester course 2 practicum hours. 2 credits. May be repeated with a different course for credit. Enrollment restricted to students who have completed the relevant course with a minimum grade of B and who have a minimum cumulative GPA of 3.0. Permission of instructor is required prior to registration. Preceptors assist instructors in lecture (BIOL) or laboratory (BIOZ) courses. Responsibilities vary and may include, but are not limited to, attending class, conducting review sessions and preparing course study/review materials. Graded as pass/fail. A maximum of four combined credits from BIOL 496 and BIOL 499 may be applied to degree requirements.

BIOL 497. Ecological Service Learning. 1 Hour.

Semester course 1 lecture hour. 1 credit. Prerequisite: BIOL 317 with a minimum grade of C. A service-learning course coupled to course content and material taught in BIOL 317. Students will seek out ecologically relevant opportunities with local, state and federal community partners who will provide experiences to enhance academic enrichment and personal growth and will help foster a sense of civic responsibility. Students must complete a minimum of 20 service-learning hours with community partner(s).

BIOL 498. Insects and Plants Service-learning. 2 Hours.

Semester course 2 field experience hours. 2 credits. Prerequisites: BIOL 317 or BIOL 318 with a minimum grade of C, and permission of the instructor. A service-learning course related to insect-plant interactions. Field experience with community partners, including public parks, botanical gardens and organic farms. Designed to expand academic instruction, enhance personal growth and foster a sense of civic responsibility. Students must complete a minimum of 40 service-learning hours with a community partner.

BIOL 499. Biology Lead Preceptorship. 2 Hours.

Semester course 2 practicum hours. 2 credits. Prerequisite: BIOL 496 in the same course with a grade of Pass. Enrollment is restricted to students who have completed the relevant course with a minimum grade of B and who have a minimum cumulative GPA of 3.0. Permission of the instructor is required prior to registration. Lead preceptors assist instructors in lecture (BIOL) or laboratory (BIOZ) courses. Responsibilities cumulate beyond those required in the prerequisite course. Responsibilities vary and may include, but are not are limited to, organizing preceptor teams for large enrollment courses, preceptor mentorship, data entry of course materials, execution of group work, etc. Graded as pass/fail. A maximum of four combined credits from BIOL 496 and BIOL 499 may be applied to degree requirements.

BIOL 502. Microbial Biotechnology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: MICR/BIOC 503 or BIOC 530, 531, 532 and 533 or equivalent, and MICR/BIOC 504 or equivalent. Open to qualified seniors and graduate students only. Discussion of the application of basic principles to the solution of commercial problems. The course will cover the historical principles in biotransformations as related to primary and secondary metabolism, as well as recombinant DNA technology and monoclonal antibodies and products resulting from the application of recombinant DNA technology.

BIOL 503. Fish Biology. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisite: BIOL 317 or equivalent. Open to qualified seniors and graduate students only. Classification, behavior, physiology and ecology of fishes. Laboratories will emphasize field collection of fish and identification of specimens.

BIOL 507. Aquatic Microbiology. 4 Hours.

Semester course 2 lecture and 4 laboratory hours. 4 credits. Prerequisites: BIOL 303 and 307 or equivalents. Open to qualified seniors and graduate students only. This course will involve a practical approach to the methods used to culture, identify and enumerate specific microorganisms that affect the cycling of elements in aquatic systems and those that affect or indicate water quality.

BIOL 508. Barrier Island Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 317 or equivalent, or permission of instructor. A study of the physical factors affecting the formation of barrier islands, adaptations of plants and animals for colonization and persistence in these harsh environments, and how coastal ecological processes conform to general ecological theory. Examples and problems pertaining to Virginia and the southeastern United States are emphasized.

BIOL 509. Microbial Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 317 or equivalent with a grade of C or better. Open only to qualified seniors and graduate students. Explores the interactions of microorganisms and their environment, including discussion of microbial diversity, nutrient cycling, symbiosis and selected aspects of applied microbiology.

BIOL 510. Conservation Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Open to qualified seniors and graduate students only. Explores the accelerated loss of species due to increasing human population pressure and the biological, social and legal processes involved in conserving biodiversity.

BIOL 512. Plant Diversity and Evolution. 4 Hours.

Semester course 3 lecture and 4 laboratory hours. 4 credits. Prerequisites: BIOL 300 and 310 or equivalents, or permission of instructor. Taxonomy, diversity and evolutionary history of vascular plants (including ferns, gymnosperms and flowering plants). Lecture emphasis on evolutionary relationships laboratory emphasis on plant recognition and identification, especially of the Virginia flora, including some field trips to areas of local botanical interest.

BIOL 514. Stream Ecology. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisite: BIOL 317. Open to qualified seniors and graduate students only. A study of the ecology of streams and rivers. Laboratory emphasis is on the structure and functioning of aquatic communities in mountain to coastal streams.

BIOL 516. Population Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: STAT/BIOS 543. Theoretical and empirical analyses of how demographic and evolutionary processes influence neutral and adaptive genetic variation within populations.

BIOL 518. Plant Ecology. 4 Hours.

Semester course 3 lecture and 2 laboratory hours. One three-day field trip is required. 4 credits. Prerequisite: BIOL 317. Open to qualified seniors and graduate students only. A lecture, field and laboratory course concerned with the development, succession and dynamics of plant communities and their interrelations with climate, soil, biotic and historic factors.

BIOL 519. Forest Ecology. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisite: BIOL 317 or equivalent. Enrollment restricted to graduate students and upper-level undergraduates. Covers advanced topics in forest ecology, with a particular emphasis on Virginia’s diverse forest ecosystems. Students gain an understanding of the principal controls on forest structure, growth and distribution and apply these principles to the development and execution of a graduate-level field research project.

BIOL 520. Population Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 310 and BIOL 317 or permission of instructor. Open to qualified seniors and graduate students only. Theoretical and empirical analysis of processes that occur within natural populations, including population genetics, population growth and fluctuation, demography, evolution of life history strategies and interspecific interactions. Quantitative models will be used extensively to explore ecological concepts.

BIOL 521. Community Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 317 or equivalent. Open to qualified seniors and graduate students only. Theoretical and empirical analysis of the structure and function of natural communities, ecosystems and landscapes.

BIOL 522. Evolution and Speciation. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 310 or equivalent. Open to qualified seniors and graduate students only. Evolutionary principles, with emphasis on genetic and environmental factors leading to changes in large and small populations of plants and animals, and the mechanisms responsible for speciation.

BIOL 524. Endocrinology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 and CHEM 301-302 and CHEZ 301L, 302L or equivalent. Open to qualified seniors and graduate students only. Hormonal control systems at the organ, tissue and cellular level. Although the major emphasis will be on vertebrate endocrine systems, some discussion of invertebrate and plant control systems will be covered.

BIOL 530. Introduction to Human Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Enrollment restricted to qualified seniors and graduate students. Basic knowledge of genetics is recommended. Provides a comprehensive examination of the fundamentals of human genetics. Explores topics including Mendelian and non-Mendelian inheritance, pedigree analysis, cytogenetics, aneuploid syndromes, cancer, gene structure and function, epigenetics, gene expression, biochemical genetics, and inborn errors of metabolism.

BIOL 535. Wetlands Ecology. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Prerequisite: BIOL 317 or equivalent or permission of instructor. A study of the ecology of freshwater and coastal wetlands, including the physical and biological aspects of these systems, wetland functions at local, landscape and global scales, and wetland regulations and restoration. Students will acquire skills with analytical techniques used in laboratory settings and in field-based applications for purposes of identifying and delineating wetland ecosystems.

BIOL 540. Fundamentals of Molecular Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 310 or consent of instructor. The basic principles and methodologies of molecular biology and genetics are applied to genome organization, replication, expression, regulation, mutation and reorganization. Emphasis will be placed on a broad introduction to and integration of important topics in prokaryotic and eukaryotic systems. Crosslisted as: BNFO 540.

BIOL 541. Laboratory in Molecular Genetics. 2 Hours.

Semester course 1 lecture and 4 laboratory hours. 2 credits. Pre- or corequisite: BIOL 540 or equivalent. Experiments are designed to apply advanced techniques and concepts of molecular biology and genetics using prokaryotic and eukaryotic systems. Emphasis will be placed on experimental design, integrating results throughout the semester, making use of relevant published literature, scientific writing and providing hands-on experience with advanced equipment and methodologies. Crosslisted as: BNFO 541.

BIOL 545. Biological Complexity. 3 Hours.

Semester course 2 lecture and 2 laboratory hours. 3 credits. Prerequisites: physics and calculus, or permission of instructor. Open only to graduate students and qualified seniors. An introduction to the basis of complexity theory and the principles of emergent properties within the context of integrative life sciences. The dynamic interactions among biological, physical and social components of systems are emphasized, ranging from the molecular to ecosystem level. Modeling and simulation methods for investigating biological complexity are illustrated. Crosslisted as: LFSC 510.

BIOL 548. Bioinformatic Technologies. 2 Hours.

Semester course 2 lecture hours. 2 credits. Prerequisite: BIOL 545/LFSC 510 or permission of instructor. Introduction to the hardware and software used in computational biology, proteomics, genomics, ecoinformatics and other areas of data analysis in the life sciences. The course also will introduce students to data mining, the use of databases, meta-data analysis and techniques to access information. Crosslisted as: LFSC 520.

BIOL 550. Ecological Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Open to qualified seniors and graduate students only. Introduces the principles of ecological genetics, especially those with foundations in population and quantitative genetics, and illustrates conceptual difficulties encountered by resource stewards who wish to apply genetic principles. Explores various types of biological technologies employed by conservation geneticists and provides means for students to gain experience in analyzing and interpreting ecological genetic data.

BIOL 560. Conservation Medicine. 3 Hours.

Semester course 3 lecture hours. 3 credits. Introduces students to key elements of wildlife diseases, zoonoses, emerging infectious diseases associated with wildlife and humans, and both the conservation and health impacts of these topics. Included are discussions of the interactions among environmental quality and wildlife and human diseases and health. Topics include diseases of fish, amphibians, reptiles, birds and mammals, the effects of environmental contaminants and climate on those diseases, and their interaction with human health.

BIOL 565. Advances in Cell Signaling. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 300 or equivalent. Topical course focusing on advances in cellular communication by cytokines, hormones and neurotransmitters. Each semester, the course focuses on a different topic. Past topics have included cancer biology, allergy and asthma, and autoimmunity.

BIOL 580. Eukaryotic Biotechnology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisites: BIOL 300 and BIOL 310, both with a minimum grade of C, or graduate standing in biology or a related field. Enrollment is restricted to graduate students and senior undergraduates. Discussion of principles, concepts, techniques, applications and current advances in cellular and molecular biology aspects of biotechnology for animal and plant cells. The course will cover molecular construction of foreign genes DNA cloning technologies for DNA, RNA and protein analyses nonvector and vector-mediated genetic transformation gene regulation in transgenic cells cell and tissue culture cell fusion and agricultural, medical and other industrial applications.

BIOL 591. Special Topics in Biology. 1-4 Hours.

Semester course 1-4 credits. An in-depth study of a selected topic in biology. See the Schedule of Classes for specific topics to be offered each semester and prerequisites. If several topics are offered, students may elect to take more than one.

BIOL 601. Integrated Bioinformatics. 4 Hours.

Semester course 3 lecture and 3 laboratory hours. 4 credits. Enrollment requires permission of instructor. Presents major concepts in bioinformatics through a series of real-life problems to be solved by students. Problems addressed will include but not be limited to issues in genomic analysis, statistical analysis and modeling of complex biological phenomena. Emphasis will be placed on attaining a deep understanding of a few widely used tools of bioinformatics. Crosslisted as: BNFO 601.

BIOL 602. Professional and Career Development in Biology. 1 Hour.

Semester course 1 lecture hour. 1 credit. Enrollment is restricted to students with graduate standing. This course will equip students early in their graduate experience with the knowledge, resources and skills to rapidly and successfully complete the requirements for an M.S. in Biology while enhancing their communication and planning skills in several critical formats and areas, as well as exploring alternative career paths based on their personal goals and values.

BIOL 603. Fundamentals of Scientific Leadership. 3 Hours.

Semester course 3 lecture hours. 3 credits. Enrollment restricted to students with graduate standing. The purpose of this course is to prepare students to successfully work as members and leaders of diverse scientific teams during their graduate studies and in multiple scientific career paths. Students will be familiarized and gain experience with key concepts of teams and leading teams, including values-based missions and goals, effective communication and feedback, stages of team development and leadership, diversity and inclusivity, mentoring and coaching, resolving conflict, project management, leading change, leaving a legacy, and assessment.

BIOL 604. Research Integrity. 1 Hour.

Semester course 1 lecture hour. 1 credit. Enrollment is restricted to students with graduate standing. This course is designed to provide a discussion-based approach to research integrity. By the end of the course students will be acutely aware of how science interacts with and informs society. They will have digested an array of topical issues relating to responsible conduct of research and be able to clearly articulate ethical and legal solutions to problems posed. This course addresses issues across a broad biosciences background including laboratory and field studies. This course targets master's- and entry-level Ph.D. students. Graded as pass/fail.

BIOL 605. Diversity and Inclusion in Science. 1 Hour.

Semester course 1 lecture hour. 1 credit. Enrollment is restricted to students with graduate standing. This course will familiarize and engage students with multiple forms of diversity in science through presentations, diverse guest speakers, class discussions and student assignments, preparing them to recognize and leverage this diversity by employing inclusiveness throughout their scientific careers and lives.

BIOL 606. Quantitative Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Principles and applications of mathematical ecology at the community level, including experimental design sampling techniques, assumptions and limitations and the use of cluster analysis, gradient analysis and ordination to evaluate, summarize and compare large data sets.

BIOL 607. Science Communication: Fundamentals. 2 Hours.

Semester course 2 lecture hours. 2 credits. Enrollment is restricted to students with graduate standing. The goal of this course is to provide training in science communication to diverse audiences from scientific and nonscientific backgrounds and across diverse career paths. The course covers fundamental rules of writing, the writing process, technical writing, visual presentation, oral presentation, engaging audiences and communication with the public. Students will attain science communication skills through writing exercises, videotaped oral exercises and peer review to prepare them for graduate school and beyond.

BIOL 608. Science Communication: Research Proposals. 2 Hours.

Semester course 2 lecture hours. 2 credits. Enrollment is restricted to students with graduate standing. The goal of this course is to provide training in writing competitive research proposals. Students will learn the necessary skills for the proposal-writing stage of scientific research preparatory stage, including reference managers, annotated bibliographies, selling the idea, mock review panels, short-form proposals, long-form proposals and thesis/dissertation proposals. Students will learn proposal-writing skills that will provide an edge in applications for a diversity of funding sources.

BIOL 609. Scientific Communication: Public Discourse. 1 Hour.

Semester course 1 lecture hour. 1 credit. Prerequisite: BIOL 607. Enrollment is restricted to students with graduate standing. The mission of this course is to train students nearing completion of a thesis/dissertation to apply skills they learned in the prerequisite course to effectively communicate their own thesis/dissertation research, and its relevance to global issues in biology, to nonscientific audiences. Students successfully completing this course will be able to effectively communicate the science and relevance of their own research in verbal and written formats with non-scientists in the lay public, government and nongovernment institutions and the media. Graded as satisfactory/unsatisfactory.

BIOL 610. Conservation Applications. 3 Hours.

Semester course 3 lecture hours. 3 credits. Covers the implementation of conservation techniques including monitoring, planning, education, habitat management and combining conservation with human development strategies. Focuses on how to make conservation work where biodiverstiy and human livelihoods must be reconciled. Students will utilize a number of computer programs to analyze and interpret management strategies.

BIOL 618. Ecosystems Ecology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: BIOL 317 or equivalent or permission by instructor. Introduction to the structure and functioning of aquatic and terrestrial ecosystems. The course complements other offerings in the graduate program by considering ecological processes at higher orders of organization and in the context of abiotic factors. Students will gain discipline-specific knowledge through lectures and readings while building quantitative and critical thinking.

BIOL 620. Biogeochemistry. 3 Hours.

Semester course 3 lecture hours. 3 credits. Enrollment restricted to graduate students. This course will examine the biogeochemical cycles of carbon, nitrogen, phosphorus, sulfur and iron on Earth from both a historical perspective and in the context of global environmental change, considering the cycles individually while also acknowledging that there are significant interactions between these cycles. Examples of biogeochemical processes will be drawn from multiple ecosystems, ranging from terrestrial soils to the deep ocean.

BIOL 626. Physiological Ecology. 4 Hours.

Semester course 4 lecture hours. 4 credits. Prerequisite: BIOL 317 or equivalent. This course examines the physiological adjustments and adaptations made by organisms in response to their environment.

BIOL 630. Patterns of Mammalian Reproduction. 3 Hours.

Semester course 3 lecture hours. 3 credits. A comprehensive ecological and evolutionary study of specializations and adaptive radiation in mammalian reproductive anatomy, the reproductive cycle, seasonality of reproduction and factors affecting litter size and developmental state of neonates. Human reproductive biology is included when pertinent.

BIOL 640. Evolution and Molecular Markers. 3 Hours.

Semester course 3 lecture hours. 3 credits. Methodologies and applications of molecular biology as they pertain to the study of evolution, with a focus on systematics, speciation and biogeography. The course provides proficiency in the understanding, interpretation and choice of appropriate molecular markers for evolutionary research, with particular attention to current methods and recent literature. Designed to benefit students of both natural history (ecologists, systematics, evolutionary biologists) and molecular biology.

BIOL 650. Conservation Genetics. 3 Hours.

Semester course 3 lecture hours. 3 credits. Covers the application of molecular genetics to biodiversity conservation. Essential topics include molecular measures of genetic diversity, estimating loss of genetic diversity in small populations, detecting inbreeding, resolution of taxonomic uncertainties, genetic management of T&E species, captive breeding and reintroduction. Students will utilize a number of computer programs to analyze and interpret molecular genetic data.

BIOL 654. Environmental Remote Sensing. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: ENVS 602, or permission of the instructor. This course provides a basic and applied understanding on the use of digital remote sensor data to detect, identify and characterize earth resources. Students are required to demonstrate an understanding of the spectral attributes of soils, vegetation and water resources through various labs involving both image- and non-image-based optical spectral data. Crosslisted as: ENVS 654/URSP 654.

BIOL 660. Developmental Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: biochemistry or cell biology or their equivalent. Molecular and cellular principles of developmental biology in model systems, including flies, worms, fish and mammals. Understanding of morphogen gradients, transcription, cell movements and signaling in development. Advanced methods are taught enabling students to interpret and present findings from the primary literature.

BIOL 676. Plant and Animal Cell Biology. 3 Hours.

Semester course 3 lecture hours. 3 credits. Prerequisite: biochemistry or cell biology or permission of instructor. Molecular and cellular principles of cell behavior and function in plant and animal cells. Topics include intracellular transport, cell cycle control, signaling and cell motility. Advanced methods are taught enabling students to interpret and present findings from the primary literature in this field.

BIOL 690. Biology Seminar. 1 Hour.

Semester course 1 credit. May be repeated for credit. Presentations by faculty and visiting lecturers, and discussions of research and developments in biology and related fields. Graded as S/U/F.

BIOL 691. Special Topics in Biology. 1-4 Hours.

Semester course variable hours. 1-4 credits. An advanced study of a selected topic in biology. See the Schedule of Classes for specific topics to be offered each semester and prerequisites. If several topics are offered, students may elect to take more than one.

BIOL 692. Independent Study. 1-4 Hours.

Semester course hours to be arranged. Credits to be arranged. Determination of the amount of credit and permission of instructor, adviser and department chair must be obtained prior to registration for this course. A course designed to provide an opportunity for independent research in any area of biology outside the graduate student thesis area.

BIOL 693. Current Topics in Biology. 1 Hour.

Semester course 1 lecture hour. 1 credit. May be repeated for credit. Designed to develop skills in preparing and delivering oral presentations in conjunction with an in-depth study of a current topic in biology. Students present talks and lead discussions on the selected topic.

BIOL 698. Thesis. 1-16 Hours.

Semester course hours to be arranged. Credits to be arranged. Independent research by students in areas of systematics, environmental, developmental, behavioral, cellular and molecular biology, and comparative physiology.


Watch the video: Αντιμετωπίστε τους μύκητες των ποδιών με φυσικούς τρόπους. Teta Kampoureli (June 2022).


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