Posts tagged: Biology

Lauren Rasmussen, ’17

Rasmussen, L., & Olapade, O. A. (2016). Influence of zinc on bacterial populations and their proteolytic enzyme activities in freshwater environments: a cross-site comparison. Canadian Journal of Microbiology, 1-9.

Abstract: Temporal responses of indigenous bacterial populations and proteolytic enzyme (i.e., aminopeptidase) activities in the bacterioplankton assemblages from 3 separate freshwater environments were examined after exposure to various zinc (Zn) concentrations under controlled microcosm conditions. Zn concentrations (ranging from 0 to 10 μmol/L) were added to water samples collected from the Kalamazoo River, Rice Creek, and Huron River and examined for bacterial abundance and aminopeptidase activities at various time intervals over a 48 h incubation period in the dark. The results showed that the Zn concentrations did not significantly influence total bacterial counts directly; however, aminopeptidase activities varied significantly to increasing zinc treatments over time. Also, analysis of variance and linear regression analyses revealed significant positive relationships between bacterial numbers and their hydrolytic enzyme activities, suggesting that both probably co-vary with increasing Zn concentrations in aquatic systems. The results from this study serve as additional evidence of the ecological role of Zn as an extracellular peptidase cofactor on the dynamics of bacterial assemblages in aquatic environments.

Allison McClish, ’15

Erhard, K. F., Talbot, J., Deans, N. C., McClish, A. E., & Hollick, J. B. (2015). Nascent Transcription Affected by RNA Polymerase IV in Zea mays. Genetics, 199(4), 1107-U1355.

Abstract: All eukaryotes use three DNA-dependent RNA polymerases (RNAPs) to create cellular RNAs from DNA templates. Plants have additional RNAPs related to Pol II, but their evolutionary role(s) remain largely unknown. Zea mays (maize) RNA polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs), and transcriptional regulation of specific alleles. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based regulation. Comparisons of WT and rpd1 mutant GRO-seq profiles indicate that Pol IV globally affects transcription at both transcriptional start sites and immediately downstream of polyadenylation addition sites. We found no evidence of divergent transcription from gene promoters as seen in mammalian GRO-seq profiles. Statistical comparisons identify genes and TEs whose transcription is affected by RPD1. Most examples of significant increases in genic antisense transcription appear to be initiated by 3′-proximal long terminal repeat retrotransposons. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for specific regions of the maize genome including genes having developmental significance.

Adam Ronk, ’13

Olapade, O. A., & Ronk, A. J. (2014). Isolation, Characterization and Community Diversity of Indigenous Putative Toluene-Degrading Bacterial Populations with Catechol-2,3-Dioxygenase Genes in Contaminated Soils. Microbial Ecology, 1-7.

Abstract: Indigenous bacterial assemblages with putative hydrocarbon-degrading capabilities were isolated, characterized and screened for the presence of the catechol-2,3-dioxygenase (C23O) gene after exposure to toluene in two different (i.e., pristine and conditioned) soil communities. The indigenous bacterial populations were exposed to the hydrocarbon substrate by the addition of toluene concentrations, ranging from 0.5 % to 10 % V/W in 10 g of each soil and incubated at 30 °C for upwards of 12 days. In total, 25 isolates (11 in pristine soil and 14 in conditioned soil) were phenotypically characterized according to standard microbiological methods and also screened for the 238-bp C23O gene fragment. Additionally, 16S rRNA analysis of the isolates identified some of them as belonging to the genera Bacillus, Exiguobacterium, Enterobacter, Pseudomonas and Stenotrophomonas. Furthermore, the two clone libraries that were constructed from these toluene-contaminated soils also revealed somewhat disparate phylotypes (i.e., 70 % Actinobacteria and Firmicutes to 30 % Proteobacteria in conditioned soil, whereas in pristine soil: 66 % Actinobacteria and Firmicutes; 21 % Proteobacteria and 13 % Bacteroidetes). The differences observed in bacterial phylotypes between these two soil communities may probably be associated with previous exposure to hydrocarbon sources by indigenous populations in the conditioned soil as compared to the pristine soil.

Kayleigh Pung, ’11

Olapade, O., & Pung, K. (2012). Plant-associated bacterial populations on native and invasive plant species: comparisons between 2 freshwater environments. Canadian Journal of Microbiology, 58(6), 767-775.

Abstract: Plant–microbial interactions have been well studied because of the ecological importance of such relationships in aquatic systems. However, general knowledge regarding the composition of these biofilm communities is still evolving, partly as a result of several confounding factors that are attributable to plant host properties and to hydrodynamic conditions in aquatic environments. In this study, the occurrences of various bacterial phylogenetic taxa on 2 native plants, i.e., mayapple (Podophyllum peltatum L.) and cow parsnip (Heracleum maximum Bartram), and on an invasive species, i.e., garlic mustard (Alliaria petiolata (M. Bieb.) Cavara & Grande), were quantitatively examined using nucleic acid staining and fluorescence in situ hybridization. The plants were incubated in triplicates for about a week within the Kalamazoo River and Pierce Cedar Creek as well as in microcosms. The bacterial groups targeted for enumeration are known to globally occur in relatively high abundance and are also ubiquitously distributed in freshwater environments. Fluorescence in situ hybridization analyses of the bacterioplankton assemblages revealed that the majority of bacterial cells that hybridized with the different probes were similar between the 2 sites. In contrast, the plant-associated populations while similar on the 3 plants incubated in Kalamazoo River, their representations were highest on the 2 native plants relative to the invasive species in Pierce Cedar Creek. Overall, our results further suggested that epiphytic bacterial assemblages are probably under the influences of and probably subsequently respond to multiple variables and conditions in aquatic milieus.

Kayleigh Pung, 11, Erin Goldman, ’11

Olapade, O. A., Pung, K., Goldman, E., & Lyons-Sobaski, S. (2011). Occurrence and diversity of epiphytic bacterial communities on two native plant species in a Michigan Creek. Journal of Freshwater Ecology, 26(2), 267 – 276.

Abstract: We examined the occurrence and diversity of bacteria of different phylogenetic groups in epiphytic assemblages on two native Michigan plant species mayapple (Podophyllum peltatum) and cow parsnip (Heracleum maximum) when the plant leaves were submerged in fresh water. Fresh leaves were incubated in triplicate for about a week within a creek in Hasting, Michigan, and in laboratory microcosm to develop mature epiphytic assemblages. We enumerated bacteria in these assemblages by nucleic acid staining (i.e., total direct counts using 4′,6-diamidino-2-phenyllindole) and fluorescent in situ hybridization (FISH), while community diversity was determined based on 16S rRNA gene sequencing. FISH indicated the dominance of members of the γProteobacterial subclass (20%) on both plant species, while the 16S rRNA gene analysis revealed the predominance of the βProteobacteria (51%) on mayapple and the Fermicutes (26%) on cow parsnip, with the Bacteroidetes present equally within the epiphytic assemblages on both plants.

Jeff Stephens, ’09

Tingley, R., Herman, T., Pulsifer, M., McCurdy, D., & Stephens, J. (2010). Intra-Specific Niche Partitioning Obscures the Importance of Fine-Scale Habitat Data in Species Distribution Models. Biodiversity and Conservation, 19(9), 2455-2467.

Abstract: Geographic information systems (GIS) allow researchers to make cost-effective, spatially explicit predictions of species’ distributions across broad geographic areas. However, there has been little research on whether using fine-scale habitat data collected in the field could produce more robust models of species’ distributions. Here we used radio-telemetry data collected on a declining species, the North American wood turtle (Glyptemys insculpta), to test whether fine-scale habitat variables were better predictors of occurrence than land-cover and topography variables measured in a GIS. Patterns of male and female occurrence were similar in the spring; however, females used a much wider array of land-cover types and topographic positions in the summer and early fall, making it difficult for GIS-based models to accurately predict female occurrence at this time of year. Males on the other hand consistently selected flat, low-elevation, riparian areas throughout the year, and this consistency in turn led to the development of a strong GIS-based model. These results demonstrate the importance of taking a more sex-specific and temporally dynamic view of the environmental niche.

Adrienne VanZomeren-Dohm, ’07, Paul Beach, ’08, Wendy Simanton Holland, ’07

Flannery, E., VanZomeren-Dohm, A., Beach, P., Simanton Holland, W., & Duman-Scheel, M. (2010). Induction of Cellular Growth by the Axon Guidance Regulators Netrin a and Semaphorin-1a. Developmental Neurobiology, 70(7), 473-484.

Abstract: Although neurite outgrowth has been linked to axon guidance regulators, the effects of guidance molecules on cellular growth are not well understood. Use of the Drosophila wing imaginal disc, an epithelial tissue and a well-characterized system for analysis of cellular growth regulation, permits analysis of the impacts of guidance molecules on cellular growth in a setting in which axon guidance is not a confounding factor. In this investigation, the impacts of Netrin A (NetA) and Semaphorin-1a (Sema1a) signaling on cellular growth are examined during wing development. Levels of these genes were modulated in somatic clones in the developing wing disc, and clone areas, as well as individual sizes of clonal cells were assessed. NetA and Sema1a signaling were found to induce cellular growth in these assays. Furthermore, immunohistochemical analyses indicated that NetA and Sema1a signaling induce expression of several growth regulators, including myc, cycD, cdk4, PCNA, and MapK in the wing disc. These data illustrate that NetA and Sema1a can specifically promote growth through induction of key cellular growth regulators. The abilities of NetA and Sema1a to regulate cellular growth are likely critical to their functions in both nervous system development and oncogenesis. © 2010 Wiley Periodicals, Inc.

Elizabeth Weage, ’08

Olapade, O. A., & Weage, E. A. (2010). Comparison of Fecal Indicator Bacterial Populations in Surface Waters of the Kalamazoo River, USA. Microbes and Environments, 25(1).

Abstract: Surface waters along the Kalamazoo River, USA, were examined for occurrence and population trends of fecal indicator bacteria (FIB) with culture-based and culture-independent methods. The two methods recorded discrepancies in FIB counts, with the culture-independent method revealing more consistent numbers between the river sites. FIB cells that hybridized with the ECO1482 probe were highest in the downstream site, while the upstream site recorded higher ENF343 hybridized cells. Spatial and temporal differences in FIB populations were probably attributable to contrasting fecal pollution influences, vegetation type, varying environmental conditions as well as several in-stream factors between the two river sites.

Wendy Simanton, ’07, Stephanie Clark, ’06, Adrienne Farrell-VanZomeren, ’07, Paul Beach, ’08

Simanton, W., Clark, S., Clemons, A., Jacowski, C., Farrell-VanZomeren, A., Beach, P., et al. (2009). Conservation of Arthropod Midline Netrin Accumulation Revealed with a Cross-Reactive Antibody Provides Evidence for Midline Cell Homology. Evolution & Development, 11(3), 260-268.

Abstract: Although many similarities in arthropod CNS development exist, differences in axonogenesis and the formation of midline cells, which regulate axon growth, have been observed. For example, axon growth patterns in the ventral nerve cord of Artemia franciscana differ from that of Drosophila melanogaster. Despite such differences, conserved molecular marker expression at the midline of several arthropod species indicates that midline cells may be homologous in distantly related arthropods. However, data from additional species are needed to test this hypothesis. In this investigation, nerve cord formation and the putative homology of midline cells were examined in distantly related arthropods, including: long- and short-germ insects (D. melanogaster, Aedes aeygypti, and Tribolium castaneum), branchiopod crustaceans (A. franciscana and Triops longicauditus), and malacostracan crustaceans (Porcellio laevis and Parhyale hawaiensis). These comparative analyses were aided by a cross-reactive antibody generated against the Netrin (Net) protein, a midline cell marker and regulator of axonogenesis. The mechanism of nerve cord formation observed in Artemia is found in Triops, another branchiopod, but is not found in the other arthropods examined. Despite divergent mechanisms of midline cell formation and nerve cord development, Net accumulation is detected in a well-conserved subset of midline cells in branchiopod crustaceans, malacostracan crustaceans, and insects. Notably, the Net accumulation pattern is also conserved at the midline of the amphipod P. hawaiensis, which undergoes split germ-band development. Conserved Net accumulation patterns indicate that arthropod midline cells are homologous, and that Nets function to regulate commissure formation during CNS development of Tetraconata.

Daniel Painter, ’06, Michael Kopec, ’05, Diana Lancaster, ’06

McCurdy, D. G., Painter, D. C., ’06, Kopec, M. T., ’05, Lancaster, D., ’06, Cook, K. A., & Forbes, M. R. (2008). Reproductive Behavior of Intersexes of an Intertidal Amphipod Corophium Volutator. Invertebrate Biology, 127(4), 417-425.

Abstract: Intersexes are common in crustaceans. Typically, these intersexes are sterile or function as females, but prior evidence from laboratory experiments suggests that intersexes of a key species of gammaridean amphipod, Corophium volutator, might function as males. We observed that intersexes of C. volutator behaved as males by crawling (mate-searching) on a mudflat during ebb tides and pairing in burrows with female amphipods. In the laboratory, intersexes and males did not differ in aspects of crawling such as movement rate and measures of burrow investigation. I`ntersexuality was costly in that intersexes crawled less often than males on a mudflat, formed fewer pairs with females than males, and remained in tandem less often with receptive females than males. The use of PCR-based identification methods failed to identify the presence of transovarial, feminizing, microsporidian parasites as a major cause of intersexuality in this species in that infected females did not produce broods that contained more intersexes than broods produced by uninfected females. Because intersexes may be mistaken as females, the percentage of functional males in amphipod populations may be underestimated: an important consideration given male limitation in populations of C. volutator. The occurrence of intersexes has significant implications for studies on the evolution and ecology of sex ratios, and the use of crustaceans as indicators of environmental quality.

Natalie Dubois

Dubois, N. S., Kennedy, E. D., & Getty, T. (2006). Surplus Nest Boxes and the Potential for Polygyny Affect Clutch Size and Offspring Sex Ratio in House Wrens. Proceedings of the Royal Society B-Biological Sciences, 273(1595), 1751-1757.

Abstract: Females of many species can gain benefits from being choosy about their mates and even exhibit context-dependent investment in reproduction in response to the quality of their breeding situation. Here, we show that if a male house wren is provided with surplus nest boxes in his territory, his mate lays a larger clutch with a significantly higher proportion of sons. This response to a territory characteristic directly associated with male competitive ability, and ultimately to male reproductive success, suggests that male competition over access to high-quality territories with surplus nest boxes (i.e. those able to support polygyny) may influence female reproductive investment decisions. The results of this study have interesting implications, particularly considering the important role that studies of cavity nesting birds utilizing nest boxes have played in advancing our understanding of behaviour, ecology and evolution.

Stephanie Clark, Eric Grunow, Andrew Hasley, Brandon Hill, and Wendy Simanton

Duman-Scheel, M., Clark, S. M., Grunow, E. T., Hasley, A. O., Hill, B. L., & Simanton, W. L. (2007). Delayed Onset of Midline Netrin Expression in Artemia Franciscana Coincides with Commissural Axon Growth and Provides Evidence for Homology of Midline Cells in Distantly Related Arthropods. Evolution & Development, 9(2), 131-140.

Abstract: Although many similarities in arthropod central nervous systems (CNS) development exist, differences in midline cell formation and ventral nerve cord axonogenesis have been noted in arthropods. It is possible that changes in the expression of axon guidance molecules such as Netrin, which functions during commissural axon guidance in Drosophila and many other organisms, may parallel these differences. In this investigation, we analyze this hypothesis by examining Netrin accumulation during development of the brine shrimp Artemia franciscana, a branchiopod crustacean. An Artemia franciscana netrin (afrnet) orthologue was cloned. An antibody to the afrNet protein was generated and used to examine the pattern of afrNet accumulation during Artemia development. Despite differences between Drosophila and Artemia nerve cord development, examination of afrNet accumulation suggests that this protein functions to regulate commissure formation during Artemia CNS development. However, detection of afrNet at the midline and on commissural axons occurs at a relatively later time point in Artemia as compared with Drosophila. Detection of afrNet in a subset of midline cells that closely resemble Netrin-expressing cells at the Drosophila midline provides evidence for homology of midline cells in arthropods. Expression of Netrins in many other tissues is comparable, suggesting that Netrin proteins may play many conserved roles during arthropod development.

Sean Logan and Diana Lancaster

McCurdy, D. G., Forbes, M. R., Logan, S. P., Lancaster, D., & Mautner, S. I. (2005). Foraging and Impacts by Benthic Fish on the Intertidal Amphipod Corophium Volutator. Journal of Crustacean Biology, 25(4), 558-564.

Abstract: We studied feeding site selection and impacts by benthic fish (flounder and skates) on the amphipod Corophium volutator, an ecologically-important species in muddy intertidal communities. We determined that benthic fish foraged mainly in areas that had high densities of amphipods, on a mudflat in Nova Scotia, Canada. This observation was based on recording sediments displaced by benthic fish in areas where samples of amphipods also were taken. From gut-content analysis, we found that benthic fish fed almost entirely on C. volutator, and most consumed smaller amphipods than expected based on samples of amphipods collected from the substrate. Benthic fish also fed on male amphipods more than expected. We determined that daily foraging pressure by benthic fish on amphipods was low (about 0.3% per day) by measuring the new appearance of feeding traces made by fish. Nonetheless, fish are expected to have substantial impacts on demography of C. volutator due to the length of the fish foraging season and because fish appear to contribute to extreme female-biased sex ratios typically seen in this species.

Kristine Degel

Degel, K. and D. G. McCurdy. 2006. Impacts of temperature on emergence of trematode cercariae from the mud snail Ilyanassa obsoleta (Say). MarSci.(3).

Abstract: We assessed prevalence of trematode parasites and impacts of temperature on shedding of parasites infecting mud snails, Ilyanassa obsoleta (Say), collected from Maine. Six species of trematodes were found to infect mud snails: Austrobilharzia variglandis, Zoögonus rubellus, Stephanostomum tenue, Gynaecotyla adunca, Himasthla quissetensis, and Lepocreadium setiferoides. As predicted, snails were more likely to shed cercarial forms of six species of trematodes when experimentally exposed to elevated water temperatures for single 24-hour periods. We argue that even small-scale changes in temperature might have implications for individuals and populations of marine animals that serve as second-intermediate hosts and final hosts of trematodes shed by infected mud snails (e.g., clams, baitworms, birds, fish, humans). We also establish new northern limits for several species of marine trematodes.

Sarah Hudson and Adam Herrman

Erbeznik, M., Hudson, S. E., Herrman, A. B., & Strobel, H. J. (2004). Molecular Analysis of the Xylfgh Operon, Coding for Xylose Abc Transport, in Thermoanaerobacter Ethanolicus. Current Microbiology, 48(4), 295-299.

Abstract: A xylose ABC (ATP-binding cassette) transport operon, xylFGH, was cloned from Thermoanaerobacter ethanolicus, a thermophilic ethanol-producing eubacterium. The cistrons code for a periplasmic D-xylose-binding protein (XylF, partial sequence of 250 amino acids), ATP-binding protein (XylG, 505 amino acids), and integral membrane protein (XylH, 388 amino acids). These results, together with previous work, indicate that duplicate copies of both xylF and xylH are present in the T. ethanolicus chromosome, suggesting ancient gene duplication or lateral gene transfer events. XylG resembles other eubacterial monosaccharide ABC-ATPases in that its two nucleotide-binding domains (NBDs) are highly homologous, yet significantly different with respect to putative catalytic residues. Unlike most other integral membrane ABC transport proteins, XylH apparently contains 11 or 12 transmembrane segments (TMS) and is similar to a small group of ABC permeases that defy the ldquo2 × 6rdquo helix paradigm. This is the first report of a monosaccharide ABC transport operon in a thermophilic anaerobic eubacterium.

Sean Logan and Michael Kopec

McCurdy, D., Forbes, M., Logan, S., Kopec, M., & Mautner, S. (2004).  The functional significance of intersexes in the intertidal amphipod Corophium volutator.  Journal of Crustacean Biology, 24, 261-265.

Abstract: We investigated the functional significance of intersexuality in the amphipod Corophium volutator, a key species in soft-bottom intertidal communities. Intersexes in this species possess morphological and anatomical characters of both males and females. Two broad types of intersexes were identified: those with nonsetose oostegites and two penial papillae (Type I), and those with setose oostegites and one or two penial papillae (Type II). We found little evidence that intersexes function as females, but some females housed experimentally with intersexes became ovigerous, indicating that intersexes can function as males. Females that mated with Type II intersexes produced smaller broods than those that mated with Type I intersexes or males, suggesting that this form of intersexuality may be costly to amphipods (most Type II intersexes possessed only a single testis). Male function of intersexes may be important in populations of C. volutator because males are frequently the limiting sex due to extremely female-biased sex ratios.

Nick Whitney

Whitney, N., Pratt Jr., H. L., & Carrier, J. (2004).  Group courtship, mating behaviour, and siphon sac function in the Whitetip Reef Shark, Triaenodon obesus. Animal Behaviour, 68, 1435-1442.

Abstract: We analysed video records of three mating events involving nine free-living whitetip reef sharks in Cocos Islands, Costa Rica to examine reproductive behaviour in this species. We describe several behaviours never before documented in this species, and four behaviours never before documented in any elasmobranch. Here, we also present the first hypothesis for the function of the male’s paired reproductive organs, the siphon sacs, to be based on observations of mating sharks. We introduce terminology for three separate siphon sac structural components that are externally visible during courtship and mating in this species. Based on our analyses, as well as evidence from past mating studies, the siphon sacs in whitetip reef sharks appear to be used to propel sperm into the female’s reproductive tract, not for flushing the female’s reproductive tract of sperm from previous males. We discuss the implications of ‘group courtship’, ‘siphon isthmus constriction’, ‘reverse thrusting’, ‘postrelease gaping’ and ‘noncopulatory ejaculation’.

Daniel Holland

Holland, D., & Lee, J. (2003). A study of Z-scheme photosynthesisJournal of Undergraduate Research, U.S. Department of Energy, Office of Science, 3, 78.

Brad Slaughter

Slaughter, B. S., & Skean Jr., J. D. (2003). Comparison of cedar and tamarack stands in a relict conifer swamp at Pierce Cedar Creek Institute, Barry County, Michigan. Michigan Botanist, 42, 111-127.

Brad Slaughter

Slaughter, B. S., & Skean Jr., J. D. ( 2003). Annotated checklist of vascular plants in the vicinity of Cedar Creek and Brewster Lake, Pierce Cedar Creek Institute, Barry County, Michigan. Michigan Botanist, 42, 129-150.

Andrea Lindley and Eleanora Maries

Saville, K. J., Lindley, A. M., Maries, E. G., Carrier, J. C., & Pratt Jr., H. L. (2002).  Multiple paternity in the Nurse Shark, Ginglymostoma cirratum. Environmental Biology of Fishes, 63, 347-351.

Abstract: For over a decade, we have been studying the reproductive behavior of the nurse shark, Ginglymostoma cirratum, in the Dry Torugas off the Florida Keys, an important mating and nursery ground for this species. In the course of these studies, we have used a variety of tags and tagging protocols to monitor individual animals. Here we report the use of molecular methods for the genetic analysis of nurse sharks. Specifically we have analyzed genetic variation at the MHC II alpha locus using the polymerase chain reaction (PCR) followed by restriction fragment length polymorphism (RFLP) analysis of the amplified products. We found this technique to be a relatively rapid and reliable method for identifying genetic differences between individual sharks. Applying this method to a family of sharks consisting of a mother and 32 pups, we demonstrate that at least four fathers must have fathered this brood. Multiple paternity in the nurse shark suggests a mechanism by which populations of this species may maximize genetic variability. This seems especially valuable for philopatric species whose migratory movement, and thus potential for genetic diversity, is limited.

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