Biology Commons^™

Desiccation Induces Viable But Non-Culturable Cells In Sinorhizobium Meliloti 1021, Jan A.C. Vriezen, Frans J. De Bruijn, Klaus R. Nüsslein

Biological Sciences: Faculty Publications

Sinorhizobium meliloti is a microorganism commercially used in the production of e.g. Medicago sativa seed inocula. Many inocula are powder-based and production includes a drying step. Although S. meliloti survives drying well, the quality of the inocula is reduced during this process. In this study we determined survival during desiccation of the commercial strains 102F84 and 102F85 as well as the model strain USDA1021.

The survival of S. meliloti 1021 was estimated during nine weeks at 22% relative humidity. We found that after an initial rapid decline of colony forming units, the decline slowed to a steady 10-fold reduction …

Effect Of Wine And Vinegar Processing Of Rhizoma Corydalis On The Tissue Distribution Of Tetrahydropalmatine, Protopine And Dehydrocorydaline In Rats, Zhiying Dou, Kefeng Li, Ping Wang, Liu Cao

Michigan Tech Publications, Part 1

Vinegar and wine processing of medicinal plants are two traditional pharmaceutical techniques which have been used for thousands of years in China. Tetrahydropalmatine (THP), dehydrocorydaline (DHC) and protopine are three major bioactive molecules in Rhizoma Corydalis. In this study, a simple and reliable HPLC method was developed for simultaneous analysis of THP, DHC and protopine in rat tissues after gastric gavage administration of Rhizoma Corydalis. The validated HPLC method was successfully applied to investigate the effect of wine and vinegar processing on the compounds’ distribution in rat tissues. Our results showed that processing mainly affect the T_max and mean …

A Multicenter Evaluation Of Diagnostic Tools To Define Endpoints For Programs To Eliminate Bancroftian Filariasis, Katherine Gass, Madsen V.E. Beau De Rochars, Daniel Boakye, Mark Bradley, Peter U. Fischer, John Gyapong, Makoto Itoh, Nese Ituaso-Conway, Hayley Joseph, Dominique Kyelem, Sandra J. Laney, Anne-Marie Legrand, Tilaka S. Liyanage, Wayne Melrose, Khalfan Mohammed, Nils Pilotte, Eric A. Ottesen, Catherine Plichart, Kapa Ramaiah, Ramakrishna U. Rao, Jeffrey Talbot, Gary J. Weil, Steven A. Williams, Kimberly Y. Won, Patrick J. Lammie

Biological Sciences: Faculty Publications

Successful mass drug administration (MDA) campaigns have brought several countries near the point of Lymphatic Filariasis (LF) elimination. A diagnostic tool is needed to determine when the prevalence levels have decreased to a point that MDA campaigns can be discontinued without the threat of recrudescence. A six-country study was conducted assessing the performance of seven diagnostic tests, including tests for microfilariae (blood smear, PCR), parasite antigen (ICT, Og4C3) and antifilarial antibody (Bm14, PanLF, Urine SXP). One community survey and one school survey were performed in each country. A total of 8,513 people from the six countries participated in the study, …

High Altitude Diving In River Otters: Coping With Combined Hypoxic Stresses, Jamie R. Crait, Henry D. Prange, Noah A. Marshall, Henry J. Harlow, Clark Cotton, Merav Ben-David

Biology Faculty Publications

River otters (Lontra canadensis) are highly active, semi-aquatic mammals indigenous to a range of elevations and represent an appropriate model for assessing the physiological responses to diving at altitude. In this study, we performed blood gas analyses and compared blood chemistry of river otters from a high-elevation (2357 m) population at Yellowstone Lake with a sea-level population along the Pacific coast. Comparisons of oxygen dissociation curves (ODC) revealed no significant difference in hemoglobin-oxygen (Hb-O₂) binding affinity between the two populations - potentially because of demands for tissue oxygenation. Instead, high-elevation otters had greater Hb concentrations (18.7 …

Library Impact Statement For Bio 553 Regulatory Processes In Eucaryotic Cells, Michael A. Cerbo Ii

Library Impact Statements

Library Impact Statement for BIO 553 Regulatory Processes in Eucaryotic Cells new course proposal. No new library resources are needed to support this course. Responding library faculty member: Michael A. Cerbo II. Requesting faculty member: Joanna Norris.

Investigating The Spectrum Of Biological Activity Of Substituted Quinoline-2-Carboxamides And Their Isosteres, Jiahui Guo, Et. Al.

Department of Biological Sciences Publications

In this study, a series of thirty-five substituted quinoline-2-carboxamides and thirty-three substituted naphthalene-2-carboxamides were prepared and characterized. They were tested for their activity related to the inhibition of photosynthetic electron transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. Primary in vitro screening of the synthesized compounds was also performed against four mycobacterial species. N-Cycloheptylquinoline-2-carboxamide, N-cyclohexylquinoline-2-carboxamide and N-(2-phenylethyl)quinoline-2-carboxamide showed higher activity against M. tuberculosis than the standards isoniazid or pyrazinamide and 2-(pyrrolidin-1-ylcarbonyl)quinoline and 1-(2-naphthoyl)pyrrolidine expressed higher activity against M. kansasii and M. avium paratuberculosis than the standards isoniazid or pyrazinamide. The most effective antimycobacterial compounds demonstrated insignificant toxicity against the human …

Philopatry Drives Genetic Differentiation In An Island Archipelago: Comparative Population Genetics Of Galapagos Nazca Boobies (Sula Granti) And Great Frigatebirds (Fregata Minor), Iris Levin, Patricia Parker

Biology Department Faculty Works

Seabirds are considered highly mobile, able to fly great distances with few apparent barriers to dispersal. However, it is often the case that seabird populations exhibit strong population genetic structure despite their potential vagility. Here we show that Galapagos Nazca booby (Sula granti) populations are substantially differentiated, even within the small geographic scale of this archipelago. On the other hand, Galapagos great frigatebird (Fregata minor) populations do not show any genetic structure. We characterized the genetic differentiation by sampling five colonies of both species in the Galapagos archipelago and analyzing eight microsatellite loci and three mitochondrial genes. Using an F‐statistic …

Protein Docking Prediction Using Predicted Protein-Protein Interface., Bin Lin, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations.

Results

We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which …

Tumor Suppression By Cell Competition Through Regulation Of The Hippo Pathway, Chiao-Lin Chen, Molly C. Schroeder, Madhuri Kango-Singh, Chunyao Tao, Georg Halder

Biology Faculty Publications

Homeostatic mechanisms can eliminate abnormal cells to prevent diseases such as cancer. However, the underlying mechanisms of this surveillance are poorly understood. Here we investigated how clones of cells mutant for the neoplastic tumor suppressor gene scribble (scrib) are eliminated from Drosophila imaginal discs. When all cells in imaginal discs are mutant for scrib, they hyperactivate the Hippo pathway effector Yorkie (Yki), which drives growth of the discs into large neoplastic masses. Strikingly, when discs also contain normal cells, the scrib− cells do not overproliferate and eventually undergo apoptosis through JNK-dependent mechanisms. However, induction of apoptosis does …

Aquaporin 4 Is A Ubiquitously Expressed Isoform In The Dogfish (Squalus Acanthias) Shark, Christopher P. Cutler, Bryce Maciver, Gordon Cramb, Mark L. Zeidel

Biology: Faculty Publications

The dogfish ortholog of aquaporin 4 (AQP4) was amplified from cDNA using degenerate PCR followed by cloning and sequencing. The complete coding region was then obtained using 5′ and 3′ RACE techniques. Alignment of the sequence with AQP4 amino acid sequences from other species showed that dogfish AQP4 has high levels (up to 65.3%) of homology with higher vertebrate sequences but lower levels of homology to Agnathan (38.2%) or teleost (57.5%) fish sequences. Northern blotting indicated that the dogfish mRNA was approximately 3.2 kb and was highly expressed in the rectal gland (a shark fluid secretory organ). Semi-quantitative PCR further …

Differences In Spectral Sensitivity Within And Among Species Of Darters (Genus Etheostoma), Jennifer M. Gumm, Ellis R. Lowe, Tamra C. Mendelson

Faculty Publications

We examined variation in the visual system both within and among seven species of darters, colorful freshwater fishes of the genus Etheostoma. Using microspectrophotometry, we found that darters possess rod photoreceptor cells, single cone photoreceptor cells containing middle wavelength sensitive (MWS) visual pigments, and twin photoreceptor cells containing (LWS) visual pigments. No variation in peak sensitivity was detected among species or individuals in the rod class. In the MWS class, significant variation was detected among species and a strong statistical trend suggests differences among individuals. By contrast, all differences in the LWS class could be attributed to variation among individuals. …

Chemical And Isotopic Evaluation Of Sulfur Sources And Cycling In The Pecos River, New Mexico, Usa, Fasong Yuan, Bernhard Mayer

Biological, Geological, and Environmental Faculty Publications

The use of stable isotopes in studies of watershed biogeochemical processes has increased greatly throughout the last several decades. Much of the sulfur cycling research has addressed the influence of changes in atmospheric acid deposition on sulfur dynamics in temperate ecosystems. Little is known about sulfur cycling in dryland ecosystems such as those in the American Southwest. To identify the sources and assess the cycling of sulfur in dryland ecosystems, chemical and isotopic compositions of water were measured on samples collected from the Pecos River (New Mexico, USA) during a reconnaissance survey in spring 2010. Based on the chemical and …

Sirtuin-Induced Protein Deacetylation Affects The Heat Shock Response In Blue Mussel Congeners (Mytilus), M. Beam, M. Zuzow, L. Tomanek

Biological Sciences

The warm-adapted Mediterranean blue mussel species Mytilus galloprovincialis invaded southern California during the last century and has since replaced the cold-adapted native M. trossulus from its southern range, possibly due to climate change. Based on previous proteomic analyses, we hypothesized that the more heat-sensitive M. trossulus switches from NADH-producing metabolic pathways that may generate reactive oxygen species (ROS) to NADPH-producing pathways that are able to scavenge ROS during severe heat stress (32°C). We further linked these changes to the activity of the mitochondrial NAD-dependent deacetylase, sirtuin-5, which has been shown to regulate many metabolic pathways. To test the latter hypothesis, …

The Proteomic Response To Acute Heat Stress After Acclimation To Fluctuating Temperatures In The Eurythermal Porcelain Crab, Petrolisthes Cinctipes, Michael A. Garland, Holland Elder, David A. Hurt, Jonathon H. Stillman, Lars Tomanek

Biological Sciences

The porcelain crab Petrolisthes cinctipes inhabits the high intertidal along the Pacific coast between British Columbia and central California and is an emerging model organism to study the effects of environmental stress. In its habitat it experiences not only variability in average temperature but also variability in temperature fluctuations. To investigate the effect of temperature fluctuations, we characterized the heat shock response at 30°C for 6 h by acclimating individuals to three different acclimation treatments: 10°C, 10-20°C (4 h), and 10-30°C (4 h) on a daily basis for one month. We dissected claw muscle and separated proteins by 2D gel …

Experimentally Altered Navigational Demands Induce Changes In The Cortical Forebrain Of Free-Ranging Northern Pacific Rattlesnakes (Crotalus O. Oreganus), Matthew L. Holding, Julius A. Frazier, Emily N. Taylor, Christine R. Strand

Biological Sciences

The hippocampus of birds and mammals plays a crucial role in spatial memory and navigation. The hippocampus exhibits plasticity in adulthood in response to diverse environmental factors associated with spatial demands placed on an animal. The medial and dorsal cortices of the telencephalon of squamate reptiles have been implicated as functional homologues to the hippocampus. This study sought to experimentally manipulate the navigational demands placed on free-ranging northern Pacific rattlesnakes (Crotalus o. oreganus) to provide direct evidence of the relationship between spatial demands and neuroplasticity in the cortical telencephalon of the squamate brain. Adult male rattlesnakes were radio-tracked for 2 …

The Proteomic Response Of Mytilus Californianus To Acute Oxidative Stress In The Presence Of A Sirtuin Inhibitor, H. Chilton, J. Mier, M. Zuzow, L. Tomanek

Biological Sciences

The ribbed mussel (Mytilus californianus) occurs in the in the rocky intertidal zone along the Pacific coast of North America where it experiences greatly varying environmental conditions in terms of temperature and hypoxia, stressors that are known to induce oxidative stress. It has been hypothesized that while under acute heat stress, related Mytilus congeners undergo a shift in redox potential through the reduction of NADH fueled respiration pathways to the production of the reducing agent NADPH as a potential defensive mechanism against the production of reactive oxygen species. In addition, it has been hypothesized that sirtuins (a family …

Proteomic Responses Of Mytilus Congeners To Hypo-Saline Stress, M. Z. Zuzow, L. Serafini, L. Hitt, J. Valenzuela, L. Tomanek

Biological Sciences

The invading Mediterranean blue mussel species Mytilus galloprovincialis requires higher salinity levels than the more hypo-saline tolerant and native M.trossulus,which it replaced from its southern range in California, possibly due to climate change.It is also the warm-adapted congener.Hypo-salinity,due to an increase in extreme precipitation events,has been hypothesized to limit the expansion of the invader.By comparing the proteomic responses of the congeners to acute hypo-saline stress we were trying to identify the interspecific differences that set limits to hypo-saline stress and assess their contribution to the range shifts.We exposed mussels to acute hypo-saline(100%, 85% and 70% salinity)stress for 4h followed …

Proteomic Analysis Of Hyposalinity Stress In The Ascidian Species Ciona Savignyi And C. Intestinalis, James S. Koman, Lars Tomanek

Biological Sciences

The ascidian species Ciona savignyi and C. intestinalis are invasive species but show interspecific differences in their population response to hypo-saline stress associated with heavy winter-run off events that are predicted to become more frequent due to climate change. Despite an almost world-wide distribution, C. intestinalis seems to be more susceptible to hypo-saline stress than the geographically more limited C. savignyi. Given that the genomes of both species are fully sequenced, we were able to compare their proteomic response to both acute and chronic salinity to characterize the mechanisms that are responsible for setting tolerance limits to hyposaline conditions …

Proteomic Response Of Tidal-Rhythm Entrained Mytilus Californianus To Acute Aerial Heat Stress, D. Hernandez, M. Schuman, L. Tomanek

Biological Sciences

The rocky intertidal mussel species Mytilus californianus is native to the Pacific coast of North America. It is frequently exposed to temperatures that can induce the cellular stress response due to the tidal rhythm. Instead of acclimating mussels to common conditions in the laboratory for several weeks, we collected mussels from a site with mussel body temperature recordings (specimens’ thermal history) and immediately started experimentation by mimicking the tidal rhythm with different levels of heat stress over multiple low tides and with different recovery periods. By using individuals that were entrained to the tidal rhythm and by maintaining it, we …

[Accepted Article Manuscript Version (Postprint)] Plant Peroxisomes: Biogenesis And Function, Jianping Hu, Alison Baker, Bonnie Bartel, Nicole Linka, Robert Mullen, Sigrun Reumann, Bethany Zolman

Biology Department Faculty Works

Peroxisomes are eukaryotic organelles that are highly dynamic both in morphology and metabolism. Plant peroxisomes are involved in numerous processes, including primary and secondary metabolism, development, and responses to abiotic and biotic stresses. Considerable progress has been made in the identification of factors involved in peroxisomal biogenesis, revealing mechanisms that are both shared with and diverged from non-plant systems. Furthermore, recent advances have begun to reveal an unexpectedly large plant peroxisomal proteome and have increased our understanding of metabolic pathways in peroxisomes. Coordination of the biosynthesis, import, biochemical activity, and degradation of peroxisomal proteins allows for highly dynamic responses of …

Library Impact Statement For Bio 485x Salt Marsh Ecology, Michael A. Cerbo Ii

Library Impact Statements

Library Impact Statement for BIO 485X Salt Marsh Ecology new course proposal. No new library resources are needed to support this course. Responding library faculty member: Michael A. Cerbo II. Requesting faculty member: Serena Moseman-Valtierra.

Library Impact Statement For Bio 585x Salt Marsh Ecology, Michael A. Cerbo Ii

Library Impact Statements

Library Impact Statement for BIO 585X Salt Marsh Ecology new course proposal. No new library resources are needed to support this course. Responding library faculty member: Michael A. Cerbo II. Requesting faculty member: Serena Moseman-Valtierra.

Construction And Transformation Of A Thermotoga-E. Coli Shuttle Vector, Zhaohui Xu, Dongmei Han, Stephen M. Norris

Biological Sciences Faculty Publications

Background: Thermotoga spp. are attractive candidates for producing biohydrogen, green chemicals, and thermostable enzymes. They may also serve as model systems for understanding life sustainability under hyperthermophilic conditions. A lack of genetic tools has hampered the investigation and application of these organisms. This study aims to develop a genetic transfer system for Thermotoga spp. Results: Methods for preparing and handling Thermotoga solid cultures under aerobic conditions were optimized. A plating efficiency of similar to 50% was achieved when the bacterial cells were embedded in 0.3% Gelrite. A Thermotoga-E. coli shuttle vector pDH10 was constructed using pRQ7, a cryptic mini-plasmid found …

It’S My Body: The Biomedical Ethics Of Cell And Organ Harvest, Christina Perri

Common Reading Essay Contest Winners

First Place

Increased Variability Of Microbial Communities In Restored Salt Marshes Nearly 30 Years After Tidal Flow Restoration, Anne E. Bernhard, David Marshall, Lazaros Yiannos

Biology Faculty Publications

We analyzed microbial diversity and community composition from four salt marsh sites that were impounded for 40–50 years and subsequently restored and four unimpounded sites in southeastern Connecticut over one growing season. Community composition and diversity were assessed by terminal restriction fragment length polymorphism (TRFLP) and sequence analysis of 16S ribosomal RNA (rRNA) genes. Our results indicated diverse communities, with sequences representing 14 different bacterial divisions. Proteobacteria, Bacteroidetes, and Planctomycetes dominated clone libraries from both restored and unimpounded sites. Multivariate analysis of the TRFLP data suggest significant site, sample date, and restoration status effects, but the exact causes of these …

Global Tests Of P-Values For Multifactor Dimensionality Reduction Models In Selection Of Optimal Number Of Target Genes, Madhusudan Bhandary

Faculty Bibliography

Background: Multifactor Dimensionality Reduction (MDR) is a popular and successful data mining method developed to characterize and detect nonlinear complex gene-gene interactions (epistasis) that are associated with disease susceptibility. Because MDR uses a combinatorial search strategy to detect interaction, several filtration techniques have been developed to remove genes (SNPs) that have no interactive effects prior to analysis. However, the cutoff values implemented for these filtration methods are arbitrary, therefore different choices of cutoff values will lead to different selections of genes (SNPs). Methods: We suggest incorporating a global test of p-values to filtration procedures to identify the optimal number of …

The Number Of X Chromosomes Causes Sex Differences In Adiposity In Mice, Jenny Link, Xuqi Chen, Rebecca Mcclusky, Simon W. Beaven, Peter Tontonoz, Arthur P. Arnold, Karen Reue

Biology

Sexual dimorphism in body weight, fat distribution, and metabolic disease has been attributed largely to differential effects of male and female gonadal hormones. Here, we report that the number of X chromosomes within cells also contributes to these sex differences. We employed a unique mouse model, known as the “four core genotypes,” to distinguish between effects of gonadal sex (testes or ovaries) and sex chromosomes (XX or XY). With this model, we produced gonadal male and female mice carrying XX or XY sex chromosome complements. Mice were gonadectomized to remove the acute effects of gonadal hormones and to uncover effects …

Macroevolutionary Dynamics And Historical Biogeography Of Primate Diversification Inferred From A Species Supermatrix, Christopher A. Emerling, Mark S. Springer, Robert W. Meredith, John Gatesy, Jong Park, Daniel L. Rabosky, Tanja Stadler, Cynthia Steiner, Oliver A. Ryder, Jan E. JanecˇKa, Colleen A. Fisher, William J. Murphy

Biology

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs …

A Natural Language Interface Plug-In For Cooperative Query Answering In Biological Databases, Hasan M. Jamil

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed …

Purification And Characterization Of Endoxylanase Xln-2 From Aspergillus Niger B03, Georgi Dobrev, Boriana Zhekova

Turkish Journal of Biology

An extracellular multiple form of endoxylanase was isolated from the xylanolytic complex of Aspergillus niger B03. The enzyme was purified to a homogenous form using ultrafiltration, anion exchange chromatography, and gel filtration. It was a nonglycosylated protein with a molecular weight of 20,000 Da as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and 21,000 Da as determined by gel filtration. The optimal pH for the enzyme action was 5.0 and the optimal temperature was 55 °C. Endoxylanase stability was significantly improved in the presence of glycerol and sorbitol. The enzyme activity was activated by Mn^{2+} and Co^{2+}, and it was …