Biology Commons^™

Connectivity And Nitrate Uptake Potential Of Intermittent Streams In The Northeast Usa, Kelly Addy, Arthur J. Gold, Molly K. Welsh, Peter V. August, Mark H. Stolt, Clay P. Arango, Peter M. Groffman

All Faculty Scholarship for the College of the Sciences

Non-perennial streams dominate the extent of stream networks worldwide. Intermittent streams can provide ecosystem services to the entire network—including nitrate uptake to alleviate eutrophication of coastal waters—and are threatened by lack of legal protection. We examined 12 intermittent streams in the temperate, humid climate of the Northeast USA. Over 3 years of monitoring, continuous flow was observed a median of 277 d yr−1, with no-flow conditions from early summer into fall. Estimated median discharge was 2.9 L s−1 or 0.36mm d−1. All intermittent streams originated from source wetlands (median area: 0.27 ha) and the median length of the intermittent stream …

Global Patterns And Drivers Of Ecosystem Functioning In Rivers And Riparian Zones, Scott D. Tiegs, Clay Arango

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River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth’s biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints …

Historical Species Distribution Models Predict Species Limits In Western Plethodon Salamanders, Tara A. Pelletier, Charlie Crisafulli, Steve Wagner, Amanda J. Zellmer, Brian C. Carstens

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Allopatry is commonly used to predict boundaries in species delimitation investigations under the assumption that currently allopatric distributions are indicative of reproductive isolation; however, species ranges are known to change over time. Incorporating a temporal perspective of geographic distributions should improve species delimitation; to explore this, we investigate three species of western Plethodon salamanders that have shifted their ranges since the end of the Pleistocene. We generate species distribution models (SDM) of the current range, hindcast these models onto a climatic model 21 Ka, and use three molecular approaches to delimit species in an integrated fashion. In contrast to expectations …

Antimicrobial And Antiinsectan Phenolic Metabolites Of Dalea Searlsiae, Gil Belofsky, Mario Aronica, Eric Foss, Jane Diamond, Felipe Santana, Jacob Darley, Patrick F. Dowd, Christina M. Coleman, Daneel Ferreira

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Continued interest in the chemistry of Dalea spp. led to investigation of Dalea searlsiae, a plant native to areas of the western United States. Methanol extractions of D. searlsiae roots and subsequent chromatographic fractionation afforded the new prenylated and geranylated flavanones malheurans A–D (1–4) and known flavanones (5 and 6). Known rotenoids (7 and 8) and isoflavones (9 and 10) were isolated from aerial portions. Structure determination of pure compounds was accomplished primarily by extensive 1D- and 2D-NMR spectroscopy. The absolute configurations of compounds 1–5, 7 …

Grizzly Bear Monitoring By The Heiltsuk People As A Crucible For First Nation Conservation Practice, William G. Housty, Anna Noson, Gerald W. Scoville, John Boulanger, Richard M. Jeo, Chris T. Darimont, Christopher E. Filardi

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Guided by deeply held cultural values, First Nations in Canada are rapidly regaining legal authority to manage natural resources. We present a research collaboration among academics, tribal government, provincial and federal government, resource managers, conservation practitioners, and community leaders supporting First Nation resource authority and stewardship. First, we present results from a molecular genetics study of grizzly bears inhabiting an important conservation area within the territory of the Heiltsuk First Nation in coastal British Columbia. Noninvasive hair sampling occurred between 2006 and 2009 in the Koeye watershed, a stronghold for grizzly bears, salmon, and Heiltsuk people. Molecular demographic analyses revealed …

Rigidity Analysis Of Protein Biological Assemblies And Periodic Crystal Structures, Filip Jagodzinski, Pamela Clark, Jessica Grant, Tiffany Liu, Samantha Monastra, Ileana Streinu

All Faculty Scholarship for the College of the Sciences

Background

We initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. The goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. We use experimental X-ray crystallography data from the Protein Data Bank (PDB). The analysis relies on an effcient graph-based algorithm. Computational experiments were performed using new protein rigidity analysis tools available in the new release of our KINARI-Web server http://kinari.cs.umass.edu.

Results

We provide two types of results: on biological assemblies and on crystals. We found that when only isolated …

A Conservation And Rigidity Based Method For Detecting Critical Protein Residues, Bahar Akbal-Delibas, Filip Jagodzinski, Nurit Haspel

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Background

Certain amino acids in proteins play a critical role in determining their structural stability and function. Examples include flexible regions such as hinges which allow domain motion, and highly conserved residues on functional interfaces which allow interactions with other proteins. Detecting these regions can aid in the analysis and simulation of protein rigidity and conformational changes, and helps characterizing protein binding and docking. We present an analysis of critical residues in proteins using a combination of two complementary techniques. One method performs in-silico mutations and analyzes the protein's rigidity to infer the role of a point substitution to Glycine …

A Proposed Mechanism For Nitrogen Acquisition By Grass Seedlings Through Oxidation Of Symbiotic Bacteria, James F. White Jr., Holly Crawford, Mónica S. Torres, Robert Mattera, Ivelisse Irizarry, Marshall Bergen

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In this paper we propose and provide evidence for a mechanism, oxidative nitrogen scavenging (ONS), whereby seedlings of some grass species may extract nitrogen from symbiotic diazotrophic bacteria through oxidation by plant-secreted reactive oxygen species (ROS). Experiments on this proposed mechanism employ tall fescue (Festuca arundinaceae) seedlings to elucidate features of the oxidative mechanism. We employed 15N₂ gas assimilation experiments to demonstrate nitrogen fixation, direct microscopic visualization of bacteria on seedling surfaces to visualize the bacterial oxidation process, reactive oxygen probes to test for the presence of H₂O₂ and cultural experiments to assess conditions …

Flank Gland-Secreted Putative Chemosignals Pertaining To Photoperiod, Endocrine States, And Sociosexual Behavior In Golden Hamsters, Ying-Juan Liu, Da-Wei Wang, Lixing Sun, Jin-Hua Zhang, Jian-Xu Zhang

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Behavioral studies have shown that flank glands are involved in chemical communication in golden hamsters Mesocricetus auratus but little chemical analysis has been conducted on volatiles arising from these glands. Using gas chromatography- mass spectrometry, we detected compounds from the flank glands of males, only eight of which were also produced in females. Based on these chemical data we performed a number of further experiments. By manipulating light we found that males exposed to short-photoperiods developed smaller flank glands than those exposed to long-photoperiods. Six flank gland volatiles reduced in relative abundance, which possibly coded for reproductive status of males …

Community-Based Inquiry Improves Critical Thinking In General Education Biology, Ian J. Quitadamo, Celia L. Faiola, James E. Johnson, Martha J. Kurtz

All Faculty Scholarship for the College of the Sciences

National stakeholders are becoming increasingly concerned about the inability of college graduates to think critically. Research shows that, while both faculty and students deem critical thinking essential, only a small fraction of graduates can demonstrate the thinking skills necessary for academic and professional success. Many faculty are considering nontraditional teaching methods that incorporate undergraduate research because they more closely align with the process of doing investigative science. This study compared a research-focused teaching method called community-based inquiry (CBI) with traditional lecture/laboratory in general education biology to discover which method would elicit greater gains in critical thinking. Results showed significant critical-thinking …

Sex- And Gonad-Affecting Scent Compounds And 3 Male Pheromones In The Rat, Jian-Xu Zhang, Lixing Sun, Jin-Hua Zhang, Zhi-Yong Feng

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This study was aimed at identifying sex pheromones of the rat (Rattus norvegicus). We characterized the volatiles and semivolatiles of rat preputial gland and voided urine by using gas chromatography–mass spectrometry (GC–MS) and quantified them by their GC areas (abundances) and percentage of GC areas (relative abundances). Although all the compounds other than 4-heptanone and phenol detected were shared by males and females, the quantities for some of these sex-common compounds exhibited sexual dimorphism and decreased with gonadectomy. Thus, these compounds might be sex pheromones. Among them, squalene from preputial glands and 2-heptanone and 4-ethyl phenol from urine …

The Parallel Worm Tracker: A Platform For Measuring Average Speed And Drug-Induced Paralysis In Nematodes, Daniel Ramot, Brandon E. Johnson, Tommie L. Berry Jr., Lucinda Carnell, Miriam B. Goodman

All Faculty Scholarship for the College of the Sciences

Background

Caenorhabditis elegans locomotion is a simple behavior that has been widely used to dissect genetic components of behavior, synaptic transmission, and muscle function. Many of the paradigms that have been created to study C. elegans locomotion rely on qualitative experimenter observation. Here we report the implementation of an automated tracking system developed to quantify the locomotion of multiple individual worms in parallel.

Methodology/Principal Findings

Our tracking system generates a consistent measurement of locomotion that allows direct comparison of results across experiments and experimenters and provides a standard method to share data between laboratories. The tracker utilizes a video camera …

The Complete Plastid Genome Sequence Of Welwitschia Mirabilis: An Unusually Compact Plastome With Accelerated Divergence Rates, Skip R. Mccoy, Jennifer V. Kuehl, Jeffrey L. Boore, Linda A. Raubeson

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Background

Welwitschia mirabilis is the only extant member of the family Welwitschiaceae, one of three lineages of gnetophytes, an enigmatic group of gymnosperms variously allied with flowering plants or conifers. Limited sequence data and rapid divergence rates have precluded consensus on the evolutionary placement of gnetophytes based on molecular characters. Here we report on the first complete gnetophyte chloroplast genome sequence, from Welwitschia mirabilis, as well as analyses on divergence rates of protein-coding genes, comparisons of gene content and order, and phylogenetic implications.

Results

The chloroplast genome of Welwitschia mirabilis [GenBank: EU342371] is comprised of 119,726 base pairs and exhibits …

Comparative Chloroplast Genomics: Analyses Including New Sequences From The Angiosperms Nuphar Advena And Ranunculus Macranthus, Linda A. Raubeson, Rhiannon Peery, Timothy W. Chumley, Chris Dziubek, H. Matthew Fourcade, Jeffrey L. Boore, Robert K. Jansen

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Background

The number of completely sequenced plastid genomes available is growing rapidly. This array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is often useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (a basal eudicot). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution …

Standard-Level Herbivory In An Old-Growth Conifer Forest Canopy, David C. Shaw, Kristina A. Ernest, H. Bruce Rinker, Margaret D. Lowman

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Herbivory is an important ecological process in forest canopies but is difficult to measure, especially for whole stands. We used the Wind River Canopy Crane in Washington State to access 101 randomly-located sample points throughout the forest canopy. This provided a relatively quick and convenient way to estimate herbivory for a whole stand. The overall level of herbivory was estimated at 1.6% of leaf area. The distribution was strongly skewed to the lower canopy where broad-leafed species experienced higher levels of herbivory. Herbivory averaged 0.3% in conifers and 13.5% in broad-leafed species. Fully half of the sample points had no …

Distance-Based Genome Rearrangement Phylogeny, Li-San Wang, Tandy Warnow, Bernard M.E. Moret, Robert K. Jansen, Linda A. Raubeson

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Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, transpositions, and inverted transpositions, as well as through operations, such as duplications, losses, and transfers, that also affect the gene content of the genomes. Because these events are rare relative to nucleotide substitutions, gene order data offer the possibility of resolving ancient branches in the tree of life; the combination of gene order data with sequence data also has the potential to provide more robust phylogenetic reconstructions, since each can elucidate evolution at different time scales. Distance corrections greatly improve the accuracy of phylogeny reconstructions from DNA …

The Effect Of Male Competition On Female Choice In Brandt’S Vole, Lasiopodomys Brandti, Jianjun Zhang, Dazhao Shi, Lixing Sun

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The effect of male competition on female choice in the Brandt’s vole (Lasiopodomys brandti) was studied in the laboratory. Using a two-way choice test, we showed that when males did not compete, estrous females preferred and mated with the dominant males, but non-estrous females preferred subordinate males. However, when males competed, all dominant males gained the priority to mate, and the amicable behaviour between males, regardless of their dominant status, and between non-estrous females increased, compared with the behaviour between males and the estrous females. These results showed that interactions among Brandt’s voles were not only influenced by …

Chloroplast Dna Rearrangements In Campanulaceae: Phylogenetic Utility Of Highly Rearranged Genomes, Mary E. Cosner, Linda A. Raubeson, Robert K. Jansen

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Background

The Campanulaceae (the "hare bell" or "bellflower" family) is a derived angiosperm family comprised of about 600 species treated in 35 to 55 genera. Taxonomic treatments vary widely and little phylogenetic work has been done in the family. Gene order in the chloroplast genome usually varies little among vascular plants. However, chloroplast genomes of Campanulaceae represent an exception and phylogenetic analyses solely based on chloroplast rearrangement characters support a reasonably well-resolved tree.

Results

Chloroplast DNA physical maps were constructed for eighteen representatives of the family. So many gene order changes have occurred among the genomes that characterizing individual mutational …

Organization And Polarity Of Protoplasm, John P. Munson

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In higher forms of life, we usually concede the presence of an organ specialized for the performance of a function. In these higher forms coordination of organs, which entails a regular sequence in their functions, is readily made out; and it seems a mere platitude to say, of these, that organization determines the functions of the organism. To what extent can functions exist in the absence of organization; does the one precede the other; or have function and organization developed simultaneously, out of matter devoid of both structure and function? In my studies on the cell, I have kept these …

Spermatogenesis Of The Butterfly, Papilio Rutulus, John P. Munson

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For a number of years I have been studying the spermatogenesis of Papilio rutulus (pl. 12, fig. 1) not ,with any one single problem especially in view, but with the aim of ascertaining the entire life history of its sperm cell, its various phases of development, its mode of growth and differentiation, the history of its several parts, and its relation to the organism.