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Biology Faculty Publications

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Full-Text Articles in Life Sciences

The Effects Of Bacterial Endotoxin Lps On Synaptic Transmission At The Neuromuscular Junction, Robin L. Cooper, Micaiah Mcnabb, Jeremy Nadolski Mar 2019

The Effects Of Bacterial Endotoxin Lps On Synaptic Transmission At The Neuromuscular Junction, Robin L. Cooper, Micaiah Mcnabb, Jeremy Nadolski

Biology Faculty Publications

The direct action of bacterial lipopolysaccharides (LPS) endotoxin was shown to enhance synaptic transmission and hyperpolarize the membrane potential at low doses, but block glutamatergic receptors and decrease observable spontaneous events at a high dosage. The dosage effects are LPS type specific. The hyperpolarization is not due to voltage-gated potassium channels or to activation of nitric oxide synthase (NOS). The effects are induced directly by LPS, independent of an immune response.


The Effect Of Phylogenetic Uncertainty And Imputation On Edge Scores, K. Bodie Weedop, Arne Ø. Mooers, Caroline M. Tucker, William D. Pearse Mar 2019

The Effect Of Phylogenetic Uncertainty And Imputation On Edge Scores, K. Bodie Weedop, Arne Ø. Mooers, Caroline M. Tucker, William D. Pearse

Biology Faculty Publications

Faced with the challenge of saving as much diversity as possible given financial and time constraints, conservation biologists are increasingly prioritizing species on the basis of their overall contribution to evolutionary diversity. Metrics such as EDGE (Evolutionary Distinct and Globally Endangered) have been used to set such evolutionarily based conservation priorities for a number of taxa, such as mammals, birds, corals, amphibians, and sharks. Each application of EDGE has required some form of correction to account for species whose positions within the tree of life are unknown. Perhaps the most advanced of these corrections is phylogenetic imputation, but to date …


Consequences Of Intraspecific Variation In Seed Dispersal For Plant Demography, Communities, Evolution And Global Change, Rebecca S. Snell, Noelle G. Beckman, Evan Fricke, Bette A. Loiselle, Carolina S. Carvalho, Landon R. Jones, Nathanael I. Lichti, Nicky Lustenhouwer, Sebastian J. Schreiber, Christopher Strickland, Lauren L. Sullivan, Brittany R. Cavazos, Itamar Giladi, Alan Hastings, Kimberly M. Holbrook, Eelke Jongejans, Oleg Kogan, Flavia Montaño-Centellas, Javiera Rudolph, Haldre S. Rogers, Rafal Zwolak, Eugene W. Schupp Mar 2019

Consequences Of Intraspecific Variation In Seed Dispersal For Plant Demography, Communities, Evolution And Global Change, Rebecca S. Snell, Noelle G. Beckman, Evan Fricke, Bette A. Loiselle, Carolina S. Carvalho, Landon R. Jones, Nathanael I. Lichti, Nicky Lustenhouwer, Sebastian J. Schreiber, Christopher Strickland, Lauren L. Sullivan, Brittany R. Cavazos, Itamar Giladi, Alan Hastings, Kimberly M. Holbrook, Eelke Jongejans, Oleg Kogan, Flavia Montaño-Centellas, Javiera Rudolph, Haldre S. Rogers, Rafal Zwolak, Eugene W. Schupp

Biology Faculty Publications

As the single opportunity for plants to move, seed dispersal has an important impact on plant fitness, species distributions and patterns of biodiversity. However, models that predict dynamics such as risk of extinction, range shifts and biodiversity loss tend to rely on the mean value of parameters and rarely incorporate realistic dispersal mechanisms. By focusing on the mean population value, variation among individuals or variability caused by complex spatial and temporal dynamics is ignored. This calls for increased efforts to understand individual variation in dispersal and integrate it more explicitly into population and community models involving dispersal. However, the sources, …


Susceptibility Of Wild-Caught Lutzomyia Longipalpis (Diptera: Psychodidae) Sand Flies To Insecticide After An Extended Period Of Exposure In Western São Paulo, Brazil, Mikel A. González, Melissa J. Bell, Scott A. Bernhardt, Reginaldo P. Brazil, Erin Dilger, Orin Courtenay, James G. C. Hamilton Mar 2019

Susceptibility Of Wild-Caught Lutzomyia Longipalpis (Diptera: Psychodidae) Sand Flies To Insecticide After An Extended Period Of Exposure In Western São Paulo, Brazil, Mikel A. González, Melissa J. Bell, Scott A. Bernhardt, Reginaldo P. Brazil, Erin Dilger, Orin Courtenay, James G. C. Hamilton

Biology Faculty Publications

Background

In Brazil, members of the sand fly species complex Lutzomyia longipalpis transmit Leishmania infantum, a protist parasite that causes visceral leishmaniasis. Male Lu. longipalpis produce a sex pheromone that is attractive to both females and males. During a cluster randomised trial, to determine the combined effect of synthetic sex-aggregation pheromone and insecticide on Le. infantum transmission Lu. longipalpis had been continuously exposed to insecticide for 30 months. The objective of this study was to determine the effect of continuous exposure to the insecticides used in the trial on the susceptibility of Lu. longipalpis population.

Methods

During the trial …


A Stimulatory Role For Cytokinin In The Arbuscular Mycorrhizal Symbiosis Of Pea, Dane M. Goh, Marco Cosme, Anna B. Kislala, Samantha Mulholland, Zakaria M.F. Said, Lukáš Spíchal, R.J. Neil Emery, Stéphane Declerck, Frédérique C. Guinel Mar 2019

A Stimulatory Role For Cytokinin In The Arbuscular Mycorrhizal Symbiosis Of Pea, Dane M. Goh, Marco Cosme, Anna B. Kislala, Samantha Mulholland, Zakaria M.F. Said, Lukáš Spíchal, R.J. Neil Emery, Stéphane Declerck, Frédérique C. Guinel

Biology Faculty Publications

The arbuscular mycorrhizal (AM) symbiosis between terrestrial plants and AM fungi is regulated by plant hormones. For most of these, a role has been clearly assigned in this mutualistic interaction; however, there are still contradictory reports for cytokinin (CK). Here, pea plants, the wild type (WT) cv. Sparkle and its mutant E151 (Pssym15), were inoculated with the AM fungus Rhizophagus irregularis. E151 has previously been characterized as possessing high CK levels in non-mycorrhizal (myc-) roots and exhibiting high number of fungal structures in mycorrhizal (myc+) roots. Myc- and myc+ plants were …


Lack Of Antinociceptive Cross-Tolerance With Co-Administration Of Morphine And Fentanyl Into The Periaqueductal Gray Of Male Sprague-Dawley Rats, Erin N. Bobeck, Shauna M. Schoo, Susan L. Ingram, Michael M. Morgan Mar 2019

Lack Of Antinociceptive Cross-Tolerance With Co-Administration Of Morphine And Fentanyl Into The Periaqueductal Gray Of Male Sprague-Dawley Rats, Erin N. Bobeck, Shauna M. Schoo, Susan L. Ingram, Michael M. Morgan

Biology Faculty Publications

Tolerance to the antinociceptive effect of mu-opioid receptor (MOPr) agonists, such as morphine and fentanyl, greatly limits their effectiveness for long-term use to treat pain. Clinical studies have shown that combination therapy and opioid rotation can be used to enhance opioid-induced antinociception once tolerance has developed. The mechanism and brain regions involved in these processes are unknown. The purpose of this study was to evaluate the contribution of the ventrolateral periaqueductal gray (vlPAG) to antinociceptive tolerance and cross-tolerance between administration and co- administration of morphine and fentanyl. Tolerance was induced by pretreating rats with morphine or fentanyl or low-dose combination …


Silkworms With Spider Silklike Fibers Using Synthetic Silkworm Chow Containing Calcium Lignosulfonate, Carbon Nanotubes, And Graphene, Xiaoli Zhang, Ana Laura Licon, Thomas I. Harris, Paula F. Oliveira, Bailey J. Mcfarland, Blake E. Taurone, Brittney J. Walsh, Brianne E. Bell, Caleb T. Walker, Randolph V. Lewis, Justin A. Jones Mar 2019

Silkworms With Spider Silklike Fibers Using Synthetic Silkworm Chow Containing Calcium Lignosulfonate, Carbon Nanotubes, And Graphene, Xiaoli Zhang, Ana Laura Licon, Thomas I. Harris, Paula F. Oliveira, Bailey J. Mcfarland, Blake E. Taurone, Brittney J. Walsh, Brianne E. Bell, Caleb T. Walker, Randolph V. Lewis, Justin A. Jones

Biology Faculty Publications

Silkworm silk has become increasingly relevant for material applications. However, the industry as a whole is retracting because of problems with mass production. One of the key problems is the inconsistent properties of the silk. A means by which to improve the silk material properties is through enhanced sericulture techniques. One possible technique is altering the feed of the silkworms to include single-wall carbon nanotubes (SWNTs) or graphene (GR). Recently published results have demonstrated substantial improvement in fiber mechanical properties. However, the effect of the surfactant used to incorporate those materials into the feed on the fiber mechanical properties in …


Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals, Allison Mcdonald, Dmytro V. Gospodaryov Mar 2019

Alternative Nad(P)H Dehydrogenase And Alternative Oxidase: Proposed Physiological Roles In Animals, Allison Mcdonald, Dmytro V. Gospodaryov

Biology Faculty Publications

The electron transport systems in mitochondria of many organisms contain alternative respiratory enzymes distinct from those of the canonical respiratory system depicted in textbooks. Two of these enzymes, the alternative NADH dehydrogenase and the alternative oxidase, were of interest to a limited circle of researchers until they were envisioned as gene therapy tools for mitochondrial disease treatment. Recently, these enzymes were discovered in several animals. Here, we analyse the functioning of alternative NADH dehydrogenases and oxidases in different organisms. We propose that both enzymes ensure bioenergetic and metabolic flexibility during environmental transitions or other conditions which may compromise the operation …


Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei Mar 2019

Diversity Of Resistance Mechanisms In Carbapenem-Resistant Enterobacteriaceae At A Health Care System In Northern California, From 2013 To 2016, Fiona Senchyna, Rajiv L. Gaur, Johanna Sandlund, Cynthia Truong, Guillaume Tremintin, Dietmar Kültz, Carlos A. Gomez, Fiona B. Tamburini, Tessa Andermann, Ami Bhatt, Isabella A. Tickler, Nancy Watz, Indre Budvytiene, Gongyi Shi, Fred C. Tenover, Niaz Banaei

Biology Faculty Publications

The mechanism of resistance in carbapenem-resistant Enterobacteriaceae (CRE) has therapeutic implications. We comprehensively characterized emerging mechanisms of resistance in CRE between 2013 and 2016 at a health system in Northern California. A total of 38.7% (24/62) of CRE isolates were carbapenemase gene-positive, comprising 25.0% (6/24) blaOXA-48 like, 20.8% (5/24) blaKPC, 20.8% (5/24) blaNDM, 20.8% (5/24) blaSME, 8.3% (2/24) blaIMP, and 4.2% (1/24) blaVIM. Between carbapenemases and porin loss, the resistance mechanism was identified in 95.2% (59/62) of CRE isolates. Isolates expressing blaKPC were 100% susceptible to ceftazidime–avibactam, meropenem–vaborbactam, …


An Interactive Application For Tracking The Movement Of The Limulus Polyphemus Throughout Long Island Sound (Lis), Ismael Youssef, Samah Senbel, Jennifer Mattei Mar 2019

An Interactive Application For Tracking The Movement Of The Limulus Polyphemus Throughout Long Island Sound (Lis), Ismael Youssef, Samah Senbel, Jennifer Mattei

Biology Faculty Publications

Poster presented at the Long Island Sound Research Conference held March 15, 2019 in Port Jefferson, New York.


Draft Genome Assembly And Population Genetics Of An Agricultural Pollinator, The Solitary Alkali Bee (Halictidae: Nomia Melanderi), Karen M. Kapheim, Hailin Pan, Cai Li, Charles Blatti Ill, Brock A. Harpur, Panagiotis Ioannidis, Beryl M. Jones, Clement F. Kent, Livio Ruzzante, Laura Sloofman, Eckart Stolle, Robert M. Waterhouse, Amro Zayed, Guojie Zhang, William T. Wcislo Mar 2019

Draft Genome Assembly And Population Genetics Of An Agricultural Pollinator, The Solitary Alkali Bee (Halictidae: Nomia Melanderi), Karen M. Kapheim, Hailin Pan, Cai Li, Charles Blatti Ill, Brock A. Harpur, Panagiotis Ioannidis, Beryl M. Jones, Clement F. Kent, Livio Ruzzante, Laura Sloofman, Eckart Stolle, Robert M. Waterhouse, Amro Zayed, Guojie Zhang, William T. Wcislo

Biology Faculty Publications

Alkali bees (Nomia melanderi) are solitary relatives of the halictine bees, which have become an important model for the evolution of social behavior, but for which few solitary comparisons exist. These ground-nesting bees defend their developing offspring against pathogens and predators, and thus exhibit some of the key traits that preceded insect sociality. Alkali bees are also efficient native pollinators of alfalfa seed, which is a crop of major economic value in the United States. We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. Repetitive content makes up more than one-third of …


Congruent Phylogenetic Relationships Of Melaphidina Aphids (Aphididae: Eriosomatinae: Fordini) According To Nuclear And Mitochondrial Dna Data With Taxonomic Implications On Generic Limits, Zhumei Ren, Carol D. Von Dohlen, A. J. Harris, Rebecca B. Dikow, Xu Su, Jun Wen Feb 2019

Congruent Phylogenetic Relationships Of Melaphidina Aphids (Aphididae: Eriosomatinae: Fordini) According To Nuclear And Mitochondrial Dna Data With Taxonomic Implications On Generic Limits, Zhumei Ren, Carol D. Von Dohlen, A. J. Harris, Rebecca B. Dikow, Xu Su, Jun Wen

Biology Faculty Publications

Melaphidina aphids (Rhus-gall aphids; Eriosomatinae: Fordini) comprise five genera from eastern Asia and one monotypic genus from eastern North America. Melaphidina are unique in feeding on plant species of Rhus subgenus Rhus (Anacardiaceae), on which they form galls during the summer. The phylogenetic relationships among some species of Melaphidina aphids remain controversial. In this study, we sought to resolve the backbone phylogeny of Melaphidina aphids by sampling 15 accessions representing all six genera, all species, and all subspecies except Meitanaphis microgallis using 20 gene regions: five nuclear genes as well as 13 protein-coding genes and two rRNA genes …


A Cross-Species Analysis Reveals A General Role For Piezo2 In Mechanosensory Specialization Of Trigeminal Ganglia From Tactile Specialist Birds, Eve R. Schneider, Evan O. Anderson, Viktor V. Feketa, Marco Mastrotto, Yury A. Nikolaev, Elena O. Gracheva, Sviatoslav N. Bagriantsev Feb 2019

A Cross-Species Analysis Reveals A General Role For Piezo2 In Mechanosensory Specialization Of Trigeminal Ganglia From Tactile Specialist Birds, Eve R. Schneider, Evan O. Anderson, Viktor V. Feketa, Marco Mastrotto, Yury A. Nikolaev, Elena O. Gracheva, Sviatoslav N. Bagriantsev

Biology Faculty Publications

A major challenge in biology is to link cellular and molecular variations with behavioral phenotypes. Here, we studied somatosensory neurons from a panel of bird species from the family Anatidae, known for their tactile-based foraging behavior. We found that tactile specialists exhibit a proportional expansion of neuronal mechanoreceptors in trigeminal ganglia. The expansion of mechanoreceptors occurs via neurons with intermediately and slowly inactivating mechanocurrent. Such neurons contain the mechanically gated Piezo2 ion channel whose expression positively correlates with the expression of factors responsible for the development and function of mechanoreceptors. Conversely, Piezo2 expression negatively correlates with expression of molecules mediating …


Dacar Cas/Somali Red Aloe: A New Species Of Aloe (Asphodelaceae) From Somaliland, Mary E. Barkworth, Ahmed Ibrahim Awale, Faisal Jama Gelle Feb 2019

Dacar Cas/Somali Red Aloe: A New Species Of Aloe (Asphodelaceae) From Somaliland, Mary E. Barkworth, Ahmed Ibrahim Awale, Faisal Jama Gelle

Biology Faculty Publications

A new species of Aloe (Asphodelaceae) is described from Somaliland. It differs from other species in forming large clumps and in having sap that is initially yellow but quickly turns bright red and then dark red or reddish-brown, paniculate red-flowered inflorescences and uniformly coloured leaves with red teeth. Its recognition raises the number of species known from the combined area of Somaliland and Somalia s.s. from 31 to 36. A map portraying species density of Aloe by country, as that genus is now interpreted, shows that Aloe has its highest density on islands in the Indian Ocean but that, within …


Employing Plant Functional Groups To Advance Seed Dispersal Ecology And Conservation, Clare Aslan, Noelle G. Beckman, Haldre S. Rogers, Judie Bronstein, Damaris Zurell, Florian Hartig, Katriona Shea, Liba Pejchar, Mike Neubert, John Poulsen, Janneke Hillerislambers, Maria Miriti, Bette Loiselle, Edu Effiom, Jenny Zambrano, Eugene W. Schupp, Et Al. Feb 2019

Employing Plant Functional Groups To Advance Seed Dispersal Ecology And Conservation, Clare Aslan, Noelle G. Beckman, Haldre S. Rogers, Judie Bronstein, Damaris Zurell, Florian Hartig, Katriona Shea, Liba Pejchar, Mike Neubert, John Poulsen, Janneke Hillerislambers, Maria Miriti, Bette Loiselle, Edu Effiom, Jenny Zambrano, Eugene W. Schupp, Et Al.

Biology Faculty Publications

Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether …


Biogeochemical Recuperation Of Lowland Tropical Forest During Succession, Benjamin W. Sullivan, Rachel L. Nifong, Megan K. Nasto, Silvia Alvarez-Clare, Camie M. Dencker, Fiona M. Soper, Kevin T. Shoemaker, F. Yoko Ishida, Joana Zaragoza-Castells, Eric A. Davidson, Cory C. Cleveland Feb 2019

Biogeochemical Recuperation Of Lowland Tropical Forest During Succession, Benjamin W. Sullivan, Rachel L. Nifong, Megan K. Nasto, Silvia Alvarez-Clare, Camie M. Dencker, Fiona M. Soper, Kevin T. Shoemaker, F. Yoko Ishida, Joana Zaragoza-Castells, Eric A. Davidson, Cory C. Cleveland

Biology Faculty Publications

High rates of land conversion and land use change have vastly increased the proportion of secondary forest in the lowland tropics relative to mature forest. As secondary forests recover following abandonment, nitrogen (N) and phosphorus (P) must be present in sufficient quantities to sustain high rates of net primary production and to replenish the nutrients lost during land use prior to secondary forest establishment. Biogeochemical theory and results from individual studies suggest that N can recuperate during secondary forest recovery, especially relative to P. Here, we synthesized 23 metrics of N and P in soil and plants from 45 secondary …


Identification Of The Alternative Oxidase Gene And Its Expression In The Copepod Tigriopus Californicus, Allison Mcdonald, Carly E. Tward, Willie Cygelfarb, Jaspreet Singh Feb 2019

Identification Of The Alternative Oxidase Gene And Its Expression In The Copepod Tigriopus Californicus, Allison Mcdonald, Carly E. Tward, Willie Cygelfarb, Jaspreet Singh

Biology Faculty Publications

In addition to the typical electron transport system (ETS) in animal mitochondria responsible for oxidative phosphorylation, in some species there exists an alternative oxidase (AOX) pathway capable of catalyzing the oxidation of ubiquinol and the reduction of oxygen to water. The discovery of AOX in animals is recent and further investigations into its expression, regulation, and physiological role have been hampered by the lack of a tractable experimental model organism. Our recent DNA database searches using bioinformatics revealed an AOX sequence in several marine copepods including Tigriopus californicus. This species lives in tidepools along the west coast of North …


A Chromosome-Scale Assembly Of The Axolotl Genome, Jeramiah J. Smith, Nataliya Y. Timoshevskaya, Vladimir A. Timoshevskiy, Melissa C. Keinath, Drew Hardy, S. Randal Voss Feb 2019

A Chromosome-Scale Assembly Of The Axolotl Genome, Jeramiah J. Smith, Nataliya Y. Timoshevskaya, Vladimir A. Timoshevskiy, Melissa C. Keinath, Drew Hardy, S. Randal Voss

Biology Faculty Publications

The axolotl (Ambystoma mexicanum) provides critical models for studying regeneration, evolution, and development. However, its large genome (∼32 Gb) presents a formidable barrier to genetic analyses. Recent efforts have yielded genome assemblies consisting of thousands of unordered scaffolds that resolve gene structures, but do not yet permit large-scale analyses of genome structure and function. We adapted an established mapping approach to leverage dense SNP typing information and for the first time assemble the axolotl genome into 14 chromosomes. Moreover, we used fluorescence in situ hybridization to verify the structure of these 14 scaffolds and assign each to its …


Seed Germination Responses To Seasonal Temperature And Drought Stress Are Species‐Specific But Not Related To Seed Size In A Desert Steppe: Implications For Effect Of Climate Change On Community Structure, Fengyan Yi, Zhaoren Wang, Carol C. Baskin, Jerry M. Baskin, Ruhan Ye, Hailian Sun, Yuanyuan Zhang, Xuehua Ye, Guofang Liu, Xuejun Yang, Zhenying Huang Feb 2019

Seed Germination Responses To Seasonal Temperature And Drought Stress Are Species‐Specific But Not Related To Seed Size In A Desert Steppe: Implications For Effect Of Climate Change On Community Structure, Fengyan Yi, Zhaoren Wang, Carol C. Baskin, Jerry M. Baskin, Ruhan Ye, Hailian Sun, Yuanyuan Zhang, Xuehua Ye, Guofang Liu, Xuejun Yang, Zhenying Huang

Biology Faculty Publications

Investigating how seed germination of multiple species in an ecosystem responds to environmental conditions is crucial for understanding the mechanisms for community structure and biodiversity maintenance. However, knowledge of seed germination response of species to environmental conditions is still scarce at the community level. We hypothesized that responses of seed germination to environmental conditions differ among species at the community level, and that germination response is not correlated with seed size. To test this hypothesis, we determined the response of seed germination of 20 common species in the Siziwang Desert Steppe, China, to seasonal temperature regimes (representing April, May, June, …


Burning And Mowing Similarly Increase Prairie Plant Production In The Spring, But Not Due To Increased Soil Temperatures, Timothy L. Dickson Feb 2019

Burning And Mowing Similarly Increase Prairie Plant Production In The Spring, But Not Due To Increased Soil Temperatures, Timothy L. Dickson

Biology Faculty Publications

Burning and mowing are two of the most common grassland disturbances across millions of hectares worldwide, but uncertainty remains about when and why these disturbances increase plant production. One of the main hypotheses for increased plant production is that disturbances increase soil temperature in the early growing season and thereby increase plant growth. I tested this hypothesis using a multi‐decade study of the frequency (annual or quadrennial) and season (spring, summer, or autumn) of reconstructed tallgrass prairie burning and mowing. To determine plant production, I measured aboveground biomass during three periods of the 2015 growing season: (1) prior to mid‐May; …


Sleeping Through Anything: The Effects Of Unpredictable Disruptions On Mouse Sleep, Healing, And Affect, Amy Robinson-Junker, Bruce O'Hara, Abigail Durkes, Brianna Gaskill Jan 2019

Sleeping Through Anything: The Effects Of Unpredictable Disruptions On Mouse Sleep, Healing, And Affect, Amy Robinson-Junker, Bruce O'Hara, Abigail Durkes, Brianna Gaskill

Biology Faculty Publications

Many aspects of the laboratory environment are not tailored to the needs of rodents, which may cause stress. Unpredictable stressors can cause ulcers, prolonged pituitary-adrenal activation, and anhedonia. Similarly, pain has been demonstrated to slow wound healing, and mice experiencing pain exhibit altered behavior. However it is unknown how husbandry, which occurs when the mice are inactive, and lack of analgesia, specifically in a punch biopsy procedure, effects animal physiology, behavior, and welfare, particularly as it relates to sleep fragmentation. We hypothesized that sleep fragmentation, induced by unpredictable husbandry and lack of pain management will slow wound healing. Two main …


Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf Jan 2019

Refernment: An R Package For Annotating Rna Editing In Plastid Genomes, Tanner A. Robison, Paul G. Wolf

Biology Faculty Publications

PREMISE OF THE STUDY: In the absence of cDNA, the annotation of RNA editing in plastomes must be done manually, representing a significant time cost to those studying the organellar genomes of ferns and hornworts.

METHODS AND RESULTS: We developed an R package to automatically annotate apparent nonsense mutations in plastid genomes. The software successfully annotates such sites and results in no false positives for data with no sequencing or assembly errors.

CONCLUSIONS: Compared to manual annotation, ReFernment offers greater speed and accuracy for annotating RNA editing sites. This software should be especially useful for researchers generating large numbers of …


Co-Cultures Of Oophila Amblystomatis Between Ambystoma Maculatum And Ambystoma Gracile Hosts Show Host-Symbiont Fidelity, Ryan R. Kerney, Jasper S. Leavitt, Elizabeth M. Hill, Huanjia Zhang, Eunsoo Kim, John Burns Jan 2019

Co-Cultures Of Oophila Amblystomatis Between Ambystoma Maculatum And Ambystoma Gracile Hosts Show Host-Symbiont Fidelity, Ryan R. Kerney, Jasper S. Leavitt, Elizabeth M. Hill, Huanjia Zhang, Eunsoo Kim, John Burns

Biology Faculty Publications

A unique symbiosis occurs between embryos of the spotted salamander (Ambystoma maculatum) and a green alga (Oophila amblystomatis). Unlike most vertebrate host-symbiont relationships, which are ectosymbiotic, A. maculatum exhibits both an ecto- and an endo-symbiosis, where some of the green algal cells living inside egg capsules enter embryonic tissues as well as individual salamander cells. Past research has consistently categorized this symbiosis as a mutualism, making this the first example of a “beneficial” microbe entering vertebrate cells. Another closely related species of salamander, Ambystoma gracile, also harbors beneficial Oophila algae in its egg capsules. However, our …


Creative Citizen Science Illuminates Complex Ecological Responses To Climate Change, Abraham J. Miller-Rushing, Amanda S. Gallinat, Richard B. Primack Jan 2019

Creative Citizen Science Illuminates Complex Ecological Responses To Climate Change, Abraham J. Miller-Rushing, Amanda S. Gallinat, Richard B. Primack

Biology Faculty Publications

Climate change is causing the timing of key behaviors (i.e., phenology) to shift differently across trophic levels and among some interacting organisms (e.g., plants and pollinators, predators and prey), suggesting that interactions among species are being disrupted (1, 2). Studying the phenology of interactions, however, is difficult, which has limited researchers’ ability to zero in on changes in specific interactions or on the consequences of mismatches. In PNAS, Hassall et al. (3) use a combination of citizen science techniques to investigate the effects of climate change on dozens of specific interactions. They focus on a Batesian mimicry complex involving stinging …


Some Current Trends And Challenges In Philippine Aquaculture, With An Emphasis On Synergies With Biodiversity Initiatives, Ronald Allan L. Cruz, Vikas Kumar, Janice A. Ragaza Jan 2019

Some Current Trends And Challenges In Philippine Aquaculture, With An Emphasis On Synergies With Biodiversity Initiatives, Ronald Allan L. Cruz, Vikas Kumar, Janice A. Ragaza

Biology Faculty Publications

No abstract provided.


A Rapid And Accurate Minion-Based Workflow For Tracking Species Biodiversity In The Field, Hendrik Freitag, Simone Maestri, Emanuela Cosentino, Marta Paterno, Jhoana M. Garces, Luca Marcolungo, Massimiliano Alfano, Iva Njunjić, Menno Schilthuizen, Ferry Slik, Michele Menegon, Marzia Rossato, Massimo Delledonne Jan 2019

A Rapid And Accurate Minion-Based Workflow For Tracking Species Biodiversity In The Field, Hendrik Freitag, Simone Maestri, Emanuela Cosentino, Marta Paterno, Jhoana M. Garces, Luca Marcolungo, Massimiliano Alfano, Iva Njunjić, Menno Schilthuizen, Ferry Slik, Michele Menegon, Marzia Rossato, Massimo Delledonne

Biology Faculty Publications

Genetic markers (DNA barcodes) are often used to support and confirm species identification. Barcode sequences can be generated in the field using portable systems based on the Oxford Nanopore Technologies (ONT) MinION sequencer. However, to achieve a broader application, current proof-of-principle workflows for on-site barcoding analysis must be standardized to ensure a reliable and robust performance under suboptimal field conditions without increasing costs. Here, we demonstrate the implementation of a new on-site workflow for DNA extraction, PCR-based barcoding, and the generation of consensus sequences. The portable laboratory features inexpensive instruments that can be carried as hand luggage and uses standard …


Nell2 Regulates The Contralateral-Versus-Ipsilateral Visual Projection As A Domain-Specific Positional Cue, Chizu Nakamoto, Elaine Durward, Masato Horie, Masaru Nakamoto Jan 2019

Nell2 Regulates The Contralateral-Versus-Ipsilateral Visual Projection As A Domain-Specific Positional Cue, Chizu Nakamoto, Elaine Durward, Masato Horie, Masaru Nakamoto

Biology Faculty Publications

In mammals with binocular vision, retinal ganglion cell (RGC) axons from each eye project to eye-specific domains in the contralateral and ipsilateral dorsal lateral geniculate nucleus (dLGN), underpinning disparity-based stereopsis. Although domain-specific axon guidance cues that discriminate contralateral and ipsilateral RGC axons have long been postulated as a key mechanism for development of the eye-specific retinogeniculate projection, the molecular nature of such cues has remained elusive. Here, we show that the extracellular glycoprotein Nell2 (neural epidermal growth factor-like-like 2) is expressed in the dorsomedial region of the dLGN, which ipsilateral RGC axons terminate in and contralateral axons avoid. In Nell2 …


Unique Features Of Caenothus Trace To Earliest Stages Of Flower Development, W. John Hayden Jan 2019

Unique Features Of Caenothus Trace To Earliest Stages Of Flower Development, W. John Hayden

Biology Faculty Publications

The basics of flower structure are straightforward. A “typical” flower (Figure 1) has four whorls of floral organs arranged in stereotypical order: sepals (lowermost and outermost), petals, stamens, and, finally, one or more carpels (pistils) located in the innermost (or uppermost) position. This is not rocket science. Names of these floral organs and their relative placement within the flower can be grasped readily by schoolchildren. Also “typical” but seldom emphasized in elementary lessons is the fact that the organs of each successive whorl occupy alternate radii; i.e., petals are routinely positioned between sepals, and stamens (if only one whorl) are …


Multiple Connections Between Amazonia And Atlantic Forest Shaped The T Phylogenetic And Morphological Diversity Of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae), Rafael O. De Sá, João Filipe Riva Tonini, Hannah Van Huss, Alex Long, Travis Cuddy, Mauricio C. Forlani, Pedro L.V. Peloso, Hussam Zaher, Célio F.B. Haddad Jan 2019

Multiple Connections Between Amazonia And Atlantic Forest Shaped The T Phylogenetic And Morphological Diversity Of Chiasmocleis Mehely, 1904 (Anura: Microhylidae: Gastrophryninae), Rafael O. De Sá, João Filipe Riva Tonini, Hannah Van Huss, Alex Long, Travis Cuddy, Mauricio C. Forlani, Pedro L.V. Peloso, Hussam Zaher, Célio F.B. Haddad

Biology Faculty Publications

Chiasmocleis is the most species-rich genus of Neotropical microhylids. Herein, we provide the first comprehensive multilocus phylogeny for the genus, including all but 3 of the 34 recognized species and multiple individuals per species. We discuss cryptic speciation, species discovery, patterns of morphological evolution, and provide a historical biogeographic analysis to account for the current distribution of the genus. Diversification of Chiasmocleis from other New World microhylids began during the Eocene, app. 40 mya, in forested areas, and current diversity seems to be a product of recurrent connections between the Atlantic Forest and Amazonia. Small-sized species evolved independently three times …


Fungus Creates Zombie Insects On Dogwood, W. John Hayden Jan 2019

Fungus Creates Zombie Insects On Dogwood, W. John Hayden

Biology Faculty Publications

I have something I need to get off my chest. I have an obsession with, of all things, a fungus! And not just any fungus, but a fungus that infects, I am embarrassed to admit, Flowering Dogwood, the VNPS Wildflower of the Year for 2018. Yes, maybe I’ve gone off my rocker. But this fungus is so cool, so devious, so elegantly convoluted and weird—in a creepy sort of way—that I find myself utterly enthralled. Perhaps sharing my obsession with this fungus will prove therapeutic and permit me to return to my more socially respectable obsessive fascination with plants.