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School of Biological Sciences: Faculty Publications

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Full-Text Articles in Biology

Genome Sequence Of Streptomyces Aureofaciens Atcc Strain 10762, Julien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G. Oliver, Etsuko N. Moriyama Jan 2016

Genome Sequence Of Streptomyces Aureofaciens Atcc Strain 10762, Julien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G. Oliver, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracycline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain 10762.


Range-Wide Patterns Of Geographic Variation In Songs Of Golden-Crowned Sparrows (Zonotrichia Atricapilla), Daizaburo Shizuka, M. Ross Lein, Glen Chilton Jan 2016

Range-Wide Patterns Of Geographic Variation In Songs Of Golden-Crowned Sparrows (Zonotrichia Atricapilla), Daizaburo Shizuka, M. Ross Lein, Glen Chilton

School of Biological Sciences: Faculty Publications

Discrete geographic variation, or dialects, in songs of songbirds arise as a consequence of complex interactions between ecology and song learning. Four of the five species of Zonotrichia sparrows, including the model species White-crowned Sparrow (Z. leucophrys), have been studied with respect to the causes and consequences of geographic variation in song. Within White-crowned Sparrows, subspecies that migrate farther have larger range size of dialects. Here, we assessedgeographic patterns of song variation in the fifth species of this genus, the Golden-crowned Sparrow (Z. atricapilla). We analyzed field-recorded songs from 2 sampling periods (1996–1998 and 2006–2013) covering …


Corrigendum: The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova Jan 2016

Corrigendum: The Arabidopsis Homologs Of Trithorax (Atx1) And Enhancer Of Zeste (Clf) Establish ‘Bivalent Chromatin Marks’ At The Silent Agamous Locus, Abdelaty Saleh, Ayed Al-Abdallat, Ivan Ndamukong, Raul Alvarez-Venegas, Zoya Avramova

School of Biological Sciences: Faculty Publications

The authors wish to draw the attention to two irregularities in Figures 2a and 4. Both concern errors in duplicating images of "empty" lanes illustrating absence of DNA bands. We regret these omissions and apologize to readers for the inconvenience caused. The results and conclusions remain valid.


Climate Modifies Response Of Non-Native And Native Species Richness To Nutrient Enrichment, Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. Macdougall, Lara G. Reichmann, Juan Alberti, Selene Baez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M.H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D.B. Leakey, Rebecca L. Mcculley, Joslin L. Moore, Jesus Pascual, Elizabeth T. Borer Jan 2016

Climate Modifies Response Of Non-Native And Native Species Richness To Nutrient Enrichment, Habacuc Flores-Moreno, Peter B. Reich, Eric M. Lind, Lauren L. Sullivan, Eric W. Seabloom, Laura Yahdjian, Andrew S. Macdougall, Lara G. Reichmann, Juan Alberti, Selene Baez, Jonathan D. Bakker, Marc W. Cadotte, Maria C. Caldeira, Enrique J. Chaneton, Carla M. D'Antonio, Philip A. Fay, Jennifer Firn, Nicole Hagenah, W. Stanley Harpole, Oscar Iribarne, Kevin P. Kirkman, Johannes M.H. Knops, Kimberly J. La Pierre, Ramesh Laungani, Andrew D.B. Leakey, Rebecca L. Mcculley, Joslin L. Moore, Jesus Pascual, Elizabeth T. Borer

School of Biological Sciences: Faculty Publications

Ecosystem eutrophication often increases domination by non-natives and causes displacement of native taxa. However, variation in environmental conditions may affect the outcome of interactions between native and non-native taxa in environments where nutrient supply is elevated. We examined the interactive effects of eutrophication, climate variability and climate average conditions on the success of native and non-native plant species using experimental nutrient manipulations replicated at 32 grassland sites on four continents. We hypothesized that effects of nutrient addition would be greatest where climate was stable and benign, owing to reduced niche partitioning. We found that the abundance of non-native species increased …


The Importance Of Cross-Validation, Accuracy, And Precision For Measuring Plumage Color: A Comment On Vaquero-Alba Et Al. (2016), Joanna K. Hubbard, Amanda K. Hund, Iris I. Levin, Kevin J. Mcgraw, Matt Wilkins, Rebecca J. Safran Jan 2016

The Importance Of Cross-Validation, Accuracy, And Precision For Measuring Plumage Color: A Comment On Vaquero-Alba Et Al. (2016), Joanna K. Hubbard, Amanda K. Hund, Iris I. Levin, Kevin J. Mcgraw, Matt Wilkins, Rebecca J. Safran

School of Biological Sciences: Faculty Publications

Vaquero-Alba and colleagues published a study in The Auk: Ornithological Advances comparing objective color measurements of plumage taken in the field directly on a bird’s body to those taken in the lab on collected feathers arranged to emulate the appearance of a bird’s natural plumage. Although the field measures of plumage color were less repeatable than lab measures, the authors concluded that measurements taken in the field were more representative of a bird’s ‘‘true color.’’ Accordingly, they recommend that researchers should bring spectrophotometers into the field to measure color on live birds. We question the assumption that their field measurements …


Biotin Auxotrophy And Biotin Enhanced Germ Tube Formation In Candida Albicans, Nur Ahmad Hussin, Ruvini U. Pathirana, Sahar Hasim, Swetha Tati, Jessica A. Scheib-Owens, Kenneth Nickerson Jan 2016

Biotin Auxotrophy And Biotin Enhanced Germ Tube Formation In Candida Albicans, Nur Ahmad Hussin, Ruvini U. Pathirana, Sahar Hasim, Swetha Tati, Jessica A. Scheib-Owens, Kenneth Nickerson

School of Biological Sciences: Faculty Publications

Due to the increased number of immunocompromised patients, infections with the pathogen Candida albicans have significantly increased in recent years. C. albicans transition from yeast to germ tubes is one of the essential factors for virulence. In this study we noted that Lee’s medium, commonly used to induce filamentation, contained 500-fold more biotin than needed for growth and 40-fold more biotin than is typically added to growth media. Thus, we investigated the effects of excess biotin on growth rate and filamentation by C. albicans in different media. At 37 ˚C, excess biotin (4 µM) enhanced germ tube formation (GTF) ca. …


Polymorphisms And Resistance Mutations Of Hepatitis C Virus On Sequences In The European Hepatitis C Virus Database, Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini Da Veiga, Angelo Alves De Mattos, Charles Wood Jan 2016

Polymorphisms And Resistance Mutations Of Hepatitis C Virus On Sequences In The European Hepatitis C Virus Database, Dimas Alexandre Kliemann, Cristiane Valle Tovo, Ana Beatriz Gorini Da Veiga, Angelo Alves De Mattos, Charles Wood

School of Biological Sciences: Faculty Publications

AIM: To evaluate the occurrence of resistant mutations in treatment-naïve hepatitis C virus (HCV) sequences deposited in the European hepatitis C virus database (euHCVdb).

METHODS: The sequences were downloaded from the euHCVdb (https://euhcvdb.ibcp.fr/euHCVdb/). The search was performed for full-length NS3 protease, NS5A and NS5B polymerase sequences of HCV, separated by genotypes 1a, 1b, 2a, 2b and 3a, and resulted in 798 NS3, 708 NS5A and 535 NS5B sequences from HCV genotypes 1a, 1b, 2a, 2b and 3a, after the exclusion of sequences containing errors and/or gaps or incomplete sequences, and sequences from patients previously treated with direct antiviral agents (DAA). …


How Many Kinds Of Birds Are There And Why Does It Matter?, George F. Barrowclough, Joel Cracraft, John Klicka, Robert M. Zink Jan 2016

How Many Kinds Of Birds Are There And Why Does It Matter?, George F. Barrowclough, Joel Cracraft, John Klicka, Robert M. Zink

School of Biological Sciences: Faculty Publications

Estimates of global species diversity have varied widely, primarily based on variation in the numbers derived from different inventory methods of arthropods and other small invertebrates. Within vertebrates, current diversity metrics for fishes, amphibians, and reptiles are known to be poor estimators, whereas those for birds and mammals are often assumed to be relatively well established. We show that avian evolutionary diversity is significantly underestimated due to a taxonomic tradition not found in most other taxonomic groups. Using a sample of 200 species taken from a list of 9159 biological species determined primarily by morphological criteria, we applied a diagnostic, …


Student Buy-In To Active Learning In A College Science Course, Andrew J. Cavanagh, Oriana R. Aragon, Xinnian Chen, Brian A. Couch, Mary F. Durham, Aiyana Bobrownicki, David I. Hanauer, Mark J. Graham Jan 2016

Student Buy-In To Active Learning In A College Science Course, Andrew J. Cavanagh, Oriana R. Aragon, Xinnian Chen, Brian A. Couch, Mary F. Durham, Aiyana Bobrownicki, David I. Hanauer, Mark J. Graham

School of Biological Sciences: Faculty Publications

The benefits of introducing active learning in college science courses are well established, yet more needs to be understood about student buy-in to active learning and how that process of buy-in might relate to student outcomes. We test the exposure–persuasion– identification–commitment (EPIC) process model of buy-in, here applied to student (n = 245) engagement in an undergraduate science course featuring active learning. Student buy-in to active learning was positively associated with engagement in self-regulated learning and students’ course performance. The positive associations among buy-in, self-regulated learning, and course performance suggest buy-in as a potentially important factor leading to student …


Characterizing Student Perceptions Of And Buy-In Toward Common Formative Assessment Techniques, Kathleen R. Brazeal, Tanya L. Brown, Brian A. Couch Jan 2016

Characterizing Student Perceptions Of And Buy-In Toward Common Formative Assessment Techniques, Kathleen R. Brazeal, Tanya L. Brown, Brian A. Couch

School of Biological Sciences: Faculty Publications

Formative assessments (FAs) can occur as preclass assignments, in-class activities, or postclass homework. FAs aim to promote student learning by accomplishing key objectives, including clarifying learning expectations, revealing student thinking to the instructor, providing feedback to the student that promotes learning, facilitating peer interactions, and activating student ownership of learning. While FAs have gained prominence within the education community, we have limited knowledge regarding student perceptions of these activities. We used a mixed-methods approach to determine whether students recognize and value the role of FAs in their learning and how students perceive course activities to align with five key FA …


A Guide For Graduate Students Interested In Postdoctoral Positions In Biology Education Research, Melissa L. Aikens, Lisa A. Corwin, Tessa C. Andrews, Brian A. Couch, Sarah L. Eddy, Lisa Mcdonnell, Gloriana Trujillo Jan 2016

A Guide For Graduate Students Interested In Postdoctoral Positions In Biology Education Research, Melissa L. Aikens, Lisa A. Corwin, Tessa C. Andrews, Brian A. Couch, Sarah L. Eddy, Lisa Mcdonnell, Gloriana Trujillo

School of Biological Sciences: Faculty Publications

Postdoctoral positions in biology education research (BER) are becoming increasingly common as the field grows. However, many life science graduate students are unaware of these positions or do not understand what these positions entail or the careers with which they align. In this essay, we use a backward-design approach to inform life science graduate students of postdoctoral opportunities in BER. Beginning with the end in mind, we first discuss the types of careers to which BER postdoctoral positions lead. We then discuss the different types of BER postdoctoral positions, drawing on our own experiences and those of faculty mentors. Finally, …


Knowing Your Own: A Classroom Case Study Using The Scientific Method To Investigate How Birds Learn To Recognize Their Offspring, Joanna K. Hubbard, Daizaburo Shizuka, Brian A. Couch Jan 2016

Knowing Your Own: A Classroom Case Study Using The Scientific Method To Investigate How Birds Learn To Recognize Their Offspring, Joanna K. Hubbard, Daizaburo Shizuka, Brian A. Couch

School of Biological Sciences: Faculty Publications

Understanding the scientific method provides students with a necessary foundation for careers in science-related fields. Moreover, students can apply scientific inquiry skills in many aspects of their daily lives and decision making. Thus, the ability to apply the scientific method represents an essential skill that students should learn during undergraduate science education. We designed an interrupted case study in which students learn about and apply the scientific method to investigate and recapitulate the findings of a published research article. This research article addresses the question of how parents recognize their own young in a system where birds of the same …


Heterochromatin And Genetic Conflict, Colin D. Meiklejohn Jan 2016

Heterochromatin And Genetic Conflict, Colin D. Meiklejohn

School of Biological Sciences: Faculty Publications

Meiosis is a dangerous business. The two alleles in diploid organisms share an evolutionary interest in the survival and reproduction of their host individual; however, as soon as they segregate into haploid gametes, these alleles find themselves competing for transmission to the next generation (1). In males, the development of all four meiotic products into functional gametes fosters the evolution of alleles that disrupt the development or viability of gametes carrying the alternate allele. Systems that distort Mendelian segregation (hence, segregation distorters) typically comprise at least two loci: a trans-acting drive locus (such as a gene that encodes a …


Unraveling The Consequences Of The Terminal Pleistocene Megafauna Extinction On Mammal Community Assembly, Felisa A. Smith, Catalina P. Tomé, Emma A. Elliott Smith, S. Kathleen Lyons, Seth D. Newsome, Thomas W. Stafford Jan 2016

Unraveling The Consequences Of The Terminal Pleistocene Megafauna Extinction On Mammal Community Assembly, Felisa A. Smith, Catalina P. Tomé, Emma A. Elliott Smith, S. Kathleen Lyons, Seth D. Newsome, Thomas W. Stafford

School of Biological Sciences: Faculty Publications

Recent studies connecting the decline of large predators and consumers with the disintegration of ecosystems often overlook that this natural experiment already occurred. As recently as 14 ka, tens of millions of large-bodied mammals were widespread across the American continents. Within 1000 yr of the arrival of humans, ∼80% were extinct including all > 600 kg. While the cause of the late Pleistocene (LP) extinction remains contentious, largely overlooked are the ecological consequences of the loss of millions of large-bodied animals. Here, we examine the influence of the LP extinction on a local mammal community. Our study site is Hall’s Cave …


Comparative Anatomy Of The Bony Labyrinth Of Extant And Extinct Porpoises (Cetacea: Phocoenidae), Rachel A. Racicot, William Gearty, Naoki Kohno, John J. Flynn Jan 2016

Comparative Anatomy Of The Bony Labyrinth Of Extant And Extinct Porpoises (Cetacea: Phocoenidae), Rachel A. Racicot, William Gearty, Naoki Kohno, John J. Flynn

School of Biological Sciences: Faculty Publications

The inner ear anatomy of cetaceans, now more readily accessible by means of nondestructive high-resolution X-ray computed tomographic (CT) scanning, provides a window into their acoustic abilities and ecological preferences. Inner ear labyrinths also may be a source for additional morphological characters for phylogenetic analyses. In this study, we explore digital endocasts of the inner ear labyrinths of representative species of extinct and extant porpoises (Mammalia: Cetacea: Phocoenidae), a clade of some of the smallest odontocete cetaceans, which produce some of the highest-frequency clicks for biosonar and communication. Metrics used to infer hearing ranges based on cochlear morphology indicate that …


Target Dose Conversion Modeling From Pencil Beam (Pb) To Monte Carlo (Mc) For Lung Sbrt, Dandan Zheng, Xiaofeng Zhu, Qinghui Zhang, Xiaoying Liang, Weining Zhen, Chi Lin, Vivek Verma, Shuo Wang, Andrew Wahl, Yu Lei, Sumin Zhou, Chi Zhang Jan 2016

Target Dose Conversion Modeling From Pencil Beam (Pb) To Monte Carlo (Mc) For Lung Sbrt, Dandan Zheng, Xiaofeng Zhu, Qinghui Zhang, Xiaoying Liang, Weining Zhen, Chi Lin, Vivek Verma, Shuo Wang, Andrew Wahl, Yu Lei, Sumin Zhou, Chi Zhang

School of Biological Sciences: Faculty Publications

Background: A challenge preventing routine clinical implementation of Monte Carlo (MC)-based lung SBRT is the difficulty of reinterpreting historical outcome data calculated with inaccurate dose algorithms, because the target dose was found to decrease to varying degrees when recalculated with MC. The large variability was previously found to be affected by factors such as tumour size, location, and lung density, usually through sub-group comparisons. We hereby conducted a pilot study to systematically and quantitatively analyze these patient factors and explore accurate target dose conversion models, so that large-scale historical outcome data can be correlated with more accurate MC dose without …


The Influence Of Balanced And Imbalanced Resource Supply On Biodiversity–Functioning Relationship Across Ecosystems, Aleksandra M. Lewandowska, Antje Biermann, Elizabeth T. Borer, Miguel A. Cebrián-Piqueras, Steven A.J. Declerck, Luc De Meester, Ellen Van Donk, Lars Ganfeldt, Daniel S. Gruner, Nicole Hagenah, W. Stanley Harpole, Kevin P. Kirkman, Christopher A. Klausmeier, Michael Kleyer, Johannes M. H. Knops, Pieter Lemmens, Eric M. Lind, Elena Litchman, Jasmin Mantilla-Contreras, Koen Martens, Sandra Meier, Vanessa Minden, Joslin L. Moore, Harry Olde Venterink, Eric W. Seabloom, Ulrich Sommer, Maren Striebel, Anastasia Trenkamp, Juliane Trinogga, Jotaro Urabe, Wim Vyverman, Dedmer B. Van De Waal, Claire E. Widdicombe, Helmut Hillebrand Jan 2016

The Influence Of Balanced And Imbalanced Resource Supply On Biodiversity–Functioning Relationship Across Ecosystems, Aleksandra M. Lewandowska, Antje Biermann, Elizabeth T. Borer, Miguel A. Cebrián-Piqueras, Steven A.J. Declerck, Luc De Meester, Ellen Van Donk, Lars Ganfeldt, Daniel S. Gruner, Nicole Hagenah, W. Stanley Harpole, Kevin P. Kirkman, Christopher A. Klausmeier, Michael Kleyer, Johannes M. H. Knops, Pieter Lemmens, Eric M. Lind, Elena Litchman, Jasmin Mantilla-Contreras, Koen Martens, Sandra Meier, Vanessa Minden, Joslin L. Moore, Harry Olde Venterink, Eric W. Seabloom, Ulrich Sommer, Maren Striebel, Anastasia Trenkamp, Juliane Trinogga, Jotaro Urabe, Wim Vyverman, Dedmer B. Van De Waal, Claire E. Widdicombe, Helmut Hillebrand

School of Biological Sciences: Faculty Publications

Numerous studies show that increasing species richness leads to higher ecosystem productivity. This effect is often attributed to more efficient portioning of multiple resources in communities with higher numbers of competing species, indicating the role of resource supply and stoichiometry for biodiversity–ecosystem functioning relationships. Here, we merged theory on ecological stoichiometry with a framework of biodiversity–ecosystem functioning to understand how resource use transfers into primary production. We applied a structural equation model to define patterns of diversity– productivity relationships with respect to available resources. Meta-analysis was used to summarize the findings across ecosystem types ranging from aquatic ecosystems to grasslands …


A Dataset For Assessing Temporal Changes In Gene Expression During The Aging Process Of Adult Drosophila Melanogaster, Kimberly A. Carlson, Chi Zhang, Lawrence G. Harshman Jan 2016

A Dataset For Assessing Temporal Changes In Gene Expression During The Aging Process Of Adult Drosophila Melanogaster, Kimberly A. Carlson, Chi Zhang, Lawrence G. Harshman

School of Biological Sciences: Faculty Publications

A Drosophila melanogaster genome-wide transcriptome dataset is

available for studies on temporal patterns of gene expression. Gene

expression was measured using two-dye color oligonucleotide arrays

derived from Version 2 of the Drosophila Genomics Resource Center.

A total of 15,158 oligonucleotide probes corresponded to a high

proportion of the coding genes in the genome. The source of the flies

was a highly genetically heterogeneous population maintained in an

overlapping generation population regime. This regime was

designed to maintain life history traits so that they were similar to

those found in natural populations. Flies collected for the cohorts

were obtained in a …


Genome Sequence Of Streptomyces Aureofaciens Atcc Strain 10762, Julien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G. Oliver, Etsuko N. Moriyama Jan 2016

Genome Sequence Of Streptomyces Aureofaciens Atcc Strain 10762, Julien Gradnigo, Greg Somerville, Michael J. Huether, Richard J. Kemmy, Craig M. Johnson, Michael G. Oliver, Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

Streptomyces aureofaciens is a Gram-positive actinomycete that produces the antibiotics tetracycline and chlortetracycline. Here, we report the assembly and initial annotation of the draft genome sequence of S. aureofaciens ATCC strain 10762.


Candida Albicans Isw2 Regulates Chlamydospore Suspensor Cell Formation And Virulence In Vivo In A Mouse Model Of Disseminated Candidiasis, Dhammika Navarathna, Ruvini U. Pathirana, Michail S. Lionakis, Kenneth W. Nickerson, David D. Roberts Jan 2016

Candida Albicans Isw2 Regulates Chlamydospore Suspensor Cell Formation And Virulence In Vivo In A Mouse Model Of Disseminated Candidiasis, Dhammika Navarathna, Ruvini U. Pathirana, Michail S. Lionakis, Kenneth W. Nickerson, David D. Roberts

School of Biological Sciences: Faculty Publications

Formation of chlamydospores by Candida albicans was an established medical diagnostic test to confirm candidiasis before the molecular era. However, the functional role and pathological relevance of this in vitro morphological transition to pathogenesis in vivo remain unclear. We compared the physical properties of in vitro-induced chlamydospores with those of large C. albicans cells purified by density gradient centrifugation from Candida infected mouse kidneys. The morphological and physical properties of these cells in kidneys of mice infected intravenously with wild type C. albicans confirmed that chlamydospores can form in infected kidneys. A previously reported chlamydospore-null Δisw2/ …


Targeted Therapy For Acute Autoimmune Myocarditis With Nano-Sized Liposomal Fk506 In Rats, Keiji Okuda, Hai Ying Fu, Takashi Matsuzaki, Ryo Araki, Shota Tsuchida, Punniyakoti V. Thanikachalam, Tatsuya Fukuta, Tomohiro Asai, Masaki Yamato, Shoji Sanada, Hiroshi Asanuma, Yoshihiro Asano, Masanori Asakura, Haruo Hanawa, Hiroyuki Hao, Naoto Oku, Seiji Takashima, Masafumi Kitakaze, Yasushi Sakata, Tetsuo Minamino Jan 2016

Targeted Therapy For Acute Autoimmune Myocarditis With Nano-Sized Liposomal Fk506 In Rats, Keiji Okuda, Hai Ying Fu, Takashi Matsuzaki, Ryo Araki, Shota Tsuchida, Punniyakoti V. Thanikachalam, Tatsuya Fukuta, Tomohiro Asai, Masaki Yamato, Shoji Sanada, Hiroshi Asanuma, Yoshihiro Asano, Masanori Asakura, Haruo Hanawa, Hiroyuki Hao, Naoto Oku, Seiji Takashima, Masafumi Kitakaze, Yasushi Sakata, Tetsuo Minamino

School of Biological Sciences: Faculty Publications

Immunosuppressive agents are used for the treatment of immune-mediated myocarditis; however, the need to develop a more effective therapeutic approach remains. Nano-sized liposomes may accumulate in and selectively deliver drugs to an inflammatory lesion with enhanced vascular permeability. The aims of this study were to investigate the distribution of liposomal FK506, an immunosuppressive drug encapsulated within liposomes, and the drug’s effects on cardiac function in a rat experimental autoimmune myocarditis (EAM) model. We prepared polyethylene glycol-modified liposomal FK506 (mean diameter: 109.5 ± 4.4 nm). We induced EAM by immunization with porcine myosin and assessed the tissue distribution of the nano-sized …


Advantages Of An Improved Rhesus Macaque Genome For Evolutionary Analyses, Julien S. Gradnigo, Abhishek Majumdar, Robert B. Norgren Jr., Etsuko N. Moriyama Jan 2016

Advantages Of An Improved Rhesus Macaque Genome For Evolutionary Analyses, Julien S. Gradnigo, Abhishek Majumdar, Robert B. Norgren Jr., Etsuko N. Moriyama

School of Biological Sciences: Faculty Publications

The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct. The rhesus macaque provides a unique opportunity to determine whether an …


Is The Relationship Between Mast-Seeding And Weather In Oaks Related To Their Life-History Or Phylogeny?, Walter D. Koenig, Reyes Alejano, Maria Dolores Carbonero, Pilar Fernández-Rebollo, Johannes Knops, Teodoro Marañón, Carmen M. Padilla-Díaz, Ian S. Pearse, Ignacio M. Pérez-Ramos, Javier Vázquez-Piqué, Mario B. Pesendorfer Jan 2016

Is The Relationship Between Mast-Seeding And Weather In Oaks Related To Their Life-History Or Phylogeny?, Walter D. Koenig, Reyes Alejano, Maria Dolores Carbonero, Pilar Fernández-Rebollo, Johannes Knops, Teodoro Marañón, Carmen M. Padilla-Díaz, Ian S. Pearse, Ignacio M. Pérez-Ramos, Javier Vázquez-Piqué, Mario B. Pesendorfer

School of Biological Sciences: Faculty Publications

Although the functional basis of variable and synchronous seed production (masting behavior) has been extensively investigated, only recently has attention been focused on the proximate mechanisms driving this phenomenon. We analyzed the relationship between weather and acorn production in 15 species of oaks (genus Quercus) from three geographic regions on two continents, with the goals of determining the extent to which similar sets of weather factors affect masting behavior across species and to explore the ecological basis for the similarities detected. Lag-1 temporal autocorrelations were predominantly negative, supporting the hypothesis that stored resources play a role in masting behavior …


Experimental Microbial Evolution Of Extremophiles, Paul H. Blum, Deepak Rudrappa, Raghuveer Singh, Samuel Mccarthy, Benjamin J. Pavlik Jan 2016

Experimental Microbial Evolution Of Extremophiles, Paul H. Blum, Deepak Rudrappa, Raghuveer Singh, Samuel Mccarthy, Benjamin J. Pavlik

School of Biological Sciences: Faculty Publications

Experimental microbial evolutions (EME) involves studying closely a microbial population after it has been through a large number of generations under controlled conditions (Kussell 2013). Adaptive laboratory evolution (ALE) selects for fitness under experimentally imposed conditions (Bennett and Hughes 2009; Dragosits and Mattanovich 2013). However, experimental evolution studies focusing on the contributions of genetic drift and natural mutation rates to evolution are conducted under non-selective conditions to avoid changes imposed by selection (Hindré et al. 2012).

To understand the application of experimental evolutionary methods to extremophiles it is essential to consider the recent growth in this field over the last …


A Stenotrophomonas Maltophilia Strain Evades A Major Caenorhabditis Elegans Defense Pathway, Corin V. White, Brian J. Darby, Robert J. Breeden, Robert J. Breeden, Michael A. Herman Jan 2016

A Stenotrophomonas Maltophilia Strain Evades A Major Caenorhabditis Elegans Defense Pathway, Corin V. White, Brian J. Darby, Robert J. Breeden, Robert J. Breeden, Michael A. Herman

School of Biological Sciences: Faculty Publications

Stenotrophomonas maltophilia is a ubiquitous bacterium and an emerging nosocomial pathogen. This bacterium is resistant to many antibiotics, associated with a number of infections, and a significant health risk, especially for immunocompromised patients. Given that Caenorhabditis elegans shares many conserved genetic pathways and pathway components with higher organisms, the study of its interaction with bacterial pathogens has biomedical implications. S. maltophilia has been isolated in association with nematodes from grassland soils, and it is likely that C. elegans encounters this bacterium in nature. We found that a local S. maltophilia isolate, JCMS, is more virulent than the other S. maltophilia …


Displaying To Females May Lower Male Foraging Time And Vigilance In A Lekking Bird, Sarah A. Cowles, Robert M. Gibson Nov 2015

Displaying To Females May Lower Male Foraging Time And Vigilance In A Lekking Bird, Sarah A. Cowles, Robert M. Gibson

School of Biological Sciences: Faculty Publications

Males of many species use courtship behavior to attract mates. However, by doing so males may face the associated costs of increased energetic expenditure, reduced foraging time, and elevated predation risk. We investigated the costs of display in lekking male Sharp-tailed Grouse (Tympanuchus phasianellus). We used lek-wide scan sampling to study how males allocated time among courtship display (‘‘dancing’’), agonism, foraging, and inactivity in relation to female numbers both within and across days. We also addressed the limited attention hypothesis and estimated visual attentiveness by videotaping 13 males and scoring head turns during these different activities. We found that the …


Exploring The Influence Of Ancient And Historic Megaherbivore Extirpations On The Global Methane Budget, Felisa A. Smith, John I. Hammond, Meghan A. Balk, Scott M. Elliott, S. Kathleen Lyons, Melissa I. Pardi, Catalina P. Tomé, Peter J. Wagner, Marie L. Westover, Christopher E. Doughty Aug 2015

Exploring The Influence Of Ancient And Historic Megaherbivore Extirpations On The Global Methane Budget, Felisa A. Smith, John I. Hammond, Meghan A. Balk, Scott M. Elliott, S. Kathleen Lyons, Melissa I. Pardi, Catalina P. Tomé, Peter J. Wagner, Marie L. Westover, Christopher E. Doughty

School of Biological Sciences: Faculty Publications

Globally, large-bodied wild mammals are in peril. Because “megamammals” have a disproportionate influence on vegetation, trophic interactions, and ecosystem function, declining populations are of considerable conservation concern. However, this is not new; trophic downgrading occurred in the past, including the African rinderpest epizootic of the 1890s, the massive Great Plains bison kill-off in the 1860s, and the terminal Pleistocene extinction of megafauna. Examining the consequences of these earlier events yields insights into contemporary ecosystem function. Here, we focus on changes inmethane emissions, produced as a byproduct of enteric fermentation by herbivores. Although methane is ∼200 times less abundant than carbon …


Interspecific Egg Rejection As Ecological Collateral Damage From Selection Driven By Conspecific Brood Parasitism, Bruce E. Lyon, Daizaburo Shizuka, John M. Eadie May 2015

Interspecific Egg Rejection As Ecological Collateral Damage From Selection Driven By Conspecific Brood Parasitism, Bruce E. Lyon, Daizaburo Shizuka, John M. Eadie

School of Biological Sciences: Faculty Publications

Distinguishing between interspecific and intraspecific coevolution as the selective driver of traits can be difficult in some taxa. A previous study of an avian obligate brood parasite, the black-headed duck, Heteronetta atricapilla, suggested that egg rejection by its two main hosts (two species of coot) is an incidental by-product of selection from conspecific brood parasitism within the hosts, not selection imposed by the interspecific parasite. However, although both species of coot can recognize and reject eggs of conspecific brood parasites, which closely resemble their own, they paradoxically also accept a moderate fraction of duck eggs (40–60%), which differ strikingly …


Composite Random Search Strategies Based On Non-Directional Sensory Cues, Ben C. Nolting, Travis M. Hinkelman, Chad Brassil, Brigitte Tenhumberg Apr 2015

Composite Random Search Strategies Based On Non-Directional Sensory Cues, Ben C. Nolting, Travis M. Hinkelman, Chad Brassil, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Many foraging animals find food using composite random search strategies, which consist of intensive and extensive search modes. Models of composite search can generate predictions about how optimal foragers should behave in each search mode, and how they should determine when to switch between search modes. Most of these models assume that foragers use resource encounters to decide when to switch between search modes. Empirical observations indicate that a variety of organisms use nondirectional sensory cues to identify areas that warrant intensive search. These cues are not precise enough to allow a forager to directly orient itself to a resource, …


The Molecular Biology Capstone Assessment: A Concept Assessment For Upper-Division Molecular Biology Students, Brian A. Couch, William B. Wood, Jennifer K. Knight Apr 2015

The Molecular Biology Capstone Assessment: A Concept Assessment For Upper-Division Molecular Biology Students, Brian A. Couch, William B. Wood, Jennifer K. Knight

School of Biological Sciences: Faculty Publications

Measuring students’ conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty …