Life Sciences Commons^™

High-Throughput Amplicon Sequencing Of Rrna Genes Requires A Copy Number Correction To Accurately Reflect The Effects Of Management Practices On Soil Nematode Community Structure, B. J. Darby, T. C. Todd, M. A. Herman

School of Biological Sciences: Faculty Publications

Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. …

Do Bacterial And Fungal Communities In Soils Of The Bolivian Altiplano Change Under Shorter Fallow Periods?, L. Gomez-Montano, A. Jumpponen, M. A. Gonzales, J. Cusicanqui, C. Valdivia, P. P. Motavalli, M. Herman, K. A. Garrett

School of Biological Sciences: Faculty Publications

Traditional fallow periods in the Bolivian highlands are being shortened in an effort to increase short-term crop yields, with potential long-term impacts on soil microbial communities and their functions. In addition, native vegetation, such as Parasthrephia sp. or Baccharis sp. (both locally known as “thola”) are often removed as a fuel for cooking. We evaluated the effects of fallow period and thola on soils in 29 farmers’ fields in two municipalities in the Bolivian Altiplano (Umala and Ancoraimes). Soil fungal and bacterial community responses were characterized using 454-pyrosequencing. Soils in Ancoraimes had significantly higher levels of organic matter, nitrogen, and …

Low Seroprevalent Species D Adenovirus Vectors As Influenza Vaccines, Eric A. Weaver, Michael A. Barry

School of Biological Sciences: Faculty Publications

Seasonal and pandemic influenza remains a constant threat. While standard influenza vaccines have great utility, the need for improved vaccine technologies have been brought to light by the 2009 swine flu pandemic, highly pathogenic avian influenza infections, and the most recent early and widespread influenza activity. Species C adenoviruses based on serotype 5 (AD5) are potent vehicles for gene-based vaccination. While potent, most humans are already immune to this virus. In this study, low seroprevalent species D adenoviruses Ad26, 28, and 48 were cloned and modified to express the influenza virus A/PR/8/34 hemagglutinin gene for vaccine studies. When studied in …

Disturbance Frequency And Vertical Distribution Of Seeds Affect Long-Term Population Dynamics: A Mechanistic Seed Bank Model, Eric A. Eager, Chirakkal V. Haridas, Diana Pilson, Richard Rebarber, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Seed banks are critically important for disturbance specialist plants because seeds of these species germinate only in disturbed soil. Disturbance and seed depth affect the survival and germination probability of seeds in the seed bank, which in turn affect population dynamics. We develop a density-dependent stochastic integral projection model to evaluate the effect of stochastic soil disturbances on plant population dynamics with an emphasis on mimicking how disturbances vertically redistribute seeds within the seed bank. We perform a simulation analysis of the effect of the frequency and mean depth of disturbances on the population’s quasi-extinction probability, as well as the …

Comparison Of Systemic And Mucosal Immunization Withhelper-Dependent Adenoviruses For Vaccination Against Mucosal Challenge With Shiv, Eric A. Weaver, Pramod N. Nehete, Bharti P. Nehete, Guojun Yang, Stephanie J. Buchl, Patrick W. Hanley, Donna Palmer, David C. Montefiori, Guido Ferrari, Philip Ng, K. Jagannadha Sastry, Michael A. Barry

School of Biological Sciences: Faculty Publications

Most HIV-1 infections are thought to occur at mucosal surfaces during sexual contact. It has been hypothesized that vaccines delivered at mucosal surfaces may mediate better protection against HIV-1 than vaccines that are delivered systemically. To test this, rhesus macaques were vaccinated by intramuscular (i.m.) or intravaginal (ivag.) routes with helperdependent adenoviral (HD-Ad) vectors expressing HIV-1 envelope. Macaques were first immunized intranasally with species C Ad serotype 5 (Ad5) prior to serotype-switching with species C HD-Ad6, Ad1, Ad5, and Ad2 vectors expressing env followed by rectal challenge with CCR5-tropic SHIV-SF162P3. Vaccination by the systemic route generated stronger systemic CD8 T …

Melanin Concentration Gradients In Modern And Fossil Feathers, Daniel J. Field, Liliana D’Alba, Jakob Vinther, Samuel M. Webb, William Gearty, Matthew D. Shawkey

School of Biological Sciences: Faculty Publications

In birds and feathered non-avian dinosaurs, within-feather pigmentation patterns range from discrete spots and stripes to more subtle patterns, but the latter remain largely unstudied. A ,55 million year old fossil contour feather with a dark distal tip grading into a lighter base was recovered from the Fur Formation in Denmark. SEM and synchrotron-based trace metal mapping confirmed that this gradient was caused by differential concentration of melanin. To assess the potential ecological and phylogenetic prevalence of this pattern, we evaluated 321 modern samples from 18 orders within Aves. We observed that the pattern was found most frequently in distantly …

Nitrogen Uptake Strategies Of Edaphically Specialized Bornean Tree Species, Sabrina E. Russo, Amy Kochsiek, Jocelyn Olney, Lauren Thompson, Amy E. Miller, Sylvester Tan

School of Biological Sciences: Faculty Publications

The association of tree species with particular soil types contributes to high b diversity in forests, but the mechanisms producing such distributions are still debated. Soil nitrogen (N) often limits growth and occurs in differentially available chemical forms. In a Bornean forest where tree species composition changes dramatically along a soil gradient varying in supplies of different N-forms, we investigated whether tree species’ N-uptake and soil specialization strategies covaried. We analyzed foliar ¹⁵N natural abundance for a total of 216 tree species on clay or sandy loam (the soils at the gradient’s extremes) and conducted a ¹⁵N-tracer experiment …

An Incompatibility Between A Mitochondrial Trna And Its Nuclear-Encoded Trna Synthetase Compromises Development And Fitness In Drosophila, Colin D. Meiklejohn, Marissa A. Holmbeck, Mohammed A. Siddiq, Dawn N. Abt, David M. Rand, Kristi L. Montooth

School of Biological Sciences: Faculty Publications

Mitochondrial transcription, translation, and respiration require interactions between genes encoded in two distinct genomes, generating the potential for mutations in nuclear and mitochondrial genomes to interact epistatically and cause incompatibilities that decrease fitness. Mitochondrial-nuclear epistasis for fitness has been documented within and between populations and species of diverse taxa, but rarely has the genetic or mechanistic basis of these mitochondrial–nuclear interactions been elucidated, limiting our understanding of which genes harbor variants causing mitochondrial–nuclear disruption and of the pathways and processes that are impacted by mitochondrial–nuclear coevolution. Here we identify an amino acid polymorphism in the Drosophila melanogaster nuclear-encoded mitochondrial tyrosyl–tRNA …

Plant Mitochondrial Genome Evolution Can Be Explained By Dna Repair Mechanisms, Alan C. Christensen

School of Biological Sciences: Faculty Publications

Plant mitochondrial genomes are notorious for their large and variable size, nonconserved open reading frames of unknown function, and high rates of rearrangement. Paradoxically, the mutation rates are very low. However, mutation rates can only be measured in sequences that can be aligned—a very small part of plant mitochondrial genomes. Comparison of the complete mitochondrial genome sequences of two ecotypes of Arabidopsis thaliana allows the alignment of noncoding as well as coding DNA and estimation of the mutation rates in both. A recent chimeric duplication is also analyzed. A hypothesis is proposed that the mechanisms of plant mitochondrial DNA repair …

Delayed Amyloid Plaque Deposition And Behavioral Deficits In Outcrossed Aβpp/Ps1 Mice, Brian A. Couch, Meghan E. Kerrisk, Adam C. Kaufman, Haakon B. Nygaard, Stephen M. Strittmatter, Anthony J. Koleske

School of Biological Sciences: Faculty Publications

Alzheimer’s disease (AD) is a progressive neurodegenerative dementia characterized by amyloid plaque accumulation, synapse/dendrite loss, and cognitive impairment. Transgenic mice expressing mutant forms of amyloid-β precursor protein (AβPP) and presenilin-1 (PS1) recapitulate several aspects of this disease and provide a useful model system for studying elements of AD progression. AβPP/PS1 mice have been previously shown to exhibit behavioral deficits and amyloid plaque deposition between 4–9 months of age. We crossed AβPP/PS1 animals with mice of a mixed genetic background (C57BL/6 × 129/SvJ) and investigated the development of AD-like features in the resulting outcrossed mice. The onset of memory-based behavioral impairment …

Effects Of Nitrogen Availability On The Fate Of Litter-Carbon And Soil Organic Matter Decomposition, Amy Kochsiek, Johannes Knops

School of Biological Sciences: Faculty Publications

Aims: To determine whether addition of inorganic nitrogen (N) directly to maize litter (stalk and leaf) with differing tissue quality impacts litter and soil organic matter (SOM) decomposition. We tested whether N addition leads to 1) faster litter decomposition, 2) less SOM-C decomposition and 3) increased incorporation of organic-C into soil-C fractions thereby increasing C sequestration potential in maize-based systems.

Methodology: We investigated decomposition of two types of maize litter (stalk and leaf) with differing tissue quality both in the field and in a laboratory incubation experiment. In the field, litter was placed on the soil surface and at …

Little Evidence For Demasculinization Of The Drosophila X Chromosome Among Genes Expressed In The Male Germline, Colin D. Meiklejohn, Daven C. Presgraves

School of Biological Sciences: Faculty Publications

Male-biased genes—those expressed at higher levels in males than in females—are underrepresented on the X chromosome of Drosophila melanogaster. Several evolutionary models have been posited to explain this so-called demasculinization of the X. Here, we show that the apparent paucity of male-biased genes on the X chromosome is attributable to global X-autosome differences in expression in Drosophila testes, owing to a lack of sex chromosome dosage compensation in the male germline, but not to any difference in the density of testis-specific or testis-biased genes on the X chromosome. First,using genome-wide gene expression data from 20 tissues,we find no evidence …

Tlr-Trif Pathway Enhances The Expression Of Kshv Replication And Transcription Activator, Florencia Meyer, Erica Ehlers, Andrew Steadman, Thomas Waterbury, Mingxia Cao, Luwen Zhang

School of Biological Sciences: Faculty Publications

Background: Host innate immunity is against virus infection and replication.

Results: Toll-like receptor 3 activation leads to enhanced expression of a key Kaposi’s sarcoma-associated herpesvirus (KSHV) protein.

Conclusion: KSHV uses host Toll-like receptor pathway to augment its critical gene expression. Significance: A virus may usurp host innate immunity for its own benefits.

Widespread Selection Across Coding And Noncoding Dna In The Pea Aphid Genome, Ryan D. Bickel, Joseph P. Dunham, Jennifer A. Brisson

School of Biological Sciences: Faculty Publications

Genome-wide patterns of diversity and selection are critical measures for understanding how evolution has shaped the genome. Yet, these population genomic estimates are available for only a limited number of model organisms. Here we focus on the population genomics of the pea aphid (Acyrthosiphon pisum). The pea aphid is an emerging model system that exhibits a range of intriguing biological traits not present in classic model systems. We performed low-coverage genome resequencing of 21 clonal pea aphid lines collected from alfalfa host plants in North America to characterize genome-wide patterns of diversity and selection. We observed an excess …

Four Distinct Types Of Dehydration Stress Memory Genes In Arabidopsis Thaliana, Yong Ding, Ning Liu, Laetitia Virlouvet, Jean-Jack Riethoven, Michael E. Fromm, Zoya Avramova

School of Biological Sciences: Faculty Publications

Background: How plants respond to dehydration stress has been extensively researched. However, how plants respond to multiple consecutive stresses is virtually unknown. Pre-exposure to various abiotic stresses (including dehydration) may alter plants’ subsequent responses by improving resistance to future exposures. These observations have led to the concept of ‘stress memory’ implying that during subsequent exposures plants provide responses that are different from those during their first encounter with the stress. Genes that provide altered responses in a subsequent stress define the ‘memory genes’ category; genes responding similarly to each stress form the ‘non-memory’ category.

Results: Using a genome-wide …

Regional Contingencies In The Relationship Between Aboveground Biomass And Litter In The World’S Grasslands, Lydia R. O’Halloran, Elizabeth T. Borer, Eric W. Seabloom, Andrew S. Macdougall, Elsa E. Cleland, Rebecca L. Mcculley, Sarah Hobbie, W. Stanley Harpole, Nicole M. Decrappeo, Chengjin Chu, Jonathan D. Bakker, Kendi F. Davies, Guozhen Du, Jennifer Firn, Nicole Hagenah, Kirsten S. Hofmockel, Johannes Knops, Wei Li, Brett A. Melbourne, John W. Morgan, John L. Orrock, Suzanne M. Prober, Carly J. Stevens

School of Biological Sciences: Faculty Publications

Based on regional-scale studies, aboveground production and litter decomposition are thought to positively covary, because they are driven by shared biotic and climatic factors. Until now we have been unable to test whether production and decomposition are generally coupled across climatically dissimilar regions, because we lacked replicated data collected within a single vegetation type across multiple regions, obfuscating the drivers and generality of the association between production and decomposition. Furthermore, our understanding of the relationships between production and decomposition rests heavily on separate meta-analyses of each response, because no studies have simultaneously measured production and the accumulation or decomposition of …

Cd20 Antibody Primes B Lymphocytes For Type I Interferon Production, Dongsheng Xu, Andrew Staedman, Luwen Zhang

School of Biological Sciences: Faculty Publications

CD20 is a B cell surface marker that is expressed in various stages in B lymphocytes and certain lymphomas. Clinical administration of CD20 antibody, such as rituximab, is used widely to treat human B-cell lymphomas and other diseases. However, CD20 antibody failed to treat systemic lupus erythematosus (SLE or lupus). The reason for the failure is currently unknown. Type I interferons (IFN) are a major component for the host innate immunity, and a key pathogenic factor in lupus. We found that CD20 antibody potentiated human B cells for its production of IFNs in vitro. This function was specific to …

Deer Mouse Hemoglobin Exhibits A Lowered Oxygen Affinity Owing To Mobility Of The E Helix. Corrigendum, Noriko Inoguchi, Jake R. Oshlo, Chandrasekhar Natarajan, Roy E. Weber, Angela Fago, Jay F. Storz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

In the article by Inoguchi et al. (2013) the affiliation for two of the authors, Angela Fago and Roy E. Weber, was given incorrectly. The correct affiliation is Zoophysiology, Department of Bioscience, Aarhus University, Aarhus, Denmark.

Long-Term Nitrogen Amendment Alters The Diversity And Assemblage Of Soil Bacterial Communities In Tallgrass Prairie, Joseph D. Coolon, Kenneth L. Jones, Timothy C. Todd, John M. Blair, Michael A. Herman

School of Biological Sciences: Faculty Publications

Anthropogenic changes are altering the environmental conditions and the biota of ecosystems worldwide. In many temperate grasslands, such as North American tallgrass prairie, these changes include alteration in historically important disturbance regimes (e.g., frequency of fires) and enhanced availability of potentially limiting nutrients, particularly nitrogen. Such anthropogenically-driven changes in the environment are known to elicit substantial changes in plant and consumer communities aboveground, but much less is known about their effects on soil microbial communities. Due to the high diversity of soil microbes and methodological challenges associated with assessing microbial community composition, relatively few studies have addressed specific taxonomic changes …

A Whole-Cell Biosensor For The Detection Of Gold, Carla M. Zammit, Davide Quaranta, Shane Gibson, Anita J. Zaitouna, Christine Ta, Joel Brugger, Rebecca Y. Lai, Gregor Grass, Frank Reith

School of Biological Sciences: Faculty Publications

Geochemical exploration for gold (Au) is becoming increasingly important to the mining industry. Current processes for Au analyses require sampling materials to be taken from often remote localities. Samples are then transported to a laboratory equipped with suitable analytical facilities, such as Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) or Instrumental Neutron Activation Analysis (INAA). Determining the concentration of Au in samples may take several weeks, leading to long delays in exploration campaigns. Hence, a method for the on-site analysis of Au, such as a biosensor, will greatly benefit the exploration industry. The golTSB genes from Salmonella enterica serovar typhimurium are selectively …

Inge Revsbech Wins The Journal Of Experimental Biology’S Outstanding Paper Prize 2013, Nicola Stead, Inge G. Revsbech, Hideaki Moriyama, Jay F. Storz, Angela Fago

School of Biological Sciences: Faculty Publications

The Editors of The Journal of Experimental Biology are pleased to announce that Inge Revsbech from Aarhus University, Denmark, is the winner of this year’s JEB Outstanding paper prize. The prize is awarded in memory of Bob Boutillier (JEB Editor-in-Chief 1994–2003) to a junior author who has made the most significant contribution to an outstanding paper. ‘The prize aims to promote and reward the hard work that individual young scientists have put into solving different riddles of any particular species using ingenuity, perseverance and sound technology and methodology’, explains Hans Hoppeler, Editor-In-Chief.

Revsbech was the first author on the paper …

Role Of Merh In Mercury Resistance In The Archaeon Sulfolobus Solfataricus, James Schelert, Deepak Rudrappa, Tyler Johnson, Paul H. Blum

School of Biological Sciences: Faculty Publications

Crenarchaeota include extremely thermoacidophilic organisms that thrive in geothermal

environments dominated by sulfidic ores and heavy metals such as mercury. Mercuric ion, Hg(II),

inactivates transcription in the crenarchaeote Sulfolobus solfataricus and simultaneously

derepresses transcription of a resistance operon, merHAI, through interaction with the MerR

transcription factor. While mercuric reductase (MerA) is required for metal resistance, the role of

MerH, an adjacent small and predicted product of an ORF, has not been explored. Inactivation of

MerH either by nonsense mutation or by in-frame deletion diminished Hg(II) resistance of mutant

cells. Promoter mapping studies indicated that Hg(II) sensitivity of the merH …

Antelope Mating Strategies Facilitate Invasion Of Grasslands By A Woody Weed, Shivani Jadeja, Soumya Prasad, Suhel Quader, Kavita Isvaran

School of Biological Sciences: Faculty Publications

Intra and interspecific variation in frugivore behaviour can have important consequences for seed dispersal outcomes. However, most information comes from among-species comparisons, and within-species variation is relatively poorly understood. We examined how large intraspecific differences in the behaviour of a native disperser, blackbuck antelope Antilope cervicapra, influence dispersal of a woody invasive, Prosopis juliflora, in a grassland ecosystem. Blackbuck disperse P. juliflora seeds through their dung. In lekking blackbuck populations, males defend clustered or dispersed mating territories. Territorial male movement is restricted, and within their territories males defecate on dung-piles. In contrast, mixed-sex herds range over large areas …

Predicting Invasion In Grassland Ecosystems: Is Exotic Dominance The Real Embarrassment Of Richness?, Eric W. Seabloom, Elizabeth T. Borer, Yvonne Buckley, Elsa E. Cleland, Kendi Davies, Jennifer Firn, W. Stanley Harpole, Yann Hautier, Eric Lind, Andrew Macdougall, John L. Orrock, Suzanne M. Prober, Peter Andler, Juan Alberti, T. Michael Anderson, Jonathan D. Bakker, Lori A. Biederman, Dana Blumenthal, Cynthia S. Brown, Lars A. Brudvig, Maria Caldeira, Chengjin Chu, Michael J. Crawley, Pedro Daleo, Ellen I. Damschen, Carla M. D'Antonio, Nicole M. Decrappeo, Chris R. Dickman, Guozhen Du, Philip A. Fay, Paul Frater, Daniel S. Gruner, Nicole Hagenah, Andrew Hector, Aveliina Helm, Helmut Hillebrand, Kirsten S. Hofmockel, Hope C. Humphries, Oscar Iribarne, Virginia L. Jin, Adam Kay, Kevin P. Kirkman, Julia A. Klein, Johannes M. H. Knops, Kimberly J. La Pierre, Laura M. Ladwig, John G. Lambrinos, Andrew D. B. Leakey, Qi Li, Wei Li, Rebecca Mcculley, Brett Melbourne, Charles E. Mitchell, Joslin L. Moore, John Morgan, Brent Mortensen, Lydia R. O'Halloran, Meelis Partel, Jesus Pascual, David A. Pyke, Anita C. Risch, Roberto Salguero-Gomez, Mahesh Sankaran, Martin Schuetz, Anna Simonsen, Melinda Smith, Carly Stevens, Lauren L. Sullivan, Glenda M. Wardle, Elizabeth M. Wolkovich, Peter D. Wragg, Justin Wright, Louie Yang

School of Biological Sciences: Faculty Publications

Invasions have increased the size of regional species pools, but are typically assumed to reduce native diversity. However, global-scale tests of this assumption have been elusive because of the focus on exotic species richness, rather than relative abundance. This is problematic because low invader richness can indicate invasion resistance by the native community or, alternatively, dominance by a single exotic species. Here, we used a globally replicated study to quantify relationships between exotic richness and abundance in grass-dominated ecosystems in 13 countries on six continents, ranging from salt marshes to alpine tundra. We tested effects of human land use, native …

The Mid-Domain Effect: It’S Not Just About Space, Andrew D. Letten, S. Kathleen Lyons, Angela T. Moles

School of Biological Sciences: Faculty Publications

Ecologists and biogeographers have long sought to understand how and why diversity varies across space. Up until the late 20th century, the dominant role of environmental gradients and historical processes in driving geographical species richness patterns went largely undisputed. However, almost 20 years ago, Colwell & Hurtt (1994) proposed a radical reappraisal of ecological gradient theory that called into question decades of empirical and theoretical research. That controversial idea was later termed the ‘the mid-domain effect’: the simple proposition that in the absence of environmental gradients, the random placement of species ranges within a bounded domain will give rise to …

Different Modes Of Evolution In Males And Females Generate Dichromatism In Fairy-Wrens (Maluridae), Allison E. Johnson, J. Jordan Price, Stephen Pruett-Jones

School of Biological Sciences: Faculty Publications

Sexual dichromatism in birds is often attributed to selection for elaboration in males. However, evolutionary changes in either sex can result in plumage differences between them, and such changes can result in either gains or losses of dimorphism. We reconstructed the evolution of plumage colors in both males and females of species in Maluridae, a family comprising the fairy-wrens (Malurus, Clytomias, Sipodotus), emu-wrens (Stipiturus), and grasswrens (Amytornis). Our results show that, across species, males and females differ in their patterns of color evolution. Male plumage has diverged at relatively steady rates, whereas …

Candida Albicans Czf1 And Efg1 Coordinate The Response To Farnesol During Quorum Sensing, White-Opaque Thermal Dimorphism, And Cell Death, Melanie L. Langford, Jessica C. Hargarten, Krista D. Patefield, Elizabeth Marta, Jill R. Blankenship, Saranna Fanning, Kenneth W. Nickerson, Audrey L. Atkin

School of Biological Sciences: Faculty Publications

Quorum sensing by farnesol in Candida albicans inhibits filamentation and may be directly related to its ability to cause both mucosal and systemic diseases. The Ras1-cyclic AMP signaling pathway is a target for farnesol inhibition. However, a clear understanding of the downstream effectors of the morphological farnesol response has yet to be unraveled. To address this issue, we screened a library for mutants that fail to respond to farnesol. Six mutants were identified, and the czf1Δ/czf1Δ mutant was selected for further characterization. Czf1 is a transcription factor that regulates filamentation in embedded agar and also whiteto- opaque switching. We found …

Large-Scale Spatial Synchrony And Cross-Synchrony In Acorn Production By Two California Oaks, Walter D. Koenig, Johannes M.H. Knops

School of Biological Sciences: Faculty Publications

Seed production that varies greatly from year to year, known as ‘‘masting’’ or ‘‘mast-fruiting’’ behavior, is a population-level phenomenon known to exhibit geographic synchrony extending, at least in some cases, hundreds of kilometers. The two main nonexclusive hypotheses for the driver of such geographically extensive synchrony are (1) environmental factors (the Moran effect), and (2) the mutual dependence of trees on outcrossed pollen (pollen coupling). We tested 10 predictions relevant to these two hypotheses using 18 years of acorn production data on two species of California oaks. Data were obtained across the entire ranges of the two species at 12 …

Deer Mouse Hemoglobin Exhibits A Lowered Oxygen Affinity Owing To Mobility Of The E Helix, Noriko Inoguchi, Jake R. Oshlo, Chandrasekhar Natarajan, Roy E. Weber, Angela Fago, Jay F. Storz, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin was solved. Recombinant hemoglobin was expressed in Escherichia coli and was purified by ion-exchange chromatography. Recombinant hemoglobin was crystallized by the hangingdrop vapor-diffusion method using polyethylene glycol as a precipitant. The obtained orthorhombic crystal contained two subunits in the asymmetric unit. The refined structure was interpreted as the aquo-met form. Structural comparisons were performed among hemoglobins from deer mouse, house mouse and human. In contrast to human hemoglobin, deer mouse hemoglobin lacks the …

Reductive Evolution And The Loss Of Pdc/Pas Domains From The Genus Staphylococcus, Neethu Shah, Rosmarie Gaupp, Hideaki Moriyama, Kent M. Eskridge, Etsuko N. Moriyama, Greg A. Somerville

School of Biological Sciences: Faculty Publications

Background: The Per-Arnt-Sim (PAS) domain represents a ubiquitous structural fold that is involved in bacterial sensing and adaptation systems, including several virulence related functions. Although PAS domains and the subclass of PhoQ-DcuS-CitA (PDC) domains have a common structure, there is limited amino acid sequence similarity. To gain greater insight into the evolution of PDC/PAS domains present in the bacterial kingdom and staphylococci in specific, the PDC/PAS domains from the genomic sequences of 48 bacteria, representing 5 phyla, were identified using the sensitive search method based on HMM-to-HMM comparisons (HHblits).

Results: A total of 1,007 PAS domains and 686 …