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Louisiana State University

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Microbiological, Physicochemical, And Immunological Analysis Of A Commercial Cashew Nut-Based Yogurt, Christopher P. Mattison, Kayanush Aryana, Kristen Clermont, Eric Prestenburg, Steven W. Lloyd, Casey .. Grimm, Richard L. Wasserman Nov 2020

Microbiological, Physicochemical, And Immunological Analysis Of A Commercial Cashew Nut-Based Yogurt, Christopher P. Mattison, Kayanush Aryana, Kristen Clermont, Eric Prestenburg, Steven W. Lloyd, Casey .. Grimm, Richard L. Wasserman

Faculty Publications

Nut-based milks and yogurts are gaining popularity, but may not offer the same benefits as dairy yogurts to consumers. Cashew nuts often cause severe allergic reactions, and cashew nut allergens are stable to several types of processing. To compare its characteristics to dairy yogurt and characterize the effects of fermentation on the Ana o 1-3 cashew nut allergens, a commercial yogurt made from cashew nuts (Cashewgurt) was evaluated for microbiological, physiochemical, and immunological properties. Average counts for lactobacilli and Streptococcus thermophilus were greater than 10 million colony forming units per milliliter, indicating the capacity to provide a health benefit. Cashewgurt …

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Speciation-By-Depth On Coral Reefs: Sympatric Divergence With Gene Flow Or Cryptic Transient Isolation?, Carlos Prada, Michael E. Hellberg Nov 2020

Speciation-By-Depth On Coral Reefs: Sympatric Divergence With Gene Flow Or Cryptic Transient Isolation?, Carlos Prada, Michael E. Hellberg

Faculty Publications

The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data. Here, we revisit the case of two depth-segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange …

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Reducing Host Dna Contamination In 16s Rrna Gene Surveys Of Anthozoan Microbiomes Using Pna Clamps, Alicia M. Reigel, Sarah M. Owens, Michael E. Hellberg Oct 2020

Reducing Host Dna Contamination In 16s Rrna Gene Surveys Of Anthozoan Microbiomes Using Pna Clamps, Alicia M. Reigel, Sarah M. Owens, Michael E. Hellberg

Faculty Publications

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgoniansEunicea flexuosaandGorgonia ventalina,and the scleractinianPorites panamensis. The 20-bp PNA clamp was designed using DNA fromE. flexuosa. Adding the …

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Fish Assemblages Associated With Artificial Reefs Assessed Using Multiple Gear Types In The Northwest Gulf Of Mexico, Jeffrey D. Plumlee, Kaylan M. Dance, Michael A. Dance, Hay R. Rooker, Thomas C. Tinhan, J. Brooke Shipley, R. J. David Wells Oct 2020

Fish Assemblages Associated With Artificial Reefs Assessed Using Multiple Gear Types In The Northwest Gulf Of Mexico, Jeffrey D. Plumlee, Kaylan M. Dance, Michael A. Dance, Hay R. Rooker, Thomas C. Tinhan, J. Brooke Shipley, R. J. David Wells

Faculty Publications

Quantitative surveys of fishes associated with artificial reefs in the northwest Gulf of Mexico were conducted over a 4-yr period (2014-2017). Artificial reefs surveyed were comprised of three types: concrete structures, rig jackets, and decommissioned ships. All reefs were surveyed using vertical long line ( VLL), fish traps, and Adaptive Resolution Imaging Sonar (ARIS 1800). Mean fish abundance did not significantly differ using VLL [1.7 ind set(-1) (SD 2.2)] among the three reef types. However, relative abundance among all fishes collected was significantly highest on rig reefs using traps [6.2 ind soak(-1) (SD 3.8)], while results from sonar surveys indicated …

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All-Atomic Molecular Dynamic Studies Of Human And Drosophila Cdk8: Insights Into Their Kinase Domains, The Lxxll Motifs, And Drug Binding Site, Wu Xu, Xiao-Jun Xie, Ali K. Faust, Mengmeng Liu, Xiao Li, Feng Chen, Ashlin A. Naquin, Avery C. Walton, Peter W. Kishbaugh, Jun-Yuan Ji Oct 2020

All-Atomic Molecular Dynamic Studies Of Human And Drosophila Cdk8: Insights Into Their Kinase Domains, The Lxxll Motifs, And Drug Binding Site, Wu Xu, Xiao-Jun Xie, Ali K. Faust, Mengmeng Liu, Xiao Li, Feng Chen, Ashlin A. Naquin, Avery C. Walton, Peter W. Kishbaugh, Jun-Yuan Ji

Faculty Publications

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 …

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Behavioral Strategies During Incubation Influence Nest And Female Survival Of Wild Turkeys, Ashley K. Lohr, James A. Martin, Gregory T. Wann, Bradley S. Cohen, Bret A. Collier, Michael J. Chamberlain Sep 2020

Behavioral Strategies During Incubation Influence Nest And Female Survival Of Wild Turkeys, Ashley K. Lohr, James A. Martin, Gregory T. Wann, Bradley S. Cohen, Bret A. Collier, Michael J. Chamberlain

Faculty Publications

Females must balance physiological and behavioral demands of producing offspring with associated expenditures, such as resource acquisition and predator avoidance. Nest success is an important parameter underlying avian population dynamics. Galliforms are particularly susceptible to low nest success due to exposure of ground nests to multiple predator guilds, lengthy incubation periods, and substantive reliance on crypsis for survival. Hence, it is plausible that nesting individuals prioritize productivity and survival differently, resulting in a gradient of reproductive strategies. Fine-scale movement patterns during incubation are not well documented in ground-nesting birds, and the influence of reproductive movements on survival is largely unknown. …

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Phyr: Anrpackage For Phylogenetic Species-Distribution Modelling In Ecological Communities, Daijiang Li, Russell Dinnage, Lucas A. Nell, Matthew R. Helmus, Anthony Ives Sep 2020

Phyr: Anrpackage For Phylogenetic Species-Distribution Modelling In Ecological Communities, Daijiang Li, Russell Dinnage, Lucas A. Nell, Matthew R. Helmus, Anthony Ives

Faculty Publications

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. To fill this gap, therpackagephyr(pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other …

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Gomcl: A T Gomcl: A Toolkit T Oolkit To Cluster O Cluster, Evaluate, And Extr Aluate, And Extract Non-R Act Non-Redundant Edundant Associations Of Gene Ontology-Based Functions, Guannan Wang, Dong-Ha Oh, Maheshi Dassanayake Apr 2020

Gomcl: A T Gomcl: A Toolkit T Oolkit To Cluster O Cluster, Evaluate, And Extr Aluate, And Extract Non-R Act Non-Redundant Edundant Associations Of Gene Ontology-Based Functions, Guannan Wang, Dong-Ha Oh, Maheshi Dassanayake

Faculty Publications

Background Functional enrichment of genes and pathways based on Gene Ontology (GO) has been widely used to describe the results of various -omics analyses. GO terms statistically overrepresented within a set of a large number of genes are typically used to describe the main functional attributes of the gene set. However, these lists of overrepresented GO terms are often too large and contains redundant overlapping GO terms hindering informative functional interpretations. Results We developed GOMCL to reduce redundancy and summarize lists of GO terms effectively and informatively. This lightweight python toolkit efficiently identifies clusters within a list of GO terms …

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Hinge Region In Dna Packaging Terminase Pul15 Of Herpes Simplex Virus: A Potential Allosteric Target For Antiviral Drugs, Lana F. Thaljeh, J. Ainsley Rothschild, Misagh Naderi, Lyndon M. Coghill Oct 2019

Hinge Region In Dna Packaging Terminase Pul15 Of Herpes Simplex Virus: A Potential Allosteric Target For Antiviral Drugs, Lana F. Thaljeh, J. Ainsley Rothschild, Misagh Naderi, Lyndon M. Coghill

Faculty Publications

Approximately 80% of adults are infected with a member of the herpesviridae family. Herpesviruses establish life-long latent infections within neurons, which may reactivate into lytic infections due to stress or immune suppression. There are nine human herpesviruses (HHV) posing health concerns from benign conditions to life threatening encephalitis, including cancers associated with viral infections. The current treatment options for most HHV conditions mainly include several nucleoside and nucleotide analogs targeting viral DNA polymerase. Although these drugs help manage infections, their common mechanism of action may lead to the development of drug resistance, which is particularly devastating in immunocompromised patients. Therefore, …

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Hinge Region In Dna Packaging Terminase Pul15 Of Herpes Simplex Virus: A Potential Allosteric Target For Antiviral Drugs, Lana F. Thaljeh, J. Ainsley Rothschild, Misagh Naderi, Lyndon M. Coghill, Jeremy M. Brown, Michal Brylinski Oct 2019

Hinge Region In Dna Packaging Terminase Pul15 Of Herpes Simplex Virus: A Potential Allosteric Target For Antiviral Drugs, Lana F. Thaljeh, J. Ainsley Rothschild, Misagh Naderi, Lyndon M. Coghill, Jeremy M. Brown, Michal Brylinski

Faculty Publications

Approximately 80% of adults are infected with a member of the herpesviridae family. Herpesviruses establish life-long latent infections within neurons, which may reactivate into lytic infections due to stress or immune suppression. There are nine human herpesviruses (HHV) posing health concerns from benign conditions to life threatening encephalitis, including cancers associated with viral infections. The current treatment options for most HHV conditions mainly include several nucleoside and nucleotide analogs targeting viral DNA polymerase. Although these drugs help manage infections, their common mechanism of action may lead to the development of drug resistance, which is particularly devastating in immunocompromised patients. Therefore, …

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Fisetin, A 3,7,3 ',4 '-Tetrahydroxyflavone Inhibits The Pi3k/Akt/Mtor And Mapk Pathways And Ameliorates Psoriasis Pathology In 2d And 3d Organotypic Human Inflammatory Skin Models, Konstantin G. Kousoulas Sep 2019

Fisetin, A 3,7,3 ',4 '-Tetrahydroxyflavone Inhibits The Pi3k/Akt/Mtor And Mapk Pathways And Ameliorates Psoriasis Pathology In 2d And 3d Organotypic Human Inflammatory Skin Models, Konstantin G. Kousoulas

Faculty Publications

Psoriasis is a chronic immune-mediated skin disease that involves the interaction of immune and skin cells, and is characterized by cytokine-driven epidermal hyperplasia, deviant differentiation, inflammation, and angiogenesis. Because the available treatments for psoriasis have significant limitations, dietary products are potential natural sources of therapeutic molecules, which can repair the molecular defects associated with psoriasis and could possibly be developed for its management. Fisetin (3,7,3 ',4 '-tetrahydroxyflavone), a phytochemical naturally found in pigmented fruits and vegetables, has demonstrated proapoptotic and antioxidant effects in several malignancies. This study utilized biochemical, cellular, pharmacological, and tissue engineering tools to characterize the effects of …

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Histone H4 H75e Mutation Attenuates Global Genomic And Rad26-Independent Transcription-Coupled Nucleotide Excision Repair, Shisheng Li, Kathiresan Selvam, Sheikh Arafatur Rahman Aug 2019

Histone H4 H75e Mutation Attenuates Global Genomic And Rad26-Independent Transcription-Coupled Nucleotide Excision Repair, Shisheng Li, Kathiresan Selvam, Sheikh Arafatur Rahman

Faculty Publications

Nucleotide excision repair (NER) consists of global genomic NER (GG-NER) and transcription coupled NER (TC-NER) subpathways. In eukaryotic cells, genomic DNA is wrapped around histone octamers (an H3-H4 tetramer and two H2A-H2B dimers) to form nucleosomes, which are well known to profoundly inhibit the access of NER proteins. Through unbiased screening of histone H4 residues in the nucleosomal LRS (loss of ribosomal DNA-silencing) domain, we identified 24 mutations that enhance or decrease UV sensitivity of Saccharomyces cerevisiae cells. The histone H4 H75E mutation, which is largely embedded in the nucleosome and interacts with histone H2B, significantly attenuates GG-NER and Rad26-independent …

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From Pampa To Puna: Biogeography And Diversification Of A Group Of Neotropical Obligate Grassland Birds (Anthus: Motacillidae), Paul Van Els Aug 2019

From Pampa To Puna: Biogeography And Diversification Of A Group Of Neotropical Obligate Grassland Birds (Anthus: Motacillidae), Paul Van Els

Faculty Publications

The evolution of Neotropical birds of open landscapes remains largely unstudied. We investigate the diversification and biogeography of a group of Neotropical obligate grassland birds (Anthus: Motacillidae). We use a multilocus phylogeny of 22 taxa of Anthus to test the hypothesis that these birds radiated contemporaneously with the development of grasslands in South America. We employ the R package DDD to analyze the dynamics of Anthus diversification across time in Neotropical grasslands, explicitly testing for shifts in dynamics associated with the Miocene development of grasslands, the putative Pleistocene expansion of arid lowland biomes, and Pleistocene sundering of Andean highland grasslands. …

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The Nopp140 Gene In Drosophila Melanogaster Displays Length Polymorphisms In Its Large Repetitive Second Exon, Patrick J. Dimario, Sonu Shrestha Baral Aug 2019

The Nopp140 Gene In Drosophila Melanogaster Displays Length Polymorphisms In Its Large Repetitive Second Exon, Patrick J. Dimario, Sonu Shrestha Baral

Faculty Publications

Nopp140, often called the nucleolar and Cajal body phosphoprotein (NOLC1), is an evolutionarily conserved chaperone for the transcription and processing of rRNA during ribosome subunit assembly. Metazoan Nopp140 contains an amino terminal LisH dimerization domain and a highly conserved carboxyl domain. A large central domain consists of alternating basic and acidic motifs of low sequence complexity. Orthologous versions of Nopp140 contain variable numbers of repeating basic-acidic units. While vertebrate Nopp140 genes use multiple exons to encode the central domain, the Nopp140 gene in Drosophila uses exclusively exon 2 to encode the central domain. Here, we define three overlapping repeat sequence …

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Temporal And Spatial Dynamics Of Competitive Parapatry In Chewing Lice, Mark S. Hafner Jul 2019

Temporal And Spatial Dynamics Of Competitive Parapatry In Chewing Lice, Mark S. Hafner

Faculty Publications

We synthesize observations from 1979 to 2016 of a contact zone involving two subspecies of pocket gophers (Thomomys bottae connectens and T. b. opulentus) and their respective chewing lice (Geomydoecus aurei and G. centralis) along the Rio Grande Valley in New Mexico, U.S.A., to test predictions about the dynamics of the zone. Historically, the natural flood cycle of the Rio Grande prevented contact between the two subspecies of pocket gophers. Flood control measures completed in the 1930s permitted contact, thus establishing the hybrid zone between the pocket gophers and the contact zone between their lice (without hybridization). Since that time, …

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Zinc Toxicity And Iron-Sulfur Cluster Biogenesis In Escherichia Coli, Huangen Ding May 2019

Zinc Toxicity And Iron-Sulfur Cluster Biogenesis In Escherichia Coli, Huangen Ding

Faculty Publications

While zinc is an essential trace metal in biology, excess zinc is toxic to organisms. Previous studies have shown that zinc toxicity is associated with disruption of the (4Fe-4S] clusters in various dehydratases in Escherichia coli. Here, we report that the intracellular zinc overload in E. coli cells inhibits iron-sulfur cluster biogenesis without affecting the preassembled iron-sulfur clusters in proteins. Among the housekeeping iron-sulfur cluster assembly proteins encoded by the gene cluster iscSUA-hscBA-fdx-iscX in E. coli cells, the scaffold IscU, the iron chaperone IscA, and ferredoxin have strong zinc binding activity in cells, suggesting that intracellular zinc overload inhibits iron-sulfur …

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The Cure For Cultivating Fastidious Microbes, William Wischusen, Arundhati Bakshi, Austen T. Webber, Lorelei E. Patrick Apr 2019

The Cure For Cultivating Fastidious Microbes, William Wischusen, Arundhati Bakshi, Austen T. Webber, Lorelei E. Patrick

Faculty Publications

Course-Based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the …

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Amplification Dynamics Of Platy-1 Retrotransposons In The Cebidae Platyrrhine Lineage, Mark A. Batzer, Jessica M. Storer, Jackson R. Mierl, Sarah A. Brantley Apr 2019

Amplification Dynamics Of Platy-1 Retrotransposons In The Cebidae Platyrrhine Lineage, Mark A. Batzer, Jessica M. Storer, Jackson R. Mierl, Sarah A. Brantley

Faculty Publications

Platy-1 elements are Platyrrhine-specific, short interspersed elements originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared with the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in …

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Genomic, Ecological, And Morphological Approaches To Investigating Species Limits: A Case Study In Modern Taxonomy From Tropical Eastern Pacific Surgeonfishes, Prosanta Chakrabarty Apr 2019

Genomic, Ecological, And Morphological Approaches To Investigating Species Limits: A Case Study In Modern Taxonomy From Tropical Eastern Pacific Surgeonfishes, Prosanta Chakrabarty

Faculty Publications

A wide variety of species are distinguished by slight color variations. However, molecular analyses have repeatedly demonstrated that coloration does not always correspond to distinct evolutionary histories between closely related groups, suggesting that this trait is labile and can be misleading for species identification. In the present study, we analyze the evolutionary history of sister species of Prionurus surgeonfishes in the Tropical Eastern Pacific (TEP), which are distinguished by the presence or absence of dark spots on their body. We examined the species limits in this system using comparative specimen-based approaches, a mitochondrial gene (COI), more than 800 nuclear loci …

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The Aqueous Environment As An Active Participant In The Protein Folding Process, Michal Brylinski Mar 2019

The Aqueous Environment As An Active Participant In The Protein Folding Process, Michal Brylinski

Faculty Publications

Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. …

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Deepdrug3d: Classification Of Ligand-Binding Pockets In Proteins With A Convolutional Neural Network, Michal Brylinski, Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine Feb 2019

Deepdrug3d: Classification Of Ligand-Binding Pockets In Proteins With A Convolutional Neural Network, Michal Brylinski, Limeng Pu, Rajiv Gandhi Govindaraj, Jeffrey Mitchell Lemoine

Faculty Publications

Comprehensive characterization of ligand-binding sites is invaluable to infer molecular functions of hypothetical proteins, trace evolutionary relationships between proteins, engineer enzymes to achieve a desired substrate specificity, and develop drugs with improved selectivity profiles. These research efforts pose significant challenges owing to the fact that similar pockets are commonly observed across different folds, leading to the high degree of promiscuity of ligand-protein interactions at the system-level. On that account, novel algorithms to accurately classify binding sites are needed. Deep learning is attracting a significant attention due to its successful applications in a wide range of disciplines. In this communication, we …

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Host Sex, Size, And Hemoparasite Infection Influence The Effects Of Ectoparasitic Burdens On Free-Ranging Iguanas, Christine Lattin Feb 2019

Host Sex, Size, And Hemoparasite Infection Influence The Effects Of Ectoparasitic Burdens On Free-Ranging Iguanas, Christine Lattin

Faculty Publications

Investigations focusing on host-ectoparasite interactions in animals have revealed asymptomatic to severe health and fitness consequences suggesting that species mobilize different interspecific response mechanisms. Fewer studies, however, have examined intraspecific responses to ectoparasitic burdens. In this study, we analyzed host health and fitness responses to increasing ectoparasite burdens along with the presence/absence of hemoparasites of free-ranging insular rock iguanas (Cyclura cychlura) in The Bahamas. Using hematology, plasma biochemistry, as well as body condition and growth rate comparisons, we failed to find significant associations of tick burdens with annual growth rate, corticosterone, packed cell volume, total white blood cell, and heterophil, …

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Dosage Compensation Of The X Chromosomes In Bovine Germline, Early Embryos, And Somatic Tissues, Zongliang Jiang Jan 2019

Dosage Compensation Of The X Chromosomes In Bovine Germline, Early Embryos, And Somatic Tissues, Zongliang Jiang

Faculty Publications

Dosage compensation of the mammalian X chromosome (X) was proposed by Susumu Ohno as a mechanism wherein the inactivation of one X in females would lead to doubling the expression of the other. This would resolve the dosage imbalance between eutherian females (XX) versus male (XY) and between a single active X versus autosome pairs (A). Expression ratio of X- and A-linked genes has been relatively well studied in humans and mice, despite controversial results over the existence of upregulation of X-linked genes. Here we report the first comprehensive test of Ohno's hypothesis in bovine preattachment embryos, germline, and somatic …

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