Contact Patterns Among Bighorn Sheep In and Around Glacier National Park

Identifying patterns of direct contacts among individual animals is important to understanding infectious disease transmission. Social behavior can be influenced by both intrinsic and extrinsic variables and can be explored at 3 levels: social network structure, dyad structure, and contact structure. We investigated drivers of contact structure using GPS locations of 87 male and female bighorn sheep (Ovis canadensis) in and around Glacier National Park in Montana, USA. Focusing on contacts between sheep moving separately, we examined relationships between contact locations and movement variables, land cover, distances to various resources, and variables known to influence survival using a resource selection function. Used and available points were defined as simultaneous locations within 25 m (the contact-used) and 13 km (largest step length- available) of another collared bighorn sheep, thus results of this analysis describe the strengths of these variables relative to habitat use. Data were analyzed separately according to dyad type (male-male, female-female, malefemale). Most contacts occurred in March for male-male and female-female dyads and in November, December, and January for male-female dyads. For male-male dyads, contacts occurred more than expected given habitat use in conifer land cover and locations farther from perennial water sources, high NDVI, little canopy cover, and low and high solar radiation index. For female-female dyads, contacts occurred less than expected given habitat use in grass and barren land cover and locations with intermediate terrain ruggedness, high NDVI, and low and high snow water equivalent. For male-female dyads, contacts occurred most during the night, least during the day, and at locations with intermediate elevation and farther from escape terrain. Together, these results suggest that more specific conditions apply to contact locations than general locations and that we can predict locations where contacts are most likely to occur, which may be useful for disease management

Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra- and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra- or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (Kd 3.4 ± 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape-based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed. Published by Wiley-Blackwell. © 2010 The Protein Society

Direct Determination of the Site of Addition of Glucosyl Units to Maltooligosaccharide Acceptors Catalyzed by Maize Starch Synthase I

Starch synthase (SS) (ADP-glucose:1,4-α-D-glucan 4-α-D-glucosyltransferase) elongates α-(1→4)-linked linear glucans within plastids to generate the storage polymers that constitute starch granules. Multiple SS classes are conserved throughout the plant kingdom, indicating that each provides a unique function responsible for evolutionary selection. Evidence has been presented arguing for addition of glucosyl units from the ADPglucose donor to either the reducing end or the non-reducing end of the acceptor substrate, although until recently direct evidence addressing this question was not available. Characterization of newly incorporated glucosyl units determined that recombinant maize (Zea mays L.) SSIIa elongates its substrates at the non-reducing end. However, the possibility remained that other SSs might utilize distinct mechanisms, and that one or more of the conserved enzyme classes could elongate acceptors at the reducing end. This study characterized the reaction mechanism of recombinant maize SSI regarding its addition site. Newly incorporated residues were labeled with 13C, and reducing ends of the elongation products were labeled by chemical derivitization. Electrospray ionization-tandem mass spectroscopy traced the two parameters, i.e., the newly added residue and the reducing end. The results determined that SSI elongates glucans at the non-reducing end. The study also confirmed previous findings showing recombinant SSI can generate glucans of at least 25 units, that it is active using acceptors as short as maltotriose, that recombinant forms of the enzyme absolutely require an acceptor for activity, and that it is not saturable with maltooligosaccharide acceptor substrates

Prevalence and Characteristics of Self-Reported Hypothyroidism and Its Association with Nonorgan-Specific Manifestations in US Sarcoidosis Patients: A Nationwide Registry Study

Little is known about the prevalence, clinical characteristics and impact of hypothyroidism in patients with sarcoidosis. We aimed to determine the prevalence and clinical features of hypothyroidism and its relation to organ involvement and other clinical manifestations in patients with sarcoidosis. We conducted a national registry-based study investigating 3835 respondents to the Sarcoidosis Advanced Registry for Cures Questionnaire between June 2014 and August 2019. This registry is based on a self-reported, web-based questionnaire that provides data related to demographics, diagnostics, sarcoidosis manifestations and treatment. We compared sarcoidosis patients with and without self-reported hypothyroidism. We used multivariable logistic regression and adjusted for potential confounders to determine the association of hypothyroidism with nonorgan-specific manifestations. 14% of the sarcoidosis patients self-reported hypothyroidism and were generally middle-aged white women. Hypothyroid patients had more comorbid conditions and were more likely to have multiorgan sarcoidosis involvement, especially with cutaneous, ocular, joints, liver and lacrimal gland involvement. Self-reported hypothyroidism was associated with depression (adjusted odds ratio (aOR) 1.3, 95% CI 1.01–1.6), antidepressant use (aOR 1.3, 95% CI 1.1–1.7), obesity (aOR 1.7, 95% CI 1.4–2.1), sleep apnoea (aOR 1.7, 95% CI 1.3–2.2), chronic fatigue syndrome (aOR 1.5, 95% CI 1.2–2) and was borderline associated with fibromyalgia (aOR 1.3, 95% CI 1–1.8). Physical impairment was more common in patients with hypothyroidism. Hypothyroidism is a frequent comorbidity in sarcoidosis patients that might be a potentially reversible contributor to fatigue, depression and physical impairment in this population. We recommend considering routine screening for hypothyroidism in sarcoidosis patients especially in those with multiorgan sarcoidosis, fatigue and depression

Industrial and Human Ruins of Post Communist Europe

With the former industrial cities of Eastern Europe in ruin - once the pillars of these former communist economies - the attention of both investors and academics has shifted towards capital cities and their political and economic potential fueled by the rise of new governments and foreign direct investment. The failed attempts to privatize many of these former industrial spaces, has left entire cities in ruin and despair, forgotten by all but artists and preservationists, who see these spaces not only as aesthetically inspiring but also as charged with redemptive potential. This article puts forward an alternative exploration of the Eastern European post-communist transition through these ruined spaces, arguing that the aesthetic dimension of change is key to understanding the human impact of the transition. Focusing on two former industrial sites – the Hunedoara Ironworks in Romania and the Vitkovice Ironworks in the Czech Republic, the article seeks to understand the rhetorical and material relationship between these ruined spaces and the workers who once inhabited them as well as the effect that different practices of representation – mainly photography - and preservation have had on these spaces

Association between plasma metabolites and gene expression profiles in five porcine endocrine tissues

Background: Endocrine tissues play a fundamental role in maintaining homeostasis of plasma metabolites such as non-esterified fatty acids and glucose, the levels of which reflect the energy balance or the health status of animals. However, the relationship between the transcriptome of endocrine tissues and plasma metabolites has been poorly studied. Methods: We determined the blood levels of 12 plasma metabolites in 27 pigs belonging to five breeds, each breed consisting of both females and males. The transcriptome of five endocrine tissues i.e. hypothalamus, adenohypophysis, thyroid gland, gonads and backfat tissues from 16 out of the 27 pigs was also determined. Sex and breed effects on the 12 plasma metabolites were investigated and associations between genes expressed in the five endocrine tissues and the 12 plasma metabolites measured were analyzed. A probeset was defined as a quantitative trait transcript (QTT) when its association with a particular metabolic trait achieved a nominal P value < 0.01. Results: A larger than expected number of QTT was found for non-esterified fatty acids and alanine aminotransferase in at least two tissues. The associations were highly tissue-specific. The QTT within the tissues were divided into co-expression network modules enriched for genes in Kyoto Encyclopedia of Genes and Genomes or gene ontology categories that are related to the physiological functions of the corresponding tissues. We also explored a multi-tissue co-expression network using QTT for non-esterified fatty acids from the five tissues and found that a module, enriched in hypothalamus QTT, was positioned at the centre of the entire multi-tissue network. Conclusions: These results emphasize the relationships between endocrine tissues and plasma metabolites in terms of gene expression. Highly tissue-specific association patterns suggest that candidate genes or gene pathways should be investigated in the context of specific tissues

Species-Specific and Inhibitor-Dependent Conformations of LpxC: Implications for Antibiotic Design

LpxC is an essential enzyme in the lipid A biosynthetic pathway in Gram-negative bacteria. Several promising antimicrobial lead compounds targeting LpxC have been reported, though they typically display a large variation in potency against different Gram-negative pathogens. We report that inhibitors with a diacetylene scaffold effectively overcome the resistance caused by sequence variation in the LpxC substrate-binding passage. Compound binding is captured in complex with representative LpxC orthologs, and structural analysis reveals large conformational differences that mostly reflect inherent molecular features of distinct LpxC orthologs, whereas ligand-induced structural adaptations occur at a smaller scale. These observations highlight the need for a molecular understanding of inherent structural features and conformational plasticity of LpxC enzymes for optimizing LpxC inhibitors as broad-spectrum antibiotics against Gram-negative infections

A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli.

Lipid A is a highly conserved component of lipopolysaccharide (LPS), itself a major component of the outer membrane of Gram-negative bacteria. Lipid A is essential to cells and elicits a strong immune response from humans and other animals. We developed a quantitative model of the nine enzyme-catalyzed steps of Escherichia coli lipid A biosynthesis, drawing parameters from the experimental literature. This model accounts for biosynthesis regulation, which occurs through regulated degradation of the LpxC and WaaA (also called KdtA) enzymes. The LpxC degradation signal appears to arise from the lipid A disaccharide concentration, which we deduced from prior results, model results, and new LpxK overexpression results. The model agrees reasonably well with many experimental findings, including the lipid A production rate, the behaviors of mutants with defective LpxA enzymes, correlations between LpxC half-lives and cell generation times, and the effects of LpxK overexpression on LpxC concentrations. Its predictions also differ from some experimental results, which suggest modifications to the current understanding of the lipid A pathway, such as the possibility that LpxD can replace LpxA and that there may be metabolic channeling between LpxH and LpxB. The model shows that WaaA regulation may serve to regulate the lipid A production rate when the 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) concentration is low and/or to control the number of KDO residues that get attached to lipid A. Computation of flux control coefficients showed that LpxC is the rate-limiting enzyme if pathway regulation is ignored, but that LpxK is the rate-limiting enzyme if pathway regulation is present, as it is in real cells. Control also shifts to other enzymes if the pathway substrate concentrations are not in excess. Based on these results, we suggest that LpxK may be a much better drug target than LpxC, which has been pursued most often

Defining Global Gene Expression Changes of the Hypothalamic-Pituitary-Gonadal Axis in Female sGnRH-Antisense Transgenic Common Carp (Cyprinus carpio)

BACKGROUND: The hypothalamic-pituitary-gonadal (HPG) axis is critical in the development and regulation of reproduction in fish. The inhibition of neuropeptide gonadotropin-releasing hormone (GnRH) expression may diminish or severely hamper gonadal development due to it being the key regulator of the axis, and then provide a model for the comprehensive study of the expression patterns of genes with respect to the fish reproductive system. METHODOLOGY/PRINCIPAL FINDINGS: In a previous study we injected 342 fertilized eggs from the common carp (Cyprinus carpio) with a gene construct that expressed antisense sGnRH. Four years later, we found a total of 38 transgenic fish with abnormal or missing gonads. From this group we selected the 12 sterile females with abnormal ovaries in which we combined suppression subtractive hybridization (SSH) and cDNA microarray analysis to define changes in gene expression of the HPG axis in the present study. As a result, nine, 28, and 212 genes were separately identified as being differentially expressed in hypothalamus, pituitary, and ovary, of which 87 genes were novel. The number of down- and up-regulated genes was five and four (hypothalamus), 16 and 12 (pituitary), 119 and 93 (ovary), respectively. Functional analyses showed that these genes involved in several biological processes, such as biosynthesis, organogenesis, metabolism pathways, immune systems, transport links, and apoptosis. Within these categories, significant genes for neuropeptides, gonadotropins, metabolic, oogenesis and inflammatory factors were identified. CONCLUSIONS/SIGNIFICANCE: This study indicated the progressive scaling-up effect of hypothalamic sGnRH antisense on the pituitary and ovary receptors of female carp and provided comprehensive data with respect to global changes in gene expression throughout the HPG signaling pathway, contributing towards improving our understanding of the molecular mechanisms and regulative pathways in the reproductive system of teleost fish