bluuebunny/crossref_metadata_2025 huggingface dataset:
Poverty, Place, and Coal Employment across Appalachia and the United States in a New Economic Era
Authors: Lobao Linda , Zhou Minyu , Partridge Mark , Betz Michael
Published: March 2016

The impacts of employment in the coal industry remain controversial. Few studies have investigated these impacts over the decade of the great recession and in light of the nation's changing energy economy. We bring together two long‐standing rural sociological traditions to address debates framed at the national level and for Appalachian communities facing the throes of transition from the coal industry. Building from rural sociology's “poverty and place” tradition and from natural resources sociology, we examine the relationship between coal employment and communities’ economic well‐being as indicated by poverty, household income, and unemployment. The study spans U.S. and Appalachian counties from 1990 to 2010. U.S. counties with greater coal employment in 1990 had lower income and higher poverty in 2000. Overall, however, coal employment's effect is mixed in the 1990–2000 decade. By contrast, for the recent 2000–2010 decade, coal employment is positively associated with indicators of well‐being. In Appalachia, fewer employment alternatives outside mining are related to higher well‐being. Our findings extend the poverty and place literature and the natural resources literature and underscore why a just transition away from coal should focus on moving communities toward sectors offering better future livelihoods.
B and T Cell Epitope‐Based Peptides Predicted from Evolutionarily Conserved and Whole Protein Sequences of Ebola Virus as Vaccine Targets
Authors: Yasmin T. , Nabi A. H. M. Nurun
Published: March 2016

Ebola virus (EBV) has become a serious threat to public health. Different approaches were applied to predict continuous and discontinuous B cell epitopes as well as T cell epitopes from the sequence‐based and available three‐dimensional structural analyses of each protein of EBV. Peptides ‘79VPSATKRWGFRSGVPP94’ from GP1 and ‘515LHYWTTQDEGAAIGLA530’ from GP2 of Ebola were found to be the consensus peptidic sequences predicted as linear B cell epitope of which the latter contains a region 519TTQDEG524 that fulfilled all the criteria of accessibility, hydrophilicity, flexibility and beta turn region for becoming an ideal B cell epitope. Different nonamers as T cell epitopes were obtained that interacted with different numbers of MHC class I and class II alleles with a binding affinity of <100 nm. Interestingly, these alleles also bound to the MHC class I alleles mostly prevalent in African and South Asian regions. Of these, ‘LANETTQAL’ and ‘FLYDRLAST’ nonamers were predicted to be the most potent T cell epitopes and they, respectively, interacted with eight and twelve class I alleles that covered 63.79% and 54.16% of world population, respectively. These nonamers were found to be the core sequences of 15mer peptides that interacted with the most common class II allele, HLA‐DRB1*01:01. They were further validated for their binding to specific class I alleles using docking technique. Thus, these predicted epitopes may be used as vaccine targets against EBV and can be validated in model hosts to verify their efficacy as vaccine.
“Taking Back a Little Bit of Control”: Managing the Contaminated Body Through Consumption
Authors: MacKendrick Norah , Stevens Lindsay M.
Published: March 2016

In this article, we explore the lived experience of avoiding environmental chemicals through safer consumption, such as buying “eco‐friendly” products. Using focus groups and in‐depth interviews involving 50 subjects, we investigate how individuals become aware of environmental chemicals and how they adapt to this awareness. Our participants describe being surprised or alarmed to learn that chemicals are present in food and commodities that they believed were safe. They respond by developing a set of heuristics rendering the “dangerous” consumer landscape into a space that is amenable to personal control. They learn to read an ingredient label and look for organic certification seals on product packaging. We develop the idea of the “contingent boundary” to describe how participants perceive personal control as uneven: they believe they can activate a protective boundary in local and familiar contexts, but outside these contexts, they believe the boundary dissolves. They accept this contingency as normal and describe having to ignore some chemical exposures, for fear of becoming too “crazy.” We conclude that the individuals in our study accept that inverted quarantine (Szasz 2007) is out of reach, and instead try to impose order upon a ubiquitous risk.
Gender, Field, and Habitus: How Gendered Dispositions Reproduce Fields of Cultural Production
Authors: Miller Diana L.
Published: March 2016

Bourdieu argues that fields of action produce a specific habitus in participants, and views this specific habitus as a mechanism through which the field is reproduced. Although Bourdieu acknowledges the habitus as gendered, he does not theorize gender as part of the mutually constitutive relationship between field and habitus. Using evidence from two cultural fields, the Toronto heavy metal and folk music scenes, I show that gender is central to the process through which field and habitus sustain each other. The metal field produces a “metalhead habitus” that privileges gender performances centered on individual dominance and status competition. In contrast, the “folkie habitus” encourages gender performances centered on caring, emotional relations with others, and community‐building. These differently gendered habitus support different working conventions: music production occurs largely through volunteer‐based nonprofit organizations in the folk field, and individual entrepreneurship in the metal field. The gendered habitus also supports different stylistic conventions: guitar virtuosity in the metal field, and participatory music‐making in folk. Applying a gendered lens to the field–habitus relationship clarifies the mechanisms through which cultural fields shape individual action, and the mechanisms through which cultural fields are reproduced and maintained.
The Missing Organizational Dimension of Prisoner Reentry: An Ethnography of the Road to Reentry at a Nonprofit Service Provider
Authors: Mijs Jonathan J. B.
Published: March 2016

Prisoner reentry has received great interest in political sociology, criminology, and beyond. Research documents the struggles of individuals trying to find their way back into society. Less attention has been given to the organizational aspects of reentry. This is unfortunate given the rapid growth of nonprofit reentry organizations in the United States, which introduces a new set of questions about the context and challenges to prisoner reentry. Drawing on an ethnography of Safe, a nonprofit reentry organization in the Northeast, I describe the organization's pivotal role in institutionalizing the pathway to prisoner reentry: a road to reentry, which takes former prisoners through a process that reconfigures their morality, identity, and social relationships. The road‐to‐reentry concept helps bring together scholars of the welfare state and criminology by highlighting how the challenges of prisoner reentry rely on how this process is organized. The way in which prison reentry is organized, in turn, affects former prisoners’ agency and shapes the relationship between these men and women and their respective families and communities.
Sacral nerve stimulation enhances early intestinal mucosal repair following mucosal injury in a pig model
Authors: Brégeon Jérémy , Coron Emmanuel , Da Silva Anna Christina Cordeiro , Jaulin Julie , Aubert Philippe , Chevalier Julien , Vergnolle Nathalie , Meurette Guillaume , Neunlist Michel
Published: March 2016

Key points

Reducing intestinal epithelial barrier (IEB) dysfunctions is recognized as being of major therapeutic interest for various intestinal disorders.

Sacral nerve stimulation (SNS) is known to reduce IEB permeability.

Here, we report in a pig model that SNS enhances morphological and functional recovery of IEB following mucosal injury induced via 2,4,6‐trinitrobenzenesulfonic acid. These effects are associated with an increased expression of tight junction proteins such as ZO‐1 and FAK.

These results establish that SNS enhances intestinal barrier repair in acute mucosal injury. They further set the scientific basis for future use of SNS as a complementary or alternative therapeutic option for the treatment of gut disorders with IEB dysfunctions such as inflammatory bowel diseases or irritable bowel syndrome.

Intestinal epithelial barrier (IEB) dysfunctions, such as increased permeability or altered healing, are central to intestinal disorders. Sacral nerve stimulation (SNS) is known to reduce IEB permeability, but its ability to modulate IEB repair remains unknown. This study aimed to characterize the impact of SNS on mucosal repair following 2,4,6‐trinitrobenzenesulfonic acid (TNBS)‐induced lesions. Six pigs were stimulated by SNS 3 h prior to and 3 h after TNBS enema, while sham animals (n = 8) were not stimulated. The impact of SNS on mucosal changes was evaluated by combining in vivo imaging, histological and functional methods. Biochemical and transcriptomic approaches were used to analyse the IEB and mucosal inflammatory response. We observed that SNS enhanced the recovery from TNBS‐induced increase in transcellular permeability. At 24 h, TNBS‐induced alterations of mucosal morphology were significantly less in SNS compared with sham animals. SNS reduced TNBS‐induced changes in ZO‐1 expression and its epithelial pericellular distribution, and also increased pFAK/FAK expression compared with sham. Interestingly, SNS increased the mucosal density of neutrophils, which was correlated with an increase in trypsin and TGF‐β1 levels compared with sham. Finally, SNS prevented the TNBS‐induced increases in IL‐1β and IL‐4 over time that were observed with sham treatment. In conclusion, our results show that SNS enhances mucosal repair following injury. This study highlights novel mechanisms of action of SNS and identifies SNS as a new therapy for diseases with IEB repair disorders.
The mechanistic bases of the power–time relationship: muscle metabolic responses and relationships to muscle fibre type
Authors: Vanhatalo Anni , Black Matthew I. , DiMenna Fred J. , Blackwell Jamie R. , Schmidt Jakob Friis , Thompson Christopher , Wylie Lee J. , Mohr Magni , Bangsbo Jens , Krustrup Peter , Jones Andrew M.
Published: March 2016

Key points

The power‐asymptote (critical power; CP) of the hyperbolic power–time relationship for high‐intensity exercise defines a threshold between steady‐state and non‐steady‐state exercise intensities and the curvature constant (W′) indicates a fixed capacity for work >CP that is related to a loss of muscular efficiency.

The present study reports novel evidence on the muscle metabolic underpinnings of CP and W′ during whole‐body exercise and their relationships to muscle fibre type.

We show that the W′ is not correlated with muscle fibre type distribution and that it represents an elevated energy contribution from both oxidative and glycolytic/glycogenolytic metabolism.

We show that there is a positive correlation between CP and highly oxidative type I muscle fibres and that muscle metabolic steady‐state is attainable CP.

Our findings indicate a mechanistic link between the bioenergetic characteristics of muscle fibre types and the power–time relationship for high‐intensity exercise.

We hypothesized that: (1) the critical power (CP) will represent a boundary separating steady‐state from non‐steady‐state muscle metabolic responses during whole‐body exercise and (2) that the CP and the curvature constant (W′) of the power–time relationship for high‐intensity exercise will be correlated with type I and type IIx muscle fibre distributions, respectively. Four men and four women performed a 3 min all‐out cycling test for the estimation of CP and constant work rate (CWR) tests slightly >CP until exhaustion (Tlim), slightly CP Tlim isotime to test the first hypothesis. Eleven men performed 3 min all‐out tests and donated muscle biopsies to test the second hypothesis. Below CP, muscle [PCr] [42.6 ± 7.1 vs. 49.4 ± 6.9 mmol (kg d.w.)−1], [La−] [34.8 ± 12.6 vs. 35.5 ± 13.2 mmol (kg d.w.)−1] and pH (7.11 ± 0.08 vs. 7.10 ± 0.11) remained stable between ∼12 and 24 min (P > 0.05 for all), whereas these variables changed with time >CP such that they were greater [[La−] 95.6 ± 14.1 mmol (kg d.w.)−1] and lower [[PCr] 24.2 ± 3.9 mmol (kg d.w.)−1; pH 6.84 ± 0.06] (P < 0.05) at Tlim (740 ± 186 s) than during the <CP trial. The CP (234 ± 53 W) was correlated with muscle type I (r = 0.67, P = 0.025) and inversely correlated with muscle type IIx fibre proportion (r = −0.76, P = 0.01). There was no relationship between W′ (19.4 ± 6.3 kJ) and muscle fibre type. These data indicate a mechanistic link between the bioenergetic characteristics of different muscle fibre types and the power–duration relationship. The CP reflects the bioenergetic characteristics of highly oxidative type I muscle fibres, such that a muscle metabolic steady‐state is attainable below and not above CP.
Single cell transcriptome analysis of mouse carotid body glomus cells
Authors: Zhou Ting , Chien Ming‐Shan , Kaleem Safa , Matsunami Hiroaki
Published: March 2016

Key points

Carotid body (CB) glomus cells mediate acute oxygen sensing and the initiation of the hypoxic ventilatory response, yet the gene expression profile of these cells is not available.

We demonstrate that the single cell RNA‐Seq method is a powerful tool for identifying highly expressed genes in CB glomus cells.

Our single cell RNA‐Seq results characterized novel CB glomus cell genes, including members of the G protein‐coupled receptor signalling pathway, ion channels and atypical mitochondrial electron transport chain subunits.

A heterologous cell‐based screening identified acetate (which is known to affect CB glomus cell activity) as an agonist for the most highly abundant G protein‐coupled receptor (Olfr78) in CB glomus cells.

These data established the first transcriptome profile of CB glomus cells, highlighting genes with potential implications in CB chemosensory function.

The carotid body (CB) is a major arterial chemoreceptor containing glomus cells whose activities are regulated by changes in arterial blood content, including oxygen. Despite significant advancements in the characterization of their physiological properties, our understanding of the underlying molecular machinery and signalling pathway in CB glomus cells is still limited. To overcome this, we employed the single cell RNA­Seq method by performing next‐generation sequencing on single glomus cell­derived cDNAs to eliminate contamination of genes derived from other cell types present in the CB. Using this method, we identified a set of genes abundantly expressed in glomus cells, which contained novel glomus cell‐specific genes. Transcriptome and subsequent in situ hybridization and immunohistochemistry analyses identified abundant G protein‐coupled receptor signalling pathway components and various types of ion channels, as well as members of the hypoxia‐inducible factors pathway. A short‐chain fatty acid olfactory receptor Olfr78, recently implicated in CB function, was the most abundant G protein‐coupled receptor. Two atypical mitochondrial electron transport chain subunits (Ndufa4l2 and Cox4i2) were among the most specifically expressed genes in CB glomus cells, highlighting their potential roles in mitochondria‐mediated oxygen sensing. The wealth of information provided by the present study offers a valuable foundation for identifying molecules functioning in the CB.
Experimental and Numerical Investigation of the Flow Inside the Return Channel of a Centrifugal Process Compressor
Authors: Rube C. , Rossbach T. , Wedeking M. , Grates D. R. , Jeschke P.
Published: March 2016

This paper presents the first detailed experimental performance data for a new centrifugal process compressor test rig. Additional numerical simulations supported by extensive pressure measurements at various positions allow an analysis of the operational and loss behavior of the entire stage and its components. The stage investigated is a high flow rate stage of a single-shaft, multistage compressor for industrial applications and consists of a shrouded impeller, a vaneless diffuser, a U-bend, and an adjoining vaned return channel. Large channel heights due to high flow rates induce the formation of highly three-dimensional flow phenomena and thus enlarge the losses due to secondary flows. An accurate prediction of this loss behavior by means of numerical investigations is challenging. The published experimental data offer the opportunity to validate the used numerical methods at discrete measurement planes, which strengthens confidence in the numerical predictions. CFD simulations of the stage are initially validated with global performance data and extensive static pressure measurements in the vaneless diffuser. The comparison of the pressure rise and an estimation of the loss behavior inside the vaneless diffuser provide the basis for a numerical investigation of the flow phenomena in the U-bend and the vaned return channel. The flow acceleration in the U-bend is further assessed via the measured two-dimensional pressure field on the hub wall. The upstream potential field of the return channel vanes allows an evaluation of the resulting flow angle. Measurements within the return channel provide information about the deceleration and turning of the flow. In combination with the numerical simulations, loss mechanisms can be identified and are presented in detail in this paper.
Mismatched partners that achieve postpairing behavioral similarity improve their reproductive success
Authors: Laubu Chloé , Dechaume-Moncharmont François-Xavier , Motreuil Sébastien , Schweitzer Cécile
Published: March 2016

In the monogamous convict cichlid, mismatched partners become better parents by adjusting their behaviors to each other.
Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards
Authors: Daza Juan D. , Stanley Edward L. , Wagner Philipp , Bauer Aaron M. , Grimaldi David A.
Published: March 2016

Exquisitely preserved fossil lizards from 99-million-year-old Burmese amber provide new insights into paleotropical diversity.
Quantitative determination of pairing interactions for high-temperature superconductivity in cuprates
Authors: Bok Jin Mo , Bae Jong Ju , Choi Han-Yong , Varma Chandra M. , Zhang Wentao , He Junfeng , Zhang Yuxiao , Yu Li , Zhou X. J.
Published: March 2016

The extracted pairing interactions responsible for high-temperature superconductivity lead to a clear discrimination among theories.
Origin of uranium isotope variations in early solar nebula condensates
Authors: Tissot François L. H. , Dauphas Nicolas , Grossman Lawrence
Published: March 2016

Research shows that
247
Cm was present in meteorites at a level consistent with a single stellar environment of
r
-process nucleosynthesis.
Host-parasite Red Queen dynamics with phase-locked rare genotypes
Authors: Rabajante Jomar F. , Tubay Jerrold M. , Ito Hiromu , Uehara Takashi , Kakishima Satoshi , Morita Satoru , Yoshimura Jin , Ebert Dieter
Published: March 2016

Red Queen dynamics are observed in selected genotypes, whereas the rest of the genotypes remain subordinate in synchronized dynamics.
RETRACTED: A universal cooperative assembly-directed method for coating of mesoporous TiO
2
nanoshells with enhanced lithium storage properties
Authors: Guan Bu Yuan , Yu Le , Li Ju , Lou Xiong Wen (David)
Published: March 2016

A universal cooperative assembly method is developed for growing mesostructured TiO
2
shells on diverse functional particles.
Influence of Low-Shear Modeled Microgravity on Heat Resistance, Membrane Fatty Acid Composition, and Heat Stress-Related Gene Expression in Escherichia coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895
Authors: Kim H. W. , Rhee M. S.
Published: March 2016

We previously showed that modeled microgravity conditions alter the physiological characteristics of
Escherichia coli
O157:H7. To examine how microgravity conditions affect bacterial heat stress responses, D values, membrane fatty acid composition, and heat stress-related gene expression (
clpB
,
dnaK
,
grpE
,
groES
,
htpG
,
htpX
,
ibpB
, and
rpoH
),
E. coli
O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895 were cultured under two different conditions: low-shear modeled microgravity (LSMMG, an analog of spaceflight conditions) and normal gravity (NG, Earth-like conditions). When 24-h cultures were heated to 55°C, cells cultured under LSMMG conditions showed reduced survival compared with cells cultured under NG conditions at all time points (
P
< 0.05). D values of all tested strains were lower after LSMMG culture than after NG culture. Fourteen of 37 fatty acids examined were present in the bacterial membrane: nine saturated fatty acids (SFA) and five unsaturated fatty acids (USFA). The USFA/SFA ratio, a measure of membrane fluidity, was higher under LSMMG conditions than under NG conditions. Compared with control cells grown under NG conditions, cells cultured under LSMMG conditions showed downregulation of eight heat stress-related genes (average, −1.9- to −3.7-fold). The results of this study indicate that in a simulated space environment, heat resistance of
E. coli
O157:H7 decreased, and this might be due to the synergistic effects of the increases in membrane fluidity and downregulated relevant heat stress genes.

IMPORTANCE
Microgravity is a major factor that represents the environmental conditions in space. Since infectious diseases are difficult to deal with in a space environment, comprehensive studies on the behavior of pathogenic bacteria under microgravity conditions are warranted. This study reports the changes in heat stress resistance of
E. coli
O157:H7, the severe foodborne pathogen, under conditions that mimic microgravity. The results provide scientific clues for further understanding of the bacterial response under the simulated microgravity conditions. It will contribute not only to the improvement of scientific knowledge in the academic fields but also ultimately to the development of a prevention strategy for bacterial disease in the space environment.
Transcriptional Repression of the VC2105 Protein by Vibrio FadR Suggests that It Is a New Auxiliary Member of the
fad
Regulon
Authors: Gao Rongsui , Lin Jingxia , Zhang Han , Feng Youjun
Published: March 2016

Recently, our group along with others reported that the
Vibrio
FadR regulatory protein is unusual in that, unlike the prototypical
fadR
product of
Escherichia coli
, which has only one ligand-binding site,
Vibrio
FadR has two ligand-binding sites and represents a new mechanism for fatty acid sensing. The promoter region of the
vc2105
gene, encoding a putative thioesterase, was mapped, and a putative FadR-binding site (AA CTG GTA AGA GCA CTT) was proposed. Different versions of the FadR regulatory proteins were prepared and purified to homogeneity. Both electrophoretic mobility shift assay (EMSA) and surface plasmon resonance (SPR) determined the direct interaction of the
vc2105
gene with FadR proteins of various origins. Further, EMSAs illustrated that the addition of long-chain acyl-coenzyme A (CoA) species efficiently dissociates the
vc2105
promoter from the FadR regulator. The expression level of the
Vibrio cholerae vc2105
gene was elevated 2- to 3-fold in a
fadR
null mutant strain, validating that FadR is a repressor for the
vc2105
gene. The β-galactosidase activity of a
vc2105-lacZ
transcriptional fusion was increased over 2-fold upon supplementation of growth medium with oleic acid. Unlike the
fadD
gene, a member of the
Vibrio fad
regulon, the VC2105 protein played no role in bacterial growth and virulence-associated gene expression of
ctxAB
(cholera toxin A/B) and
tcpA
(toxin coregulated pilus A). Given that the transcriptional regulation of
vc2105
fits the criteria for fatty acid degradation (
fad
) genes, we suggested that it is a new member of the
Vibrio fad
regulon.

IMPORTANCE
The
Vibrio
FadR regulator is unusual in that it has two ligand-binding sites. Different versions of the FadR regulatory proteins were prepared and characterized
in vitro
and
in vivo
. An auxiliary
fad
gene (
vc2105
) from
Vibrio
was proposed that encodes a putative thioesterase and has a predicted FadR-binding site (AAC TGG TA A GAG CAC TT). The function of this putative binding site was proved using both EMSA and SPR. Further
in vitro
and
in vivo
experiments revealed that the
Vibrio
FadR is a repressor for the
vc2105
gene. Unlike
fadD
, a member of the
Vibrio fad
regulon, VC2105 played no role in bacterial growth and expression of the two virulence-associated genes (
ctxAB
and
tcpA
). Therefore, since transcriptional regulation of
vc2105
fits the criteria for
fad
genes, it seems likely that
vc2105
acts as a new auxiliary member of the
Vibrio fad
regulon.
Diversity of Clinical and Environmental Isolates of Vibrio cholerae in Natural Transformation and Contact-Dependent Bacterial Killing Indicative of Type VI Secretion System Activity
Authors: Bernardy Eryn E. , Turnsek Maryann A. , Wilson Sarah K. , Tarr Cheryl L. , Hammer Brian K.
Published: March 2016

The bacterial pathogen
Vibrio cholerae
can occupy both the human gut and aquatic reservoirs, where it may colonize chitinous surfaces that induce the expression of factors for three phenotypes: chitin utilization, DNA uptake by natural transformation, and contact-dependent bacterial killing via a type VI secretion system (T6SS). In this study, we surveyed a diverse set of 53 isolates from different geographic locales collected over the past century from human clinical and environmental specimens for each phenotype outlined above. The set included pandemic isolates of serogroup O1, as well as several serogroup O139 and non-O1/non-O139 strains. We found that while chitin utilization was common, only 22.6% of the isolates tested were proficient at chitin-induced natural transformation, suggesting that transformation is expendable. Constitutive contact-dependent killing of
Escherichia coli
prey, which is indicative of a functional T6SS, was rare among clinical isolates (only 4 of 29) but common among environmental isolates (22 of 24). These results bolster the pathoadaptive model in which tight regulation of T6SS-mediated bacterial killing is beneficial in a human host, whereas constitutive killing by environmental isolates may give a competitive advantage in natural settings. Future sequence analysis of this set of diverse isolates may identify previously unknown regulators and structural components for both natural transformation and T6SS.
Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104
Authors: Leekitcharoenphon Pimlapas , Hendriksen Rene S. , Le Hello Simon , Weill François-Xavier , Baggesen Dorte Lau , Jun Se-Ran , Ussery David W. , Lund Ole , Crook Derrick W. , Wilson Daniel J. , Aarestrup Frank M.
Published: March 2016

It has been 30 years since the initial emergence and subsequent rapid global spread of multidrug-resistant
Salmonella enterica
serovar Typhimurium DT104 (MDR DT104). Nonetheless, its origin and transmission route have never been revealed. We used whole-genome sequencing (WGS) and temporally structured sequence analysis within a Bayesian framework to reconstruct temporal and spatial phylogenetic trees and estimate the rates of mutation and divergence times of 315
S
. Typhimurium DT104 isolates sampled from 1969 to 2012 from 21 countries on six continents. DT104 was estimated to have emerged initially as antimicrobial susceptible in ∼1948 (95% credible interval [CI], 1934 to 1962) and later became MDR DT104 in ∼1972 (95% CI, 1972 to 1988) through horizontal transfer of the 13-kb
Salmonella
genomic island 1 (SGI1) MDR region into susceptible strains already containing SGI1. This was followed by multiple transmission events, initially from central Europe and later between several European countries. An independent transmission to the United States and another to Japan occurred, and from there MDR DT104 was probably transmitted to Taiwan and Canada. An independent acquisition of resistance genes took place in Thailand in ∼1975 (95% CI, 1975 to 1990). In Denmark, WGS analysis provided evidence for transmission of the organism between herds of animals. Interestingly, the demographic history of Danish MDR DT104 provided evidence for the success of the program to eradicate
Salmonella
from pig herds in Denmark from 1996 to 2000. The results from this study refute several hypotheses on the evolution of DT104 and suggest that WGS may be useful in monitoring emerging clones and devising strategies for prevention of
Salmonella
infections.
In Situ
Biomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine
Authors: Li Xiaobao , Chopp David L. , Russin William A. , Brannon Paul T. , Parsek Matthew R. , Packman Aaron I.
Published: March 2016

Microbial biofilms and mineral precipitation commonly co-occur in engineered water systems, such as cooling towers and water purification systems, and both decrease process performance. Microbial biofilms are extremely challenging to control and eradicate. We previously showed that
in situ
biomineralization and the precipitation and deposition of abiotic particles occur simultaneously in biofilms under oversaturated conditions. Both processes could potentially alter the essential properties of biofilms, including susceptibility to biocides. However, the specific interactions between mineral formation and biofilm processes remain poorly understood. Here we show that the susceptibility of biofilms to chlorination depends specifically on internal transport processes mediated by biomineralization and the accumulation of abiotic mineral deposits. Using injections of the fluorescent tracer Cy5, we show that
Pseudomonas aeruginosa
biofilms are more permeable to solutes after
in situ
calcite biomineralization and are less permeable after the deposition of abiotically precipitated calcite particles. We further show that biofilms are more susceptible to chlorine killing after biomineralization and less susceptible after particle deposition. Based on these observations, we found a strong correlation between enhanced solute transport and chlorine killing in biofilms, indicating that biomineralization and particle deposition regulate biofilm susceptibility by altering biocide penetration into the biofilm. The distinct effects of
in situ
biomineralization and particle deposition on biocide killing highlight the importance of understanding the mechanisms and patterns of biomineralization and scale formation to achieve successful biofilm control.
Chemistry of developing bordered-pit rims in balsam-fir trees
Authors: Savidge Rodney Arthur
Published: March 2016

Rims of bordered pits form on the primary walls of radially enlarged cambial derivatives prior to the onset of general secondary-wall formation. A recent report (Botany, 2014, 92(7): 495–511) raised the possibility that the chemical composition of the rim might be different from that of the secondary wall. To investigate this, early-stage nonfluorescent and late-stage autofluorescent rims were separated from cambial derivatives of Abies balsamea (L.) Mill. and purified to homogeneity by density-gradient centrifugation. Solid state nuclear magnetic resonance spectroscopy, Raman microspectroscopy, combined gas chromatography – mass spectroscopy, enzyme digestion, and chemical resilience data support the interpretation that cellulose alone is the microfibrillar polysaccharide of nonfluorescent early-stage rims. A lignin is additionally present in late-stage rims, and it evidently bonds with cellulose because rims are extraordinarily resistant to hydrolysis by either enzymes or strong acid.
A proteomic approach towards understanding the cross talk between Bacteroides fragilis and Bifidobacterium longum in coculture
Authors: Rios-Covián David , Sánchez Borja , Martínez Noelia , Cuesta Isabel , Hernández-Barranco Ana M. , de los Reyes-Gavilán Clara G. , Gueimonde Miguel
Published: March 2016

A better understanding of the interactions among intestinal microbes is needed to decipher the complex cross talk that takes place within the human gut. Bacteroides and Bifidobacterium genera are among the most relevant intestinal bacteria, and it has been previously reported that coculturing of these 2 microorganisms affects their survival. Therefore, coculturing of Bifidobacterium longum NB667 and Bacteroides fragilis DSMZ2151 was performed with the aim of unravelling the mechanisms involved in their interaction. To this end, we applied proteomic (2D-DIGE) analyses, and by chromatographic techniques we quantified the bacterial metabolites produced during coincubation. Coculture stimulated the growth of B. longum, retarding that of B. fragilis, with concomitant changes in the production of some proteins and metabolites of both bacteria. The combined culture promoted upregulation of the bifidobacterial pyruvate kinase and downregulation of the Bacteroides phosphoenolpyruvate carboxykinase — 2 enzymes involved in the catabolism of carbohydrates. Moreover, B. fragilis FKBP-type peptidyl-prolyl cis–trans isomerase, a protein with chaperone-like activity, was found to be overproduced in coculture, suggesting the induction of a stress response in this microorganism. This study provides mechanistic data to deepen our understanding of the interaction between Bacteroides and Bifidobacterium intestinal populations.
Abdominal fat reducing outcome of exercise training: fat burning or hydrocarbon source redistribution?
Authors: Kuo Chia-Hua , Harris M. Brennan
Published: March 2016

Fat burning, defined by fatty acid oxidation into carbon dioxide, is the most described hypothesis to explain the actual abdominal fat reducing outcome of exercise training. This hypothesis is strengthened by evidence of increased whole-body lipolysis during exercise. As a result, aerobic training is widely recommended for obesity management. This intuition raises several paradoxes: first, both aerobic and resistance exercise training do not actually elevate 24 h fat oxidation, according to data from chamber-based indirect calorimetry. Second, anaerobic high-intensity intermittent training produces greater abdominal fat reduction than continuous aerobic training at similar amounts of energy expenditure. Third, significant body fat reduction in athletes occurs when oxygen supply decreases to inhibit fat burning during altitude-induced hypoxia exposure at the same training volume. Lack of oxygen increases post-meal blood distribution to human skeletal muscle, suggesting that shifting the postprandial hydrocarbons towards skeletal muscle away from adipose tissue might be more important than fat burning in decreasing abdominal fat. Creating a negative energy balance in fat cells due to competition of skeletal muscle for circulating hydrocarbon sources may be a better model to explain the abdominal fat reducing outcome of exercise than the fat-burning model.
The protective effect of trimetazidine against cisplatin-induced nephrotoxicity in rats
Authors: El-Sherbeeny Nagla A. , Attia Ghalia M.
Published: March 2016

Nephrotoxicity is a dose-limiting side effect of cisplatin (CSP). The study investigated the possible protective role of trimetazidine (TMZ) against CSP-induced nephrotoxicity in rats. Rats were divided into four groups; control, TMZ, CSP, and CSP + TMZ. The CSP group showed significant deterioration in kidney function with structural changes in the form of interstitial hemorrhage, glomeruli shrinkage and peritublar capillary congestion, tubular cells vacuolation, pyknosis, shedding and necrosis, and inflammatory cell infiltrates, all indicating renal damage. CSP also caused a significant increase in the lipid peroxidation marker malondialdehyde (MDA) levels, renal nuclear factor kappa B (NF-κB) DNA-binding activity and protein expression, and tumor necrosis factor alpha (TNF-α) and IL-6 levels. Treatment with TMZ before and after CSP injection produced significant improvement of kidney function and histopathology. TMZ treatment also significantly attenuated CSP-induced oxidative stress and suppressed elevated levels of TNF-α and IL-6 and NF-κB expression and its DNA-binding activity caused by CSP administration. TMZ has a protective effect against CSP-induced nephrotoxicity mediated by reduction of oxidative stress and attenuation of CSP-induced inflammation.
Piceatannol increases the expression of hepatocyte growth factor and IL-10 thereby protecting hepatocytes in thioacetamide-induced liver fibrosis
Authors: Abd-Elgawad Hazem , Abu-Elsaad Nashwa , El-Karef Amr , Ibrahim Tarek
Published: March 2016

Piceatannol is a polyphenolic analog of resveratrol that selectively inhibits the non-receptor tyrosine kinase-Syk. This study investigates the potential ability of piceatannol to attenuate liver fibrosis and protect hepatocytes from injury. Thioacetamide was injected in adult male mice (100 mg/kg, i.p., 3 times/week) for 8 weeks. Piceatannol (1 or 5 mg/kg per day) was administered by oral gavage during the last 4 weeks. Liver function biomarkers, tissue malondialdehyde (MDA), cytokeratin-18 (CK18), hepatocyte growth factor (HGF), and interleukin-10 (IL-10) were measured. Necroinflammation, fibrosis, expression of transforming growth factor (TGF)-β1, and α-smooth muscle actin (SMA) were scored by histopathological examination and immunohistochemistry. Obtained results showed ability of piceatannol (1 mg/kg) to restore liver function and reduce inflammation. It significantly (p < 0.001) reduced MDA, CK18, TGF-β1, and α-SMA expression, and increased HGF and IL-10. It can be concluded that piceatannol at low dose can inhibit TGF-β1 induced hepatocytes apoptosis and exerts an anti-inflammatory effect attenuating fibrosis progression.
Depolarization of mitochondria in neurons promotes activation of nitric oxide synthase and generation of nitric oxide
Authors: Katakam Prasad V. G. , Dutta Somhrita , Sure Venkata N. , Grovenburg Samuel M. , Gordon Angellica O. , Peterson Nicholas R. , Rutkai Ibolya , Busija David W.
Published: March 2016

The diverse signaling events following mitochondrial depolarization in neurons are not clear. We examined for the first time the effects of mitochondrial depolarization on mitochondrial function, intracellular calcium, neuronal nitric oxide synthase (nNOS) activation, and nitric oxide (NO) production in cultured neurons and perivascular nerves. Cultured rat primary cortical neurons were studied on 7–10 days in vitro, and endothelium-denuded cerebral arteries of adult Sprague-Dawley rats were studied ex vivo. Diazoxide and BMS-191095 (BMS), activators of mitochondrial KATPchannels, depolarized mitochondria in cultured neurons and increased cytosolic calcium levels. However, the mitochondrial oxygen consumption rate was unaffected by mitochondrial depolarization. In addition, diazoxide and BMS not only increased the nNOS phosphorylation at positive regulatory serine 1417 but also decreased nNOS phosphorylation at negative regulatory serine 847. Furthermore, diazoxide and BMS increased NO production in cultured neurons measured with both fluorescence microscopy and electron spin resonance spectroscopy, which was sensitive to inhibition by the selective nNOS inhibitor 7-nitroindazole (7-NI). Diazoxide also protected cultured neurons against oxygen-glucose deprivation, which was blocked by NOS inhibition and rescued by NO donors. Finally, BMS induced vasodilation of endothelium denuded, freshly isolated cerebral arteries that was diminished by 7-NI and tetrodotoxin. Thus pharmacological depolarization of mitochondria promotes activation of nNOS leading to generation of NO in cultured neurons and endothelium-denuded arteries. Mitochondrial-induced NO production leads to increased cellular resistance to lethal stress by cultured neurons and to vasodilation of denuded cerebral arteries.
Extracellular sodium dependence of the conduction velocity-calcium relationship: evidence of ephaptic self-attenuation
Authors: George Sharon A. , Bonakdar Mohammad , Zeitz Michael , Davalos Rafael V. , Smyth James W. , Poelzing Steven
Published: March 2016

Our laboratory previously demonstrated that perfusate sodium and potassium concentrations can modulate cardiac conduction velocity (CV) consistent with theoretical predictions of ephaptic coupling (EpC). EpC depends on the ionic currents and intercellular separation in sodium channel rich intercalated disk microdomains like the perinexus. We suggested that perinexal width (WP) correlates with changes in extracellular calcium ([Ca2+]o). Here, we test the hypothesis that increasing [Ca2+]o reduces WP and increases CV. Mathematical models of EpC also predict that reducing WP can reduce sodium driving force and CV by self-attenuation. Therefore, we further hypothesized that reducing WP and extracellular sodium ([Na+]o) will reduce CV consistent with ephaptic self-attenuation. Transmission electron microscopy revealed that increasing [Ca2+]o (1 to 3.4 mM) significantly decreased WP. Optically mapping wild-type (WT) (100% Cx43) mouse hearts demonstrated that increasing [Ca2+]o increases transverse CV during normonatremia (147.3 mM), but slows transverse CV during hyponatremia (120 mM). Additionally, CV in heterozygous (∼50% Cx43) hearts was more sensitive to changes in [Ca2+]o relative to WT during normonatremia. During hyponatremia, CV slowed in both WT and heterozygous hearts to the same extent. Importantly, neither [Ca2+]o nor [Na+]o altered Cx43 expression or phosphorylation determined by Western blotting, or gap junctional resistance determined by electrical impedance spectroscopy. Narrowing WP, by increasing [Ca2+]o, increases CV consistent with enhanced EpC between myocytes. Interestingly, during hyponatremia, reducing WP slowed CV, consistent with theoretical predictions of ephaptic self-attenuation. This study suggests that serum ion concentrations may be an important determinant of cardiac disease expression.
Phosphatidylcholine kinetics in neonatal rat lungs and the effects of rhuKGF and betamethasone
Authors: Bernhard Wolfgang , Gesche Jens , Raith Marco , Poets Christian F.
Published: March 2016

Surfactant, synthesized by type II pneumocytes (PN-II), mainly comprises phosphatidylcholine (PC) and is essential to prevent neonatal respiratory distress. Furthermore, PC is essential to lung tissue growth and maintenance as a membrane component. Recent findings suggest that the lung contributes to systemic lipid homeostasis via PC export through ABC-A1 transporter expression. Hence it is important to consider pharmacological interventions in neonatal lung PC metabolism with respect to such export. Five-day-old rats were treated with carrier (control), intraperitoneal betamethasone, subcutaneous recombinant human keratinocyte growth factor (rhuKGF), or their combination for 48 h. Animals were intraperitoneally injected with 50 mg/kg [D9-methyl]choline chloride 1.5, 3.0, and 6.0 h before death at day 7, and lung lavage fluid (LLF) and tissue were harvested. Endogenous PC, D9-labeled PC species, and their water-soluble precursors (D9-)choline and (D9-)phosphocholine were determined by tandem mass spectrometry. Treatment increased secreted and tissue PC pools but did not change equilibrium composition of PC species in LLF. However, all treatments increased specific surfactant components in tissue. In control rats, peak D9-PC in lavaged lung was reached after 3 h and was decreased at 6 h. Only 13% of this net loss in lavaged lung was found in LLF. Such decrease was not present in lungs treated with betamethasone and/or with rhuKGF. D9-PC loss at 3–6 h and PC synthesis calculated from D9enrichment of phosphocholine indicated that daily synthesis rate is higher than total pool size. We conclude that lung tissue contributes to systemic PC homeostasis in neonatal rats, which is altered by glucocorticoid and rhuKGF treatment.
Human cerebrospinal fluid microRNA: temporal changes following subarachnoid hemorrhage
Authors: Powers Ciarán J. , Dickerson Ryan , Zhang Stacey W. , Rink Cameron , Roy Sashwati , Sen Chandan K.
Published: March 2016

Aneurysmal subarachnoid hemorrhage (aSAH) is a devastating form of hemorrhagic stroke with 30-day mortality between 33 and 45%. Delayed cerebral ischemia (DCI) is the chief cause of morbidity and mortality in patients who survive the initial aSAH. DCI accounts for almost 50% of deaths in patients surviving to treatment of the ruptured aneurysm. The mechanisms for brain injury after aSAH and the brain's response to this injury are not fully understood in humans. MicroRNAs (miRs) are 22- to 25-nucleotide single-stranded RNA molecules that inhibit the expression of specific messenger RNA targets. In this work, miR profiling of human cerebrospinal fluid from eight patients after aSAH was performed daily for 10 days with the goal of identifying changes in miR abundance. Using the nanoString nCounter Expression Assay, we identified two specific clusters of miR that were differentially regulated over time. Quantitative RT-PCR was performed on select miRs from each cluster. The first cluster contained miRs known to be present in blood and decreased in abundance over time. miRs in this group include miR-92a and let-7b. The second cluster contained several poorly characterized miRs that increased in abundance over time. miRs in this group included miR-491. This second cluster of miRs may be released into the CSF by the brain itself as a result of the initial SAH. Temporal changes in the abundance of specific miRs in human CSF after aSAH may provide novel insight into the role of miRs in brain injury and the brain's response.
Development of Novel Quaternary Ammonium Linkers for Antibody–Drug Conjugates
Authors: Burke Patrick J. , Hamilton Joseph Z. , Pires Thomas A. , Setter Jocelyn R. , Hunter Joshua H. , Cochran Julia H. , Waight Andrew B. , Gordon Kristine A. , Toki Brian E. , Emmerton Kim K. , Zeng Weiping , Stone Ivan J. , Senter Peter D. , Lyon Robert P. , Jeffrey Scott C.
Published: March 2016

A quaternary ammonium-based drug-linker has been developed to expand the scope of antibody–drug conjugate (ADC) payloads to include tertiary amines, a functional group commonly present in biologically active compounds. The linker strategy was exemplified with a β-glucuronidase–cleavable auristatin E construct. The drug-linker was found to efficiently release free auristatin E (AE) in the presence of β-glucuronidase and provide ADCs that were highly stable in plasma. Anti-CD30 conjugates comprised of the glucuronide-AE linker were potent and immunologically specific in vitro and in vivo, displaying pharmacologic properties comparable with a carbamate-linked glucuronide-monomethylauristatin E control. The quaternary ammonium linker was then applied to a tubulysin antimitotic drug that contained an N-terminal tertiary amine that was important for activity. A glucuronide-tubulysin quaternary ammonium linker was synthesized and evaluated as an ADC payload, in which the resulting conjugates were found to be potent and immunologically specific in vitro, and displayed a high level of activity in a Hodgkin lymphoma xenograft. Furthermore, the results were superior to those obtained with a related tubulysin derivative containing a secondary amine N-terminus for conjugation using previously known linker technology. The quaternary ammonium linker represents a significant advance in linker technology, enabling stable conjugation of payloads with tertiary amine residues. Mol Cancer Ther; 15(5); 938–45. ©2016 AACR.