bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroRNA‐29b modulates Japanese encephalitis virus‐induced microglia activation by targeting tumor necrosis factor alpha‐induced protein 3
Authors: Thounaojam Menaka Chanu , Kaushik Deepak Kumar , Kundu Kiran , Basu Anirban 
Published: November 2013

AbstractJapanese encephalitis virus (JEV), a single‐stranded RNA (ssRNA) virus, is the leading cause of encephalitis in Asia. Microglial activation is one of the key events in JEV‐induced neuroinflammation. Although the various microRNAs (miRNAs) has been shown to regulate microglia activation during pathological conditions including neuroviral infections, till date, the involvement of miRNAs in JEV infection has not been evaluated. Hence, we sought to evaluate the possible role of miRNAs in mediating JEV‐induced microglia activation. Initial screening revealed significant up‐regulation of miR‐29b in JEV‐infected mouse microglial cell line (BV‐2) and primary microglial cells. Furthermore, using bioinformatics tools, we identified tumor necrosis factor alpha‐induced protein 3, a negative regulator of nuclear factor‐kappa B signaling as a potential target of miR‐29b. Interestingly, in vitro knockdown of miR‐29b resulted in significant over‐expression of tumor necrosis factor alpha‐induced protein 3, and subsequent decrease in nuclear translocation of pNF‐κB. JEV infection in BV‐2 cell line elevated inducible nitric oxide synthase, cyclooxygenase‐2, and pro‐inflammatory cytokine expression levels, which diminished after miR‐29b knockdown. Collectively, our study demonstrates involvement of miR‐29b in regulating JEV‐ induced microglial activation.
imagemiR‐29b regulates Japanese Encephalitis Virus (JEV)‐induced microglia activation via inhibition of the anti‐inflammatory proteinTNFAIP3, which results in sustained activation of NF‐kB. Sustained NF‐?Bactivation further results in augmented secretion of pro‐inflammatory cytokines and induction of inflammatory mediators (iNOS and Cox‐2).
Triheptanoin partially restores levels of tricarboxylic acid cycle intermediates in the mouse pilocarpine model of epilepsy
Authors: Hadera Mussie G. , Smeland Olav B. , McDonald Tanya S. , Tan Kah Ni , Sonnewald Ursula , Borges Karin 
Published: November 2013

AbstractTriheptanoin, the triglyceride of heptanoate, is anticonvulsant in various epilepsy models. It is thought to improve energy metabolism in the epileptic brain by re‐filling the tricarboxylic acid (TCA) cycle with C4‐intermediates (anaplerosis). Here, we injected mice with [1,2‐13C]glucose 3.5–4 weeks after pilocarpine‐induced status epilepticus (SE) fed either a control or triheptanoin diet. Amounts of metabolites and incorporations of 13C were determined in extracts of cerebral cortices and hippocampal formation and enzyme activity and mRNA expression were quantified. The percentage enrichment with two 13C atoms in malate, citrate, succinate, and GABA was reduced in hippocampal formation of control‐fed SE compared with control mice. Except for succinate, these reductions were not found in triheptanoin‐fed SE mice, indicating that triheptanoin prevented a decrease of TCA cycle capacity. Compared to those on control diet, triheptanoin‐fed SE mice showed few changes in most other metabolite levels and their 13C labeling. Reduced pyruvate carboxylase mRNA and enzyme activity in forebrains and decreased [2,3‐13C]aspartate amounts in cortex suggest a pyruvate carboxylation independent source of C‐4 TCA cycle intermediates. Most likely anaplerosis was kept unchanged by carboxylation of propionyl‐CoA derived from heptanoate. Further studies are proposed to fully understand triheptanoin's effects on neuroglial metabolism and interaction.
imageIn the hippocampal formation (HF) of a mouse epilepsy model, formation of citrate, GABA, succinate, fumarate, and malate from 13C‐labeled glucose is reduced. Triheptanoin, the triglyceride of heptanoate, inhibits pyruvate carboxylase activity (PC, green arrow), but restores some of these metabolite levels (red arrows). The refilling of the TCA cycle via carboxylation of propionyl‐CoA is likely to contribute to triheptanoin's anticonvulsant effects.
Diagnostic Yield of Cytologic Analysis of Pericardial Effusion in Dogs
Authors: Cagle L.A. , Epstein S.E. , Owens S.D. , Mellema M.S. , Hopper K. , Burton A.G. 
Published: November 2013

BackgroundPericardial effusion cytology is believed by many to be of limited value, yet few studies have evaluated its diagnostic utility.ObjectivesTo determine the diagnostic utility of cytologic analysis of pericardial effusion in dogs and to determine if consideration of additional data could improve the diagnostic yield.AnimalsTwo hundred and fifty‐nine dogs with cytologic analysis of pericardial effusion performed between April 1990 and June 2012.MethodsElectronic medical records from a university teaching hospital were retrospectively reviewed; signalment, complete blood count, serum biochemistry, cytologic analysis of pericardial effusion, and echocardiographic data were recorded. Cytology was classified as diagnostic (infectious or neoplastic) or nondiagnostic (hemorrhagic or other) and groups were compared with multiple Student'st‐tests.ResultsCytology was grouped as nondiagnostic (92.3%) or diagnostic (7.7%) and characterized as hemorrhagic (90%), neoplastic (4.6%), infectious (3.1%), or other (2.3%). Overall cytologic analysis of pericardial effusion diagnostic utility was 7.7% and increased to 20.3% if the effusion hematocrit (HCT) <10%; echocardiographic evidence of a mass did not result in a significant increase in the diagnostic utility.Conclusions and Clinical ImportanceThe diagnostic utility of cytologic analysis of canine pericardial effusion is variable depending on the underlying etiology. In this group of dogs, the diagnostic yield of cytologic analysis was greater for pericardial effusion samples in which theHCTwas less than 10%.
Genomic architecture of ecologically divergent body shape in a pair of sympatric crater lake cichlid fishes
Authors: Franchini Paolo , Fruciano Carmelo , Spreitzer Maria L. , Jones Julia C. , Elmer Kathryn R. , Henning Frederico , Meyer Axel 
Published: November 2013

AbstractDetermining the genetic bases of adaptations and their roles in speciation is a prominent issue in evolutionary biology. Cichlid fish species flocks are a prime example of recent rapid radiations, often associated with adaptive phenotypic divergence from a common ancestor within a short period of time. In several radiations of freshwater fishes, divergence in ecomorphological traits — including body shape, colour, lips and jaws — is thought to underlie their ecological differentiation, specialization and, ultimately, speciation. The Midas cichlid species complex (Amphilophusspp.) of Nicaragua provides one of the few known examples of sympatric speciation where species have rapidly evolved different but parallel morphologies in young crater lakes. This study identified significantQTLfor body shape usingSNPs generated via ddRADsequencing and geometric morphometric analyses of a cross between two ecologically and morphologically divergent, sympatric cichlid species endemic to crater Lake Apoyo: an elongated limnetic species (Amphilophus zaliosus) and a high‐bodied benthic species (Amphilophus astorquii). A total of 453 genome‐wide informativeSNPs were identified in 240F2hybrids. These markers were used to construct a genetic map in which 25 linkage groups were resolved. Seventy‐two segregatingSNPs were linked to 11QTL. By annotating the two most highly supportedQTL‐linked genomic regions, genes that might contribute to divergence in body shape along the benthic–limnetic axis in Midas cichlid sympatric adaptive radiations were identified. These results suggest that few genomic regions of large effect contribute to early stage divergence in Midas cichlids.
Opposite carbon isotope discrimination during dark respiration in leaves versus roots – a review
Authors: Ghashghaie Jaleh , Badeck Franz W. 
Published: November 2013

SummaryIn general, leaves are 13C‐depleted compared with all other organs (e.g. roots, stem/trunk and fruits). Different hypotheses are formulated in the literature to explain this difference. One of these states that CO2 respired by leaves in the dark is 13C‐enriched compared with leaf organic matter, while it is 13C‐depleted in the case of root respiration. The opposite respiratory fractionation between leaves and roots was invoked as an explanation for the widespread between‐organ isotopic differences. After summarizing the basics of photosynthetic and post‐photosynthetic discrimination, we mainly review the recent findings on the isotopic composition of CO2 respired by leaves (autotrophic organs) and roots (heterotrophic organs) compared with respective plant material (i.e. apparent respiratory fractionation) as well as its metabolic origin. The potential impact of such fractionation on the isotopic signal of organic matter (OM) is discussed. Some perspectives for future studies are also proposed .

Contents

Summary
751

I.
Introduction
751

II.
Photosynthetic carbon isotope discrimination
752

III.
Post‐photosynthetic discrimination
753

IV.
Apparent dark respiratory fractionation in leaves
754

V.
Root‐respired CO2 is generally 13C‐depleted compared with root OM, except in C3 woody plants
757

VI.
δ13CR of leaves and roots diverges at leaf autotrophy onset
762

VII.
Metabolic pathways potentially implied in 13C depletion in root‐respired CO2
763

VIII.
A glance at stem respiration
765

IX.
Impact on carbon isotope composition of plant OM
765

X.
Conclusions
766

Acknowledgements
766

References
766
A large pholidosaurid in the Phu Kradung Formation of north‐eastern Thailand
Authors: Martin Jeremy E. , Lauprasert Komsorn , Buffetaut Eric , Liard Romain , Suteethorn Varavudh 
Published: November 2013

AbstractIn the early 1980s, the remains of a large crocodilian, consisting of a nearly complete lower jaw, were referred to a distinct species of Sunosuchus, S. thailandicus. The specimen was recovered from a road‐cut near Nong Bua Lamphu, north‐eastern Thailand, in the upper part of the continental Phu Kradung Formation, and then considered Early to Middle Jurassic in age. Since then, this age has been revised and most of the formation is now considered Early Cretaceous, although a Late Jurassic age is possible for its lowermost part. Here, we report for the first time cranial elements associated with mandibular remains assignable to ‘S’. thailandicus. An attribution to Pholidosauridae is proposed on the basis of premaxillary morphology, and the original referral of this taxon to the goniopholidid Sunosuchus is discarded. A new genus name Chalawan now designates the originally described material of S. thailandicus. Nevertheless, the newly described specimen shares a characteristic with both ‘traditional’ Goniopholididae and Pholidosauridae: the presence of a depression located on the lateral wall of the maxilla and jugal. A phylogenetic analysis confirms the inclusion of both Goniopholididae and Pholidosauridae into a common clade, Coelognathosuchia tax. nov. Although the new Thai skull is much fragmented, its original shape is reconstructed and is compared with other pholidosaurid genera, namely Elosuchus, Meridiosaurus, Oceanosuchus, Pholidosaurus, Sarcosuchus and Terminonaris. The presence of the genus Sunosuchus being highly questionable in Thailand, it cannot be used as evidence to link the Chinese and Indochinese blocks. Instead, the recognition of a freshwater pholidosaurid in a continental formation of the Indochinese block suggests that early in their evolutionary history, these crocodilians, already known from Europe, Africa and South America, were more widely distributed along the northern margin of the Tethys than previously recognized.
Anesthesia and long‐term outcomes after neonatal intensive care
Authors: Marlow Neil 
Published: November 2013

SummaryAs survival is now increasing, care of the extremely preterm infant is now directed at strategies to minimize long‐term morbidity. In this study, I review the current state‐of‐the‐art outcomes for babies born at extremely low gestations and identify strategies that may be aimed at optimizing outcomes. With respect to anesthetic practice, I then go on to discuss important issues of pain management in these babies and how this may affect long‐term outcomes.
Applications du théorème d’Ax–Lindemann hyperbolique
Authors: Ullmo Emmanuel 
Published: November 2013

AbstractWe explain how the André–Oort conjecture for a general Shimura variety can be deduced from the hyperbolic Ax–Lindemann conjecture, a good lower bound for Galois orbits of special points and the definability, in the$o$-minimal structure${ \mathbb{R} }_{\mathrm{an} , \mathrm{exp} } $, of the restriction to a fundamental set of the uniformizing map of a Shimura variety. These ingredients are known in some important cases. As a consequence a proof of the André–Oort conjecture for projective special subvarieties of${ \mathcal{A} }_{6}^{N} $for an arbitrary integer$N$is given.
Analysis of the Gull Fecal Microbial Community Reveals the Dominance of Catellicoccus marimammalium in Relation to Culturable Enterococci
Authors: Koskey Amber M. , Fisher Jenny C. , Traudt Mary F. , Newton Ryan J. , McLellan Sandra L. 
Published: November 2013

ABSTRACT

Gulls are prevalent in beach environments and can be a major source of fecal contamination. Gulls have been shown to harbor a high abundance of fecal indicator bacteria (FIB), such as
Escherichia coli
and enterococci, which can be readily detected as part of routine beach monitoring. Despite the ubiquitous presence of gull fecal material in beach environments, the associated microbial community is relatively poorly characterized. We generated comprehensive microbial community profiles of gull fecal samples using Roche 454 and Illumina MiSeq platforms to investigate the composition and variability of the gull fecal microbial community and to measure the proportion of FIB.
Enterococcaceae
and
Enterobacteriaceae
were the two most abundant families in our gull samples. Sequence comparisons between short-read data and nearly full-length 16S rRNA gene clones generated from the same samples revealed
Catellicoccus marimammalium
as the most numerous taxon among all samples. The identification of bacteria from gull fecal pellets cultured on membrane-
Enterococcus
indoxyl-β-
d
-glucoside (mEI) plates showed that the dominant sequences recovered in our sequence libraries did not represent organisms culturable on mEI. Based on 16S rRNA gene sequencing of gull fecal isolates cultured on mEI plates, 98.8% were identified as
Enterococcus
spp., 1.2% were identified as
Streptococcus
spp., and none were identified as
C. marimammalium
. Illumina deep sequencing indicated that gull fecal samples harbor significantly higher proportions of
C. marimammalium
16S rRNA gene sequences (>50-fold) relative to typical mEI culturable
Enterococcus
spp.
C. marimammalium
therefore can be confidently utilized as a genetic marker to identify gull fecal pollution in the beach environment.
Lactobacillus helveticus MIMLh5-Specific Antibodies for Detection of S-Layer Protein in Grana Padano Protected-Designation-of-Origin Cheese
Authors: Stuknytė Milda , Brockmann Eeva-Christine , Huovinen Tuomas , Guglielmetti Simone , Mora Diego , Taverniti Valentina , Arioli Stefania , De Noni Ivano , Lamminmäki Urpo 
Published: November 2013

ABSTRACT

Single-chain variable-fragment antibodies (scFvs) have considerable potential in immunological detection and localization of bacterial surface structures. In this study, synthetic phage-displayed antibody libraries were used to select scFvs against immunologically active S-layer protein of
Lactobacillus helveticus
MIMLh5. After three rounds of panning, five relevant phage clones were obtained, of which four were specific for the S-layer protein of
L. helveticus
MIMLh5 and one was also capable of binding to the S-layer protein of
L. helveticus
ATCC 15009. All five anti-S-layer scFvs were expressed in
Escherichia coli
XL1-Blue, and their specificity profiles were characterized by Western blotting. The anti-S-layer scFv PolyH4, with the highest specificity for the S-layer protein of
L. helveticus
MIMLh5, was used to detect the S-layer protein in Grana Padano protected-designation-of-origin (PDO) cheese extracts by Western blotting. These results showed promising applications of this monoclonal antibody for the detection of immunomodulatory S-layer protein in dairy (and dairy-based) foods.
Prevalence and Fimbrial Genotype Distribution of Poultry Salmonella Isolates in China (2006 to 2012)
Authors: Gong Jiansen , Zhang Jinqiu , Xu Ming , Zhu Chunhong , Yu Yan , Liu Xuexian , Kelly Patrick , Xu Bu , Wang Chengming 
Published: November 2013

ABSTRACT

In this study, a total of 323
Salmonella enterica
strains were isolated from 3,566 rectal swab samples of 51 poultry farms in seven regions of 12 provinces of China between 2006 and 2012. The prevalences of
Salmonella
sp. carriage were 12.4% in geese (66 positive/533 samples), 10.4% in turkeys (32/309), 9.8% in chickens (167/1,706), 6.8% in ducks (41/601), and 4.1% in pigeons (17/417), respectively. These isolates belonged to 20 serovars, in which the most frequent serovars were
S. enterica
serovar Gallinarum biovar Pullorum (herein,
S
. Pullorum) (55 isolates, 17.0%),
S. enterica
serovar Typhimurium (50 isolates, 15.5%), and
S. enterica
serovar Enteritidis (39 isolates, 12.1%). Overall,
S
. Typhimurium was the most commonly detected serovar; among the individual species,
S
. Pullorum was most commonly isolated from chickens,
S
. Enteritidis was most common in ducks,
S
. Typhimurium was most common in geese and pigeons, and
S. enterica
serovar Saintpaul was most common in turkeys. PCR determination of 20 fimbrial genes demonstrated the presence of
bcfD
,
csgA
,
fimA
,
stdB
, and
sthE
genes and the absence of
staA
and
stgA
genes in these isolates, and other loci were variably distributed, with frequency values ranging from 11.8 to 99.1%. These 323
Salmonella
isolates were subdivided into 41 different fimbrial genotypes, and of these isolate, 285 strains (88.2%) had 12 to 14 fimbrial genes. Our findings indicated that the
Salmonella
isolates from different poultry species were phenotypically and genetically diverse and that some fimbrial genes are more frequently associated with serovars or serogroups.
Quorum-Sensing Regulation of Constitutive Plantaricin by Lactobacillus plantarum Strains under a Model System for Vegetables and Fruits
Authors: Rizzello Carlo G. , Filannino Pasquale , Di Cagno Raffaella , Calasso Maria , Gobbetti Marco 
Published: November 2013

ABSTRACT

This study aimed at investigating the regulatory system of bacteriocin synthesis by
Lactobacillus plantarum
strains in vegetables and fruits in a model system. Sterile and neutralized cell-free supernatant (CFS) from
L. plantarum
strains grown in MRS broth showed
in vitro
antimicrobial activities toward various indicator strains. The highest activity was that of
L. plantarum
C2. The antimicrobial activity was further assayed on vegetable and fruit agar plates (solid conditions) and in juices (liquid conditions). A regulatory mechanism of bacteriocin synthesis via quorum sensing was hypothesized. The synthesis of antimicrobial compounds seemed to be constitutive under solid conditions of growth on vegetable and fruit agar plates. In contrast, it depended on the size of the inoculum when
L. plantarum
C2 was grown in carrot juice. Only the inoculum of ca. 9.0 log CFU ml
−1
produced detectable activity. The genes
plnA
,
plnEF
,
plnG
, and
plnH
were found in all
L. plantarum
strains. The genes
plnJK
and
plnN
were detected in only three or four strains. Reverse-phase high-performance liquid chromatography purification and mass spectrometry analysis revealed the presence of a mixture of eight peptides in the most active fraction of the CFS from
L. plantarum
C2. Active peptides were encrypted into bacteriocin precursors, such as plantaricins PlnJ/K and PlnH and PlnG, which are involved in the ABC transport system. A real-time PCR assay showed an increase in the expression of
plnJK
and
plnG
during growth of
L. plantarum
C2 in carrot juice.
Uncovering a Microbial Enigma: Isolation and Characterization of the Streamer-Generating, Iron-Oxidizing, Acidophilic Bacterium “Ferrovum myxofaciens”
Authors: Johnson D. Barrie , Hallberg Kevin B. , Hedrich Sabrina 
Published: November 2013

ABSTRACT

A betaproteobacterium, shown by molecular techniques to have widespread global distribution in extremely acidic (pH 2 to 4) ferruginous mine waters and also to be a major component of “acid streamer” growths in mine-impacted water bodies, has proven to be recalcitrant to enrichment and isolation. A modified “overlay” solid medium was devised and used to isolate this bacterium from a number of mine water samples. The physiological and phylogenetic characteristics of a pure culture of an isolate from an abandoned copper mine (“
Ferrovum myxofaciens
” strain P3G) have been elucidated. “
F. myxofaciens
” is an extremely acidophilic, psychrotolerant obligate autotroph that appears to use only ferrous iron as an electron donor and oxygen as an electron acceptor. It appears to use the Calvin-Benson-Bassham pathway to fix CO
2
and is diazotrophic. It also produces copious amounts of extracellular polymeric materials that cause cells to attach to each other (and to form small streamer-like growth
in vitro
) and to different solid surfaces. “
F. myxofaciens
” can catalyze the oxidative dissolution of pyrite and, like many other acidophiles, is tolerant of many (cationic) transition metals. “
F. myxofaciens
” and related clone sequences form a monophyletic group within the
Betaproteobacteria
distantly related to classified orders, with genera of the family
Nitrosomonadaceae
(lithoautotrophic, ammonium-oxidizing neutrophiles) as the closest relatives. On the basis of the phylogenetic and phenotypic differences of “
F. myxofaciens
” and other
Betaproteobacteria
, a new family, “
Ferrovaceae
,” and order, “
Ferrovales
,” within the class
Betaproteobacteria
are proposed. “
F. myxofaciens
” is the first extreme acidophile to be described in the class
Betaproteobacteria
.