bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteome Analyses of Strains ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp. under Culture Conditions Resulting in Enhanced H
2
Production
Authors: Aryal Uma K. , Callister Stephen J. , Mishra Sujata , Zhang Xiaohui , Shutthanandan Janani I. , Angel Thomas E. , Shukla Anil K. , Monroe Matthew E. , Moore Ronald J. , Koppenaal David W. , Smith Richard D. , Sherman Louis 
Published: December 2012

ABSTRACT

Cultures of the cyanobacterial genus
Cyanothece
have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N
2
-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes, and we performed quantitative proteome analysis of
Cyanothece
sp. strains ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N
2
-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome
c
oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher levels of respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in
Cyanothece
ATCC 51142 in the presence of glycerol under H
2
-producing conditions, suggesting a competition between these sources of carbon. However, in
Cyanothece
PCC 7822, the Calvin cycle still played a role in cofactor recycling during H
2
production. Our data comprise the first comprehensive profiling of proteome changes in
Cyanothece
PCC 7822 and allow an in-depth comparative analysis of major physiological and biochemical processes that influence H
2
production in both strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large-scale H
2
production.
Isolation of Acetobacterium sp. Strain AG, Which Reductively Debrominates Octa- and Pentabrominated Diphenyl Ether Technical Mixtures
Authors: Ding Chang , Chow Wai Ling , He Jianzhong 
Published: December 2012

ABSTRACT

Polybrominated diphenyl ethers (PBDEs) are a class of environmental pollutants that have been classified as persistent organic pollutants since 2009. In this study, a sediment-free enrichment culture (culture G) was found to reductively debrominate octa- and penta-BDE technical mixtures to less-brominated congeners (tetra-, tri-, and di-BDEs) via a
para
-dominant debromination pattern for the former and a strict
para
debromination pattern for the latter. Culture G could debrominate 96% of 280 nM PBDEs in an octa-BDE mixture to primarily tetra-BDEs in 21 weeks. Continuous transferring of culture G with octa-/penta-BDEs dissolved in
n
-nonane or trichloroethene (TCE) yielded two strains (
Acetobacterium
sp. strain AG and
Dehalococcoides
sp. strain DG) that retained debromination capabilities. In the presence of lactate but without TCE, strain AG could cometabolically debrominate 75% of 275 nM PBDEs in a penta-BDE mixture in 33 days. Strain AG shows 99% identity to its closest relative,
Acetobacterium malicum
. In contrast to strain AG, strain DG debrominated PBDEs only in the presence of TCE. In addition, 18 out of 19 unknown PBDE debromination products were successfully identified from octa- and penta-BDE mixtures and revealed, for the first time, a comprehensive microbial PBDE debromination pathway. As an acetogenic autotroph that rapidly debrominates octa- and penta-BDE technical mixtures,
Acetobacterium
sp. strain AG adds to the still-limited understanding of PBDE debromination by microorganisms.
Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments
Authors: Puentes-Téllez Pilar Eliana , Hansen Martin Asser , Sørensen Søren Johannes , van Elsas Jan Dirk 
Published: December 2012

ABSTRACTIn a study aiming to assess bacterial evolution in complex growth media, we evaluated the long-term adaptive response ofEscherichia coliMC1000 in Luria-Bertani (LB) medium. Seven parallel populations were founded and followed over 150 days in sequential batch cultures under three different oxygen conditions (defined environments), and 19 evolved forms were isolated. The emergence of forms with enhanced fitness was evident in competition experiments of all evolved forms versus the ancestral strain. The evolved forms were then subjected to phenotypic and genomic analyses relative to the ancestor. Profound changes were found in their phenotypes as well as whole-genome sequences. Interestingly, considerable heterogeneity was found at the intrapopulational level. However, consistently occurring parallel adaptive responses were found across all populations. The evolved forms all contained a mutation ingalR, a repressor of the galactose operon. Concomitantly, the new forms revealed enhanced growth on galactose as well as galactose-containing disaccharides. This response was likely driven by the LB medium.
HbzF Catalyzes Direct Hydrolysis of Maleylpyruvate in the Gentisate Pathway of Pseudomonas alcaligenes NCIMB 9867
Authors: Liu Kun , Liu Ting-Ting , Zhou Ning-Yi 
Published: December 2012

ABSTRACT

HbzF from
Pseudomonas alcaligenes
NCIMB 9867 was purified to homogeneity as a His-tagged protein and likely a dimer by SDS-PAGE and gel filtration. This protein was demonstrated to be a novel maleylpyruvate hydrolase, catalyzing direct hydrolysis of maleylpyruvate to maleate and pyruvate, and belongs to the fumarylacetoacetate hydrolase superfamily. This study reveals the genetic determinate for the direct maleylpyruvate hydrolysis in the gentisate pathway, complementary to the well-studied maleylpyruvate isomerization route.
Significance of Heme-Based Respiration in Meat Spoilage Caused by Leuconostoc gasicomitatum
Authors: Jääskeläinen Elina , Johansson Per , Kostiainen Olli , Nieminen Timo , Schmidt Georg , Somervuo Panu , Mohsina Marzia , Vanninen Paula , Auvinen Petri , Björkroth Johanna 
Published: December 2012

ABSTRACT

Leuconostoc gasicomitatum
is a psychrotrophic lactic acid bacterium (LAB) which causes spoilage in cold-stored modified-atmosphere-packaged (MAP) meat products. In addition to the fermentative metabolism,
L. gasicomitatum
is able to respire when exogenous heme and oxygen are available. In this study, we investigated the respiration effects on growth rate, biomass, gene expression, and volatile organic compound (VOC) production in laboratory media and pork loin. The meat samples were evaluated by a sensory panel every second or third day for 29 days. We observed that functional respiration increased the growth (rate and yield) of
L. gasicomitatum
in laboratory media with added heme and
in situ
meat with endogenous heme. Respiration increased enormously (up to 2,600-fold) the accumulation of acetoin and diacetyl, which are buttery off-odor compounds in meat. Our transcriptome analyses showed that the gene expression patterns were quite similar, irrespective of whether respiration was turned off by excluding heme from the medium or mutating the
cydB
gene, which is essential in the respiratory chain. The respiration-based growth of
L. gasicomitatum
in meat was obtained in terms of population development and subsequent development of sensory characteristics. Respiration is thus a key factor explaining why
L. gasicomitatum
is so well adapted in high-oxygen packed meat.
Analagous Population Structures for Two Alphabaculoviruses Highlight a Functional Role for Deletion Mutants
Authors: Serrano Amaya , Williams Trevor , Simón Oihane , López-Ferber Miguel , Caballero Primitivo , Muñoz Delia 
Published: December 2012

ABSTRACT

A natural
Spodoptera exigua
multiple nucleopolyhedrovirus (SeMNPV) isolate from Florida shares a strikingly similar genotypic composition to that of a natural
Spodoptera frugiperda
MNPV (SfMNPV) isolate from Nicaragua. Both isolates comprise a high proportion of large-deletion genotypes that lack genes that are essential for viral replication or transmission. To determine the likely origins of such genotypically similar population structures, we performed genomic and functional analyses of these genotypes. The homology of nucleotides in the deleted regions was as high as 79%, similar to those of other colinear genomic regions, although some SfMNPV genes were not present in SeMNPV. In addition, no potential consensus sequences were shared between the deletion flanking sequences. These results indicate an evolutionary mechanism that independently generates and sustains deletion mutants within each virus population. Functional analyses using different proportions of complete and deletion genotypes were performed with the two viruses in mixtures of occlusion bodies (OBs) or co-occluded virions. Ratios greater than 3:1 of complete/deletion genotypes resulted in reduced pathogenicity (expressed as median lethal dose), but there were no significant changes in the speed of kill. In contrast, OB yields increased only in the 1:1 mixture. The three phenotypic traits analyzed provide a broader picture of the functional significance of the most extensively deleted SeMNPV genotype and contribute toward the elucidation of the role of such mutants in baculovirus populations.
Bioluminescence Imaging Study of Spatial and Temporal Persistence of Lactobacillus plantarum and Lactococcus lactis in Living Mice
Authors: Daniel Catherine , Poiret Sabine , Dennin Véronique , Boutillier Denise , Pot Bruno 
Published: December 2012

ABSTRACT

Lactic acid bacteria, especially lactobacilli, are common inhabitants of the gastrointestinal tract of mammals, for which they have received considerable attention due to their putative health-promoting properties. In this study, we describe the development and application of luciferase-expressing
Lactobacillus plantarum
and
Lactococcus lactis
strains for noninvasive
in vivo
monitoring in the digestive tract of mice. We report for the first time the functional
in vitro
expression in
Lactobacillus plantarum
NCIMB8826 and in
Lactococcus lactis
MG1363 of the click beetle luciferase (CBluc), as well as
Gaussia
and bacterial luciferases, using a combination of vectors, promoters, and codon-optimized genes. We demonstrate that a CBluc construction is the best-performing luciferase system for the noninvasive
in vivo
detection of lactic acid bacteria after oral administration. The persistence and viability of both strains was studied by bioluminescence imaging in anesthetized mice and in mouse feces.
In vivo
bioluminescence imaging confirmed that after a single or multiple oral administrations,
L. lactis
has shorter survival times in the mouse gastrointestinal tract than
L. plantarum
, and it also revealed the precise gut compartments where both strains persisted. The application of luciferase-labeled bacteria has significant potential to allow the
in vivo
and
ex vivo
study of the interactions of lactic acid bacteria with their mammalian host.
Enterohemorrhagic Escherichia coli O157:H7 Survival in an
In Vitro
Model of the Human Large Intestine and Interactions with Probiotic Yeasts and Resident Microbiota
Authors: Thévenot Jonathan , Etienne-Mesmin Lucie , Denis Sylvain , Chalancon Sandrine , Alric Monique , Livrelli Valérie , Blanquet-Diot Stéphanie 
Published: December 2012

ABSTRACT

This is the first report on the fate of enterohemorrhagic
Escherichia coli
O157:H7 in simulated human colonic conditions. The pathogen was progressively eliminated from the bioreactor and did not modify the major populations of resident microbiota. The coadministration of the
Saccharomyces cerevisiae
CNCM I-3856 probiotic strain led to a significant increase in acetate production but did not reduce pathogen viability.
Two Doses of Bovine Viral Diarrhea Virus DNA Vaccine Delivered by Electroporation Induce Long-Term Protective Immune Responses
Authors: van Drunen Littel-van den Hurk Sylvia , Lawman Zoe , Snider Marlene , Wilson Don , van den Hurk Jan V. , Ellefsen Barry , Hannaman Drew 
Published: December 2012

ABSTRACTBovine viral diarrhea virus (BVDV) is a pathogen of major importance in cattle, so there is a need for new effective vaccines. DNA vaccines induce balanced immune responses and are relatively inexpensive and thus promising for both human and veterinary applications. In this study, newborn calves with maternal antibodies were vaccinated intramuscularly (i.m.) with a BVDV E2 DNA vaccine with the TriGrid Delivery System for i.m. delivery (TDS-IM). Two doses of this vaccine spaced 6 or 12 weeks apart were sufficient to induce significant virus-neutralizing antibody titers, numbers of activated T cells, and reduction in viral shedding and clinical presentations after BVDV-2 challenge. In contrast to the placebo-treated animals, the vaccinated calves did not lose any weight, which is an excellent indicator of the well-being of an animal and has a significant economic impact. Furthermore, the interval between the two vaccinations did not influence the magnitude of the immune responses or degree of clinical protection, and a third immunization was not necessary or beneficial. Since electroporation may enhance not only the magnitude but also the duration of immunity after DNA immunization, the interval between vaccination and challenge was extended in a second trial, which showed that two doses of this E2 DNA vaccine again significantly reduced clinical disease against BVDV for several months. These results are promising and support this technology for use against infectious diseases in cattle and large species, including humans, in general.
Morphogenetic Circuitry Regulating Growth and Development in the Dimorphic Pathogen Penicillium marneffei
Authors: Boyce Kylie J. , Andrianopoulos Alex 
Published: December 2012

ABSTRACTPenicillium marneffeiis an emerging human-pathogenic fungus endemic to Southeast Asia. Like a number of other fungal pathogens,P. marneffeiexhibits temperature-dependent dimorphic growth and grows in two distinct cellular morphologies, hyphae at 25°C and yeast cells at 37°C. Hyphae can differentiate to produce the infectious agents, asexual spores (conidia), which are inhaled into the host lung, where they are phagocytosed by pulmonary alveolar macrophages. Within macrophages, conidia germinate into unicellular yeast cells, which divide by fission. This minireview focuses on the current understanding of the genes required for the morphogenetic control of conidial germination, hyphal growth, asexual development, and yeast morphogenesis inP. marneffei.
Septin Phosphorylation and Coiled-Coil Domains Function in Cell and Septin Ring Morphology in the Filamentous Fungus Ashbya gossypii
Authors: Meseroll Rebecca A. , Occhipinti Patricia , Gladfelter Amy S. 
Published: December 2012

ABSTRACT

Septins are a class of GTP-binding proteins conserved throughout many eukaryotes. Individual septin subunits associate with one another and assemble into heteromeric complexes that form filaments and higher-order structures
in vivo
. The mechanisms underlying the assembly and maintenance of higher-order structures in cells remain poorly understood. Septins in several organisms have been shown to be phosphorylated, although precisely how septin phosphorylation may be contributing to the formation of high-order septin structures is unknown. Four of the five septins expressed in the filamentous fungus,
Ashbya gossypii
, are phosphorylated, and we demonstrate here the diverse roles of these phosphorylation sites in septin ring formation and septin dynamics, as well as cell morphology and viability. Intriguingly, the alteration of specific sites in Cdc3p and Cdc11p leads to a complete loss of higher-order septin structures, implicating septin phosphorylation as a regulator of septin structure formation. Introducing phosphomimetic point mutations to specific sites in Cdc12p and Shs1p causes cell lethality, highlighting the importance of normal septin modification in overall cell function and health. In addition to discovering roles for phosphorylation, we also present diverse functions for conserved septin domains in the formation of septin higher-order structure. We previously showed the requirement for the Shs1p coiled-coil domain in limiting septin ring size and reveal here that, in contrast to Shs1p, the coiled-coil domains of Cdc11p and Cdc12p are required for septin ring formation. Our results as a whole reveal novel roles for septin phosphorylation and coiled-coil domains in regulating septin structure and function.
Analyses of Extracellular Carbohydrates in Oomycetes Unveil the Existence of Three Different Cell Wall Types
Authors: Mélida Hugo , Sandoval-Sierra Jose V. , Diéguez-Uribeondo Javier , Bulone Vincent 
Published: December 2012

ABSTRACT

Some of the most devastating plant and animal pathogens belong to the oomycete class. The cell walls of these microorganisms represent an excellent target for disease control, but their carbohydrate composition is elusive. We have undertaken a detailed cell wall analysis in 10 species from 2 major oomycete orders, the Peronosporales and the Saprolegniales, thereby unveiling the existence of 3 clearly different cell wall types: type I is devoid of
N
-acetylglucosamine (GlcNAc) but contains glucuronic acid and mannose; type II contains up to 5% GlcNAc and residues indicative of cross-links between cellulose and 1,3-β-glucans; type III is characterized by the highest GlcNAc content (>5%) and the occurrence of unusual carbohydrates that consist of 1,6-linked GlcNAc residues. These 3 cell wall types are also distinguishable by their cellulose content and the fine structure of their 1,3-β-glucans. We propose a cell wall paradigm for oomycetes that can serve as a basis for the establishment of cell wall architectural models and the further identification of cell wall subtypes. This paradigm is complementary to morphological and molecular criteria for taxonomic grouping and provides useful information for unraveling poorly understood cell wall carbohydrate biosynthetic pathways through the identification and characterization of the corresponding enzymes.
Individual and Combined Roles of the Master Regulators AphA and LuxR in Control of the Vibrio harveyi Quorum-Sensing Regulon
Authors: van Kessel Julia C. , Rutherford Steven T. , Shao Yi , Utria Alan F. , Bassler Bonnie L. 
Published: December 2012

ABSTRACTBacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In theVibrio harveyiquorum-sensing circuit, two master transcription factors, AphA and LuxR, coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they coregulate 77 genes. LuxR strongly controls genes at both low cell density and high cell density, suggesting that it is the major quorum-sensing regulator. In contrast, AphA is absent at high cell density and acts to fine-tune quorum-sensing gene expression at low cell density. We examined two loci as case studies of coregulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum-regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group life-styles. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell density. Thus, the asymmetric production of AphA and LuxR coupled with differences in their strengths and timing of target gene regulation generate a precise temporal pattern of gene expression.
Sequential Triplex Real-Time PCR Assay for Detecting 21 Pneumococcal Capsular Serotypes That Account for a High Global Disease Burden
Authors: Pimenta Fabiana C. , Roundtree Alexis , Soysal Ahmet , Bakir Mustafa , du Plessis Mignon , Wolter Nicole , von Gottberg Anne , McGee Lesley , Carvalho Maria da Gloria , Beall Bernard 
Published: December 2012

ABSTRACT

We developed and validated a real-time PCR assay consisting of 7 triplexed reactions to identify 11 individual serotypes plus 10 small serogroups representing the majority of disease-causing isolates of
Streptococcus pneumoniae
. This assay targets the 13 serotypes included within the 13-valent conjugate vaccine and 8 additional key serotypes or serogroups. Advantages over other serotyping assays are described. The assay will be expanded to 40 serotypes/serogroups. We will provide periodic updates at our protocol website.
Rapid Hepatitis C Virus Divergence among Chronically Infected Individuals
Authors: Cruz-Rivera Mayra , Carpio-Pedroza Juan Carlos , Escobar-Gutiérrez Alejandro , Lozano Daniela , Vergara-Castaneda Arely , Rivera-Osorio Pilar , Martinez-Guarneros Armando , Chacon Carlos A. Vazquez , Fonseca-Coronado Salvador , Vaughan Gilberto 
Published: December 2012

ABSTRACT
Here, we analyze the viral divergence among hepatitis C virus (HCV) chronic cases infected with genotype 1. The intrahost viral evolution was assessed by deep sequencing using the 454 Genome Sequencer platform. The results showed a rapid nucleotide sequence divergence. This notorious short-term viral evolution is of the utmost importance for the study of HCV transmission, because direct links between related samples were virtually lost. Thus, rapid divergence of HCV significantly affects genetic relatedness studies and outbreak investigations.
Synergistic prognostic values of cardiac sympathetic innervation with left ventricular hypertrophy and left atrial size in heart failure patients without reduced left ventricular ejection fraction: a cohort study
Authors: Doi Takahiro , Nakata Tomoaki , Hashimoto Akiyoshi , Yuda Satoshi , Wakabayashi Takeru , Kouzu Hidemichi , Kaneko Naofumi , Hase Mamoru , Tsuchihashi Kazufumi , Miura Tetsuji 
Published: December 2012

ObjectivesThis study tested whether cardiac sympathetic innervation assessed by metaiodobenzylguanidine (MIBG) activity has long-term prognostic value in combination with left ventricular hypertrophy (LVH) and left atrial size in heart failure (HF) patients without reduced left ventricular ejection fraction (LVEF).DesignA single-centre prospective cohort study.Setting/participantsWith primary endpoints of cardiac death and rehospitalisation due to HF progression, 178 consecutive symptomatic HF patients with 74% men, mean age of 56 years and mean LVEF of 64.5% were followed up for 80 months. The entry criteria consisted of LVEF more than 50%, completion of predischarge clinical evaluations including cardiac MIBG and echocardiographic studies and at least more than 1-year follow-up when survived.ResultsThirty-four patients with cardiac evens had larger left atrial dimension (LAD), increased LV mass index, reduced MIBG activity quantified as heart-to-mediastinum ratio (HMR) than did the others. Multivariable Cox analysis showed that LAD and HMR were significant predictors (HR of 1.080 (95% CI 1.00 to 1.16, p=0.044) and 0.107 (95% CI 0.01 to 0.61, p=0.012, respectively). Thresholds of HMR (1.65) and LAD (37 mm) were closely related to identification of high-risk patients. In particular, HMR was a significant determinant of cardiac events in both patients with and without LV hypertrophy. Reduced HMR with enlarged LAD or LV hypertrophy identified patients at most increased risk; overall log-rank value, 11.5, p=0.0032 for LAD and 17.5, p=0.0002, respectively.ConclusionsIn HF patients without reduced LV ejection fraction, impairment of cardiac sympathetic innervation is related to cardiac outcomes independently and synergistically with LA size and LV hypertrophy. Cardiac sympathetic innervation assessment can contribute to better risk-stratification in combination with evaluation of LA size and LV mass but is needed to be evaluated for establishing aetiology-based risk assessment in HF patients at increased risk.