bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence and Genotypic Characteristics of Clostridium difficile in a Closed and Integrated Human and Swine Population
Authors: Norman Keri N. , Scott H. Morgan , Harvey Roger B. , Norby Bo , Hume Michael E. , Andrews Kathleen 
Published: July 2011

ABSTRACT

Recently, an apparent rise in the number of cases attributed to community-acquired
Clostridium difficile
infection has led researchers to explore additional sources of infection. The finding of
C. difficile
in food animals and retail meat has raised concern about potential food-borne and occupational exposures. The objective of this study was to compare
C. difficile
isolated from a closed population of healthy individuals consisting of both humans and swine in order to investigate possible food safety and occupational risks for exposure. Using a multistep enrichment isolation technique, we identified 11.8% of the human wastewater samples and 8.6% of the swine samples that were positive for
C. difficile
. The prevalences of
C. difficile
in swine production groups differed significantly (
P
< 0.05); however, the prevalences in the two human occupational group cohorts did not differ significantly (
P
= 0.81). The majority of the human and swine isolates were similar based on multiple typing methods. The similarity in
C. difficile
prevalence in the human group cohorts suggests a low occupational hazard, while a greatly decreased prevalence of
C. difficile
in later-stage swine production groups suggests a diminished risk for food-borne exposure. The similarity of strains in the two host species suggests the possibility of a common environmental source for healthy individuals in a community setting.
Detection, Isolation, and Characterization of Acidophilic Methanotrophs from Sphagnum Mosses
Authors: Kip Nardy , Ouyang Wenjing , van Winden Julia , Raghoebarsing Ashna , van Niftrik Laura , Pol Arjan , Pan Yao , Bodrossy Levente , van Donselaar Elly G. , Reichart Gert-Jan , Jetten Mike S. M. , Sinninghe Damsté Jaap S. , Op den Camp Huub J. M. 
Published: July 2011

ABSTRACT

Sphagnum
peatlands are important ecosystems in the methane cycle. Methane-oxidizing bacteria in these ecosystems serve as a methane filter and limit methane emissions. Yet little is known about the diversity and identity of the methanotrophs present in and on
Sphagnum
mosses of peatlands, and only a few isolates are known. The methanotrophic community in
Sphagnum
mosses, originating from a Dutch peat bog, was investigated using a
pmoA
microarray. A high biodiversity of both gamma- and alphaproteobacterial methanotrophs was found. With
Sphagnum
mosses as the inoculum, alpha- and gammaproteobacterial acidophilic methanotrophs were isolated using established and newly designed media. The 16S rRNA,
pmoA
,
pxmA
, and
mmoX
gene sequences showed that the alphaproteobacterial isolates belonged to the
Methylocystis
and
Methylosinus
genera. The
Methylosinus
species isolated are the first acid-tolerant members of this genus. Of the acidophilic gammaproteobacterial strains isolated, strain M5 was affiliated with the
Methylomonas
genus, and the other strain, M200, may represent a novel genus, most closely related to the genera
Methylosoma
and
Methylovulum
. So far, no acidophilic or acid-tolerant methanotrophs in the
Gammaproteobacteria
class are known. All strains showed the typical features of either type I or II methanotrophs and are, to the best of our knowledge, the first isolated (acidophilic or acid-tolerant) methanotrophs from
Sphagnum
mosses.
Gpd1 and Gpd2 Fine-Tuning for Sustainable Reduction of Glycerol Formation in Saccharomyces cerevisiae
Authors: Hubmann Georg , Guillouet Stephane , Nevoigt Elke 
Published: July 2011

ABSTRACT

Gpd1 and Gpd2 are the two isoforms of glycerol 3-phosphate dehydrogenase (GPDH), which is the rate-controlling enzyme of glycerol formation in
Saccharomyces cerevisiae.
The two isoenzymes play crucial roles in osmoregulation and redox balancing. Past approaches to increase ethanol yield at the cost of reduced glycerol yield have most often been based on deletion of either one or two isogenes (
GPD1
and
GPD2
). While single deletions of
GPD1
or
GPD2
reduced glycerol formation only slightly, the
gpd1
Δ
gpd2
Δ double deletion strain produced zero glycerol but showed an osmosensitive phenotype and abolished anaerobic growth. Our current approach has sought to generate “intermediate” phenotypes by reducing both isoenzyme activities without abolishing them. To this end, the
GPD1
promoter was replaced in a
gpd2
Δ background by two lower-strength
TEF1
promoter mutants. In the same manner, the activity of the
GPD2
promoter was reduced in a
gpd1Δ
background. The resulting strains were crossed to obtain different combinations of residual
GPD1
and
GPD2
expression levels. Among our engineered strains we identified four candidates showing improved ethanol yields compared to the wild type. In contrast to a
gpd1
Δ
gpd2
Δ double-deletion strain, these strains were able to completely ferment the sugars under quasi-anaerobic conditions in both minimal medium and during simultaneous saccharification and fermentation (SSF) of liquefied wheat mash (wheat liquefact). This result implies that our strains can tolerate the ethanol concentration at the end of the wheat liquefact SSF (up to 90 g liter
−1
). Moreover, a few of these strains showed no significant reduction in osmotic stress tolerance compared to the wild type.
A Genomewide Screen for Tolerance to Cationic Drugs Reveals Genes Important for Potassium Homeostasis in Saccharomyces cerevisiae
Authors: Barreto Lina , Canadell David , Petrezsélyová Silvia , Navarrete Clara , Marešová Lydie , Peréz-Valle Jorge , Herrera Rito , Olier Iván , Giraldo Jesús , Sychrová Hana , Yenush Lynne , Ramos José , Ariño Joaquín 
Published: July 2011

ABSTRACT

Potassium homeostasis is crucial for living cells. In the yeast
Saccharomyces cerevisiae
, the uptake of potassium is driven by the electrochemical gradient generated by the Pma1 H
+
-ATPase, and this process represents a major consumer of the gradient. We considered that any mutation resulting in an alteration of the electrochemical gradient could give rise to anomalous sensitivity to any cationic drug independently of its toxicity mechanism. Here, we describe a genomewide screen for mutants that present altered tolerance to hygromycin B, spermine, and tetramethylammonium. Two hundred twenty-six mutant strains displayed altered tolerance to all three drugs (202 hypersensitive and 24 hypertolerant), and more than 50% presented a strong or moderate growth defect at a limiting potassium concentration (1 mM). Functional groups such as protein kinases and phosphatases, intracellular trafficking, transcription, or cell cycle and DNA processing were enriched. Essentially, our screen has identified a substantial number of genes that were not previously described to play a direct or indirect role in potassium homeostasis. A subset of 27 representative mutants were selected and subjected to diverse biochemical tests that, in some cases, allowed us to postulate the basis for the observed phenotypes.
RNA Interference in Fungi: Pathways, Functions, and Applications
Authors: Dang Yunkun , Yang Qiuying , Xue Zhihong , Liu Yi 
Published: July 2011

ABSTRACT

Small RNA molecules of about 20 to 30 nucleotides function in gene regulation and genomic defense via conserved eukaryotic RNA interference (RNAi)-related pathways. The RNAi machinery consists of three core components: Dicer, Argonaute, and RNA-dependent RNA polymerase. In fungi, the RNAi-related pathways have three major functions: genomic defense, heterochromatin formation, and gene regulation. Studies of
Schizosaccharomyces pombe
and
Neurospora
, and other fungi have uncovered surprisingly diverse small RNA biogenesis pathways, suggesting that fungi utilize RNAi-related pathways in various cellular processes to adapt to different environmental conditions. These studies also provided important insights into how RNAi functions in eukaryotic systems in general. In this review, we will discuss our current understanding of the fungal RNAi-related pathways and their functions, with a focus on filamentous fungi. We will also discuss how RNAi can be used as a tool in fungal research.
Polycyclic Aromatic Hydrocarbon Metabolic Network in Mycobacterium vanbaaleniiPYR-1
Authors: Kweon Ohgew , Kim Seong-Jae , Holland Ricky D. , Chen Hongyan , Kim Dae-Wi , Gao Yuan , Yu Li-Rong , Baek Songjoon , Baek Dong-Heon , Ahn Hongsik , Cerniglia Carl E. 
Published: July 2011

ABSTRACT

This study investigated a metabolic network (MN) from
Mycobacterium vanbaalenii
PYR-1 for polycyclic aromatic hydrocarbons (PAHs) from the perspective of structure, behavior, and evolution, in which multilayer omics data are integrated. Initially, we utilized a high-throughput proteomic analysis to assess the protein expression response of
M. vanbaalenii
PYR-1 to seven different aromatic compounds. A total of 3,431 proteins (57.38% of the genome-predicted proteins) were identified, which included 160 proteins that seemed to be involved in the degradation of aromatic hydrocarbons. Based on the proteomic data and the previous metabolic, biochemical, physiological, and genomic information, we reconstructed an experiment-based system-level PAH-MN. The structure of PAH-MN, with 183 metabolic compounds and 224 chemical reactions, has a typical scale-free nature. The behavior and evolution of the PAH-MN reveals a hierarchical modularity with funnel effects in structure/function and intimate association with evolutionary modules of the functional modules, which are the ring cleavage process (RCP), side chain process (SCP), and central aromatic process (CAP). The 189 commonly upregulated proteins in all aromatic hydrocarbon treatments provide insights into the global adaptation to facilitate the PAH metabolism. Taken together, the findings of our study provide the hierarchical viewpoint from genes/proteins/metabolites to the network via functional modules of the PAH-MN equipped with the engineering-driven approaches of modularization and rationalization, which may expand our understanding of the metabolic potential of
M. vanbaalenii
PYR-1 for bioremediation applications.
Activity and Transcriptional Regulation of Bacterial Protein-Like Glycerol-3-Phosphate Dehydrogenase of the Haloarchaea in Haloferax volcanii
Authors: Rawls Katherine S. , Martin Jonathan H. , Maupin-Furlow Julie A. 
Published: July 2011

ABSTRACT

Glycerol is a primary energy source for heterotrophic haloarchaea and a major component of “salty” biodiesel waste. Glycerol is catabolized solely by glycerol kinase (encoded by
glpK
) to glycerol-3-phosphate (G3P) in
Haloferax volcanii
. Here we characterized the next critical step of this metabolic pathway: the conversion of G3P to dihydroxyacetone phosphate by G3P dehydrogenase (G3PDH).
H. volcanii
harbors two putative G3PDH operons: (i)
glpA1B1C1
, located on the chromosome within the neighborhood of
glpK
, and (ii)
glpA2B2C2
, on megaplasmid pHV4. Analysis of knockout strains revealed that
glpA1
(and not
glpA2
) is required for growth on glycerol. However, both
glpA1
and
glpA2
could complement a
glpA1
knockout strain (when expressed from a strong promoter in
trans
) and were required for the total G3PDH activity of cell lysates. The
glpA1B1C1
,
glpK
,
glpF
(encoding a putative glycerol facilitator), and
ptsH2
(encoding a homolog of the bacterial phosphotransferase system protein Hpr) genes were transcriptionally linked and appeared to be under the control of a strong, G3P-inducible promoter upstream of
glpA1
. Overall, this study provides fundamental insights into glycerol metabolism in
H. volcanii
and enhances our understanding of central metabolic pathways of haloarchaea.
The Sulfolobicin Genes of Sulfolobus acidocaldariusEncode Novel Antimicrobial Proteins
Authors: Ellen Albert F. , Rohulya Olha V. , Fusetti Fabrizia , Wagner Michaela , Albers Sonja-Verena , Driessen Arnold J. M. 
Published: July 2011

ABSTRACT

Crenarchaea, such as
Sulfolobus acidocaldarius
and
Sulfolobus tokodaii
, produce antimicrobial proteins called sulfolobicins. These antimicrobial proteins inhibit the growth of closely related species. Here we report the identification of the sulfolobicin-encoding genes in
S. acidocaldarius
. The active sulfolobicin comprises two proteins that are equipped with a classical signal sequence. These proteins are secreted by the cells and found to be membrane vesicle associated. Gene inactivation studies demonstrate that both proteins are required for the bacteriostatic antimicrobial activity. Sulfolobicins constitute a novel class of antimicrobial proteins without detectable homology to any other protein.
Genome Sequence of the Arctic Methanotroph Methylobacter tundripaludum SV96
Authors: Svenning Mette M. , Hestnes Anne Grethe , Wartiainen Ingvild , Stein Lisa Y. , Klotz Martin G. , Kalyuzhnaya Marina G. , Spang Anja , Bringel Françoise , Vuilleumier Stéphane , Lajus Aurélie , Médigue Claudine , Bruce David C. , Cheng Jan-Fang , Goodwin Lynne , Ivanova Natalia , Han James , Han Cliff S. , Hauser Loren , Held Brittany , Land Miriam L. , Lapidus Alla , Lucas Susan , Nolan Matt , Pitluck Sam , Woyke Tanja 
Published: July 2011

ABSTRACT

Methylobacter tundripaludum
SV96
T
(ATCC BAA-1195) is a psychrotolerant aerobic methane-oxidizing gammaproteobacterium (
Methylococcales
,
Methylococcaceae
) living in High Arctic wetland soil. The strain was isolated from soil harvested in July 1996 close to the settlement Ny-Ålesund, Svalbard, Norway (78°56′N, 11°53′E), and described as a novel species in 2006. The genome includes
pmo
and
pxm
operons encoding copper membrane monooxygenases (Cu-MMOs), genes required for nitrogen fixation, and the
nirS
gene implicated in dissimilatory nitrite reduction to NO but no identifiable inventory for further processing of nitrogen oxides. These genome data provide the basis to investigate
M. tundripaludum
SV96, identified as a major player in the biogeochemistry of Arctic environments.
Draft Genome Sequence of the Novel Agar-Digesting Marine Bacterium HQM9
Authors: Du Zongjun , Zhang Zhewen , Miao Tingting , Wu Jiayan , Lü Guoqiang , Yu Jun , Xiao Jingfa , Chen Guanjun 
Published: July 2011

ABSTRACT

Strain HQM9, an aerobic, rod-shaped marine bacterium from red algae, can produce agarases and liquefy solid plating media efficiently when agar is used as a coagulant. Here we report the draft genome sequence and the initial findings from a preliminary analysis of strain HQM9, which should be a novel species of
Flavobacteriaceae
.
Spatial orientation of the subtalar joint axis is different in subjects with and without Achilles tendon disorders
Authors: Reule Claudia A , Alt Wilfried W , Lohrer Heinz , Hochwald Harald 
Published: July 2011

BackgroundThere are many possible predisposing factors for Achilles tendon disorders suggested in the literature but their pathogenetic relevance is not proven in most cases. The asymmetric mechanical load distribution within the Achilles tendon during locomotion is frequently addressed as a major risk factor for Achilles tendon disorders. The spatial orientation of the subtalar joint axis (STA) may influence the Achilles tendon loading possibly leading to overload injuries.HypothesisThere is a significant difference between the orientation of the STA in subjects with and without Achilles tendon pathologies.Materials and methods614 subtalar joint axes determined in 307 long-distance runners with and without Achilles tendon disorders were included. Achilles tendon disorders were defined as any Achilles tendon–related pain during or following running, existing for more than 2 weeks in the past. Motion analysis of the foot was performed using an ultrasonic pulse-echo-based measurement system. The orientation of the STA was expressed by two angles.ResultsThe mean inclination angle was 42±16° and the mean deviation angle was 11±23°. There was a significant difference (p=0.002) between the mean deviation angle measured in subjects with Achilles tendon pathologies (18±23°) and those without (10±23°).ConclusionsThe results demonstrate a wide interindividual variability of the spatial orientation of the STA. In addition, the mean deviation angle in people with Achilles tendon pathologies is significantly more oblique than in people without. This finding indicates that the spatial orientation of the STA is related to the incidence of overuse injuries of the Achilles tendon in the investigated sample.
Reduced expression of desmocollin 2 is an independent prognostic biomarker for shorter patients survival in pancreatic ductal adenocarcinoma
Authors: Hamidov Zaur , Altendorf-Hofmann Annelore , Chen Yuan , Settmacher Utz , Petersen Iver , Knösel Thomas 
Published: July 2011

BackgroundCell–cell adhesion molecules such as desmosomes and cytokeratins may play a major role in epithelial–mesenchymal transition and have been suggested to have a relevant impact on tumour progression. This study investigated 15 biomarkers in pancreatic ductal adenocarcinoma (PDAC) and correlated the results with clinicopathological parameters.MethodsTissue microarrays of 115 R0-resected PDAC were constructed to evaluate the protein expression of 15 in genome‐wide expression profiling differentially expressed biomarkers.ResultsAt the protein level a high expression of desmocollin 2 (DSC2) was observed in 90.4%, DSC1 (67.6%), DSC3 (0.9%), MDM2 (16.2%), CEA (64.8%), CK7 (85.2%), CK8 (96.5%), CK18 (96.5%), CK19 (93.9%), CK20 (11.5%), CA19-9 (86.6%), TLE1 (8.7%), PITX1 (91.2%), factor H (95.7%) and mesothelin (9.6%). Reduced expression of DSC2 was statistically correlated with shorter patient survival, higher tumour grading and positive lymph node status (p=0.008, p=0.029, p=0.011, respectively). In multivariable analysis reduced expression of DSC2, higher tumour grading and positive lymph node status were independently correlated with shorter patient survival.ConclusionsReduced expression of DSC2 is independently correlated with shorter patient survival, higher tumour grading and positive lymph node status in PDAC and could serve as a prognostic marker.
What is the significance of flat epithelial atypia and what are the management implications?
Authors: Rajan Sabrina , Sharma Nisha , Dall Barbara J G , Shaaban Abeer M 
Published: July 2011

AimsTo assess the significance of flat epithelial atypia (FEA) on core biopsy by evaluating the proportion of cases upgraded to in-situ and invasive carcinoma on further sampling with vacuum-assisted biopsy (VAB) or diagnostic surgical biopsy.MethodsA retrospective analysis was performed of all core biopsies containing FEA and/or atypical intraductal proliferation (AIDP) in the pathology database from April 2008 to April 2010 (n=90). Before April 2009, the majority of core biopsies containing FEA and/or AIDP proceeded to surgical biopsy. From April 2009 onwards, a new patient management pathway was introduced incorporating VAB to sample core biopsies containing FEA and/or AIDP as an alternative to surgical biopsy.ResultsOf 90 core biopsies, the following were identified: FEA only in 42%; FEA with concomitant AIDP in 21% and AIDP only in 37%. There was a stepwise increase in the proportion of cases upgraded to in-situ or invasive carcinoma: 19% in the FEA group; 29% in the FEA and AIDP group and 53% in the AIDP group. In the FEA-only group, one invasive tumour (grade 1 tubular carcinoma) and six cases of ductal carcinoma in situ were found.ConclusionThe presence of FEA on core biopsy warrants further tissue sampling to ensure concomitant malignancy is not missed. Sampling with VAB provides sufficient tissue for histopathological evaluation, reducing the need for surgical biopsy. It is important that the utilisation of VAB is incorporated into a safe patient management pathway with careful multidisciplinary team discussion to ensure radiological–pathological concordance.
Noise exposure and serious injury to active sawmill workers in British Columbia
Authors: Kling Rakel N , Demers Paul A , Alamgir Hasanat , Davies Hugh W 
Published: July 2011

BackgroundOccupational noise might increase the risk of workplace injury through a variety of mechanisms, including interference with communication and increased stress.ObjectivesThe purpose of this study was to assess the effect of chronic noise exposure on serious workplace injury, and how the timing of exposure influenced risk.MethodsThe authors examined a cohort of 26 000 workers, who worked between 1950 and 1989. Cases were those hospitalised for a work-related injury (ICD-9 codes 800–999, and E codes E800–E999), from April 1989 to December 1998. Cumulative exposure levels were estimated for subjects based on a quantitative retrospective exposure assessment. An internal comparison of cumulative noise exposure and subchronic durations of noise exposure and injury was conducted using Poisson regression. There were 163 cases for the cumulative and 161 cases for the subchronic analysis.ResultsCumulative noise exposure were associated with a decreased risk for injuries, with the risk generally decreasing as cumulative noise levels increased, while most durations of subchronic exposure were associated with an increased risk for injury. An inverse U-shaped trend was observed with the time period of 90 days to 1 year demonstrating the most elevated RR compared with 0–1 days of exposure.ConclusionsWorkers highly exposed to noise, or exposed for long periods of time, might develop effective methods of communicating the risk and preventing injuries when exposed to noise.
Air exposure assessment of TDI and biological monitoring of TDA in urine in workers in polyurethane foam industry
Authors: Geens Tom , Dugardin Sandra , Schockaert Ann , De Cooman Geert , van Sprundel Marc 
Published: July 2011

ObjectivesToluene diisocyanate (TDI) is used in the manufacturing process of polyurethane (PU) foams and is a potent inducer of occupational asthma. The objective of this study was to evaluate the correlation between the exposure to total TDI (2,4- and 2,6-TDI) in air and the corresponding biomarker concentration of total TDA (2,4- and 2,6-TDA) in hydrolysed urine. The aim was also to propose an appropriate biological exposure limit for total TDA in urine.Methods9 workers from two production lines in a PU foam producing plant were studied. Personal exposure to TDI during four representative production shifts was monitored by an active air sampling method (filter impregnated with 1-(2-methoxyphenyl)piperazine) and quantified by high-performance liquid chromatography and diode array detection (NIOSH n° 2535, 5521). In parallel, pre-shift and post-shift urinary samples were collected from the exposed workers, and TDA concentrations were determined by gas chromatography–mass spectrometry after alkaline hydrolysis. All samples were collected on four measuring days: two Fridays (end of workweek) and two Mondays (start of workweek) separated by a weekend without exposure.ResultsStrong correlations between the personal air concentrations of total TDI and the corresponding biomarker levels of total TDA in urine (r=0.816) were observed. An increase of 18.12 μg TDA/l (post-shift minus pre-shift concentration) corresponds to an exposure of 5 ppb (37 μg/m3, the current American Conference of Governmental Industrial Hygienists threshold limit value) during the shift.ConclusionsThe increase in TDA during the shift is a suitable biomarker for exposure to TDI during the same shift. Further research is needed to evaluate the use of start of week or end of week post-shift TDA in urine as biomarker since TDA was found to accumulate during the working week and thus the moment of sampling will clearly influence the result.