bluuebunny/crossref_metadata_2025_split huggingface dataset:
High Lytic Infection Rates but Low Abundances of Prokaryote Viruses in a Humic Lake (Vassivière, Massif Central, France)
Authors: Pradeep Ram A. S. , Rasconi S. , Jobard M. , Palesse S. , Colombet J. , Sime-Ngando T. 
Published: July 2011

ABSTRACT

We explored the abundance and infection rates of viruses on a time series scale in the euphotic zone of the humic mesotrophic Lake Vassivière (Massif Central, France) and compared them to nonhumic lakes of contrasting trophy (i.e., the oligomesotrophic Lake Pavin and the eutrophic Lake Aydat) located in the same geographical region and sampled during the same period. In Lake Vassivière, the abundances of virus-like particles (range, 1.7 × 10
10
to 2.6 × 10
10
liter
−1
) were significantly (
P
< 0.001) lower than in Lakes Pavin and Aydat. The percentage of virus-infected prokaryotic cells (mean, 18.0%) was significantly higher (
P
< 0.001) in Vassivière than in Pavin (mean, 11.5%) and Aydat (mean, 9.7%). In Vassivière, the abundance of prokaryotes was a good predictor (
r
= 0.78,
P
< 0.001) of the number of virus-like particles, while the potential grazing rate from heterotrophic nanoflagellates was positively correlated to the viral infection rate (
r
= 0.75,
P
< 0.001;
n
= 20), indicating the prevalence of cycling interactions among viruses, prokaryotes, and grazers, which is in agreement with past experiments. The absence of correlation between chlorophyll
a
concentrations (Chl) and viral parameters suggested that the resources for the lytic activity of viruses in Vassivière were mainly under allochthonous control, through host activity. Indeed, compilation of data obtained from several nonhumic lakes in the French Massif Central revealed that Chl was positively correlated to the abundance of virus-like particles at concentrations above 0.5 μg Chl liter
−1
and negatively at concentrations below 0.5 μg Chl liter
−1
, suggesting that phytoplankton-derived resources could force prokaryotic growth to attain a certain threshold level when the host availability is sufficient to boost the proliferation of viruses. Therefore, based on the high level of lytic infection rates in Lake Vassivière, we conclude that viruses are key agents for prokaryotic mortality and could influence the food web dynamics in humic lakes, which may ultimately depend on the internal cycling of resources and, perhaps, mainly on the allochthonous inputs and the associated humic substances.
Microbial Removal of Atmospheric Carbon Tetrachloride in Bulk Aerobic Soils
Authors: Mendoza Y. , Goodwin K. D. , Happell J. D. 
Published: July 2011

ABSTRACT

Atmospheric concentrations of carbon tetrachloride (CCl
4
) were removed by bulk aerobic soils from tropical, subtropical, and boreal environments. Removal was observed in all tested soil types, indicating that the process was widespread. The flux measured in field chamber experiments was 0.24 ± 0.10 nmol CCl
4
(m
2
day)
−1
(average ± standard deviation [SD];
n
= 282). Removal of CCl
4
and removal of methane (CH
4
) were compared to explore whether the two processes were linked. Removal of both gases was halted in laboratory samples that were autoclaved, dry heated, or incubated in the presence of mercuric chloride (HgCl
2
). In marl soils, treatment with antibiotics such as tetracycline and streptomycin caused partial inhibition of CCl
4
(50%) and CH
4
(76%) removal, but removal was not affected in soils treated with nystatin or myxothiazol. These data indicated that bacteria contributed to the soil removal of CCl
4
and that microeukaryotes may not have played a significant role. Amendments of methanol, acetate, and succinate to soil samples enhanced CCl
4
removal by 59%, 293%, and 72%, respectively. Additions of a variety of inhibitors and substrates indicated that nitrification, methanogenesis, or biological reduction of nitrate, nitrous oxide, or sulfate (e.g., occurring in possible anoxic microzones) did not play a significant role in the removal of CCl
4
. Methyl fluoride inhibited removal of CH
4
but not CCl
4
, indicating that CH
4
and CCl
4
removals were not directly linked. Furthermore, CCl
4
removal was not affected in soils amended with copper sulfate or methane, supporting the results with MeF and suggesting that the observed CCl
4
removal was not significantly mediated by methanotrophs.
An ABC-Type Cobalt Transport System Is Essential for Growth of Sinorhizobium melilotiat Trace Metal Concentrations
Authors: Cheng Jiujun , Poduska Branislava , Morton Richard A. , Finan Turlough M. 
Published: July 2011

ABSTRACTWe report expression and mutant phenotypes for a gene cluster inSinorhizobium meliloti, designatedcbtJKL, that has been shown to encode an ABC-typecobalttransport system. Transcription ofcbtJKLinitiated 384 nucleotides upstream from thecbtJtranslation start codon, and the resulting 5′ region contained a putative B12riboswitch. Expression of thecbtJKLgenes appeared to be controlled by (cobalt-loaded) cobalamin interacting at the B12riboswitch, since (i) a putative B12riboswitch was located within this large upstream region, (ii)cbtJtranscription was repressed upon addition of cobalt or vitamin B12, and (iii) deletions in the B12riboswitch resulted in constitutivecbtJKLtranscription. Insertion mutants incbtJKLfailed to grow in LB medium, and growth was restored through the addition of cobalt but not other metals. This growth phenotype appeared to be due to the chelation of cobalt present in LB, andcbtJKLmutants also failed to grow in minimal medium containing the chelating agent EDTA unless the medium was supplemented with additional or excess cobalt. In uptake experiments,57Co2+accumulation was high in wild-type cells expressing thecbtJKLgenes, whereas wild-type cells in whichcbtJKLexpression was repressed showed reduced accumulation. IncbtJKLmutant cells,57Co2+accumulation was reduced relative to that of the wild type, and presumably, this residual cobalt transport occurred via an alternate ion uptake system(s) that is not specific to cobalt. In symbiosis, the alternate system(s) appeared to mediate cobalt transport into bacteroid cells, as lowcbtJKLexpression was detected in bacteroids andcbtJKLmutants formed N2-fixing nodules on alfalfa.
Phenylacetyl Coenzyme A Is an Effector Molecule of the TetR Family Transcriptional Repressor PaaR from Thermus thermophilusHB8
Authors: Sakamoto Keiko , Agari Yoshihiro , Kuramitsu Seiki , Shinkai Akeo 
Published: July 2011

ABSTRACT

Phenylacetic acid (PAA) is a common intermediate in the catabolic pathways of several structurally related aromatic compounds. It is converted into phenylacetyl coenzyme A (PA-CoA), which is degraded to general metabolites by a set of enzymes. Within the genome of the extremely thermophilic bacterium
Thermus thermophilus
HB8, a cluster of genes, including a TetR family transcriptional regulator, may be involved in PAA degradation. The gene product, which we named
T. thermophilus
PaaR, negatively regulated the expression of the two operons composing the gene cluster
in vitro. T. thermophilus
PaaR repressed the target gene expression by binding pseudopalindromic sequences, with a consensus sequence of 5′-CNAACGNNCGTTNG-3′, surrounding the promoters. PA-CoA is a ligand of PaaR, with a proposed binding stoichiometry of 1:1 protein monomer, and was effective for transcriptional derepression. Thus, PaaR is a functional homolog of PaaX, a GntR transcriptional repressor found in
Escherichia coli
and
Pseudomonas
strains. A three-dimensional structure of
T. thermophilus
PaaR was predicted by homology modeling. In the putative structure, PaaR adopts the typical three-dimensional structure of the TetR family proteins, with 10 α-helices. A positively charged surface at the center of the molecule is similar to the acyl-CoA-binding site of another TetR family transcriptional regulator,
T. thermophilus
FadR, which is involved in fatty acid degradation. The CoA moiety of PA-CoA may bind to the center of the PaaR molecule, in a manner similar to the binding of the CoA moiety of acyl-CoA to FadR.
The Rhodanese Domain of ThiI Is Both Necessary and Sufficient for Synthesis of the Thiazole Moiety of Thiamine in Salmonella enterica
Authors: Martinez-Gomez N. Cecilia , Palmer Lauren D. , Vivas Eugenio , Roach Peter L. , Downs Diana M. 
Published: July 2011

ABSTRACT

In
Salmonella enterica
, ThiI is a bifunctional enzyme required for the synthesis of both the 4-thiouridine modification in tRNA and the thiazole moiety of thiamine. In 4-thiouridine biosynthesis, ThiI adenylates the tRNA uridine and transfers sulfur from a persulfide formed on the protein. The role of ThiI in thiazole synthesis is not yet well understood. Mutational analysis described here found that ThiI residues required for 4-thiouridine synthesis were not involved in thiazole biosynthesis. The data further showed that the C-terminal rhodanese domain of ThiI was sufficient for thiazole synthesis
in vivo
. Together, these data support the conclusion that sulfur mobilization in thiazole synthesis is mechanistically distinct from that in 4-thiouridine synthesis and suggest that functional annotation of ThiI in genome sequences should be readdressed. Nutritional studies described here identified an additional cysteine-dependent mechanism for sulfur mobilization to thiazole that did not require ThiI, IscS, SufS, or glutathione. The latter mechanism may provide insights into the chemistry used for sulfur mobilization to thiazole in organisms that do not utilize ThiI.
Genome Sequence of Methyloversatilis universalisFAM5
T
, a Methylotrophic Representative of the Order Rhodocyclales
Authors: Kittichotirat Weerayuth , Good Nathan M. , Hall Rob , Bringel Françoise , Lajus Aurélie , Médigue Claudine , Smalley Nicole E. , Beck David , Bumgarner Roger , Vuilleumier Stéphane , Kalyuzhnaya Marina G. 
Published: July 2011

ABSTRACT

Rhodocyclales
are representative of versatile bacteria that are able to utilize a wide variety of organic compounds for growth, but only a few strains have been isolated in pure culture thus far. Here we present the genome sequence of
Methyloversatilis universalis
FAM5
T
, the first cultivable methylotrophic member of the order.
The σ
B
-Dependent
yabJ-spoVG
Operon Is Involved in the Regulation of Extracellular Nuclease, Lipase, and Protease Expression in Staphylococcus aureus
Authors: Schulthess Bettina , Bloes Dominik A. , François Patrice , Girard Myriam , Schrenzel Jacques , Bischoff Markus , Berger-Bächi Brigitte 
Published: July 2011

ABSTRACT

The alternative sigma factor σ
B
of
Staphylococcus aureus
is involved in the coordination of the general stress response, expression of virulence determinants, and modulation of antibiotic resistance levels. It controls a large regulon, either directly by recognizing conserved σ
B
promoter sequences or indirectly via σ
B
-dependent elements. The σ
B
-controlled
yabJ-spoVG
operon encodes two such putative downstream elements. We report here transcriptome analysis in
S. aureus
Newman, showing that inactivation of the
yabJ-spoVG
operon had primarily a repressing effect on a small subregulon encoding mainly virulence factors, including a nuclease (
nuc
), a protease (
splE
) and a lipase (
lip
). As a consequence, extracellular nuclease, protease, and lipase activities were reduced in a Δ
yabJ
-
spoVG
mutant.
trans
-complementation by SpoVG was sufficient to restore their reduced phenotypic expression and lowered transcription due to the
yabJ-spoVG
deletion. It did not restore, however, the changes triggered by σ
B
inactivation, indicating that both regulons only partially overlap, despite the σ
B
dependency of the
yabJ-spoVG
expression. Thus, σ
B
is likely to control additional, SpoVG-independent factors affecting the expression of numerous hydrolytic enzymes. SpoVG, on the other hand, seems to fine-tune the σ
B
-dependent regulation of a subset of virulence factors by antagonizing the σ
B
effect.
Complete Genome Sequence of Amycolicicoccus subflavusDQS3-9A1
T
, an Actinomycete Isolated from Crude Oil-Polluted Soil
Authors: Cai Man , Chen Wei-Min , Nie Yong , Chi Chang-Qiao , Wang Ya-Nan , Tang Yue-Qin , Li Guo-Ying , Wu Xiao-Lei 
Published: July 2011

ABSTRACT

Amycolicicoccus subflavus
DQS3-9A1
T
, isolated from crude oil-polluted soil in the Daqing Oilfield in China, is a type strain of a newly published novel species in the novel genus
Amycolicicoccus
. Here we report the complete genome of DQS3-9A1
T
and genes associated with oil-polluted environment.
Complete Genome Sequences of Krokinobactersp. Strain 4H-3-7-5 and Lacinutrixsp. Strain 5H-3-7-4, Polysaccharide-Degrading Members of the Family Flavobacteriaceae
Authors: Klippel Barbara , Lochner Adriane , Bruce David C. , Walston Davenport Karen , Detter Chris , Goodwin Lynne A. , Han James , Han Shunsheng , Hauser Loren , Land Miriam L. , Nolan Matt , Ovchinnikova Galina , Pennacchio Len , Pitluck Sam , Tapia Roxanne , Woyke Tanja , Wiebusch Sigrid , Basner Alexander , Abe Fumiyoshi , Horikoshi Koki , Keller Martin , Antranikian Garabed 
Published: July 2011

ABSTRACT

Two members of the family
Flavobacteriaceae
were isolated from subseafloor sediments using artificial seawater with cellulose, xylan, and chitin as the sole carbon and energy sources. Here, we present the complete genome sequences of
Krokinobacter
sp. strain 4H-3-7-5 and
Lacinutrix
sp. strain 5H-3-7-4, which both encode putatively novel enzymes involved in cellulose, hemicellulose, and chitin metabolism.
Who presents more than once? Repeat abortion among women in Britain
Authors: Stone Nicole , Ingham Roger 
Published: July 2011

Background and methodologyAround one in three sexually active women in Britain will have an abortion during their lifetime and a third of those women will experience more than one. Using data collected during the second National Survey of Sexual Attitudes and Lifestyles the characteristics of women who have presented for a second or subsequent abortion are compared to those women who have obtained only one.ResultsResults indicate that increased age and parity are key characteristics distinguishing between women who have experienced only one abortion and those women who have had more. Findings also reveal that those who have sought abortion on more than one occasion are more likely (than those who have had one abortion) to be Black, have left school at an earlier age, be living in rented accommodation, report an earlier age at first sexual experience, be less likely to have used a reliable method of contraception at sexual debut and report a greater number of sexual partners.Discussion and conclusionsIt is well recognised that attendance at abortion services presents an important opportunity for the provision of individually tailored information regarding contraception to assist women avoid the need for subsequent procedures. However, differential use of abortion services may also indicate variations in knowledge levels, attitudes to risk, attitudes towards abortion, partner communication, gender power and differential access to services. Further research is required to clarify these potential relationships so that suitable health promotion activities can be developed.
Occupational noise exposure assessment using O*NET and its application to a study of hearing loss in the US general population
Authors: Choi Yoon-Hyeong , Hu Howard , Tak SangWoo , Mukherjee Bhramar , Park Sung Kyun 
Published: July 2011

ObjectivesAlthough occupational noise is a well known risk factor for hearing loss, little epidemiological evidence has been reported on its association with hearing loss in the general population, in part, because of the difficulty in exposure assessment. This study introduced a quantitative occupational noise exposure assessment tool using the Occupational Information Network (O*NET) database and evaluated its applicability for epidemiological research using data from the National Health and Nutrition Examination Survey (NHANES) 1999–2004.MethodsThe O*NET noise exposure data were assessed by questionnaires across numerous occupations, asking the frequency of exposure to sounds and noise levels that are distracting and uncomfortable (with five possible responses from ‘never’ to ‘every day’). Means of the O*NET noise scores were computed to correspond to NHANES occupational categories and assigned to 3828 adults aged 20–69 years, who participated in the 1999–2004 NHANES. Pure-tone averages (PTA) of hearing thresholds at 0.5, 1, 2 and 4 kHz were computed, and hearing loss was defined as a PTA >25 dB in either ear. Linear and logistic regression models with either continuous or quintiles of the O*NET noise scores were fitted on log-transformed PTA and binary hearing loss, respectively.ResultsNoise scores ranged from 1.80 to 4.37 with mean±SE of 3.06±0.02. After controlling for potential confounders, the highest (vs lowest) noise score quintile had a 22.5% (95% CI 11.0% to 35.2%) increase in PTA, and there was a linear dose-dependent trend across the quintiles of noise scores (p trend<0.0001). The adjusted OR for hearing loss comparing the highest with the lowest noise score quintiles was 2.1 (95% CI 1.2 to 3.6).ConclusionThis study suggests that the O*NET noise score is a useful tool for examining occupational noise-induced health effects in the general population in the absence of actual occupational noise exposure assessment data.
Cardiac magnetic resonance imaging of non-ischaemic cardiomyopathy
Authors: Deshpande Aparna , Pakkal Mini , Agrawal Bobby , Raj Vimal 
Published: July 2011

Abstract
Cardiomyopathy is defined as a heterogeneous group of diseases of the myocardium associated with mechanical and/or electrical dysfunction due to a variety of causes that are frequently genetic. These are either confined to the heart or are part of generalised systemic disorders, often leading to cardiovascular death or progressive heart failure related disability. Determination of exact aetiology of cardiomyopathy can be difficult but remains important for both treatment and prognosis. Cardiovascular magnetic resonance imaging allows comprehensive assessment of patients suspected to have cardiomyopathy and is therefore being increasingly used in diagnosis and follow-up of these patients. This review presents the main features of common cardiomyopathies on cardiovascular magnetic resonance imaging and highlights its role in providing additional information over and above the traditional diagnostic techniques.
Increased VEGFR-2 Gene Copy Is Associated with Chemoresistance and Shorter Survival in Patients with Non–Small-Cell Lung Carcinoma Who Receive Adjuvant Chemotherapy
Authors: Yang Fei , Tang Ximing , Riquelme Erick , Behrens Carmen , Nilsson Monique B. , Giri Uma , Varella-Garcia Marileila , Byers Lauren A. , Lin Heather Y. , Wang Jing , Raso Maria G. , Girard Luc , Coombes Kevin , Lee J. Jack , Herbst Roy S. , Minna John D. , Heymach John V. , Wistuba Ignacio I. 
Published: July 2011

Abstract
VEGF receptor-2 (VEGFR-2 or kinase insert domain receptor; KDR) is a known endothelial target also expressed in NSCLC tumor cells. We investigated the association between alterations in the KDR gene and clinical outcome in patients with resected non–small-cell lung carcinoma (NSCLC; n = 248). KDR copy number gains (CNG), measured by quantitative PCR and fluorescence in situ hybridization, were detected in 32% of tumors and associated with significantly higher KDR protein and higher microvessel density than tumors without CNGs. KDR CNGs were also associated with significantly increased risk of death (HR = 5.16; P = 0.003) in patients receiving adjuvant platinum-based chemotherapy, but no differences were observed in patients not receiving adjuvant therapy. To investigate potential mechanisms for these associations, we assessed NSCLC cell lines and found that KDR CNGs were significantly associated with in vitro resistance to platinum chemotherapy as well as increased levels of nuclear hypoxia inducible factor-1α (HIF-1α) in both NSCLC tumor specimens and cell lines. Furthermore, KDR knockdown experiments using small interfering RNA reduced platinum resistance, cell migration, and HIF-1α levels in cells bearing KDR CNGs, providing evidence for direct involvement of KDR. No KDR mutations were detected in exons 7, 11, and 21 by PCR-based sequencing; however, two variant single nucleotide polymorphism genotypes were associated with favorable overall survival in adenocarcinoma patients. Our findings suggest that tumor cell KDR CNGs may promote a more malignant phenotype including increased chemoresistance, angiogenesis, and HIF-1α levels, and that KDR CNGs may be a useful biomarker for identifying patients at high risk for recurrence after adjuvant therapy, a group that may benefit from VEGFR-2 blockade. Cancer Res; 71(16); 5512–21. ©2011 AACR.
GPR56 Regulates VEGF Production and Angiogenesis during Melanoma Progression
Authors: Yang Liquan , Chen Guangchun , Mohanty Sonali , Scott Glynis , Fazal Fabeha , Rahman Arshad , Begum Shahinoor , Hynes Richard O. , Xu Lei 
Published: July 2011

Abstract
Angiogenesis is a critical step during cancer progression. The VEGF is a major stimulator for angiogenesis and is predominantly contributed by cancer cells in tumors. Inhibition of the VEGF signaling pathway has shown promising therapeutic benefits for cancer patients, but adaptive tumor responses are often observed, indicating the need for further understanding of VEGF regulation. We report that a novel G protein–coupled receptor, GPR56, inhibits VEGF production from the melanoma cell lines and impedes melanoma angiogenesis and growth, through the serine threonine proline-rich segment in its N-terminus and a signaling pathway involving protein kinase Cα. We also present evidence that the two fragments of GPR56, which are generated by autocatalyzed cleavage, played distinct roles in regulating VEGF production and melanoma progression. Finally, consistent with its suppressive roles in melanoma progression, the expression levels of GPR56 are inversely correlated with the malignancy of melanomas in human subjects. We propose that components of the GPR56-mediated signaling pathway may serve as new targets for antiangiogenic treatment of melanoma. Cancer Res; 71(16); 5558–68. ©2011 AACR.
Overexpression of MBD2 in Glioblastoma Maintains Epigenetic Silencing and Inhibits the Antiangiogenic Function of the Tumor Suppressor Gene BAI1
Authors: Zhu Dan , Hunter Stephen B. , Vertino Paula M. , Van Meir Erwin G. 
Published: July 2011

Abstract
Brain angiogenesis inhibitor 1 (BAI1) is a putative G protein–coupled receptor with potent antiangiogenic and antitumorigenic properties that is mutated in certain cancers. BAI1 is expressed in normal human brain, but it is frequently silenced in glioblastoma multiforme. In this study, we show that this silencing event is regulated by overexpression of methyl-CpG–binding domain protein 2 (MBD2), a key mediator of epigenetic gene regulation, which binds to the hypermethylated BAI1 gene promoter. In glioma cells, treatment with the DNA demethylating agent 5-aza-2′-deoxycytidine (5-Aza-dC) was sufficient to reactivate BAI1 expression. Chromatin immunoprecipitation showed that MBD2 was enriched at the promoter of silenced BAI1 in glioma cells and that MBD2 binding was released by 5-Aza-dC treatment. RNA interference–mediated knockdown of MBD2 expression led to reactivation of BAI1 gene expression and restoration of BAI1 functional activity, as indicated by increased antiangiogenic activity in vitro and in vivo. Taken together, our results suggest that MBD2 overexpression during gliomagenesis may drive tumor growth by suppressing the antiangiogenic activity of a key tumor suppressor. These findings have therapeutic implications because inhibiting MBD2 could offer a strategy to reactivate BAI1 and suppress glioma pathobiology. Cancer Res; 71(17); 5859–70. ©2011 AACR.