bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Approaches for Isolation of Previously Uncultivated Oral Bacteria
Authors: Sizova M. V. , Hohmann T. , Hazen A. , Paster B. J. , Halem S. R. , Murphy C. M. , Panikov N. S. , Epstein S. S. 
Published: November 2011

ABSTRACT

A significant number of microorganisms from the human oral cavity remain uncultivated. This is a major impediment to the study of human health since some of the uncultivated species may be involved in a variety of systemic diseases. We used a range of innovations previously developed to cultivate microorganisms from the human oral cavity, focusing on anaerobic species. These innovations include (i)
in vivo
cultivation to specifically enrich for species actively growing in the oral cavity (the “minitrap” method), (ii) single-cell long-term cultivation to minimize the effect of fast-growing microorganisms, and (iii) modifications of conventional enrichment techniques, using media that did not contain sugar, including glucose. To enable cultivation of obligate anaerobes, we maintained strict anaerobic conditions in most of our cultivation experiments. We report that, on a per cell basis, the most successful recovery was achieved using minitrap enrichment (11%), followed by single-cell cultivation (3%) and conventional plating (1%). Taxonomically, the richest collection was obtained using the single-cell cultivation method, followed by minitrap and conventional enrichment, comprising representatives of 13, 9, and 4 genera, respectively. Interestingly, no single species was isolated by all three methods, indicating method complementarity. An important result is the isolation and maintenance in pure culture of 10 strains previously only known by their molecular signatures, as well as representatives of what are likely to be three new microbial genera. We conclude that the ensemble of new methods we introduced will likely help close the gap between cultivated and uncultivated species from the human oral cavity.
Molecular Survey and Genetic Identification of Anaplasma Species in Goats from Central and Southern China
Authors: Liu Zhijie , Ma Miling , Wang Zhaowen , Wang Jing , Peng Yulv , Li Youquan , Guan Guiquan , Luo Jianxun , Yin Hong 
Published: November 2011

ABSTRACTAnaplasmaspecies are obligate intracellular rickettsial pathogens that impact the health of humans and animals. Few studies have been carried out onAnaplasmainfections in central and southern China. This study was conducted to determine the coinfection rates ofAnaplasma ovis,A. bovis, andA. phagocytophilumfrom 262 field blood samples of goats in these regions. The average prevalences of single infection ofA. ovis,A. bovis, andA. phagocytophilumwere 15.3, 16.0, and 6.1%, respectively. Coinfection ofA. ovisandA. boviswas dominant, with an infection rate of 27.1%. Coinfection ofA. ovisandA. phagocytophilumwas 1.9% and that ofA. bovisandA. phagocytophilumwas 4.2%. Three-pathogen coinfection was found in three of four investigated provinces with a prevalence between 0 and 5.3%. The accuracy of the PCR results was corroborated by sequencing. Analysis of the 16S rRNA gene sequences ofA. bovisandA. phagocytophilumconfirmed the presence of these pathogens at the investigated sites and indicated the possible genetic diversity ofA. phagocytophilum. Field blood inoculation of experimental animals led to successful identification and observation of the morphological shapes ofA. bovisin the infected monocytes of sheep. Phylogenetic study withmsp4sequences ofA. ovisindicated that theA. ovisgenotypes from sheep in the north differed from the genotypes of goats in the investigated sites.
The Neurospora crassa DCC-1 Protein, a Putative Histidine Kinase, Is Required for Normal Sexual and Asexual Development and Carotenogenesis
Authors: Barba-Ostria Carlos , Lledías Fernando , Georgellis Dimitris 
Published: November 2011

ABSTRACT

Two-component signaling pathways based on phosphoryl group transfer between histidine kinase and response regulator proteins regulate environmental responses in bacteria, archaea, plants, slime molds, and fungi. Here we characterize a mutant form of DCC-1, a putative histidine kinase encoded by the NCU00939 gene of the filamentous fungus
Neurospora crassa
. We show that this protein participates in the regulation of processes such as conidiation, perithecial development, and, to a certain degree, carotenogenesis. Furthermore, DCC-1 is suggested to exert its effect by promoting cyclic AMP production, thereby placing this protein within the context of a signaling pathway.
FtsZ-ZapA-ZapB Interactome of Escherichia coli
Authors: Galli Elisa , Gerdes Kenn 
Published: November 2011

ABSTRACT

Bacterial cell division relies on the formation and contraction of the Z ring, coordinated and regulated by a dynamic protein complex called the divisome. The cell division factor ZapA interacts directly with FtsZ and thereby increases FtsZ protofilament association and Z-ring stability. Here, we investigated ZapB interaction with ZapA and its effect on Z-ring formation and FtsZ protofilament bundling. The combination of the
ftsZ84
allele that encodes an FtsZ variant that polymerizes inefficiently with a
zapB
null mutant resulted in a synthetic defective phenotype. Overproduction of ZapA led to the formation of aberrant FtsZ helical structures and delocalization of ZapB. The N-terminal end of ZapB was essential for ZapB-ZapA interaction, and amino acid changes close to the N terminus of ZapB exhibited reduced interaction with ZapA. Sedimentation assays showed that ZapB interacts strongly with ZapA and reduces ZapA's interaction with FtsZ
in vitro
. The morphology of the structures formed by ZapA and ZapB together was similar to the cables formed by ZapB in the presence of CaCl
2
, a known ZapB bundling agent. The
in vivo
and
in vitro
data support a model in which ZapA interacts strongly with ZapB and the ZapA-ZapB interaction is favored over ZapA-FtsZ.
Rhodobacter sphaeroides Uses a Reductive Route via Propionyl Coenzyme A To Assimilate 3-Hydroxypropionate
Authors: Schneider Kathrin , Asao Marie , Carter Michael S. , Alber Birgit E. 
Published: November 2011

ABSTRACT

3-Hydroxypropionate is a product or intermediate of the carbon metabolism of organisms from all three domains of life. However, little is known about how carbon derived from 3-hydroxypropionate is assimilated by organisms that can utilize this C
3
compound as a carbon source. This work uses the model bacterium
Rhodobacter sphaeroides
to begin to elucidate how 3-hydroxypropionate can be incorporated into cell constituents. To this end, a quantitative assay for 3-hydroxypropionate was developed by using recombinant propionyl coenzyme A (propionyl-CoA) synthase from
Chloroflexus aurantiacus
. Using this assay, we demonstrate that
R. sphaeroides
can utilize 3-hydroxypropionate as the sole carbon source and energy source. We establish that acetyl-CoA is not the exclusive entry point for 3-hydroxypropionate into the central carbon metabolism and that the reductive conversion of 3-hydroxypropionate to propionyl-CoA is a necessary route for the assimilation of this molecule by
R. sphaeroides
. Our conclusion is based on the following findings: (i) crotonyl-CoA carboxylase/reductase, a key enzyme of the ethylmalonyl-CoA pathway for acetyl-CoA assimilation, was not essential for growth with 3-hydroxypropionate, as demonstrated by mutant analyses and enzyme activity measurements; (ii) the reductive conversion of 3-hydroxypropionate or acrylate to propionyl-CoA was detected in cell extracts of
R. sphaeroides
grown with 3-hydroxypropionate, and both activities were upregulated compared to the activities of succinate-grown cells; and (iii) the inactivation of
acuI
, encoding a candidate acrylyl-CoA reductase, resulted in a 3-hydroxypropionate-negative growth phenotype.
Roles of Endonuclease V, Uracil-DNA Glycosylase, and Mismatch Repair in Bacillus subtilis DNA Base-Deamination-Induced Mutagenesis
Authors: López-Olmos Karina , Hernández Martha P. , Contreras-Garduño Jorge A. , Robleto Eduardo A. , Setlow Peter , Yasbin Ronald E. , Pedraza-Reyes Mario 
Published: November 2011

ABSTRACT

The disruption of
ung
, the unique uracil-DNA-glycosylase-encoding gene in
Bacillus subtilis
, slightly increased the spontaneous mutation frequency to rifampin resistance (Rif
r
), suggesting that additional repair pathways counteract the mutagenic effects of uracil in this microorganism. An alternative excision repair pathway is involved in this process, as the loss of YwqL, a putative endonuclease V homolog, significantly increased the mutation frequency of the
ung
null mutant, suggesting that Ung and YwqL both reduce the mutagenic effects of base deamination. Consistent with this notion, sodium bisulfite (SB) increased the Rif
r
mutation frequency of the single
ung
and double
ung
ywqL
strains, and the absence of Ung and/or YwqL decreased the ability of
B. subtilis
to eliminate uracil from DNA. Interestingly, the Rif
r
mutation frequency of single
ung
and
mutSL
(mismatch repair [MMR] system) mutants was dramatically increased in a
ung
knockout strain that was also deficient in MutSL, suggesting that the MMR pathway also counteracts the mutagenic effects of uracil. Since the mutation frequency of the
ung mutSL
strain was significantly increased by SB, in addition to Ung, the mutagenic effects promoted by base deamination in growing
B. subtilis
cells are prevented not only by YwqL but also by MMR. Importantly, in nondividing cells of
B. subtilis
, the accumulations of mutations in three chromosomal alleles were significantly diminished following the disruption of
ung
and
ywqL
. Thus, under conditions of nutritional stress, the processing of deaminated bases in
B. subtilis
may normally occur in an error-prone manner to promote adaptive mutagenesis.
A Rickettsia Genome Overrun by Mobile Genetic Elements Provides Insight into the Acquisition of Genes Characteristic of an Obligate Intracellular Lifestyle
Authors: Gillespie Joseph J. , Joardar Vinita , Williams Kelly P. , Driscoll Timothy , Hostetler Jessica B. , Nordberg Eric , Shukla Maulik , Walenz Brian , Hill Catherine A. , Nene Vishvanath M. , Azad Abdu F. , Sobral Bruno W. , Caler Elisabet 
Published: November 2011

ABSTRACT

We present the draft genome for the
Rickettsia
endosymbiont of
Ixodes scapularis
(REIS), a symbiont of the deer tick vector of Lyme disease in North America. Among
Rickettsia
species (
Alphaproteobacteria: Rickettsiales
), REIS has the largest genome sequenced to date (>2 Mb) and contains 2,309 genes across the chromosome and four plasmids (pREIS1 to pREIS4). The most remarkable finding within the REIS genome is the extraordinary proliferation of mobile genetic elements (MGEs), which contributes to a limited synteny with other
Rickettsia
genomes. In particular, an integrative conjugative element named RAGE (for
Rickettsiales
amplified genetic element), previously identified in scrub typhus rickettsiae (
Orientia tsutsugamushi
) genomes, is present on both the REIS chromosome and plasmids. Unlike the pseudogene-laden RAGEs of
O. tsutsugamushi
, REIS encodes nine conserved RAGEs that include F-like type IV secretion systems similar to that of the
tra
genes encoded in the
Rickettsia bellii
and
R. massiliae
genomes. An unparalleled abundance of encoded transposases (>650) relative to genome size, together with the RAGEs and other MGEs, comprise ∼35% of the total genome, making REIS one of the most plastic and repetitive bacterial genomes sequenced to date. We present evidence that conserved rickettsial genes associated with an intracellular lifestyle were acquired via MGEs, especially the RAGE, through a continuum of genomic invasions. Robust phylogeny estimation suggests REIS is ancestral to the virulent spotted fever group of rickettsiae. As REIS is not known to invade vertebrate cells and has no known pathogenic effects on
I. scapularis
, its genome sequence provides insight on the origin of mechanisms of rickettsial pathogenicity.
Public health on-call in Scotland: how much experience is sufficient?
Authors: McCartney G , Dunbar J K , Morling J , Johnman C , Gilmour H 
Published: November 2011

Abstract

Objectives
To quantify the out-of-hours experience obtained by public health trainees in Scotland and to assess whether this is sufficient to meet the Faculty of Public Health guidelines.

Study design
Prospective survey.

Methods
All public health trainees in Scotland were invited to participate in a prospective survey of out-of-hours experience. Data were collected from March 2009 to March 2010. The variation in the experience between trainees was compared according to the size, urban/rural mix, and deprivation of the population for which they were responsible. The variation in the experiences gained were then compared to the requirements of the Faculty of Public Health.

Results
18 trainees participated from 6 areas, collecting data on 391 shifts and a total of 276 calls. For every 50 shifts the median number of notifications of probable meningococcus was 3.7 and the median number of chemical incidents and Escherichia coli O157 notifications was 0.0. This variation is difficult to interpret because some trainees collected data for only a short period. The variation between trainees was not significantly related to population size, deprivation or rurality. Pooling the data from all trainees, there was a mean of 2.9 probable meningococcus notifications, 2.4 E coli O157 calls, and 0.3 chemical incident calls per 50 shifts.

Conclusions
There is a large and unpredictable degree of variation in the on-call experience of Scottish trainees. The minimum recommended number of on-call shifts may not be adequate to ensure a high proportion of trainees are prepared for unsupervised on-call.
The use of fungicide Nova to mitigate infection of Sphagnum by parasitic fungi in the greenhouse
Authors: Landry J. , Martinez C. , Rochefort L. 
Published: November 2011

A common problem when growing Sphagnum mosses in the greenhouse is the propagation of parasitic fungi. Since no clear procedure is available to correct the situation, the aim of this experiment is to give scientists and growers a tool to control fungi invasions in the greenhouse. First, eight fungicides and the effect of temperature were tested on Petri dishes inoculated with two fungi commonly found in Sphagnum: Lyophyllum palustre (Peck) Singer and Chaetomium sp. To assess Sphagnum tolerance to fungicides, the four most efficient treatments were tested on healthy Sphagnum carpet, at maximum and minimum concentrations. Finally, the most promising fungicide, Nova (myclobutanil), was tested on Sphagnum carpets infected by L. palustre and Chaetomium sp. Since the concentration of this fungicide had no effect on biomass accumulation, the maximum concentration (0.54 g/L) was tested. Because of the high absorbency of Sphagnum, Nova was applied at the recommended dose (1 L/10 m2) and at three times the recommended dose (3 L/10 m2). An evaluation of infected Sphagnum individuals was carried out after a frequency of two and three applications. The recommendation for controlling the invasion of Sphagnum by L. palustre and Chaetomium sp. in the greenhouse is the application of Nova fungicide at three times the recommended dose. The frequency of applications had no significant effect.
Childhood Brain Tumors and Maternal Cured Meat Consumption in Pregnancy: Differential Effect by GlutathioneS-Transferases
Authors: Nielsen Susan Searles , Mueller Beth A. , Preston-Martin Susan , Farin Federico M. , Holly Elizabeth A. , McKean-Cowdin Roberta 
Published: November 2011

AbstractBackground: Some epidemiologic studies suggest that maternal consumption of cured meat during pregnancy may increase risk of brain tumors in offspring. We explored whether this possible association was modified by fetal genetic polymorphisms in genes coding for glutathione S-transferases (GSTs) that may inactivate nitroso compounds.Methods: We assessed six GST variants: GSTM1 null, GSTT1 null, GSTP1I105V (rs1695), GSTP1A114V (rs1138272), GSTM3*B (3-bp deletion), and GSTM3A-63C (rs1332018) within a population-based case-control study with data on maternal prenatal cured meat consumption (202 cases and 286 controls born in California or Washington, 1978–1990).Results: Risk of childhood brain tumor increased with increasing cured meat intake by the mother during pregnancy among children without GSTT1 [OR = 1.29; 95% confidence interval (95% CI), 1.07–1.57 for each increase in the frequency of consumption per week] or with potentially reduced GSTM3 (any −63C allele; OR = 1.14; 95% CI, 1.03–1.26), whereas no increased risk was observed among those with GSTT1 or presumably normal GSTM3 levels (interaction P = 0.01 for each).Conclusions: Fetal ability to deactivate nitrosoureas may modify the association between childhood brain tumors and maternal prenatal consumption of cured meats.Impact: These results support the hypothesis that maternal avoidance during pregnancy of sources of some nitroso compounds or their precursors may reduce risk of brain tumors in some children. Cancer Epidemiol Biomarkers Prev; 20(11); 2413–9. ©2011 AACR.
Nicotine, Carbon Monoxide, and Carcinogen Exposure after a Single Use of a Water Pipe
Authors: Jacob Peyton , Raddaha Ahmad H. Abu , Dempsey Delia , Havel Christopher , Peng Margaret , Yu Lisa , Benowitz Neal L. 
Published: November 2011

Abstract
Background: Smoking tobacco preparations in a water pipe (hookah) is widespread in many places of the world, including the United States, where it is especially popular among young people. Many perceive water pipe smoking to be less hazardous than cigarette smoking. We studied systemic absorption of nicotine, carbon monoxide, and carcinogens from one water pipe smoking session.
Methods: Sixteen subjects smoked a water pipe on a clinical research ward. Expired carbon monoxide and carboxyhemoglobin were measured, plasma samples were analyzed for nicotine concentrations, and urine samples were analyzed for the tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1- butanol (NNAL) and polycyclic aromatic hydrocarbon (PAH) metabolite biomarker concentrations.
Results: We found substantial increases in plasma nicotine concentrations, comparable to cigarette smoking, and increases in carbon monoxide levels that are much higher than those typically observed from cigarette smoking, as previously published. Urinary excretion of NNAL and PAH biomarkers increased significantly following water pipe smoking.
Conclusions: Absorption of nicotine in amounts comparable to cigarette smoking indicates a potential for addiction, and absorption of significant amounts of carcinogens raise concerns of cancer risk in people who smoke tobacco products in water pipes.
Impact: Our data contribute to an understanding of the health impact of water pipe use. Cancer Epidemiol Biomarkers Prev; 20(11); 2345–53. ©2011 AACR.
Circulation of Progenitor Cells in Obese and Lean Colorectal Cancer Patients
Authors: Bellows Charles F. , Zhang Yan , Chen Jinyun , Frazier Marsha L. , Kolonin Mikhail G. 
Published: November 2011

Abstract
Background: Colorectal cancer (CRC) is a common life-threatening malignancy; risk and progression are elevated in obesity. The purpose of this study was to measure the frequency of circulating CD34-positive endothelial and progenitor cells in the circulation and evaluate their potential values as CRC biomarkers.
Methods: Blood was collected from 45 patients with CRC and compared with cancer-free control donors. Detection and enumeration of cells was carried out by flow cytometry on the basis of immunophenotypes established for the cell populations of interest: hematopoietic and endothelial circulating progenitor cells, endothelial cells, mesenchymal stromal cells (MSC), and CD34bright leukocytes (CD34b LC). Groups were compared using multivariate regression analysis. Receiver-operating characteristic (ROC) curve analysis was used to evaluate the diagnostic values.
Results: After adjusting for age and body mass index (BMI), the mean frequencies of MSCs and CD34b LCs were significantly higher in the circulation of patients with CRC than in controls. The areas under the ROC curve were 0.77 and 0.82 for MSCs and CD34b LCs, respectively. The frequency of circulating MSCs, but not of the other cell populations, was also found to be significantly higher in the circulation of obese patients with CRC (BMI ≥ 30 kg/m2) than in lean patients with CRC and obese controls.
Conclusions: Increased frequency of MSCs and CD34b LCs in the peripheral blood may represent a new diagnostic marker for CRC.
Impact: BMI-dependent changes in circulating MSCs, potentially mobilized from white adipose tissue may reveal their trafficking to tumors, which could be one of the mechanistic links between obesity and cancer progression. Cancer Epidemiol Biomarkers Prev; 20(11); 2461–8. ©2011 AACR.
Tumor Suppressor MicroRNA-493 Decreases Cell Motility and Migration Ability in Human Bladder Cancer Cells by Downregulating RhoC and FZD4
Authors: Ueno Koji , Hirata Hiroshi , Majid Shahana , Yamamura Soichiro , Shahryari Varahram , Tabatabai Z. Laura , Hinoda Yuji , Dahiya Rajvir 
Published: November 2011

Abstract
The purpose of this study was to identify new tumor suppressor microRNAs (miRNA; miR) in bladder cancer, conduct functional analysis of their suppressive role, and identify their specific target genes. To explore tumor suppressor miRs in bladder cancer, miR microarray was conducted using SV-HUC-1, T24, J82, and TCCSUP cells. Expression of miR-493 in bladder cancer (T24, J82, and TCCSUP) cells was downregulated compared with normal SV-HUC-1 cells. Also, the expression of miR-493 was significantly lower in bladder cancer tissues than in their corresponding noncancerous tissues. Transfection of miR-493 into T24 or J82 cells decreased their cell growth and migration abilities. On the basis of this result, to identify potential miR-493 target genes, we used target scan algorithms to identify target oncogenes related to invasion and migration. miR-493 decreased 3′-untranslated region luciferase activity and protein expression of FZD4 and RhoC. miR-493 also decreased binding of RhoC and Rock-1. miR-493 is a new tumor suppressor miRNA in bladder cancer and inhibits cell motility through downregulation of RhoC and FZD4. Mol Cancer Ther; 11(1); 244–53. ©2011 AACR.