bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is dispersal guided by the environment? A comparison of interspecific gene flow estimates among differentiated regions of a newt hybrid zone
Authors: Espregueira Themudo G. , Nieman A. M. , Arntzen J. W. 
Published: September 2012

AbstractHow frequently genes pass through a hybrid zone may be influenced by the environment. Accordingly, in long hybrid zones that span more than one environmental setting, different patterns may emerge. The varied conditions allow testing of hypotheses on dispersal as a function of the environment. We reconstruct the amount and direction of gene flow across a heterogeneous hybrid zone of two species of marbled newts (Triturus marmoratusandTriturus pygmaeus), in four widely separated areas of theIberianPeninsula from one mitochondrial and three nuclear genes. The main variables associated with the position of the contact zone are precipitation, rivers, altitude and relief. In some sections of the contact zone, however, its position is not correlated with any environmental factor and is instead determined by the shortest geographical distance between fixed positions at either side (mountains in theEast and river in theWest). In areas where the position of the zone is stable, gene flow was bidirectional. External data show thatT. pygmaeushas supersededT. marmoratusover a large area and here gene flow was unidirectional. The prediction that a major river would reduce gene flow was not confirmed.
Asexual reproduction in introduced and native populations of the ant Cerapachys biroi
Authors: Kronauer Daniel J. C. , Pierce Naomi E. , Keller Laurent 
Published: September 2012

AbstractAsexual reproduction is particularly common among introduced species, probably because it helps to overcome the negative effects associated with low population densities during colonization. The ant Cerapachys biroi has been introduced to tropical and subtropical islands around the world since the beginning of the last century. In this species, workers can reproduce via thelytokous parthenogenesis. Here, we use genetic markers to reconstruct the history of anthropogenic introductions of C. biroi, and to address the prevalence of female parthenogenesis in introduced and native populations. We show that at least four genetically distinct lineages have been introduced from continental Asia and have led to the species' circumtropical establishment. Our analyses demonstrate that asexual reproduction dominates in the introduced range and is also common in the native range. Given that C. biroi is the only dorylomorph ant that has successfully become established outside of its native range, this unusual mode of reproduction probably facilitated the species' worldwide spread. On the other hand, the rare occurrence of haploid males and at least one clear case of sexual recombination in the introduced range show that C. biroi has not lost the potential for sex. Finally, we show that thelytoky in C. biroi probably has a genetic rather than an infectious origin, and that automixis with central fusion is the most likely underlying cytological mechanism. This is in accordance with what is known for other thelytokous eusocial Hymenoptera.
Splenocyte apoptosis in Plasmodium berghei ANKA infection: possible role of TNF‐α and TGF‐β
Authors: Keswani T. , Bhattacharyya A. 
Published: September 2012

SummaryCerebral malaria is associated with the circulating levels of tumour necrosis factor alpha (TNF‐α) and transforming growth factor β (TGF‐β), but association between these two cytokines and implications in splenocyte apoptosis remain largely obscured. We have evaluated the outcome of TGF‐β and TNF‐α production in the context of splenocyte apoptosis during Plasmodium berghei ANKA (PbA) infection. Blood‐stage PbA infection confirmed blood–brain barrier disruption, disarray of white pulp, increase in percentage of sub‐G0/G1 and splenocyte apoptosis. Flow cytometric analysis reveals up‐regulation of Fas‐L followed by caspase‐8 and caspase‐3 activation and signifies possible involvement of Fas‐L‐mediated splenocyte apoptosis. We have observed down‐regulation of TGF‐β and up‐regulation of TNF‐α in tissue and serum level, respectively, during PbA infection. Association between the production of TGF‐β and the severity of malaria infection in splenocytes was verified with TGF‐β inhibitor that exacerbated the apoptotic process. In contrary, TNF‐α inhibitor causes significant delay in apoptotic process, but could not alter the lethality of parasite. Thus, results from this study suggest that the critical balance between TGF‐β and TNF‐α might have a key role on Fas‐L‐mediated splenocyte apoptosis during experimental cerebral malaria.
The antiapoptotic activity of Heligmosomoides polygyrus antigen fractions
Authors: Doligalska M. , Brodaczewska K. , Donskow‐ Łysoniewska K. 
Published: September 2012

SummaryOur study identified Heligmosomoides polygyrus antigen factors with potential activity for regulation of T‐cell proliferation and surviving of CD4+CD25−, CD4+CD25hi and CD3+CD8+ cell populations. The antiapoptotic activity of antigenic fractions separated by HPLC was evaluated in vitro after exposure of cells to DEX and rTNF‐α. Different populations of cells responded to antigen fractions in distinct pattern; the most sensitive population of cells to H. polygyrus products were CD4+CD25hi after exposure to DEX and CD3+CD8+ T cells after exposure to rTNF‐α. H. polygyrus antigens may influence survival of CD8+ T cells by regulation of c‐FLIP rather than Bcl‐2, which affects survival of CD4+CD25hi Treg cells and CD4+ T cells. Activation of NF‐κB subunits, for example, p50 and p65 was essential for resistance of cells to apoptosis, and antigenic fractions F9 and F17 exerted different effect to F13. The most active fraction in inhibition of apoptosis was F9, which includes Hsp‐60, calumenin, ferritin, galectin and thrombospondin. This study may provide new clues for recognition of factors that regulate the immune response during infection and which engage the TNF‐α receptor‐mediated and the mitochondria‐mediated death pathway.
Cardiac damage induced by immunization with heat‐killed Trypanosoma cruzi is not antibody mediated
Authors: Bonney K. M. , Gifford K. M. , Taylor J. M. , Chen C.‐I. , Engman D. M. 
Published: September 2012

SummaryCardiac inflammation that develops during infection with Trypanosoma cruzi may result in part from autoimmunity, which may occur after bystander activation, after parasite‐induced cardiomyocyte damage, or molecular mimicry. A/J mice infected with T. cruzi or immunized with heat‐killed T. cruzi (HKTC) develop strong autoimmunity accompanied by cardiac damage. To determine whether this cardiac damage occurs via an antibody‐dependent mechanism, we analysed T. cruzi‐infected and HKTC‐immunized mice for the presence of autoantibodies, cardiac antibody deposition, and serum cardiac troponin I as a measure of cardiac damage. We also performed a serum transfer experiment in which sera from T. cruzi‐infected and T. cruzi‐immunized mice (and controls) were transferred into naïve recipients, which were then analysed for the presence of antibodies and serum troponin. Unlike T. cruzi‐infected mice, T. cruzi‐immunized mice did not show significant antibody deposition in the myocardium. These results indicate that antibody deposition does not precede cardiac damage and inflammation in mice immunized with or infected with T. cruzi. Serum adoptive transfer did not induce cardiac damage in any recipients. Based on these findings, we conclude that the cardiac damage induced by immunization with HKTC is not mediated by antibodies.
Analysis of serum cytokine levels in children with chronic cough associated with Toxocara canis infection
Authors: Nagy D. , Bede O. , Danka J. , SzÉnási Z. , Sipka S. 
Published: September 2012

SummaryToxocara infection is associated with an increased prevalence of airway symptoms and may be a possible aetiologic agent of chronic cough. The occurrence of toxocariasis in Hungary is mild and/or sporadic. The purpose of this study was to investigate the levels of serum cytokines (IL‐1, IL‐2, IL‐4, IL‐5, IL‐6, IL‐10, IL‐13, IFN‐gamma and TNF‐alpha) and total IgE, the blood eosinophil count, the results of skin prick and non‐specific bronchus provocation tests in Toxocara‐seropositive children with chronic cough relative to those in healthy controls. The patients exhibited moderate eosinophilia, significantly elevated levels of serum total IgE, IL‐6, IL‐10, IL‐13 and IFN‐gamma, and higher skin reactivity to common allergens, whereas the bronchial hyperreactivity was similar in the two groups. The protective proinflammatory cytokines (IL‐6, IFN‐gamma and IL‐13) in association with the anti‐inflammatory cytokine (IL‐10) were simultaneously increased in Toxocara‐infected children with chronic cough. During infections, the activation and suppression of immune processes occur simultaneously and cytokines of Th1/Th2 and regulatory T cells contribute to the regulation of the immune response evoked by helminth infections (depending on the parasite load, the timing and duration of the infection and the status of the host immune system).
A method of dose reconstruction for moving targets compatible with dynamic treatments
Authors: Poulsen Per Rugaard , Schmidt Mai Lykkegaard , Keall Paul , Worm Esben Schjødt , Fledelius Walther , Hoffmann Lone 
Published: September 2012

Purpose:To develop a method that allows a commercial treatment planning system (TPS) to perform accurate dose reconstruction for rigidly moving targets and to validate the method in phantom measurements for a range of treatments including intensity modulated radiation therapy (IMRT), volumetric arc therapy (VMAT), and dynamic multileaf collimator (DMLC) tracking.Methods:An in‐house computer program was developed to manipulate Dicom treatment plans exported from a TPS (Eclipse, Varian Medical Systems) such that target motion during treatment delivery was incorporated into the plans. For each treatment, a motion including plan was generated by dividing the intratreatment target motion into 1 mm position bins and construct sub‐beams that represented the parts of the treatment that were delivered, while the target was located within each position bin. For each sub‐beam, the target shift was modeled by a corresponding isocenter shift. The motion incorporating Dicom plans were reimported into the TPS, where dose calculation resulted in motion including target dose distributions. For experimental validation of the dose reconstruction a thorax phantom with a moveable lung equivalent rod with a tumor insert of solid water was first CT scanned. The tumor insert was delineated as a gross tumor volume (GTV), and a planning target volume (PTV) was formed by adding margins. A conformal plan, two IMRT plans (step‐and‐shoot and sliding windows), and a VMAT plan were generated giving minimum target doses of 95% (GTV) and 67% (PTV) of the prescription dose (3 Gy). Two conformal fields with MLC leaves perpendicular and parallel to the tumor motion, respectively, were generated for DMLC tracking. All treatment plans were delivered to the thorax phantom without tumor motion and with a sinusoidal tumor motion. The two conformal fields were delivered with and without portal image guided DMLC tracking based on an embedded gold marker. The target dose distribution was measured with a radiochromic film in the moving rod and compared with the reconstructed doses using gamma tests.Results:Considerable interplay effects between machine motion and target motion were observed for the treatments without tracking. For nontracking experiments, the mean 2 mm/2% gamma pass rate over all investigated scenarios was 99.6% between calculated and measured doses. For tracking experiments, the mean gamma pass rate was 99.4%.Conclusions:A method for accurate dose reconstruction for moving targets with dynamic treatments was developed and experimentally validated in a variety of delivery scenarios. The method is suitable for integration into TPSs, e.g., for reconstruction of the dose delivered to moving tumors or calculation of target doses delivered with DMLC tracking.
Genome Sequence of Lactobacillus ingluviei, a Bacterium Associated with Weight Gain in Animals
Authors: Merhej Vicky , Armougom Fabrice , Robert Catherine , Raoult Didier 
Published: September 2012

ABSTRACT

We report the draft genome sequence of
Lactobacillus ingluviei
strain Autruche 4 (CSURP209) isolated from an ostrich.
L. ingluviei
is associated with weight gain in mice. This genome sequence may help us understand the obesity-induced mechanisms of intestinal bacteria.
Complete Genome Sequence of Amycolatopsis mediterranei S699 Based on
De Novo
Assembly via a Combinatorial Sequencing Strategy
Authors: Tang Biao , Zhao Wei , Zheng Huajun , Zhuo Ying , Zhang Lixin , Zhao Guo-Ping 
Published: September 2012

ABSTRACT

The genome of
Amycolatopsis mediterranei
S699 was resequenced and assembled
de novo
. By comparing the sequences of S699 previously released and that of
A. mediterranei
U32, about 10 kb of major indels was found to differ between the two S699 genomes, and the differences are likely attributable to their different assembly strategies.
Genome Sequence of the Alkaliphilic Bacterium Nitritalea halalkaliphila Type Strain LW7, Isolated from Lonar Lake, India
Authors: Jangir Pramod Kumar , Singh Ajit , Shivaji S. , Sharma Rakesh 
Published: September 2012

ABSTRACT

An alkaliphilic bacterium,
Nitritalea halalkaliphila
LW7, which belongs to the family
Cyclobacteriacae
in the phylum
Bacteroidetes
, was isolated from Lonar Lake in Maharastra, India. Here we announce the draft genome sequence of the type strain LW7, which contains 3,633,701 bp with a G+C content of 48.58%.
Draft Genome Sequences of Two Campylobacter jejuni Clinical Isolates, NW and D2600
Authors: Jerome John P. , Klahn Brian D. , Bell Julia A. , Barrick Jeffrey E. , Brown C. Titus , Mansfield Linda S. 
Published: September 2012

ABSTRACT

The
Campylobacter jejuni
human clinical isolates NW and D2600 colonized C57BL/6 interleukin-10-deficient (IL-10
−/−
) mice without inducing a robust inflammatory response (J. A. Bell et al., BMC Microbiol. 9:57, 2009). We announce draft genome sequences of NW and D2600 to facilitate comparisons with strains that induce gastrointestinal inflammation in this mouse model.
Complete Genome Sequence of Helicobacter cinaedi Type Strain ATCC BAA-847
Authors: Miyoshi-Akiyama Tohru , Takeshita Nozomi , Ohmagari Norio , Kirikae Teruo 
Published: September 2012

ABSTRACT

Here we report the completely annotated genome sequence of the
Helicobacter cinaedi
type strain (ATCC BAA-847), which is an emerging pathogen that causes cellulitis and bacteremia. The genome sequence will provide new insights into the diagnosis, pathogenic mechanisms, and drug resistance of
H. cinaedi
.
Draft Genome Sequence of Weissella koreensis KCTC 3621T
Authors: Lee Je Hee , Bae Jin-Woo , Chun Jongsik 
Published: September 2012

ABSTRACTWeissella koreensisis a Gram-positive, rod-shaped, nonmotile, and facultative anaerobic species belonging to the lactic acid bacteria (LAB). The members of this species have been repeatedly isolated from kimchi (a traditional Korean fermented food) and are known for their beneficial effects on human and animal intestinal microflora through producing various clinically important amino acids such as γ-aminobutyric acid and ornithine. Here we report the genome sequence of the type strain ofW. koreensis(KCTC 3621T) to provide taxonomic and functional insights into the species.
Genome Sequence of Enterococcus sp. Strain C1, an Azo Dye Decolorizer
Authors: Chan Giek Far , Gan Han Ming , Rashid Noor Aini Abdul 
Published: September 2012

ABSTRACT

Enterococcus
sp. strain C1 is a facultative anaerobe which was coisolated with
Citrobacter
sp. strain A1 from a sewage oxidation pond. Strain C1 could degrade azo dyes very efficiently via azo reduction and desulfonation in a microaerophilic environment. Here the draft genome sequence of
Enterococcus
sp. C1 is reported.
Draft Genome Sequence of Klebsiella pneumoniae subsp. pneumoniae DSM 30104
T
Authors: Lee Je Hee , Cheon In Su , Shim Byoung-Shik , Kim Dong Wook , Kim Suhng Wook , Chun Jongsik , Song Manki 
Published: September 2012

ABSTRACT

Klebsiella pneumoniae
is a Gram-negative, rod-shaped, nonmotile, and opportunistic pathogenic species with clinical importance. It is a part of natural flora of humans and animals. Here we report the draft genome sequence of the type strain of
Klebsiella pneumoniae
subsp.
pneumoniae
(DSM 30104
T
) to provide taxonomic and functional insights into the species.
MetR-Regulated Vibrio cholerae Metabolism Is Required for Virulence
Authors: Bogard Ryan W. , Davies Bryan W. , Mekalanos John J. 
Published: September 2012

ABSTRACT

LysR-type transcriptional regulators (LTTRs) are the largest, most diverse family of prokaryotic transcription factors, with regulatory roles spanning metabolism, cell growth and division, and pathogenesis. Using a sequence-defined transposon mutant library, we screened a panel of
V. cholerae
El Tor mutants to identify LTTRs required for host intestinal colonization. Surprisingly, out of 38 LTTRs, only one severely affected intestinal colonization in the suckling mouse model of cholera: the methionine metabolism regulator, MetR. Genetic analysis of genes influenced by MetR revealed that
glyA1
and
metJ
were also required for intestinal colonization. Chromatin immunoprecipitation of MetR and quantitative reverse transcription-PCR (qRT-PCR) confirmed interaction with and regulation of
glyA1
, indicating that misregulation of
glyA1
is likely responsible for the colonization defect observed in the
metR
mutant. The
glyA1
mutant was auxotrophic for glycine but exhibited wild-type trimethoprim sensitivity, making folate deficiency an unlikely cause of its colonization defect. MetJ regulatory mutants are not auxotrophic but are likely altered in the regulation of amino acid-biosynthetic pathways, including those for methionine, glycine, and serine, and this misregulation likely explains its colonization defect. However, mutants defective in methionine, serine, and cysteine biosynthesis exhibited wild-type virulence, suggesting that these amino acids can be scavenged in vivo. Taken together, our results suggest that glycine biosynthesis may be required to alleviate an in vivo nutritional restriction in the mouse intestine; however, additional roles for glycine may exist. Irrespective of the precise nature of this requirement, this study illustrates the importance of pathogen metabolism, and the regulation thereof, as a virulence factor.

IMPORTANCE
Vibrio cholerae
continues to be a severe cause of morbidity and mortality in developing countries. Identification of
V. cholerae
factors critical to disease progression offers the potential to develop or improve upon therapeutics and prevention strategies. To increase the efficiency of virulence factor discovery, we employed a regulator-centric approach to multiplex our in vivo screening capabilities and allow whole regulons in
V. cholerae
to be interrogated for pathogenic potential. We identified MetR as a new virulence regulator and serine hydroxymethyltransferase GlyA1 as a new MetR-regulated virulence factor, both required by
V. cholerae
to colonize the infant mouse intestine. Bacterial metabolism is a prerequisite to virulence, and current knowledge of in vivo metabolism of pathogens is limited. Here, we expand the known role of amino acid metabolism and regulation in virulence and offer new insights into the in vivo metabolic requirements of
V. cholerae
within the mouse intestine.
β-1,3-Glucan, Which Can Be Targeted by Drugs, Forms a Trabecular Scaffold in the Oocyst Walls ofToxoplasmaandEimeria
Authors: Bushkin G. Guy , Motari Edwin , Magnelli Paula , Gubbels Marc-Jan , Dubey Jitender P. , Miska Katarzyna B. , Bullitt Esther , Costello Catherine E. , Robbins Phillips W. , Samuelson John 
Published: September 2012

ABSTRACTThe walls of infectious pathogens, which are essential for transmission, pathogenesis, and diagnosis, contain sugar polymers that are defining structural features, e.g., β-1,3-glucan and chitin in fungi, chitin inEntamoebacysts, β-1,3-GalNAc inGiardiacysts, and peptidoglycans in bacteria. The goal here was to determine in which of three walled forms ofToxoplasma gondii(oocyst, sporocyst, or tissue cyst) is β-1,3-glucan, the product of glucan synthases and glucan hydrolases predicted by whole-genome sequences of the parasite. The three most important discoveries were as follows. (i) β-1,3-glucan is present in oocyst walls ofToxoplasmaandEimeria(a chicken parasite that is a model for intestinal stages ofToxoplasma) but is absent from sporocyst and tissue cyst walls. (ii) Fibrils of β-1,3-glucan are part of a trabecular scaffold in the inner layer of the oocyst wall, which also includes a glucan hydrolase that has a novel glucan-binding domain. (iii) Echinocandins, which target the glucan synthase and kill fungi, arrest development of theEimeriaoocyst wall and prevent release of the parasites into the intestinal lumen. In summary, β-1,3-glucan, which can be targeted by drugs, is an important component of oocyst walls ofToxoplasmabut is not a component of sporocyst and tissue cyst walls.IMPORTANCEWe show here that walls ofToxoplasmaoocysts, the infectious stage shed by cats, contain β-1,3-glucan, a sugar polymer that is a major component of fungal walls. In contrast to fungi, β-1,3-glucan is part of a trabecular scaffold in the inner layer of the oocyst wall that is independent of the permeability barrier formed by the outer layer of the wall. While glucan synthase inhibitors kill fungi, these inhibitors arrest the development of the oocyst walls ofEimeria(an important chicken pathogen that is a surrogate forToxoplasma) and block release of oocysts into the intestinal lumen. The absence of β-1,3-glucan in tissue cysts ofToxoplasmasuggests that drugs targeted at the glucan synthase might be used to treatEimeriain chickens but not to treatToxoplasmain people.
Cardiac testing and outcomes in infants after an apparent life-threatening event
Authors: Hoki Robert , Bonkowsky Joshua L , Minich L LuAnn , Srivastava Rajendu , Pinto Nelangi M 
Published: September 2012

ObjectivesWe sought to determine the yield of cardiac testing and to identify predictors of cardiac disease in infants with an apparent life-threatening event (ALTE).DesignRetrospective longitudinal cohort study.SettingPaediatric hospital providing primary and tertiary care that is part of an integrated healthcare system.PatientsInfants hospitalised for an ALTE from 1999 to 2003.Main exposuresCardiac testing used at time of ALTE and results, and clinical risk factors for cardiac disease.Outcome measuresShort-term (during hospitalisation) and long-term (through November 2009) follow-up for any diagnosis of significant cardiac anatomic or rhythm abnormality.ResultsStudy criteria were met by 485 infants (mean age 1.9, SD±2.2 months; 49% boys). Cardiac testing was performed on 219 (45%) patients during ALTE hospitalisation, identifying two patients with significant cardiac disease (cardiomyopathy, ventricular pre-excitation). During 7.7 years of follow-up, three additional significant cardiac diagnoses (ventricular pre-excitation, frequent ventricular ectopy, moderate aortic stenosis) were identified. All cardiac tests had low positive predictive value (PPV). Significant cardiac disease was associated with prematurity (22% vs 80%, p=0.002), but not age, gender, prior ALTE or rescue breaths.ConclusionsThis longitudinal study of an ALTE cohort revealed significant cardiac disease in <1% of patients. Prematurity was the only clinical predictor identified. ECG was sensitive for identifying significant cardiac disease, but routine testing warrants further investigation because of the low PPV.