bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetically Engineered Immunomodulatory Streptococcus thermophilus Strains Producing Antioxidant Enzymes Exhibit Enhanced Anti-Inflammatory Activities
Authors: del Carmen Silvina , de Moreno de LeBlanc Alejandra , Martin Rebeca , Chain Florian , Langella Philippe , Bermúdez-Humarán Luis G. , LeBlanc Jean Guy 
Published: November 2013

ABSTRACT

The aims of this study were to develop strains of lactic acid bacteria (LAB) having both immunomodulatory and antioxidant properties and to evaluate their anti-inflammatory effects both
in vitro
, in different cellular models, and
in vivo
, in a mouse model of colitis. Different
Lactobacillus delbrueckii
subsp.
bulgaricus
and
Streptococcus thermophilus
strains were cocultured with primary cultures of mononuclear cells. Analysis of the pro- and anti-inflammatory cytokines secreted by these cells after coincubation with candidate bacteria revealed that
L. delbrueckii
subsp.
bulgaricus
CRL 864 and
S. thermophilus
CRL 807 display the highest anti-inflammatory profiles
in vitro
. Moreover, these results were confirmed
in vivo
by the determination of the cytokine profiles in large intestine samples of mice fed with these strains.
S. thermophilus
CRL 807 was then transformed with two different plasmids harboring the genes encoding catalase (CAT) or superoxide dismutase (SOD) antioxidant enzymes, and the anti-inflammatory effects of recombinant streptococci were evaluated in a mouse model of colitis induced by trinitrobenzenesulfonic acid (TNBS). Our results showed a decrease in weight loss, lower liver microbial translocation, lower macroscopic and microscopic damage scores, and modulation of the cytokine production in the large intestines of mice treated with either CAT- or SOD-producing streptococci compared to those in mice treated with the wild-type strain or control mice without any treatment. Furthermore, the greatest anti-inflammatory activity was observed in mice receiving a mixture of both CAT- and SOD-producing streptococci. The addition of
L. delbrueckii
subsp.
bulgaricus
CRL 864 to this mixture did not improve their beneficial effects. These findings show that genetically engineering a candidate bacterium (e.g.,
S. thermophilus
CRL 807) with intrinsic immunomodulatory properties by introducing a gene expressing an antioxidant enzyme enhances its anti-inflammatory activities.
Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes
Authors: Tsaousis Anastasios D. , Gentekaki Eleni , Eme Laura , Gaston Daniel , Roger Andrew J. 
Published: November 2013

ABSTRACT

The cytosolic iron/sulfur cluster assembly (CIA) machinery is responsible for the assembly of cytosolic and nuclear iron/sulfur clusters, cofactors that are vital for all living cells. This machinery is uniquely found in eukaryotes and consists of at least eight proteins in opisthokont lineages, such as animals and fungi. We sought to identify and characterize homologues of the CIA system proteins in the anaerobic stramenopile parasite
Blastocystis
sp. strain NandII. We identified transcripts encoding six of the components—Cia1, Cia2, MMS19, Nbp35, Nar1, and a putative Tah18—and showed using immunofluorescence microscopy, immunoelectron microscopy, and subcellular fractionation that the last three of them localized to the cytoplasm of the cell. We then used comparative genomic and phylogenetic approaches to investigate the evolutionary history of these proteins. While most
Blastocystis
homologues branch with their eukaryotic counterparts, the putative
Blastocystis
Tah18 seems to have a separate evolutionary origin and therefore possibly a different function. Furthermore, our phylogenomic analyses revealed that all eight CIA components described in opisthokonts originated before the diversification of extant eukaryotic lineages and were likely already present in the last eukaryotic common ancestor (LECA). The Nbp35, Nar1 Cia1, and Cia2 proteins have been conserved during the subsequent evolutionary diversification of eukaryotes and are present in virtually all extant lineages, whereas the other CIA proteins have patchy phylogenetic distributions. Cia2 appears to be homologous to SufT, a component of the prokaryotic sulfur utilization factors (SUF) system, making this the first reported evolutionary link between the CIA and any other Fe/S biogenesis pathway. All of our results suggest that the CIA machinery is an ubiquitous biosynthetic pathway in eukaryotes, but its apparent plasticity in composition raises questions regarding how it functions in nonmodel organisms and how it interfaces with various iron/sulfur cluster systems (i.e., the iron/sulfur cluster, nitrogen fixation, and/or SUF system) found in eukaryotic cells.
Mitochondrial and Nucleolar Localization of Cysteine Desulfurase Nfs and the Scaffold Protein Isu in Trypanosoma brucei
Authors: Kovářová Julie , Horáková Eva , Changmai Piya , Vancová Marie , Lukeš Julius 
Published: November 2013

ABSTRACT

Trypanosoma brucei
has a complex life cycle during which its single mitochondrion is subjected to major metabolic and morphological changes. While the procyclic stage (PS) of the insect vector contains a large and reticulated mitochondrion, its counterpart in the bloodstream stage (BS) parasitizing mammals is highly reduced and seems to be devoid of most functions. We show here that key Fe-S cluster assembly proteins are still present and active in this organelle and that produced clusters are incorporated into overexpressed enzymes. Importantly, the cysteine desulfurase Nfs, equipped with the nuclear localization signal, was detected in the nucleolus of both
T. brucei
life stages. The scaffold protein Isu, an interacting partner of Nfs, was also found to have a dual localization in the mitochondrion and the nucleolus, while frataxin and both ferredoxins are confined to the mitochondrion. Moreover, upon depletion of Isu, cytosolic tRNA thiolation dropped in the PS but not BS parasites.
Kinetics of
nif
Gene Expression in a Nitrogen-Fixing Bacterium
Authors: Poza-Carrión César , Jiménez-Vicente Emilio , Navarro-Rodríguez Mónica , Echavarri-Erasun Carlos , Rubio Luis M. 
Published: November 2013

ABSTRACT

Nitrogen fixation is a tightly regulated trait. Switching from N
2
fixation-repressing conditions to the N
2
-fixing state is carefully controlled in diazotrophic bacteria mainly because of the high energy demand that it imposes. By using quantitative real-time PCR and quantitative immunoblotting, we show here how nitrogen fixation (
nif
) gene expression develops in
Azotobacter vinelandii
upon derepression. Transient expression of the transcriptional activator-encoding gene,
nifA
, was followed by subsequent, longer-duration waves of expression of the nitrogenase biosynthetic and structural genes. Importantly, expression timing, expression levels, and NifA dependence varied greatly among the
nif
operons. Moreover, the exact concentrations of Nif proteins and their changes over time were determined for the first time. Nif protein concentrations were exquisitely balanced, with FeMo cofactor biosynthetic proteins accumulating at levels 50- to 100-fold lower than those of the structural proteins. Mutants lacking nitrogenase structural genes or impaired in FeMo cofactor biosynthesis showed overenhanced responses to derepression that were proportional to the degree of nitrogenase activity impairment, consistent with the existence of at least two negative-feedback regulatory mechanisms. The first such mechanism responded to the levels of fixed nitrogen, whereas the second mechanism appeared to respond to the levels of the mature NifDK component. Altogether, these findings provide a framework to engineer N
2
fixation in nondiazotrophs.
Saturating Mutagenesis of an Essential Gene: a Majority of the Neisseria gonorrhoeae Major Outer Membrane Porin (PorB) Is Mutable
Authors: Chen Adrienne , Seifert H. Steven 
Published: November 2013

ABSTRACT

The major outer membrane porin (PorB) of
Neisseria gonorrhoeae
is an essential protein that mediates ion exchange between the organism and its environment and also plays multiple roles in human host pathogenesis. To facilitate structure-function studies of porin's multiple roles, we performed saturating mutagenesis at the
porB
locus and used deep sequencing to identify essential versus mutable residues. Random mutations in
porB
were generated in a plasmid vector, and mutant gene pools were transformed into
N. gonorrhoeae
to select for alleles that maintained bacterial viability. Deep sequencing of the input plasmid pools and the output
N. gonorrhoeae
genomic DNA pools identified mutations present in each, and the mutations in both pools were compared to determine which changes could be tolerated by the organism. We examined the mutability of 328 amino acids in the mature PorB protein and found that 308 of them were likely to be mutable and that 20 amino acids were likely to be nonmutable. A subset of these predictions was validated experimentally. This approach to identifying essential amino acids in a protein of interest introduces an additional application for next-generation sequencing technology and provides a template for future studies of both porin and other essential bacterial genes.
Genomic and Proteomic Studies on Plesiomonas shigelloides Lipopolysaccharide Core Biosynthesis
Authors: Aquilini Eleonora , Merino Susana , Regué Miguel , Tomás Juan M. 
Published: November 2013

ABSTRACT

We report here the identification of
waa
clusters with the genes required for the biosynthesis of the core lipopolysaccharides (LPS) of two
Plesiomonas shigelloides
strains. Both
P. shigelloides
waa
clusters shared all of the genes besides the ones flanking
waaL
. In both strains, all of the genes were found in the
waa
gene cluster, although one common core biosynthetic gene (
wapG
) was found in a different chromosome location outside the cluster. Since
P. shigelloides
and
Klebsiella pneumoniae
share a core LPS carbohydrate backbone extending up at least to the second outer-core residue, the functions of the common
P. shigelloides
genes were elucidated by genetic complementation studies using well-defined
K. pneumoniae
mutants. The function of strain-specific inner- or outer-core genes was identified by using as a surrogate acceptor LPS from three well-defined
K. pneumoniae
core LPS mutants. Using this strategy, we were able to assign a proteomic function to all of the
P. shigelloides
waa
genes identified in the two strains encoding six new glycosyltransferases (WapA, -B, -C, -D, -F, and -G).
P. shigelloides
demonstrated an important variety of core LPS structures, despite being a single species of the genus, as well as high homologous recombination in housekeeping genes.
Factors influencing clinical trial site selection in Europe: the Survey of Attitudes towards Trial sites in Europe (the SAT-EU Study)
Authors: Gehring Marta , Taylor Rod S , Mellody Marie , Casteels Brigitte , Piazzi Angela , Gensini Gianfranco , Ambrosio Giuseppe 
Published: November 2013

ObjectivesApplications to run clinical trials in Europe fell 25% between 2007 and 2011. Costs, speed of approvals and shortcomings of European Clinical Trial Directive are commonly invoked to explain this unsatisfactory performance. However, no hard evidence is available on the actual weight of these factors or has it been previously investigated whether other criteria may also impact clinical trial site selection.DesignThe Survey of Attitudes towards Trial sites in Europe (SAT-EU Study) was an anonymous, cross-sectional web-based survey that systematically assessed factors impacting European clinical trial site selection. It explored 19 factors across investigator-driven, hospital-driven and environment-driven criteria, and costs. It also surveyed perceptions of the European trial environment.Setting and participantsClinical research organisations (CROs), academic clinical trial units (CTUs) and industry invited to respond.Outcome measuresPrimary outcome: weight assigned to each factor hypothesised to impact trial site selection and trial incidence. Secondary outcome: desirability of European countries to run clinical trials.ResultsResponses were obtained from 485 professionals in 34 countries: 49% from BioPharma, 40% from CTUs or CROs. Investigator-dependent, environment-dependent and hospital-dependent factors were rated highly important, costs being less important (p<0.0001). Within environment-driven criteria, pool of eligible patients, speed of approvals and presence of disease-management networks were significantly more important than costs or government financial incentives (p<0.0001). The pattern of response was consistent across respondent groupings (CTU vs CRO vs industry). Considerable variability was demonstrated in the perceived receptivity of countries to undertake clinical trials, with Germany, the UK and the Netherlands rated the best trial markets (p<0.0001).ConclusionsInvestigator-dependent factors and ease of approval dominate trial site selection, while costs appear less important. Fostering competitiveness of European clinical research may not require additional government spending/incentives. Rather, harmonisation of approval processes, greater visibility of centres of excellence and reduction of ‘hidden’ indirect costs, may bring significantly more clinical trials to Europe.
Evidence for the aetiology of human papillomavirus in oesophageal squamous cell carcinoma in the Chinese population: a meta-analysis
Authors: Liyanage Surabhi S , Rahman Bayzidur , Gao Zhanhai , Zheng Yang , Ridda Iman , Moa Aye , Newall Anthony T , Seale Holly , Li Qian , Liu Jun-Feng , MacIntyre C Raina 
Published: November 2013

ObjectivesWe aimed to conduct a meta-analysis of human papillomavirus (HPV) as a risk factor for oesophageal squamous cell carcinoma (OSCC) in China, using all eligible studies published in the English and Chinese language literature.DesignThe random effect model was used to analyse the pooled OR. The I2and Q tests were included in the subgroup analyses.SettingLiterature searches of databases including MEDLINE, PUBMED, EMBASE and Chinese National Knowledge Infrastructure (CNKI) and other available resources were performed to retrieve studies investigating OSCC tissue from Chinese participants for the presence of HPV DNA.Primary outcome measureA collective analysis of OSCC cases and control specimens was carried out from 15 case–control studies (6 in the English language and 9 in the Chinese language) for HPV prevalence.ResultsOf a total of 1177 OSCC and 1648 oesophageal control samples, 55% (642/1177) of cancer specimens and 27% (445/1648) of control samples were positive for HPV DNA. A positive strong association between HPV DNA and OSCC was observed among the included studies, with a pooled OR of 3.69 (95% CI 2.74 to 4.96). Heterogeneity and publication bias were not observed in the analysis. Subgroup analyses of the included studies also supported the measure of association of causal links between HPV and OSCC.ConclusionsThis meta-analysis provides the strongest evidence until now of an association between HPV and OSCC in the Chinese population. China has a high burden of OSCC, making this an important research finding. A strength and new contribution of this study is combining data from the English and Chinese language literature to analyse all studies conducted in China. These findings may inform the population level use of prophylactic HPV vaccination to reduce the burden of OSCC in China.
Nurse and manager perceptions of nurse initiated and managed antiretroviral therapy (NIMART) implementation in South Africa: a qualitative study
Authors: Davies Natasha Elaine Claire Garai , Homfray Mike , Venables Emilie Charlotte 
Published: November 2013

ObjectiveTo explore nurse and facility and programme manager perceptions of nurse initiated and managed antiretroviral therapy (NIMART) implementation in Gauteng, South Africa.DesignIn this qualitative study, in-depth interviews and focus group discussions were conducted to gain insight into participants’ experiences of NIMART implementation.SettingParticipants came from urban, peri-urban and rural primary healthcare clinics in two Gauteng Province municipalities.Participants25 nurses and 18 managers who were actively involved in NIMART implementation were purposively sampled.ResultsThe findings from this study reveal that, despite encountering numerous challenges including human resources, training and clinical mentoring and health systems issues, NIMART nurses and managers remained optimistic about their work. Study participants felt empowered by their expanded roles. Increased responsibilities associated with NIMART implementation encouraged better use of creative problem-solving and teamwork to facilitate integration of NIMART into existing clinic services. NIMART nurses perceived antiretroviral therapy (ART) patients to be more insightful about their illness, engaged in their HIV treatment and aware of the importance of adherence which enhanced nurse–patient relationships and increased their sense of job satisfaction.ConclusionsAlthough the implementation of NIMART is complex, when NIMART is implemented well, ART access is increased and patient outcomes are improved. Supportive interventions which address the specific challenges faced by nurses providing NIMART now need to be implemented. Attempts should be made to replicate the positive aspects of NIMART implementation identified by participants as this may improve healthcare providers’ experiences of task-shifting.
The impact of new prehospital practitioners on ambulance transportation to the emergency department: a systematic review and meta-analysis
Authors: Tohira Hideo , Williams Teresa A , Jacobs Ian , Bremner Alexandra , Finn Judith 
Published: November 2013

ObjectiveTo conduct a systematic review and meta-analysis to examine the impact of new prehospital practitioners (NPPs), including emergency care practitioners (EmCPs), paramedic practitioners and extended care paramedics (ECPs), on ambulance transportation to the emergency department (ED).MethodsWe searched MEDLINE, Embase, CINAHL and AUSTHealth databases, and hand searched emergency medicine journals and journal reference lists for relevant papers. To be included, studies were required to target one type of NPP and compare outcomes such as the frequencies of conveyance to the ED, discharge at scene, subsequent ED attendance and/or appropriateness of care between NPPs and conventional ambulance crews. Three investigators independently selected relevant studies. The risk of bias in individual studies was assessed using a validated checklist. We conducted meta-analyses for comparisons which had acceptable heterogeneity (I2<75%) and reported pooled estimates of ORs with 95% CIs.Results13 studies were identified from 16 584 citation reports. EmCPs were most frequently studied. The majority of studies (77%) did not fully report important potential confounders. NPPs were less likely to convey patients to the ED and more likely to discharge patients at the scene than conventional ambulance crews. Pooled ORs for conveyance to the ED and discharge at the scene by ECPs were 0.09 (95% CI 0.04 to 0.18) and 10.5 (95% CI 5.8 to 19), respectively. The evidence for subsequent ED attendance and appropriateness of care was equivocal.ConclusionsThe NPP schemes reduced transport to the ED; however, the appropriateness of the decision of the NPPs and the safety of patients were not well supported by the reported studies.
A Novel EGFR Isoform Confers Increased Invasiveness to Cancer Cells
Authors: Zhou Min , Wang Hai , Zhou Keke , Luo Xiaoying , Pan Xiaorong , Shi Bizhi , Jiang Hua , Zhang Jiqin , Li Kesang , Wang Hua-Mao , Gao Huiping , Lu Shun , Yao Ming , Mao Ying , Wang Hong-Yang , Yang Shengli , Gu Jianren , Li Chuanyuan , Li Zonghai 
Published: November 2013

Abstract
As a validated therapeutic target in several human cancers, the EGF receptor (EGFR) provides a focus to gain deeper insights into cancer pathophysiology. In this study, we report the identification of a naturally occurring and widely expressed EGFR isoform termed EGFRvA, which substitutes a Ser/Thr-rich peptide for part of the carboxyl-terminal regulatory domain of the receptor. Intriguingly, EGFRvA expression relates more closely to histopathologic grade and poor prognosis in patients with glioma. Ectopic expression of EGFRvA in cancer cells conferred a higher invasive capacity than EGFR in vitro and in vivo. Mechanistically, EGFRvA stimulated expression of STAT3, which upregulated heparin-binding EGF (HB-EGF). Reciprocally, HB-EGF stimulated phosphorylation of EGFRvA at Y845 along with STAT3, generating a positive feedback loop that may reinforce invasive function. The significance of EGFRvA expression was reinforced by findings that it is attenuated by miR-542-5p, a microRNA that is a known tumor suppressor. Taken together, our findings define this newfound EGFR isoform as a key theranostic molecule. Cancer Res; 73(23); 7056–67. ©2013 AACR.
Targeting Small Cell Lung Cancer Harboring PIK3CA Mutation with a Selective Oral PI3K Inhibitor PF-4989216
Authors: Walls Marlena , Baxi Sangita M. , Mehta Pramod P. , Liu Kevin K.-C. , Zhu JinJiang , Estrella Heather , Li Chunze , Zientek Michael , Zong Qing , Smeal Tod , Yin Min-Jean 
Published: November 2013

Abstract
Purpose: Constitutive activation of phosphoinositide 3-kinase (PI3K) occurs frequently in many human tumors via either gene mutation in the p110α catalytic subunit of PI3K or functional loss of tumor suppressor PTEN. Patients with small-cell lung cancer (SCLC) have very poor prognosis and survival rates such that an effective targeted therapy is in strong demand for these patients. In this study, we characterized the highly selective oral PI3K inhibitor, PF-4989216, in preclinical SCLC models to investigate whether targeting the PI3K pathway is an effective targeted therapy option for SCLCs that harbor a PIK3CA mutation.
Experimental Design: A panel of SCLC cell lines with PIK3CA mutation or PTEN loss were treated with PF-4989216 in several in vitro assays, including PI3K pathway signaling, cell viability, apoptosis, cell-cycle progression, and cell transformation. SCLC cell lines that were sensitive in vitro to PF-4989216 were further evaluated by in vivo animal studies to determine the pharmacokinetic/pharmacodynamic relationship and tumor growth inhibition (TGI) by PF-4989216 treatment.
Results: PF-4989216 inhibited PI3K downstream signaling and subsequently led to apoptosis induction, and inhibition in cell viability, transformation, and xenograft tumor growth in SCLCs harboring PIK3CA mutation. In SCLCs with PTEN loss, PF-4989216 also inhibited PI3K signaling but did not induce BCL2-interacting mediator (BIM)-mediated apoptosis nor was there any effect on cell viability or transformation. These results implicate differential tumorigenesis and apoptosis mechanisms in SCLCs harboring PIK3CA mutation versus PTEN loss.
Conclusions: Our results suggest that PF-4989216 is a potential cancer drug candidate for patients with SCLC with PIK3CA mutation but not PTEN loss. Clin Cancer Res; 20(3); 631–43. ©2013 AACR.