bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization of Commensal Escherichia coli Adapted to Different Compartments of the Porcine Gastrointestinal Tract
Authors: Abraham Sam , Gordon David M. , Chin James , Brouwers Huub J. M. , Njuguna Peter , Groves Mitchell D. , Zhang Ren , Chapman Toni A. 
Published: July 2012

ABSTRACT

The role of
Escherichia coli
as a pathogen has been the focus of considerable study, while much less is known about it as a commensal and how it adapts to and colonizes different environmental niches within the mammalian gut. In this study, we characterize
Escherichia coli
organisms (
n
= 146) isolated from different regions of the intestinal tracts of eight pigs (dueodenum, ileum, colon, and feces). The isolates were typed using the method of random amplified polymorphic DNA (RAPD) and screened for the presence of bacteriocin genes and plasmid replicon types. Molecular analysis of variance using the RAPD data showed that
E. coli
isolates are nonrandomly distributed among different gut regions, and that gut region accounted for 25% (
P
< 0.001) of the observed variation among strains. Bacteriocin screening revealed that a bacteriocin gene was detected in 45% of the isolates, with 43% carrying colicin genes and 3% carrying microcin genes. Of the bacteriocins observed (H47, E3, E1, E2, E7, Ia/Ib, and B/M), the frequency with which they were detected varied with respect to gut region for the colicins E2, E7, Ia/Ib, and B/M. The plasmid replicon typing gave rise to 25 profiles from the 13 Inc types detected. Inc F types were detected most frequently, followed by Inc HI1 and N types. Of the Inc types detected, 7 were nonrandomly distributed among isolates from the different regions of the gut. The results of this study indicate that not only may the different regions of the gastrointestinal tract harbor different strains of
E. coli
but also that strains from different regions have different characteristics.
Rerouting Citrate Metabolism in Lactococcus lactis to Citrate-Driven Transamination
Authors: Pudlik Agata M. , Lolkema Juke S. 
Published: July 2012

ABSTRACT

Oxaloacetate is an intermediate of the citrate fermentation pathway that accumulates in the cytoplasm of
Lactococcus lactis
ILCitM(pFL3) at a high concentration due to the inactivation of oxaloacetate decarboxylase. An excess of toxic oxaloacetate is excreted into the medium in exchange for citrate by the citrate transporter CitP (A. M. Pudlik and J. S. Lolkema, J. Bacteriol. 193:4049–4056, 2011). In this study, transamination of amino acids with oxaloacetate as the keto donor is described as an additional mechanism to relieve toxic stress. Redirection of the citrate metabolic pathway into the transamination route in the presence of the branched-chain amino acids Ile, Leu, and Val; the aromatic amino acids Phe, Trp, and Tyr; and Met resulted in the formation of aspartate and the corresponding α-keto acids. Cells grown in the presence of citrate showed 3.5 to 7 times higher transaminase activity in the cytoplasm than cells grown in the absence of citrate. The study demonstrates that transaminases of
L. lactis
accept oxaloacetate as a keto donor. A significant fraction of 2-keto-4-methylthiobutyrate formed from methionine by citrate-driven transamination
in vivo
was further metabolized, yielding the cheese aroma compounds 2-hydroxy-4-methylthiobutyrate and methyl-3-methylthiopropionate. Reducing equivalents required for the former compound were produced in the citrate fermentation pathway as NADH. Similarly, phenylpyruvate, the transamination product of phenylalanine, was reduced to phenyllactate, while the dehydrogenase activity was not observed for the branched-chain keto acids. Both α-keto acids and α-hydroxy acids are known substrates of CitP and may be excreted from the cell in exchange for citrate or oxaloacetate.
FlbD, a Myb Transcription Factor of Aspergillus nidulans, Is Uniquely Involved in both Asexual and Sexual Differentiation
Authors: Arratia-Quijada Jenny , Sánchez Olivia , Scazzocchio Claudio , Aguirre Jesús 
Published: July 2012

ABSTRACT

In the fungus
Aspergillus nidulans
, inactivation of the
flbA
to
-E
,
fluG
,
fluF
, and
tmpA
genes results in similar phenotypes, characterized by a delay in conidiophore and asexual spore production.
flbB
to
-D
encode transcription factors needed for proper expression of the
brlA
gene, which is essential for asexual development. However, recent evidence indicates that FlbB and FlbE also have nontranscriptional functions. Here we show that
fluF1
is an allele of
flbD
which results in an R47P substitution. Amino acids C46 and R47 are highly conserved in FlbD and many other Myb proteins, and C46 has been proposed to mediate redox regulation. Comparison of Δ
flbD
and
flbD

R47P

mutants uncovered a new and specific role for
flbD
during sexual development. While
flbD

R47P

mutants retain partial function during conidiation, both
ΔflbD
and
flbD

R47P

mutants are unable to develop the peridium, a specialized external tissue that differentiates during fruiting body formation and ends up surrounding the sexual spores. This function, unique among other
fluffy
genes, does not affect the viability of the naked ascospores produced by mutant strains. Notably, ascospore development in these mutants is still dependent on the NADPH oxidase NoxA. We generated R47K, C46D, C46S, and C46A mutant alleles and evaluated their effects on asexual and sexual development. Conidiation defects were most severe in
ΔflbD
mutants and stronger in R47P, C46D, and C46S strains than in R47K strains. In contrast, mutants carrying the
flbD

C46A

allele exhibited conidiation defects in liquid culture only under nitrogen starvation conditions. The R47K, R47P, C46D, and C46S mutants failed to develop any peridial tissue, while the
flbD

C46A

strain showed normal peridium development and increased cleistothecium formation. Our results show that FlbD regulates both asexual and sexual differentiation, suggesting that both processes require FlbD DNA binding activity and that FlbD is involved in the response to nitrogen starvation.
A Detoxifying Oxygen Reductase in the Anaerobic Protozoan Entamoeba histolytica
Authors: Vicente João B. , Tran Vy , Pinto Liliana , Teixeira Miguel , Singh Upinder 
Published: July 2012

ABSTRACT

We report the characterization of a bacterial-type oxygen reductase abundant in the cytoplasm of the anaerobic protozoan parasite
Entamoeba histolytica
. Upon host infection,
E. histolytica
is confronted with various oxygen tensions in the host intestine, as well as increased reactive oxygen and nitrogen species at the site of local tissue inflammation. Resistance to oxygen-derived stress thus plays an important role in the pathogenic potential of
E. histolytica
. The genome of
E. histolytica
has four genes that encode flavodiiron proteins, which are bacterial-type oxygen or nitric oxide reductases and were likely acquired by lateral gene transfer from prokaryotes. The
EhFdp1
gene has higher expression in virulent than in nonvirulent
Entamoeba
strains and species, hinting that the response to oxidative stress may be one correlate of virulence potential. We demonstrate that EhFdp1 is abundantly expressed in the cytoplasm of
E. histolytica
and that the protein levels are markedly increased (up to ∼5-fold) upon oxygen exposure. Additionally, we produced fully functional recombinant EhFdp1 and demonstrated that this enzyme is a specific and robust oxygen reductase but has poor nitric oxide reductase activity. This observation represents a new mechanism of oxygen resistance in the anaerobic protozoan pathogen
E. histolytica
.
Peroxide-Sensing Transcriptional Regulators in Bacteria
Authors: Dubbs James M. , Mongkolsuk Skorn 
Published: July 2012

ABSTRACT

The ability to maintain intracellular concentrations of toxic reactive oxygen species (ROS) within safe limits is essential for all aerobic life forms. In bacteria, as well as other organisms, ROS are produced during the normal course of aerobic metabolism, necessitating the constitutive expression of ROS scavenging systems. However, bacteria can also experience transient high-level exposure to ROS derived either from external sources, such as the host defense response, or as a secondary effect of other seemingly unrelated environmental stresses. Consequently, transcriptional regulators have evolved to sense the levels of ROS and coordinate the appropriate oxidative stress response. Three well-studied examples of these are the peroxide responsive regulators OxyR, PerR, and OhrR. OxyR and PerR are sensors of primarily H
2
O
2
, while OhrR senses organic peroxide (ROOH) and sodium hypochlorite (NaOCl). OxyR and OhrR sense oxidants by means of the reversible oxidation of specific cysteine residues. In contrast, PerR senses H
2
O
2
via the Fe-catalyzed oxidation of histidine residues. These transcription regulators also influence complex biological phenomena, such as biofilm formation, the evasion of host immune responses, and antibiotic resistance via the direct regulation of specific proteins.
ThechbGGene of the Chitobiose (chb) Operon of Escherichia coli Encodes a Chitooligosaccharide Deacetylase
Authors: Verma Subhash Chandra , Mahadevan Subramony 
Published: July 2012

ABSTRACTThechboperon ofEscherichia coliis involved in the utilization of the β-glucosides chitobiose and cellobiose. The function ofchbG(ydjC), the sixth open reading frame of the operon that codes for an evolutionarily conserved protein is unknown. We show thatchbGencodes a monodeacetylase that is essential for growth on the acetylated chitooligosaccharides chitobiose and chitotriose but is dispensable for growth on cellobiose and chitosan dimer, the deacetylated form of chitobiose. The predicted active site of the enzyme was validated by demonstrating loss of function upon substitution of its putative metal-binding residues that are conserved across the YdjC family of proteins. We show that activation of thechbpromoter by the regulatory protein ChbR is dependent on ChbG, suggesting that deacetylation of chitobiose-6-P and chitotriose-6-P is necessary for their recognition by ChbR as inducers. Strains carrying mutations inchbRconferring the ability to grow on both cellobiose and chitobiose are independent ofchbGfunction for induction, suggesting that gain of function mutations in ChbR allow it to recognize the acetylated form of the oligosaccharides. ChbR-independent expression of the permease and phospho-β-glucosidase from a heterologous promoter did not support growth on both chitobiose and chitotriose in the absence ofchbG, suggesting an additional role ofchbGin the hydrolysis of chitooligosaccharides. The homologs ofchbGin metazoans have been implicated in development and inflammatory diseases of the intestine, indicating that understanding the function ofE. colichbGhas a broader significance.
Convergent Molecular Evolution of Genomic Cores in Salmonella enterica and Escherichia coli
Authors: Chattopadhyay Sujay , Paul Sandip , Kisiela Dagmara I. , Linardopoulou Elena V. , Sokurenko Evgeni V. 
Published: July 2012

ABSTRACTOne of the strongest signals of adaptive molecular evolution of proteins is the occurrence of convergent hot spot mutations: repeated changes in the same amino acid positions. We performed a comparative genome-wide analysis of mutation-driven evolution of core (omnipresent) genes in 17 strains ofSalmonella entericasubspecies I and 22 strains ofEscherichia coli. More than 20% of core genes in bothSalmonellaandE. coliaccumulated hot spot mutations, with a predominance of identical changes having recent evolutionary origin. There is a significant overlap in the functional categories of the adaptively evolving genes in both species, although mostly via separate molecular mechanisms. As a strong evidence of the link between adaptive mutations and virulence inSalmonella, two human-restricted serovars, Typhi and Paratyphi A, shared the highest number of genes with serovar-specific hot spot mutations. Many of the core genes affected by Typhi/Paratyphi A-specific mutations have known virulence functions. For each species, a list of nonrecombinant core genes (and the hot spot mutations therein) under positive selection is provided.
Chromosomal Replication Initiation Machinery of Low-G+C-Content Firmicutes
Authors: Briggs Geoffrey S. , Smits Wiep Klaas , Soultanas Panos 
Published: July 2012

ABSTRACT

Much of our knowledge of the initiation of DNA replication comes from studies in the Gram-negative model organism
Escherichia coli
. However, the location and structure of the origin of replication within the
E. coli
genome and the identification and study of the proteins which constitute the
E. coli
initiation complex suggest that it might not be as universal as once thought. The archetypal low-G+C-content Gram-positive
Firmicutes
initiate DNA replication via a unique primosomal machinery, quite distinct from that seen in
E. coli
, and an examination of
oriC
in the
Firmicutes
species
Bacillus subtilis
indicates that it might provide a better model for the ancestral bacterial origin of replication. Therefore, the study of replication initiation in organisms other than
E. coli
, such as
B. subtilis
, will greatly advance our knowledge and understanding of these processes as a whole. In this minireview, we highlight the structure-function relationships of the
Firmicutes
primosomal proteins, discuss the significance of their
oriC
architecture, and present a model for replication initiation at
oriC
.
Inability To Catabolize Galactose Leads to Increased Ability To Compete for Nodule Occupancy in Sinorhizobium meliloti
Authors: Geddes Barney A. , Oresnik Ivan J. 
Published: July 2012

ABSTRACTA mutant unable to utilize galactose was isolated inSinorhizobium melilotistrain Rm1021. The mutation was found to be in a gene annotateddgoK1, a putative 2-keto-3-deoxygalactonokinase. The genetic region was isolated on a complementing cosmid and subsequently characterized. Based on genetic and bioinformatic evidence, the locus encodes all five enzymes (galD,dgoK,dgoA,SMc00883, andilvD1) involved in the De Ley-Doudoroff pathway for galactose catabolism. Although all five genes are present, genetic analysis suggests that the galactonase (SMc00883) and the dehydratase (ilvD1) are dispensable with respect to the ability to catabolize galactose. In addition, we show that the transport of galactose is partially facilitated by the arabinose transporter (AraABC) and that both glucose and galactose compete with arabinose for transport. Quantitative reverse transcription-PCR (qRT-PCR) data show that in adgoKbackground, the galactose locus is constitutively expressed, and the induction of thearalocus seems to be enhanced. Assays of competition for nodule occupancy show that the inability to catabolize galactose is correlated with an increased ability to compete for nodule occupancy.
Outcomes of hip arthroscopy. A prospective analysis and comparison between patients under 25 and over 25 years of age
Authors: Cooper Anthony Philip , Basheer Sheba Z , Maheshwari Rajan , Regan Laura , Madan Sanjeev S 
Published: July 2012

ObjectiveTo compare the results of hip arthroscopy in patients under the age of 25 with those over 25 years.DesignFrom March 2006 until May 2010, data were collected on all patients who underwent hip arthroscopy for symptomatic intra-articular hip pathology. The patients were divided into two groups based on age (less than 25 years and over 25 years). Patients completed the modified Harris hip score (MHHS), non-arthritic hip score (NAHS) and hip dysfunction and osteoarthritis outcome score (HOOS) questionnaires at baseline then at 6 weeks, 6 months, 12 months and at latest follow-up.Participants88 patients who underwent 94 hip arthroscopies by the senior author. Mean age was 24.3 (range 11–57 years).ResultsThe mean NAHS and HOOS subscales for pain and activities of daily living were worse at baseline in over 25 groups. Follow-up ranged from 9 to 68 months. 45 hips had greater than 3 year follow-up. The MHHS improved in both groups with a mean difference in the under-25 group of 16.22, and 20.88 in the over 25s. Improvements in the NAHS and HOOS subscales were also of a similar magnitude. There was no statistically significant difference between outcome scores of the two groups at the latest follow-up visit.ConclusionsWe found a comparable improvement in outcome between those patients under 25 years and those over 25 years. We propose that hip arthroscopy is of potential benefit to patients with symptoms of femoroacetabular impingement regardless of age.
Cystatin C in a composite risk score for mortality in patients with infective endocarditis: a cohort study
Authors: Bjurman Christian , Snygg-Martin Ulrika , Olaison Lars , Fu Michael L X , Hammarsten Ola 
Published: July 2012

ObjectiveTo develop a multimarker prognostic score for infective endocarditis (IE).DesignRetrospective case–control.SettingSecondary care. Single centre.Participants125 patients with definite IE.Primary outcome measures90-day and 5-year mortality.ResultsMean age was 62.7±17 years. The 90-day and 5-year mortality was 10.4% and 33.6%, respectively. CysC levels at admission and over 20% increases in CysC levels during 2 weeks of treatment were prognostic for 90-day and 5-year mortality independent of creatinine estimated glomerular filtration rate. In multivariate analyses, CysC (OR 5.42, 95% CI 1.90 to 15.5, p=0.002) and age (OR 1.06, 95% CI 1.02 to 1.10, p=0.002) remained prognostic for 5-year mortality. NT-proBNP, TnT, C reactive protein and interleukin 6 were also linked to prognosis. A composite risk scoring system using levels of CysC, NT-proBNP, age and presence of mitral valve insufficiency was able to separate a high-risk and a low-risk group.ConclusionsCysC levels at admission and increase in CysC after 2 weeks of treatment were independent prognostic markers for both 90-day and 5-year mortality in patients with IE. A multimarker composite risk scoring system including CysC identified a high-risk group.
Dose–response effects of exercise training on the subjective sleep quality of postmenopausal women: exploratory analyses of a randomised controlled trial
Authors: Kline Christopher E , Sui Xuemei , Hall Martica H , Youngstedt Shawn D , Blair Steven N , Earnest Conrad P , Church Timothy S 
Published: July 2012

ObjectiveTo investigate whether a dose–response relationship existed between exercise and subjective sleep quality in postmenopausal women. This objective represents a post hoc assessment that was not previously considered.DesignParallel-group randomised controlled trial.SettingClinical exercise physiology laboratory in Dallas, Texas.Participants437 sedentary overweight/obese postmenopausal women.InterventionParticipants were randomised to one of four treatments, each of 6 months of duration: a non-exercise control treatment (n=92) or one of three dosages of moderate-intensity exercise (50% of VO2peak), designed to meet 50% (n=151), 100% (n=99) or 150% (n=95) of the National Institutes of Health Consensus Development Panel physical activity recommendations. Exercise dosages were structured to elicit energy expenditures of 4, 8 or 12 kilocalories per kilogram of body weight per week (KKW), respectively. Analyses were intent to treat.Primary outcome measuresContinuous scores and odds of having significant sleep disturbance, as assessed by the Sleep Problems Index from the 6-item Medical Outcomes Study Sleep Scale. Outcome assessors were blinded to participant randomisation assignment.ResultsChange in the Medical Outcomes Study Sleep Problems Index score at 6 months significantly differed by treatment group (control: −2.09 (95% CI −4.58 to 0.40), 4 KKW: −3.93 (−5.87 to −1.99), 8 KKW: −4.06 (−6.45 to −1.67), 12 KKW: −6.22 (−8.68 to −3.77); p=0.04), with a significant dose–response trend observed (p=0.02). Exercise training participants had lower odds of having significant sleep disturbance at postintervention compared with control (4 KKW: OR 0.37 (95% CI 0.19 to 0.73), 8 KKW: 0.36 (0.17 to 0.77), 12 KKW: 0.34 (0.16 to 0.72)). The magnitude of weight loss did not differ between treatment conditions. Improvements in sleep quality were not related to changes in body weight, resting parasympathetic control or cardiorespiratory fitness.ConclusionExercise training induced significant improvement in subjective sleep quality in postmenopausal women, with even a low dose of exercise resulting in greatly reduced odds of having significant sleep disturbance.Trial registration numberclinicaltrials.govidentifier:NCT00011193.
Asthma and allergies in Jamaican children aged 2–17 years: a cross-sectional prevalence survey
Authors: Kahwa Eulalia K , Waldron Norman K , Younger Novie O , Edwards Nancy C , Knight-Madden Jennifer M , Bailey Kay A , Wint Yvonne B , Lewis-Bell Karen N 
Published: July 2012

ObjectiveTo determine the prevalence and severity of asthma and allergies as well as risk factors for asthma among Jamaican children aged 2–17 years.DesignA cross-sectional, community-based prevalence survey using the International Study of Asthma and Allergies in Childhood questionnaire. The authors selected a representative sample of 2017 children using stratified, multistage cluster sampling design using enumeration districts as primary sampling units.SettingJamaica, a Caribbean island with a total population of approximately 2.6 million, geographically divided into 14 parishes.ParticipantsChildren aged 2–17 years, who were resident in private households. Institutionalised children such as those in boarding schools and hospitals were excluded from the survey.Primary and secondary outcome measuresThe prevalence and severity of asthma and allergy symptoms, doctor-diagnosed asthma and risk factors for asthma.ResultsAlmost a fifth (19.6%) of Jamaican children aged 2–17 years had current wheeze, while 16.7% had self-reported doctor-diagnosed asthma. Both were more common among males than among females. The prevalence of rhinitis, hay fever and eczema among children was 24.5%, 25% and 17.3%, respectively. Current wheeze was more common among children with rhinitis in the last 12 months (44.3% vs 12.6%, p<0.001), hay fever (36.8% vs 13.8%, p<0.001) and eczema (34.1% vs 16.4%, p<0.001). Independent risk factors for current wheeze (ORs, 95% CI) were chest infections in the first year of life 4.83 (3.00 to 7.77), parental asthma 4.19 (2.8 to 6.08), rhinitis in the last 12 months 6.92 (5.16 to 9.29), hay fever 4.82 (3.62 to 6.41), moulds in the home 2.25 (1.16 to 4.45), cat in the home 2.44 (1.66 to 3.58) and dog in the home 1.81 (1.18 to 2.78).ConclusionsThe prevalence of asthma and allergies in Jamaican children is high. Significant risk factors for asthma include chest infections in the first year of life, a history of asthma in the family, allergies, moulds and pets in the home.