bluuebunny/crossref_metadata_2025_split huggingface dataset:
IRiS: Construction of ARG networks at genomic scales
Authors: Javed Asif , Pybus Marc , Melé Marta , Utro Filippo , Bertranpetit Jaume , Calafell Francesc , Parida Laxmi 
Published: July 2011

Abstract
Summary: Given a set of extant haplotypes IRiS first detects high confidence recombination events in their shared genealogy. Next using the local sequence topology defined by each detected event, it integrates these recombinations into an ancestral recombination graph. While the current system has been calibrated for human population data, it is easily extendible to other species as well.
Availability: IRiS (Identification of Recombinations in Sequences) binary files are available for non-commercial use in both Linux and Microsoft Windows, 32 and 64 bit environments from https://researcher.ibm.com/researcher/view_project.php?id = 2303
Contact: parida@us.ibm.com
Development of a Gastroenterology Educational Curriculum for Pediatric Residents Using Fellows as Teachers
Authors: Pentiuk Scott , Baker Raymond 
Published: July 2011

ABSTRACTObjectives:At many institutions, the teaching provided on subspecialty gastroenterology rotations is not structured. The purpose of the present study was to describe the development, implementation, and assessment of a structured gastroenterology curriculum for pediatric residents.Methods:A needs assessment was performed via a survey of former pediatric resident graduates presently working in general pediatrics. Topics for the curriculum were developed based upon the needs assessment. Second‐year residents on the inpatient gastroenterology rotation attended 4 case‐based, small group sessions per week for 1 month. Sessions were taught primarily by upper‐level gastroenterology fellows. The curriculum was assessed via a pre‐posttest, postrotation survey, and group feedback sessions.Results:Resident rating of education received during the rotation was high. Posttest scores increased slightly but significantly compared with pretest values. The curriculum has continued to be used >4 years after its development.Conclusions:The creation of a structured subspecialty curriculum with the use of fellows as teachers is both feasible and effective despite limitations in available time for resident teaching.
Metagenomic Insights into the Evolution, Function, and Complexity of the Planktonic Microbial Community of Lake Lanier, a Temperate Freshwater Ecosystem
Authors: Oh Seungdae , Caro-Quintero Alejandro , Tsementzi Despina , DeLeon-Rodriguez Natasha , Luo Chengwei , Poretsky Rachel , Konstantinidis Konstantinos T. 
Published: July 2011

ABSTRACT
Lake Lanier is an important freshwater lake for the southeast United States, as it represents the main source of drinking water for the Atlanta metropolitan area and is popular for recreational activities. Temperate freshwater lakes such as Lake Lanier are underrepresented among the growing number of environmental metagenomic data sets, and little is known about how functional gene content in freshwater communities relates to that of other ecosystems. To better characterize the gene content and variability of this freshwater planktonic microbial community, we sequenced several samples obtained around a strong summer storm event and during the fall water mixing using a random whole-genome shotgun (WGS) approach. Comparative metagenomics revealed that the gene content was relatively stable over time and more related to that of another freshwater lake and the surface ocean than to soil. However, the phylogenetic diversity of Lake Lanier communities was distinct from that of soil and marine communities. We identified several important genomic adaptations that account for these findings, such as the use of potassium (as opposed to sodium) osmoregulators by freshwater organisms and differences in the community average genome size. We show that the lake community is predominantly composed of sequence-discrete populations and describe a simple method to assess community complexity based on population richness and evenness and to determine the sequencing effort required to cover diversity in a sample. This study provides the first comprehensive analysis of the genetic diversity and metabolic potential of a temperate planktonic freshwater community and advances approaches for comparative metagenomics.
Isolation, Taxonomy, and Antagonistic Properties of Halophilic Actinomycetes in Saharan Soils of Algeria
Authors: Meklat Atika , Sabaou Nasserdine , Zitouni Abdelghani , Mathieu Florence , Lebrihi Ahmed 
Published: July 2011

ABSTRACT

The diversity of a population of 52 halophilic actinomycetes was evaluated by a polyphasic approach, which showed the presence of members of the
Actinopolyspora
,
Nocardiopsis
,
Saccharomonospora
,
Streptomonospora
, and
Saccharopolyspora
genera. One strain was considered to be a new member of the last genus, and several other strains seemed to be new species. Furthermore, 50% of strains were active against a broad range of indicators and contained genes encoding polyketide synthetases and nonribosomal peptide synthetases.
Biodegradation of Polyester Polyurethane by Endophytic Fungi
Authors: Russell Jonathan R. , Huang Jeffrey , Anand Pria , Kucera Kaury , Sandoval Amanda G. , Dantzler Kathleen W. , Hickman DaShawn , Jee Justin , Kimovec Farrah M. , Koppstein David , Marks Daniel H. , Mittermiller Paul A. , Núñez Salvador Joel , Santiago Marina , Townes Maria A. , Vishnevetsky Michael , Williams Neely E. , Vargas Mario Percy Núñez , Boulanger Lori-Ann , Bascom-Slack Carol , Strobel Scott A. 
Published: July 2011

ABSTRACT

Bioremediation is an important approach to waste reduction that relies on biological processes to break down a variety of pollutants. This is made possible by the vast metabolic diversity of the microbial world. To explore this diversity for the breakdown of plastic, we screened several dozen endophytic fungi for their ability to degrade the synthetic polymer polyester polyurethane (PUR). Several organisms demonstrated the ability to efficiently degrade PUR in both solid and liquid suspensions. Particularly robust activity was observed among several isolates in the genus
Pestalotiopsis
, although it was not a universal feature of this genus. Two
Pestalotiopsis microspora
isolates were uniquely able to grow on PUR as the sole carbon source under both aerobic and anaerobic conditions. Molecular characterization of this activity suggests that a serine hydrolase is responsible for degradation of PUR. The broad distribution of activity observed and the unprecedented case of anaerobic growth using PUR as the sole carbon source suggest that endophytes are a promising source of biodiversity from which to screen for metabolic properties useful for bioremediation.
Discovery of an Escherichia coli Esterase with High Activity and Enantioselectivity toward 1,2-
O
-Isopropylideneglycerol Esters
Authors: Godinho Luis F. , Reis Carlos R. , Tepper Pieter G. , Poelarends Gerrit J. , Quax Wim J. 
Published: July 2011

ABSTRACT

Escherichia coli
has been widely used as an expression host for the identification of desired biocatalysts through screening or selection assays. We have previously used
E. coli
in growth selection and screening assays for identification of
Bacillus subtilis
lipase variants (located in the periplasm) with improved activity and enantioselectivity toward 1,2-
O
-isopropylideneglycerol (IPG) esters. In the course of these studies, we discovered that
E. coli
itself exhibits significant cytoplasmic esterase activity toward IPG esters. In order to identify the enzyme (or enzymes) responsible for this esterase activity, we analyzed eight
E. coli
knockout strains, in which single esterase genes were deleted, for their ability to hydrolyze IPG butyrate. This approach led to the identification of esterase YbfF as the major
E. coli
enzyme responsible for the hydrolytic activity toward IPG esters. The gene coding for YbfF was cloned and overexpressed in
E. coli
, and the corresponding protein was purified and characterized for its biocatalytic performance. YbfF displays a high level of activity toward IPG butyrate and IPG caprylate and prefers the
R
-enantiomer of these substrates, producing the
S
-enantiomer of the IPG product with high enantiomeric excess (72 to 94%
ee
). The enantioselectivity of YbfF for IPG caprylate (
E
= 40) could be significantly enhanced when using dimethylformamide (DMF) or dimethyl sulfoxide (DMSO) as cosolvents in kinetic resolution experiments. The enzyme also shows high enantioselectivity toward 1-phenylethyl acetate (
E
≥ 200), giving the chiral product (
R
)-1-phenylethanol with >99%
ee
. The high activity and enantioselectivity of YbfF make it an attractive enzyme for organic synthesis.
pSEUDO, a Genetic Integration Standard for Lactococcus lactis
Authors: Pinto Joao P. C. , Zeyniyev Araz , Karsens Harma , Trip Hein , Lolkema Juke S. , Kuipers Oscar P. , Kok Jan 
Published: July 2011

ABSTRACT

Plasmid pSEUDO and derivatives were used to show that
llmg
_
pseudo
_
10
in
Lactococcus lactis
MG1363 and its homologous locus in
L. lactis
IL1403 are suitable for chromosomal integrations.
L. lactis
MG1363 and IL1403 nisin-induced controlled expression (NICE) system derivatives (JP9000 and IL9000) and two general stress reporter strains (NZ9000::P
hrcA
-GFP and NZ9000::P
groES
-GFP) enabling
in vivo
noninvasive monitoring of cellular fitness were constructed.
Physiological and Transcriptional Characterization of Persistent and Nonpersistent Listeria monocytogenes Isolates
Authors: Fox Edward M. , Leonard Nola , Jordan Kieran 
Published: July 2011

ABSTRACT

This study aimed to characterize physiological differences between persistent and presumed nonpersistent
Listeria monocytogenes
strains isolated at processing facilities and to investigate the molecular basis for this by transcriptomic sequencing. Full metabolic profiles of two strains, one persistent and one nonpersistent, were initially screened using Biolog's Phenotype MicroArray (PM) technology. Based on these results, in which major differences from selected antimicrobial agents were detected, another persistent strain and two nonpersistent strains were characterized using two antimicrobial PMs. Resistance to quaternary ammonium compounds (QACs) was shown to be higher among persistent strains. Growth of persistent and nonpersistent strains in various concentrations of the QACs benzethonium chloride (BZT) and cetylpyridinium chloride (CPC) was determined. Transcriptomic sequencing of a persistent and a presumed nonpersistent strain was performed to compare gene expression among these strains in the presence and absence of BZT. Two strains, designated “frequent persisters” because they were the most frequently isolated at the processing facility, showed overall higher resistance to QACs. Transcriptome analysis showed that BZT induced a complex peptidoglycan (PG) biosynthesis response, which may play a key role in BZT resistance. Comparison of persistent and nonpersistent strains indicated that transcription of many genes was upregulated among persistent strains. This included three gene operons:
pdu
,
cob-cbi
, and
eut
. These genes may play a role in the persistence of
L. monocytogenes
outside the human host.
Coevolution of Morphology and Virulence in Candida Species
Authors: Thompson Delma S. , Carlisle Patricia L. , Kadosh David 
Published: July 2011

ABSTRACTMany of the major human fungal pathogens are known to undergo morphological changes, which in certain cases are associated with virulence. Although there has been an intense research focus on morphology in fungi, very little is known about how morphology evolved in conjunction with a variety of other virulence properties. However, several recent important discoveries, primarily inCandidaspecies, are beginning to shed light on this important area and answer many longstanding questions. In this minireview, we first provide a description of the major fungal morphologies, as well as the roles of morphology and morphology-associated gene expression in virulence. Next, focusing largely onCandidaspecies, we examine the evolutionary relationships among specific morphological forms. Finally, drawing on recent findings, we begin to address the question of how specific morphological changes came to be associated with virulence ofCandidaspecies during evolution.
RNA Interference in Protozoan Parasites: Achievements and Challenges
Authors: Kolev Nikolay G. , Tschudi Christian , Ullu Elisabetta 
Published: July 2011

ABSTRACT

Protozoan parasites that profoundly affect mankind represent an exceptionally diverse group of organisms, including
Plasmodium
,
Toxoplasma
,
Entamoeba
,
Giardia
, trypanosomes, and
Leishmania
. Despite the overwhelming impact of these parasites, there remain many aspects to be discovered about mechanisms of pathogenesis and how these organisms survive in the host. Combined with the ever-increasing availability of sequenced genomes, RNA interference (RNAi), discovered a mere 13 years ago, has enormously facilitated the analysis of gene function, especially in organisms that are not amenable to classical genetic approaches. Here we review the current status of RNAi in studies of parasitic protozoa, with special emphasis on its use as a postgenomic tool.
Using Superfolder Green Fluorescent Protein for Periplasmic Protein Localization Studies
Authors: Dinh Thuy , Bernhardt Thomas G. 
Published: July 2011

ABSTRACT
Studies investigating the subcellular localization of periplasmic proteins have been hampered by problems with the export of green fluorescent protein (GFP). Here we show that a superfolding variant of GFP (sfGFP) is fluorescent following Sec-mediated transport and works best when the cotranslational branch of the pathway is employed.
Genetic Requirements for High Constitutive SOS Expression inrecA730Mutants of Escherichia coli
Authors: Vlašić Ignacija , Šimatović Ana , Brčić-Kostić Krunoslav 
Published: July 2011

ABSTRACTThe RecA protein in its functional state is in complex with single-stranded DNA, i.e., in the form of a RecA filament. In SOS induction, the RecA filament functions as a coprotease, enabling the autodigestion of the LexA repressor. The RecA filament can be formed by different mechanisms, but all of them require three enzymatic activities essential for the processing of DNA double-stranded ends. These are helicase, 5′–3′ exonuclease, and RecA loading onto single-stranded DNA (ssDNA). In some mutants, the SOS response can be expressed constitutively during the process of normal DNA metabolism. The RecA730 mutant protein is able to form the RecA filament without the help of RecBCD and RecFOR mediators since it better competes with the single-strand binding (SSB) protein for ssDNA. As a consequence, therecA730mutants show high constitutive SOS expression. In the study described in this paper, we studied the genetic requirements for constitutive SOS expression inrecA730mutants. Using a β-galactosidase assay, we showed that the constitutive SOS response inrecA730mutants exhibits different requirements in different backgrounds. In a wild-type background, the constitutive SOS response is partially dependent on RecBCD function. In arecB1080background (therecB1080mutation retains only helicase), constitutive SOS expression is partially dependent on RecBCD helicase function and is strongly dependent on RecJ nuclease. Finally, in arecB-null background, the constitutive SOS expression of therecA730mutant is dependent on the RecJ nuclease. Our results emphasize the importance of the 5′–3′ exonuclease for high constitutive SOS expression inrecA730mutants and show that RecBCD function can further enhance the excellent intrinsic abilities of the RecA730 proteinin vivo.
HlyU Is a Positive Regulator of Hemolysin Expression in Vibrio anguillarum
Authors: Li Ling , Mou Xiangyu , Nelson David R. 
Published: July 2011

ABSTRACT

The two hemolysin gene clusters previously identified in
Vibrio anguillarum
, the
vah1
cluster and the
rtxACHBDE
cluster, are responsible for the hemolytic and cytotoxic activities of
V. anguillarum
in fish. In this study, we used degenerate PCR to identify a positive hemolysin regulatory gene,
hlyU
, from the unsequenced
V. anguillarum
genome. The
hlyU
gene of
V. anguillarum
encodes a 92-amino-acid protein and is highly homologous to other bacterial HlyU proteins. An
hlyU
mutant was constructed, which exhibited an ∼5-fold decrease in hemolytic activity on sheep blood agar with no statistically significant decrease in cytotoxicity of the wild-type strain. Complementation of the
hlyU
mutation restored both hemolytic activity and cytotoxic activity. Both semiquantitative reverse transcription-PCR (RT-PCR) and quantitative real-time RT-PCR (qRT-PCR) were used to examine expression of the hemolysin genes under exponential and stationary-phase conditions in wild-type,
hlyU
mutant, and
hlyU
complemented strains. Compared to the wild-type strain, expression of
rtx
genes decreased in the
hlyU
mutant, while expression of
vah1
and
plp
was not affected in the
hlyU
mutant. Complementation of the
hlyU
mutation restored expression of the
rtx
genes and increased
vah1
and
plp
expression to levels higher than those in the wild type. The transcriptional start sites in both the
vah1-plp
and
rtxH-rtxB
genes' intergenic regions were determined using 5′ random amplification of cDNA ends (5′-RACE), and the binding sites for purified HlyU were discovered using DNA gel mobility shift experiments and DNase protection assays.
Membrane Proteases and Aminoglycoside Antibiotic Resistance
Authors: Hinz Aaron , Lee Samuel , Jacoby Kyle , Manoil Colin 
Published: July 2011

ABSTRACT

We present genetic studies that help define the functional network underlying intrinsic aminoglycoside resistance in
Pseudomonas aeruginosa
. Our analysis shows that proteolysis, particularly that controlled by the membrane protease FtsH, is a major determinant of resistance. First, we examined the consequences of inactivating genes controlled by AmgRS, a two-component regulator required for intrinsic tobramycin resistance. Three of the gene products account for resistance: a modulator of FtsH protease (YccA), a membrane protease (HtpX), and a membrane protein of unknown function (PA5528). Second, we screened mutations inactivating 66 predicted proteases and related functions. Insertions inactivating two FtsH protease accessory factors (HflK and HflC) and a cytoplasmic protease (HslUV) increased tobramycin sensitivity. Finally, we generated an
ftsH
deletion mutation. The mutation dramatically increased aminoglycoside sensitivity. Many of the functions whose inactivation increased sensitivity appeared to act independently, since multiple mutations led to additive or synergistic effects. Up to 500-fold increases in tobramycin sensitivity were observed. Most of the mutations also were highly pleiotropic, increasing sensitivity to a membrane protein hybrid, several classes of antibiotics, alkaline pH, NaCl, and other compounds. We propose that the network of proteases provides robust protection from aminoglycosides and other substances through the elimination of membrane-disruptive mistranslation products.
Rates of condom and non-condom-based anal intercourse practices among homosexually active men in Australia: deliberate HIV risk reduction?
Authors: Mao Limin , Kippax Susan C , Holt Martin , Prestage Garrett P , Zablotska Iryna B , de Wit John B F 
Published: July 2011

ObjectiveThree decades into the HIV epidemic and with the advancement of HIV treatments, condom and non-condom-based anal intercourse among gay men in resource-rich countries needs to be re-assessed.MethodsThe proportions of men engaging in a range of anal intercourse practices were estimated from the ongoing cross-sectional Gay Community Periodic Surveys in six states in Australia from 2007 to 2009. Comparisons were made between HIV-negative men, HIV-positive men with an undetectable viral load and those with a detectable viral load.ResultsCondoms play a key role in gay men's anal intercourse practices: 33.8% of HIV-negative men, 25.1% of HIV-positive men with an undetectable viral load and 22.5% of those with a detectable viral load reported consistent condom use with all male partners in the 6 months before the survey. Among HIV-negative men, the second largest group were men who had unprotected anal intercourse (UAI) only in the context of HIV-negative seroconcordant regular relationships. Among HIV-positive men, the second largest group was men who had UAI in casual encounters preceded by HIV status disclosure to some, but not all, casual partners.ConclusionsA minority, yet sizeable proportion, of men consistently engaged in a number of UAI practices in specific contexts, suggesting they have adopted deliberate HIV risk-reduction strategies. While it is important that HIV behavioural prevention continues to reinforce condom use, it needs to address both the challenges and opportunities of the substantial uptake of non-condom-based risk-reduction strategies.
Identification of Fat4 and Tsc22d1 as Novel Candidate Genes for Spontaneous Pulmonary Adenomas
Authors: Berndt Annerose , Cario Clinton L. , Silva Kathleen A. , Kennedy Victoria E. , Harrison David E. , Paigen Beverly , Sundberg John P. 
Published: July 2011

Abstract
Genetic influences that underlie spontaneous lung oncogenesis are poorly understood. The objective of this study was to determine the genetic influences on spontaneous pulmonary adenoma frequency and severity in 28 strains of mice as part of a large-scale aging study conducted at the Jackson Aging Center (http://agingmice.jax.org/). Genome-wide association studies were conducted in these strains with both low-density (132,000) and high-density (4,000,000) panel of single-nucleotide polymorphisms (SNP). Our analysis revealed that adenomas were relatively less frequent and less severe in females than males, and that loci implicated in frequency and severity were often different between male and female mice. While some of the significant loci identified mapped to genomic locations known to be responsible for carcinogen-induced cancers (e.g., Pas1), others were unique to our study. In particular, Fat4 was influential in males and Tsc22d1 was influential in females. SNPs implicated were predicted to alter amino acid sequence and change protein function. In summary, our results suggested that genetic influences that underlie pulmonary adenoma frequency are dependent on gender, and that Fat4 and Tsc22d1 are likely candidate genes to influence formation of spontaneous pulmonary adenoma in aging male and female mice, respectively. Cancer Res; 71(17); 5779–91. ©2011 AACR.