bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolism of Sialic Acid by Bifidobacterium breve UCC2003
Authors: Egan Muireann , O'Connell Motherway Mary , Ventura Marco , van Sinderen Douwe 
Published: May 2014

ABSTRACT

Bifidobacteria constitute a specific group of commensal bacteria that inhabit the gastrointestinal tracts of humans and other mammals.
Bifidobacterium breve
UCC2003 has previously been shown to utilize several plant-derived carbohydrates that include cellodextrins, starch, and galactan. In the present study, we investigated the ability of this strain to utilize the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that
B. breve
UCC2003 can cross feed on sialic acid derived from the metabolism of 3′-sialyllactose, an abundant HMO, by another infant gut bifidobacterial strain,
Bifidobacterium bifidum
PRL2010.
Stress Induces Changes in the Phosphorylation of Trypanosoma cruzi RNA Polymerase II, Affecting Its Association with Chromatin and RNA Processing
Authors: Rocha Antônio Augusto , Moretti Nilmar Silvio , Schenkman Sergio 
Published: May 2014

ABSTRACT

The phosphorylation of the carboxy-terminal heptapeptide repeats of the largest subunit of RNA polymerase II (Pol II) controls several transcription-related events in eukaryotes. Trypanosomatids lack these typical repeats and display an unusual transcription control. RNA Pol II associates with the transcription site of the spliced leader (SL) RNA, which is used in the
trans
-splicing of all mRNAs transcribed on long polycistronic units. We found that
Trypanosoma cruzi
RNA Pol II associated with chromatin is highly phosphorylated. When transcription is inhibited by actinomycin D, the enzyme runs off from SL genes, remaining hyperphosphorylated and associated with polycistronic transcription units. Upon heat shock, the enzyme is dephosphorylated and remains associated with the chromatin. Transcription is partially inhibited with the accumulation of housekeeping precursor mRNAs, except for heat shock genes. DNA damage caused dephosphorylation and transcription arrest, with RNA Pol II dissociating from chromatin although staying at the SL. In the presence of calyculin A, the hyperphosphorylated form detached from chromatin, including the SL loci. These results indicate that in trypanosomes, the unusual RNA Pol II is phosphorylated during the transcription of SL and polycistronic operons. Different types of stresses modify its phosphorylation state, affecting pre-RNA processing.
Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus
Authors: Inglis Diane O. , Skrzypek Marek S. , Liaw Edward , Moktali Venkatesh , Sherlock Gavin , Stajich Jason E. 
Published: May 2014

ABSTRACT

Cryptococcus
, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648
Cryptococcus
gene names have been published. However, these data are scattered throughout the literature and are challenging to find. Furthermore, conflicts in locus identification exist, so that named genes have been subsequently published under new names or names associated with one locus have been used for another locus. To avoid these conflicts and to provide a central source of
Cryptococcus
gene information, we have collected all published
Cryptococcus
gene names from the scientific literature and associated them with standard
Cryptococcus
locus identifiers and have incorporated them into FungiDB (
www.fungidb.org
). FungiDB is a panfungal genome database that collects gene information and functional data and provides search tools for 61 species of fungi and oomycetes. We applied these published names to a manually curated ortholog set of all
Cryptococcus
species currently in FungiDB, including
Cryptococcus neoformans
var.
neoformans
strains JEC21 and B-3501A,
C. neoformans
var.
grubii
strain H99, and
Cryptococcus gattii
strains R265 and WM276, and have written brief descriptions of their functions. We also compiled a protocol for gene naming that summarizes guidelines proposed by members of the
Cryptococcus
research community. The centralization of genomic and literature-based information for
Cryptococcus
at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen.
PvdP Is a Tyrosinase That Drives Maturation of the Pyoverdine Chromophore in Pseudomonas aeruginosa
Authors: Nadal-Jimenez Pol , Koch Gudrun , Reis Carlos R. , Muntendam Remco , Raj Hans , Jeronimus-Stratingh C. Margot , Cool Robbert H. , Quax Wim J. 
Published: May 2014

ABSTRACT

The iron binding siderophore pyoverdine constitutes a major adaptive factor contributing to both virulence and survival in fluorescent pseudomonads. For decades, pyoverdine production has allowed the identification and classification of fluorescent and nonfluorescent pseudomonads. Here, we demonstrate that PvdP, a periplasmic enzyme of previously unknown function, is a tyrosinase required for the maturation of the pyoverdine chromophore in
Pseudomonas aeruginosa
. PvdP converts the nonfluorescent ferribactin, containing two iron binding groups, into a fluorescent pyoverdine, forming a strong hexadentate complex with ferrous iron, by three consecutive oxidation steps. PvdP represents the first characterized member of a small family of tyrosinases present in fluorescent pseudomonads that are required for siderophore maturation and are capable of acting on large peptidic substrates.
The Rip1 Protease of Mycobacterium tuberculosis Controls the SigD Regulon
Authors: Schneider Jessica S. , Sklar Joseph G. , Glickman Michael S. 
Published: May 2014

ABSTRACT

Regulated intramembrane proteolysis of membrane-embedded substrates by site-2 proteases (S2Ps) is a widespread mechanism of transmembrane signal transduction in bacteria and bacterial pathogens. We previously demonstrated that the
Mycobacterium tuberculosis
S2P Rip1 is required for full virulence in the mouse model of infection. Rip1 controls transcription in part through proteolysis of three transmembrane anti-sigma factors, anti-SigK, -L, and -M, but there are also Rip1-dependent, SigKLM-independent pathways. To determine the contribution of the sigma factors K, L, and M to the Δ
rip1
attenuation phenotype, we constructed an
M. tuberculosis
Δ
sigK
Δ
sigL
Δ
sigM
mutant and found that this strain fails to recapitulate the marked attenuation of Δ
rip1
in mice. In a search for additional pathways controlled by Rip1, we demonstrated that the SigD regulon is positively regulated by the Rip1 pathway. Rip1 cleavage of transmembrane anti-SigD is required for expression of SigD target genes. In the absence of Rip1, proteolytic maturation of RsdA is impaired. These findings identify RsdA/SigD as a fourth arm of the branched pathway controlled by Rip1 in
M. tuberculosis
.
Tolerance of a Phage Element by Streptococcus pneumoniae Leads to a Fitness Defect during Colonization
Authors: DeBardeleben Hilary K. , Lysenko Elena S. , Dalia Ankur B. , Weiser Jeffrey N. 
Published: May 2014

ABSTRACT

The pathogenesis of the disease caused by
Streptococcus pneumoniae
begins with colonization of the upper respiratory tract. Temperate phages have been identified in the genomes of up to 70% of clinical isolates. How these phages affect the bacterial host during colonization is unknown. Here, we examined a clinical isolate that carries a novel prophage element, designated Spn1, which was detected in both integrated and episomal forms. Surprisingly, both lytic and lysogenic Spn1 genes were expressed under routine growth conditions. Using a mouse model of asymptomatic colonization, we demonstrate that the Spn1
−
strain outcompeted the Spn1
+
strain >70-fold. To determine if Spn1 causes a fitness defect through a
trans
-acting factor, we constructed an Spn1
+
mutant that does not become an episome or express phage genes. This mutant competed equally with the Spn1
−
strain, indicating that expression of phage genes or phage lytic activity is required to confer this fitness defect.
In vitro
, we demonstrate that the presence of Spn1 correlated with a defect in LytA-mediated autolysis. Furthermore, the Spn1
+
strain displayed increased chain length and resistance to lysis by penicillin compared to the Spn
−
strain, indicating that Spn1 alters the cell wall physiology of its host strain. We posit that these changes in cell wall physiology allow for tolerance of phage gene products and are responsible for the relative defect of the Spn1
+
strain during colonization. This study provides new insight into how bacteria and prophages interact and affect bacterial fitness
in vivo
.
How Many Initiator tRNA Genes Does Escherichia coli Need?
Authors: Samhita Laasya , Nanjundiah Vidyanand , Varshney Umesh 
Published: May 2014

ABSTRACT

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that
Escherichia coli
has four copies of initiator tRNA (tRNA

i

) genes, encoding a special tRNA (tRNA
fMet
) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between
E. coli
strains that differ in the number of tRNA

i

genes they contain. This has enabled us to uncover an unexpected link between the number of tRNA

i

genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNA

i

genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNA

i

gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.
Alginate-Dependent Gene Expression Mechanism in Sphingomonas sp. Strain A1
Authors: Hayashi Chie , Takase Ryuichi , Momma Keiko , Maruyama Yukie , Murata Kousaku , Hashimoto Wataru 
Published: May 2014

ABSTRACT

Sphingomonas
sp. strain A1, a Gram-negative bacterium, directly incorporates alginate polysaccharide into the cytoplasm through a periplasmic alginate-binding protein-dependent ATP-binding cassette transporter. The polysaccharide is degraded to monosaccharides via the formation of oligosaccharides by endo- and exotype alginate lyases. The strain A1 proteins for alginate uptake and degradation are encoded in both strands of a genetic cluster in the bacterial genome and inducibly expressed in the presence of alginate. Here we show the function of the alginate-dependent transcription factor AlgO and its mode of action on the genetic cluster and alginate oligosaccharides. A putative gene within the genetic cluster seems to encode a transcription factor-like protein (AlgO). Mutant strain A1 (ΔAlgO mutant) cells with a disrupted
algO
gene constitutively produced alginate-related proteins. DNA microarray analysis indicated that wild-type cells inducibly transcribed the genetic cluster only in the presence of alginate, while ΔAlgO mutant cells constitutively expressed the genetic cluster. A gel mobility shift assay showed that AlgO binds to the specific intergenic region between
algO
and
algS
(
algO-algS
). Binding of AlgO to the
algO-algS
intergenic region diminished with increasing alginate oligosaccharides. These results demonstrated a novel alginate-dependent gene expression mechanism. In the absence of alginate, AlgO binds to the
algO-algS
intergenic region and represses the expression of both strands of the genetic cluster, while in the presence of alginate, AlgO dissociates from the
algO-algS
intergenic region via binding to alginate oligosaccharides produced through the lyase reaction and subsequently initiates transcription of the genetic cluster. This is the first report on the mechanism by which alginate regulates the expression of the gene cluster.
Adding maps (GPS) to accelerometry data to improve study participants’ recall of physical activity: a methodological advance in physical activity research
Authors: Brown Barbara B , Wilson Laura , Tribby Calvin P , Werner Carol M , Wolf Jean , Miller Harvey J , Smith Ken R 
Published: May 2014

ObjectiveObtaining the ‘when, where and why’ of healthy bouts of moderate-to-vigorous physical activity (MVPA) provides insights into natural PA.DesignIn Salt Lake City, Utah, adults wore accelerometer and Global Positioning System (GPS) loggers for a week in a cross-sectional study to establish baseline travel and activity patterns near a planned Complete Street intervention involving a new rail line, new sidewalks and a bike path.ResultsAt the end of the week, research assistants met with the 918 participants who had at least three 10 h days of good accelerometer readings. Accelerometer and GPS data were uploaded and integrated within a custom application, and participants were provided with maps and time information for past MVPA bouts of ≥3 min to help them recall bout details. Participants said that ‘getting someplace’ was, on average, a more important motivation for their bouts than leisure or exercise. A series of recall tests showed that participants recalled most bouts they were asked about, regardless of the duration of the bout, suggesting that participant perceptions of their shorter lifestyle bouts can be studied with this methodology. Visual prompting with a map depicting where each bout took place yielded more accurate recall than prompting with time cues alone.ConclusionsThese techniques provide a novel way to understand participant memories of the context and subjective assessments associated with healthy bouts of PA. Prompts with time-stamped maps that illustrate places of MVPA offer an effective method to improve understanding of activity and its supportive sociophysical contexts.
Risky driving, mental health, and health-compromising behaviours: risk clustering in late adolescents and adults
Authors: McDonald Catherine C , Sommers Marilyn S , Fargo Jamison D 
Published: May 2014

BackgroundHealth-compromising behaviours in adolescents and adults co-occur. Because motor vehicle crashes are the leading cause of death and disability for these age groups, understanding the association between risky driving and other health-compromising behaviours is critical.MethodsWe performed a secondary analysis of data from a randomised controlled trial of an intervention for participants who screened positive for risky driving and problem drinking. Using baseline data, we examined relationships among conduct behaviour problems before and after age 15 years, depressive symptoms, sleep, problem drinking, and risky driving (hostile, reckless and drinking and driving) in late adolescents ages 18–24 (n=110) years, and adults ages 25–44 (n=202) years. We developed a measurement model for the entire sample using confirmatory factor analysis, which was then specified as a multigroup structural equation model.ResultsLate adolescents and adults had some similar associations for pathways through problem drinking to drinking and driving; depression to reckless driving; and conduct behaviour problems after 15 years of age to hostile driving. Late adolescents, however, had more complex relationships: depressive symptoms and conduct behaviour problems before 15 years of age were associated with more risky driving behaviours through multiple pathways, and males reported more risky driving.ConclusionsRisky driving is associated with other health-compromising behaviours and mental health factors. It is a multidimensional phenomenon more pronounced in late adolescence than adulthood. In order to promote safe driving, the findings support the need to consider behaviours that are a health threat in the late adolescent population during driving training and licensure.Trial registration number:NCT00164294.
Low neurologic intensive care unit hemoglobin as a predictor for intra-arterial vasospasm therapy and poor discharge modified Rankin Scale in aneurysmal subarachnoid haemorrhage-induced cerebral vasospasm
Authors: Bell Donnie L , Kimberly W Taylor , Yoo Albert J , Leslie-Mazwi Thabele M , Rabinov James D , Bell Jania E , Mehta Brijesh P , Hirsch Joshua A 
Published: May 2014

BackgroundIntra-arterial vasospasm therapy (IAVT) with vasodilators, balloon angioplasty, and cerebral blood flow augmentation devices are therapies for aneurysmal subarachnoid hemorrhage-induced symptomatic cerebral vasospasm refractory to maximal medical management. Our aim was to identify clinical factors predictive of IAVT and/or poor outcome.MethodsA cross-sectional retrospective analysis was performed of 130 patients with aneurysmal subarachnoid hemorrhage including patients without and with symptomatic cerebral vasospasm requiring IAVT. The data were analysed by Student t test, univariate analysis and binary logistic regression.ResultsThe mean±SD patient age was 54±12.2 years, admission hemoglobin was 13.6±1.5 g/dL, and neurologic intensive care unit (NICU) hemoglobin 11±1.4 g/dL. The median Hunt and Hess grade was 2 (range 1,4), Fisher grade 3 (range 3,3), and discharge modified Rankin Scale (mRS) 0.5 (range 0,2). Lower mean NICU hemoglobin was found in patients receiving IAVT than in those not receiving IAVT (M=10.4±0.9 g/dL vs M=11.2±1.4 g/dL, t(115)=−2.52, p=0.01). Further, lower mean NICU hemoglobin was associated with increased IAVT (ρ=−0.3, p<0.01) and higher discharge mRS (ρ=−0.5, p<0.01). In binary logistic regression, lower mean NICU hemoglobin was an independent predictor of IAVT (OR 0.6, 95% CI 0.4 to 0.9, p<0.05) as well as poor discharge mRS (OR 0.6, 95% CI 0.4 to 0.9, p<0.05). Hunt and Hess grade was also an independent predictor of these outcomes.ConclusionsLower mean hemoglobin during the acute phase of aneurysmal subarachnoid hemorrhage-induced cerebral vasospasm is an independent predictor of IAVT and poor discharge mRS. This relationship warrants further evaluation.
The Effects of Test Preference, Test Access, and Navigation on Colorectal Cancer Screening
Authors: Daskalakis Constantine , Vernon Sally W. , Sifri Randa , DiCarlo Melissa , Cocroft James , Sendecki Jocelyn Andrel , Myers Ronald E. 
Published: May 2014

Abstract
Background: Little is known about how colorectal cancer screening test preferences operate together with test access and navigation to influence screening adherence in primary care.
Methods: We analyzed data from a randomized trial of 945 primary care patients to assess the independent effects of screening test preference for fecal immunochemical test (FIT) or colonoscopy, mailed access to FIT and colonoscopy, and telephone navigation for FIT and colonoscopy, on screening.
Results: Preference was not associated with overall screening, but individuals who preferred FIT were more likely to complete FIT screening (P = 0.005), whereas those who preferred colonoscopy were more likely to perform colonoscopy screening (P = 0.032). Mailed access to FIT and colonoscopy was associated with increased overall screening (OR = 2.6, P = 0.001), due to a 29-fold increase in FIT use. Telephone navigation was also associated with increased overall screening (OR = 2.1, P = 0.005), mainly due to a 3-fold increase in colonoscopy performance. We estimated that providing access and navigation for both screening tests may substantially increase screening compared with a preference-tailored approach, mainly due to increased performance of nonpreferred tests.
Conclusions: Preference influences the type of screening tests completed. Test access increases FIT and navigation mainly increases colonoscopy. Screening strategies providing access and navigation to both tests may be more effective than preference-tailored approaches.
Impact: Preference tailoring in colorectal cancer screening strategies should be avoided if the objective is to maximize screening rates, although other factors (e.g., costs, necessary follow-up) should also be considered. Cancer Epidemiol Biomarkers Prev; 23(8); 1521–8. ©2014 AACR.
Risk Factors Associated with Rectal Neuroendocrine Tumors: A Cross-Sectional Study
Authors: Jung Yoon Suk , Yun Kyung Eun , Chang Yoosoo , Ryu Seungho , Park Jung Ho , Kim Hong Joo , Cho Yong Kyun , Sohn Chong Il , Jeon Woo Kyu , Kim Byung Ik , Park Dong Il 
Published: May 2014

Abstract
Background: The incidence of rectal neuroendocrine tumors (NET) has been increasing since the implementation of the screening colonoscopy. However, very little is known about risk factors associated with rectal NETs. We examined the prevalence of and the risk factors for rectal NETs in a Korean population.
Methods: A cross-sectional study was performed on 62,171 Koreans who underwent screening colonoscopy. The clinical characteristics and serum biochemical parameters of subjects with rectal NET were compared with those of subjects without rectal NET using multivariate logistic regression.
Results: Of a total of 57,819 participants, 101 [OR, 0.17%; 95% confidence interval (CI), 0.14–0.20] had a rectal NET. Young age (&lt;50 years; OR, 2.09; 95% CI, 1.06–4.15), male gender (OR, 1.92; 95% CI, 1.15–3.20), alcohol drinking [adjusted OR (AOR), 1.56; 95% CI, 1.01–2.42], and a low high-density lipoprotein-cholesterol (HDL-C) level (AOR, 1.85; 95% CI, 1.10–3.11) were independent risk factors for rectal NETs. Cigarette smoking, fatty liver, metabolic syndrome, higher triglyceride level (≥150 mg/dL), and higher homeostasis model assessment of insulin resistance (≥2.5) were not independently associated with rectal NETs, although these factors were more common in individuals with rectal NETs in the univariate analysis.
Conclusions: Young age (&lt;50 years), male gender, alcohol drinking, and a low HDL-C level were risk factors for rectal NETs. Our results suggest that gender, behavioral factors, and dyslipidemia may affect the risk for developing rectal NETs.
Impact: The findings of this study contribute to a better understanding of the influence of gender, behavioral factors, and dyslipidemia in developing rectal NETs. Cancer Epidemiol Biomarkers Prev; 23(7); 1406–13. ©2014 AACR.