bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Putative Saccharomyces cerevisiae Hydrolase Ldh1p Is Localized to Lipid Droplets
Authors: Thoms Sven , Debelyy Mykhaylo O. , Connerth Melanie , Daum Günther , Erdmann Ralf 
Published: April 2011

ABSTRACT

Here, we report the identification of a novel hydrolase in
Saccharomyces cerevisiae
. Ldh1p (systematic name, Ybr204cp) comprises the typical GXSXG-type lipase motif of members of the α/β-hydrolase family and shares some features with the peroxisomal lipase Lpx1p. Both proteins carry a putative peroxisomal targeting signal type1 (PTS1) and can be aligned with two regions of homology. While Lpx1p is known as a peroxisomal enzyme, subcellular localization studies revealed that Ldh1p is predominantly localized to lipid droplets, the storage compartment of nonpolar lipids. Ldh1p is not required for the function and biogenesis of peroxisomes, and targeting of Ldh1p to lipid droplets occurs independently of the PTS1 receptor Pex5p.
Involvement of the Saccharomyces cerevisiae Hydrolase Ldh1p in Lipid Homeostasis
Authors: Debelyy Mykhaylo O. , Thoms Sven , Connerth Melanie , Daum Günther , Erdmann Ralf 
Published: April 2011

ABSTRACT

Here, we report the functional characterization of the newly identified lipid droplet hydrolase Ldh1p. Recombinant Ldh1p exhibits esterase and triacylglycerol lipase activities. Mutation of the serine in the hydrolase/lipase motif GXSXG completely abolished esterase activity. Ldh1p is required for the maintenance of a steady-state level of the nonpolar and polar lipids of lipid droplets. A characteristic feature of the
Saccharomyces cerevisiae
Δ
ldh1
strain is the appearance of giant lipid droplets and an excessive accumulation of nonpolar lipids and phospholipids upon growth on medium containing oleic acid as a sole carbon source. Ldh1p is thought to play a role in maintaining the lipid homeostasis in yeast by regulating both phospholipid and nonpolar lipid levels.
Biological Systems Discovery In Silico: Radical
S
-Adenosylmethionine Protein Families and Their Target Peptides for Posttranslational Modification
Authors: Haft Daniel H. , Basu Malay Kumar 
Published: April 2011

ABSTRACT

Data mining methods in bioinformatics and comparative genomics commonly rely on working definitions of protein families from prior computation. Partial phylogenetic profiling (PPP), by contrast, optimizes family sizes during its searches for the cooccurring protein families that serve different roles in the same biological system. In a large-scale investigation of the incredibly diverse radical
S
-adenosylmethionine (SAM) enzyme superfamily, PPP aided in building a collection of 68 TIGRFAMs hidden Markov models (HMMs) that define nonoverlapping and functionally distinct subfamilies. Many identify radical SAM enzymes as molecular markers for multicomponent biological systems; HMMs defining their partner proteins also were constructed. Newly found systems include five groupings of protein families in which at least one marker is a radical SAM enzyme while another, encoded by an adjacent gene, is a short peptide predicted to be its substrate for posttranslational modification. The most prevalent, in over 125 genomes, featuring a peptide that we designate SCIFF (
s
ix
c
ysteines
i
n
f
orty-
f
ive residues), is conserved throughout the class
Clostridia
, a distribution inconsistent with putative bacteriocin activity. A second novel system features a tandem pair of putative peptide-modifying radical SAM enzymes associated with a highly divergent family of peptides in which the only clearly conserved feature is a run of His-Xaa-Ser repeats. A third system pairs a radical SAM domain peptide maturase with selenocysteine-containing targets, suggesting a new biological role for selenium. These and several additional novel maturases that cooccur with predicted target peptides share a C-terminal additional 4Fe4S-binding domain with PqqE, the subtilosin A maturase AlbA, and the predicted mycofactocin and Nif11-class peptide maturases as well as with activators of anaerobic sulfatases and quinohemoprotein amine dehydrogenases. Radical SAM enzymes with this additional domain, as detected by TIGR04085, significantly outnumber lantibiotic synthases and cyclodehydratases combined in reference genomes while being highly enriched for members whose apparent targets are small peptides. Interpretation of comparative genomics evidence suggests unexpected (nonbacteriocin) roles for natural products from several of these systems.
ATP Requirement for Acidic Resistance in Escherichia coli
Authors: Sun Yirong , Fukamachi Toshihiko , Saito Hiromi , Kobayashi Hiroshi 
Published: April 2011

ABSTRACT

ATP participates in many cellular metabolic processes as a major substrate to supply energy. Many systems for acidic resistance (AR) under extremely acidic conditions have been reported, but the role of ATP has not been examined. To clarify whether or not ATP is necessary for the AR in
Escherichia coli
, the AR of mutants deficient in genes for ATP biosynthesis was investigated in this study. The deletion of
purA
or
purB
, each of which encodes enzymes to produce AMP from inosinate (IMP), markedly decreased the AR. The content of ATP in these mutants decreased rapidly at pH 2.5 compared to that of the wild type. The AR was again decreased significantly by the mutation of
adk
, which encoded an enzyme to produce ADP from AMP. The DNA damage in the
purA
and
purB
mutants was higher than that in the wild type. These results demonstrated that metabolic processes that require ATP participate in survival under extremely acidic conditions, and that one such system is the ATP-dependent DNA repair system.
Genome Sequences of Salmonella enterica Serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum Strains of Well- Defined Virulence in Food-Producing Animals
Authors: Richardson Emily J. , Limaye Bhakti , Inamdar Harshal , Datta Avik , Manjari K. Sunitha , Pullinger Gillian D. , Thomson Nicholas R. , Joshi Rajendra R. , Watson Michael , Stevens Mark P. 
Published: April 2011

ABSTRACT

Salmonella enterica
is an animal and zoonotic pathogen of worldwide importance and may be classified into serovars differing in virulence and host range. We sequenced and annotated the genomes of serovar Typhimurium, Choleraesuis, Dublin, and Gallinarum strains of defined virulence in each of three food-producing animal hosts. This provides valuable measures of intraserovar diversity and opportunities to formally link genotypes to phenotypes in target animals.
Complete Genome Sequence of the Thermoacidophilic Crenarchaeon Thermoproteus uzoniensis 768-20
Authors: Mardanov Andrey V. , Gumerov Vadim M. , Beletsky Alexey V. , Prokofeva Maria I. , Bonch-Osmolovskaya Elizaveta A. , Ravin Nikolai V. , Skryabin Konstantin G. 
Published: April 2011

ABSTRACT

Thermoproteus uzoniensis
768-20 is a thermoacidophilic anaerobic crenarchaeon isolated from a solfataric field in Kamchatka, Russia. The complete genome sequence reveals genes for protein and carbohydrate-active enzymes, beta-oxidation of fatty acids, the Embden-Meyerhof and Entner-Doudoroff pathways for glucose metabolism, the tricarboxylic acid cycle, the dicarboxylate/4-hydroxybutyrate cycle, hydrogenase, and sulfur reductase.
Genome Sequence of Lactobacillus amylovorus GRL1118, Isolated from Pig Ileum
Authors: Kant Ravi , Paulin Lars , Alatalo Edward , de Vos Willem M. , Palva Airi 
Published: April 2011

ABSTRACTLactobacillus amylovorusis a common member of the beneficial microbiota present in the pig gastrointestinal tract. Here, we report the genome sequence of the surface layer (S-layer) protein-carrying and potentially probiotic strainL. amylovorusGRL1118, which was isolated from porcine ileum and which shows strong adherence to pig intestinal epithelial cells.
The Genome of Erysipelothrix rhusiopathiae, the Causative Agent of Swine Erysipelas, Reveals New Insights into the Evolution of Firmicutes and the Organism's Intracellular Adaptations
Authors: Ogawa Yohsuke , Ooka Tadasuke , Shi Fang , Ogura Yoshitoshi , Nakayama Keisuke , Hayashi Tetsuya , Shimoji Yoshihiro 
Published: April 2011

ABSTRACTErysipelothrix rhusiopathiaeis a Gram-positive bacterium that represents a new class,Erysipelotrichia, in the phylumFirmicutes. The organism is a facultative intracellular pathogen that causes swine erysipelas, as well as a variety of diseases in many animals. Here, we report the first complete genome sequence analysis of a member of the classErysipelotrichia. TheE. rhusiopathiaegenome (1,787,941 bp) is one of the smallest genomes in the phylumFirmicutes. Phylogenetic analyses based on the 16S rRNA gene and 31 universal protein families suggest thatE. rhusiopathiaeis phylogenetically close toMollicutes, which comprisesMycoplasmaspecies. Genome analyses show that the overall features of theE. rhusiopathiaegenome are similar to those of other Gram-positive bacteria; it possesses a complete set of peptidoglycan biosynthesis genes, two-component regulatory systems, and various cell wall-associated virulence factors, including a capsule and adhesins. However, it lacks many orthologous genes for the biosynthesis of wall teichoic acids (WTA) and lipoteichoic acids (LTA) and thedltABCDoperon, which is responsible ford-alanine incorporation into WTA and LTA, suggesting that the organism has an atypical cell wall. In addition, likeMollicutes, its genome shows a complete loss of fatty acid biosynthesis pathways and lacks the genes for the biosynthesis of many amino acids, cofactors, and vitamins, indicating reductive genome evolution. The genome encodes nine antioxidant factors and nine phospholipases, which facilitate intracellular survival in phagocytes. Thus, theE. rhusiopathiaegenome represents evolutionary traits of bothFirmicutesandMollicutesand provides new insights into its evolutionary adaptations for intracellular survival.
First Case of Fulminant Sepsis Due to Wohlfahrtiimonas chitiniclastica
Authors: Almuzara Marisa N. , Palombarani Susana , Tuduri Alicia , Figueroa Silvia , Gianecini Ariel , Sabater Laura , Ramirez Maria S. , Vay Carlos A. 
Published: April 2011

ABSTRACT

We report the first case of fulminant sepsis due to
Wohlfahrtiimonas chitiniclastica
. This case is also the first one reported in South America. We emphasize the importance of recognizing bacteria that live in the larvae of a parasitic fly as the causative agent of severe infections in homeless patients.
Application of TaqMan Low-Density Arrays for Simultaneous Detection of Multiple Respiratory Pathogens
Authors: Kodani Maja , Yang Genyan , Conklin Laura M. , Travis Tatiana C. , Whitney Cynthia G. , Anderson Larry J. , Schrag Stephanie J. , Taylor Thomas H. , Beall Bernard W. , Breiman Robert F. , Feikin Daniel R. , Njenga M. Kariuki , Mayer Leonard W. , Oberste M. Steven , Tondella Maria Lucia C. , Winchell Jonas M. , Lindstrom Stephen L. , Erdman Dean D. , Fields Barry S. 
Published: April 2011

ABSTRACT

The large and growing number of viral and bacterial pathogens responsible for respiratory infections poses a challenge for laboratories seeking to provide rapid and comprehensive pathogen identification. We evaluated a novel application of the TaqMan low-density array (TLDA) cards for real-time PCR detection of 21 respiratory-pathogen targets. The performance of the TLDA was compared to that of individual real-time PCR (IRTP) assays with the same primers and probes using (i) nucleic acids extracted from the 21 pathogen strains and 66 closely related viruses and bacteria and (ii) 292 clinical respiratory specimens. With spiked samples, TLDA cards were about 10-fold less sensitive than IRTP assays. By using 292 clinical specimens to generate 2,238 paired individual assays, the TLDA card exhibited 89% sensitivity (95% confidence interval [CI], 86 to 92%; range per target, 47 to 100%) and 98% specificity (95% CI, 97 to 99%; range per target, 85 to 100%) overall compared to IRTP assays as the gold standard with a threshold cycle (

C
T

) cutoff of 43. The TLDA card approach offers promise for rapid and simultaneous identification of multiple respiratory pathogens for outbreak investigations and disease surveillance.
Laboratory and Clinical Evaluation of Screening Agar Plates for Detection of Carbapenem-Resistant Enterobacteriaceae from Surveillance Rectal Swabs
Authors: Adler Amos , Navon-Venezia Shiri , Moran-Gilad Jacob , Marcos Evgeniya , Schwartz David , Carmeli Yehuda 
Published: April 2011

ABSTRACT

The increased worldwide spread of carbapenem-resistant
Enterobacteriaceae
(CRE) emphasizes the need for a sensitive screening procedure to identify these microorganisms. Gastrointestinal carriers may serve as the reservoir for cross-transmission in the health care setting, and thus active surveillance is a key part in preventing the spread of such strains. Three agar-based methods for direct CRE detection from rectal swabs were compared: CHROMagar-KPC (Chrom); MacConkey agar with imipenem at 1 μg/ml (MacI); and MacConkey plates with imipenem, meropenem, and ertapenem disks (MacD). First, we compared the levels of detection (LODs) of 10 molecularly characterized carbapenemase-producing
Enterobacteriaceae
strains by the three methods. Second, we compared their performance in a surveillance study using rectal swabs (
n
= 139). The LODs of carbapenemase-producing
Enterobacteriaceae
strains were influenced by their MICs to carbapenems and were best for MacI, followed by Chrom. The MacD method was able to detect only the strains exhibiting MICs of ≥32 μg/ml to at least ertapenem. In the surveillance study, both Chrom and MacI had greater sensitivity (85%) than MacD (76%). However, MacI was the most specific method. In conclusion, MacI appears to be most appropriate medium for the detection of CRE in settings in which multiclonal CRE strains with various MICs to carbapenems are circulating.
Intercompartmental Recombination of HIV-1 Contributes toenvIntrahost Diversity and Modulates Viral Tropism and Sensitivity to Entry Inhibitors
Authors: Brown Richard J. P. , Peters Paul J. , Caron Catherine , Gonzalez-Perez Maria Paz , Stones Leanne , Ankghuambom Chiambah , Pondei Kemebradikumo , McClure C. Patrick , Alemnji George , Taylor Stephen , Sharp Paul M. , Clapham Paul R. , Ball Jonathan K. 
Published: April 2011

ABSTRACTHIV-1 circulates within an infected host as a genetically heterogeneous viral population. Viral intrahost diversity is shaped by substitutional evolution and recombination. Although many studies have speculated that recombination could have a significant impact on viral phenotype, this has never been definitively demonstrated. We report here phylogenetic and subsequent phenotypic analyses of envelope genes obtained from HIV-1 populations present in different anatomical compartments. Assessment ofenvcompartmentalization from immunologically discrete tissues was assessed utilizing a single genome amplification approach, minimizingin vitro-generated artifacts. Genetic compartmentalization of variants was frequently observed. In addition, multiple incidences of intercompartment recombination, presumably facilitated by low-level migration of virus or infected cells between different anatomic sites and coinfection of susceptible cells by genetically divergent strains, were identified. These analyses demonstrate that intercompartment recombination is a fundamental evolutionary mechanism that helps to shape HIV-1envintrahost diversity in natural infection. Analysis of the phenotypic consequences of these recombination events showed that genetic compartmentalization often correlates with phenotypic compartmentalization and that intercompartment recombination results in phenotype modulation. This represents definitive proof that recombination can generate novel combinations of phenotypic traits which differ subtly from those of parental strains, an important phenomenon that may have an impact on antiviral therapy and contribute to HIV-1 persistencein vivo.
Temporal Profiling of the Coding and Noncoding Murine Cytomegalovirus Transcriptomes
Authors: Lacaze Paul , Forster Thorsten , Ross Alan , Kerr Lorraine E. , Salvo-Chirnside Eliane , Lisnic Vanda Juranic , López-Campos Guillermo H. , García-Ramírez José J. , Messerle Martin , Trgovcich Joanne , Angulo Ana , Ghazal Peter 
Published: April 2011

ABSTRACT

The global transcriptional program of murine cytomegalovirus (MCMV), involving coding, noncoding, and antisense transcription, remains unknown. Here we report an oligonucleotide custom microarray platform capable of measuring both coding and noncoding transcription on a genome-wide scale. By profiling MCMV wild-type and immediate-early mutant strains in fibroblasts, we found rapid activation of the transcriptome by 6.5 h postinfection, with absolute dependency on
ie3
, but not
ie1
or
ie2
, for genomic programming of viral gene expression. Evidence is also presented to show, for the first time, genome-wide noncoding and bidirectional transcription at late stages of MCMV infection.
Prevention of sport injury II: a systematic review of clinical science research
Authors: McBain Kellen , Shrier Ian , Shultz Rebecca , Meeuwisse Willem H , Klügl Martin , Garza Daniel , Matheson Gordon O 
Published: April 2011

ObjectiveTo characterise the nature of the sport injury prevention literature by reviewing published articles that evaluate specific clinical interventions designed to reduce sport injury risks.Data sourcesPubMed, Cinahl, Web of Science and Embase.Main resultsOnly 139 of 2525 articles retrieved met the inclusion criteria. Almost 40% were randomised controlled trials and 30.2% were cohort studies. The focus of the study was protective equipment in 41%, training in 32.4%, education in 7.9%, rules and regulations in 4.3%, and 13.3% involved a combination of the above. Equipment research studied stability devices (42.1%), head and face protectors (33.3%), attenuating devices (17.5%) as well as other devices (7%). Training studies often used a combination of interventions (eg, balance and stretching); most included balance and coordination (63.3%), with strength and power (36.7%) and stretching (22.5%) being less common. Almost 70% of the studies examined lower extremity injuries, and a majority of these were joint (non-bone)-ligament injuries. Contact sports were most frequently studied (41.5%), followed by collision (39.8%) and non-contact (20.3%).ConclusionThe authors found only 139 publications in the existing literature that examined interventions designed to prevent sports injury. Of these, the majority investigated equipment or training interventions whereas only 4% focused on changes to the rules and regulations that govern sport. The focus of intervention research is on acute injuries in collision and contact sports whereas only 20% of the studies focused on non-contact sports.
Patients' perspectives of the substitute decision maker: who makes better decisions?
Authors: Mirzaei Komeil , Milanifar Alireza , Asghari Fariba 
Published: April 2011

IntroductionSubstitute decision making on behalf of incapable patients is based on the ethical principle of ‘respect for autonomy’. This study was conducted to assess patients' wishes and preferences in terms of a substitute decision maker and determinants of such preferences.MethodsThe authors conducted a cross-sectional study and selected samples randomly from patients presenting at Farabi Eye Hospital clinics who were 18 years of age or older. Questionnaires were completed through interviews.Results200 patients between the ages of 18 and 83 years were interviewed. About 52% (N=105) were men and 73% (N=77) were married. Among married patients, the spouse was chosen as the substitute decision maker in only 51% of cases. Single men preferred their father first in 36% (N=9) of cases, while single girls chose their father in 5.6% (N=1) of cases and their most prevalent choice was other unmentioned people (33.3%, N=6). Most patients (93.5%) wished to be asked about their substitute decision maker when hospitalised.ConclusionThe results of this study show that the people we usually consult for decisions concerning patient treatment are significantly different from the patients' preferred substitute decision makers. The authors suggest patients be allowed to choose their substitute decision maker while conscious.
Combined endovascular and surgical resection of a giant lumbosacral arteriovenous malformation in a patient with Cobb syndrome
Authors: Spiotta Alejandro M , Hussain Muhammad Shazam , Masaryk Thomas J , Krishnaney Ajit A 
Published: April 2011

Objective and importanceCobb syndrome is a rare condition that includes a cutaneous nevus with an associated spinal vascular lesion at the same dermatome. We present a challenging case of a progressively symptomatic massive lumbosacral arteriovenous malformation (AVM) in a patient with Cobb's syndrome requiring a multimodality approach including staged preoperative transarterial and transvenous endovascular embolization followed by surgical excision and wound reconstruction.Clinical presentationThe patient presented with a massive lumbosacral AVM with symptoms of congestive heart failure. Angiography demonstrated arterial feeders predominantly from internal iliac, median sacral and lumbar segmental arteries.InterventionThe patient underwent staged transarterial and transvenous endovascular embolization resulting in 90% reduction in the AVM size, followed by surgical resection of the lesion. The patient made an excellent recovery with improvement in his symptoms of congestive heart failure.ConclusionThe treatment algorithm for massive AVMs must be individualized. A combination of staged embolization and subsequent surgery may be required to obtain a good result. Through this carefully planned multidisciplinary approach a previously incurable lesion in this patient with Cobb syndrome was able to be treated successfully.
Expression of nm23-H1 Is Associated with Poor Prognosis in Peripheral T-Cell Lymphoma, Not Otherwise Specified
Authors: Niitsu Nozomi , Nakamine Hirokazu , Okamoto Masataka 
Published: April 2011

Abstract
Purpose: We examined whether nm23-H1 is a prognostic factor of peripheral T-cell lymphoma, not otherwise specified (PTCL-NOS).
Experimental Design: We studied 102 consecutive, untreated PTCL-NOS patients from 1998 to 2008. The expression of nm23-H1 and TIA-1 was studied by immunohistochemistry.
Results: nm23-H1 was positive in 44.1% and TIA-1 in 78.4% of the PTCL-NOS patients. nm23-H1 expression was not correlated with age, performance status (PS), lactate dehydrogenase (LDH) level, or stage but was significantly correlated with the prognostic index for T-cell lymphoma. The serum nm23-H1 level was 43.44 ng/mL in the cytoplasmic nm23-H1 strongly positive, 24.32 ng/mL in the cytoplasmic nm23-H1 moderately positive, and 13.64 ng/mL in the cytoplasmic nm23-H1–negative patients. The nm23-H1–positive group had significantly shorter overall survival (OS). TIA-1 had no prognostic impact on 5-year OS rates. OS was significantly shorter in patients with the following clinicopathologic features: age 60 or more years, PS of 2 to 4, LDH level greater than normal, bone marrow involvement, or nm23-H1–positive lymphoma. Multivariate analysis confirmed nm23-H1 expression to be an independent prognostic factor.
Conclusions: The nm23-H1 protein may be an important prognostic factor in PTCL-NOS. Because our results suggested that nm23-HI is produced by lymphoma cells, we expect to see the development of new treatments targeting nm23 overexpression. Clin Cancer Res; 17(9); 2893–9. ©2011 AACR.