bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Census of Bacteria in Clean Rooms by Using DNA Microarray and Cloning Methods
Authors: La Duc Myron T. , Osman Shariff , Vaishampayan Parag , Piceno Yvette , Andersen Gary , Spry J. A. , Venkateswaran Kasthuri 
Published: August 2009

ABSTRACT
A census of clean room surface-associated bacterial populations was derived from the results of both the cloning and sequencing of 16S rRNA genes and DNA microarray (PhyloChip) analyses. Samples from the Lockheed Martin Aeronautics Multiple Testing Facility (LMA-MTF), the Kennedy Space Center Payload Hazard and Servicing Facility (KSC-PHSF), and the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) clean rooms were collected during the various assembly phases of the Phoenix and Mars Science Laboratory (MSL) spacecraft. Clone library-derived analyses detected a larger bacterial diversity prior to the arrival of spacecraft hardware in these clean room facilities. PhyloChip results were in agreement with this trend but also unveiled the presence of anywhere from 9- to 70-fold more bacterial taxa than cloning approaches. Among the facilities sampled, the JPL-SAF (MSL mission) housed a significantly less diverse bacterial population than either the LMA-MTF or KSC-PHSF (Phoenix mission). Bacterial taxa known to thrive in arid conditions were frequently detected in MSL-associated JPL-SAF samples, whereas proteobacterial lineages dominated Phoenix-associated KSC-PHSF samples. Comprehensive bacterial censuses, such as that reported here, will help space-faring nations preemptively identify contaminant biomatter that may compromise extraterrestrial life detection experiments. The robust nature and high sensitivity of DNA microarray technologies should prove beneficial to a wide range of scientific, electronic, homeland security, medical, and pharmaceutical applications and to any other ventures with a vested interest in monitoring and controlling contamination in exceptionally clean environments.
Comparative Transcriptomic Approach To Investigate Differences in Wine Yeast Physiology and Metabolism during Fermentation
Authors: Rossouw Debra , Olivares-Hernandes Roberto , Nielsen Jens , Bauer Florian F. 
Published: August 2009

ABSTRACTCommercial wine yeast strains of the speciesSaccharomyces cerevisiaehave been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level.
Identification of Flagellar Motility Genes in
Yersinia ruckeri
by Transposon Mutagenesis
Authors: Evenhuis Jason P. , LaPatra Scott E. , Verner-Jeffreys David W. , Dalsgaard Inger , Welch Timothy J. 
Published: August 2009

ABSTRACT

Here we demonstrate that flagellar secretion is required for production of secreted lipase activity in the fish pathogen
Yersinia ruckeri
and that neither of these activities is necessary for virulence in rainbow trout. Our results suggest a possible mechanism for the emergence of nonmotile biotype 2
Y. ruckeri
through the mutational loss of flagellar secretion.
Hyperglutamylation of Tubulin Can either Stabilize or Destabilize Microtubules in the Same Cell
Authors: Wloga Dorota , Dave Drashti , Meagley Jennifer , Rogowski Krzysztof , Jerka-Dziadosz Maria , Gaertig Jacek 
Published: August 2009

ABSTRACT

In most eukaryotic cells, tubulin is subjected to posttranslational glutamylation, a conserved modification of unclear function. The glutamyl side chains form as branches of the primary sequence glutamic acids in two biochemically distinct steps: initiation and elongation. The length of the glutamyl side chain is spatially controlled and microtubule type specific. Here, we probe the significance of the glutamyl side chain length regulation in vivo by overexpressing a potent side chain elongase enzyme, Ttll6Ap, in
Tetrahymena
. Overexpression of Ttll6Ap caused hyperelongation of glutamyl side chains on the tubulin of axonemal, cortical, and cytoplasmic microtubules. Strikingly, in the same cell, hyperelongation of glutamyl side chains stabilized cytoplasmic microtubules and destabilized axonemal microtubules. Our observations suggest that the cellular outcomes of glutamylation are mediated by spatially restricted tubulin interactors of diverse nature.
Allosteric Regulation of Glucosamine-6-Phosphate Deaminase (NagB) and Growth ofEscherichia colion Glucosamine
Authors: Álvarez-Añorve Laura I. , Bustos-Jaimes Ismael , Calcagno Mario L. , Plumbridge Jacqueline 
Published: August 2009

ABSTRACTGrowth onN-acetylglucosamine (GlcNAc) produces intracellularN-acetylglucosamine-6-phosphate (GlcNAc6P), which affects the regulation of the catabolism of amino sugars inEscherichia coliin two ways. First, GlcNAc6P is the inducing signal for the NagC repressor, and thus it increases the expression of the enzymes of thenagE-nagBACDoperon. Second, it is the allosteric activator of glucosamine-6P (GlcN6P) deaminase, NagB, and thus increases the catalytic capacity of this key enzyme in the metabolism of amino sugars. We showed previously that both the level of expression of thenagBgene and the transport of glucosamine were limiting the growth rate on GlcN (L. I. Álvarez-Añorve et al., J. Bacteriol. 187:2974-2982, 2005). We were unable to conclude if the lack of allosteric activation of wild-type NagB was also contributing to the slower growth rate on GlcN. Using a single-copy plasmid, with a constitutive promoter, we have separated the effects of GlcNAc6P on the NagB protein level and on deaminase activity. We show that over a range of intracellular NagB concentrations it is the quantity of the substrate, GlcN6P, which is limiting growth rather than the concentration of the allosteric activator, GlcNAc6P. On the other hand, the F174A mutant of NagB, which requires higher concentrations of GlcNAc6P for activity in vitro, grew better on GlcN in the presence of GlcNAc6P. However, wild-type NagB behaves as if it is already fully allosterically activated during growth on GlcN, and we present evidence suggesting that sufficient GlcNAc6P for allosteric activation is derived from the recycling of peptidoglycan.
Isocitrate Lyase Supplies Precursors for Hydrogen Cyanide Production in a Cystic Fibrosis Isolate of
Pseudomonas aeruginosa
Authors: Hagins Jessica M. , Locy Robert , Silo-Suh Laura 
Published: August 2009

ABSTRACT

Pseudomonas aeruginosa
colonizes and can persist in the lungs of cystic fibrosis (CF) patients for decades. Adaptation of
P. aeruginosa
to the CF lung environment causes various genotypic and phenotypic alterations in the bacterium that facilitate persistence. We showed previously that isocitrate lyase (ICL) activity is constitutively upregulated in the
P. aeruginosa
CF isolate FRD1. We show here that high ICL activity in FRD1 contributes to increased hydrogen cyanide (HCN) production by this isolate. Disruption of
aceA
, which encodes ICL, results in reduced cyanide production by FRD1 but does not affect cyanide production in the wound isolate PAO1. Cyanide production is restored to the FRD1
aceA
mutant by addition of glyoxylate, a product of ICL activity, or glycine to the growth medium. Conversion of glyoxylate to glycine may provide a mechanism for increased cyanide production by
P. aeruginosa
growing on compounds that activate the glyoxylate pathway. Consistent with this hypothesis, disruption of PA5304, encoding a putative
d
-amino acid dehydrogenase (DadA), led to decreased cyanide production by FRD1. Cyanide production was restored to the FRD1
dadA
mutant by the addition of glycine, but not glyoxylate, to the growth medium, suggesting that loss of the ability to convert glyoxylate to glycine was associated with the
dadA
mutation. This was supported by increased glycine production from toluene-treated FRD1 cells with the addition of glyoxylate compared to FRD1
dadA
cells. This study indicates a larger role for ICL in the physiology and virulence of chronic isolates of
P. aeruginosa
than previously recognized.
Inter-simple sequence repeat (ISSR) and morphological variation in the western North American range ofChrysosplenium tetrandrum(Saxifragaceae)
Authors: Levsen Nicholas D. , Mort Mark E. 
Published: August 2009

The herbaceous perennial Chrysosplenium tetrandrum (Lund ex Malmgr.) Th. Fr. (Saxifragaceae) is a self-pollinating, circumpolar species with a broad latitudinal distribution and a disjunct North American range. The southernmost populations are isolated in the Rocky Mountains of Colorado and Montana, distantly separated from elements of the main range, which is largely coincident with known glacial refugia (e.g., Beringia) and recently deglaciated regions. We employed analyses of inter-simple sequence repeats (ISSRs) and morphology to determine patterns of variation within the western North American range of C. tetrandrum and test hypotheses of glacial population history and reproductive strategy. Analyses revealed very low estimates of range-wide genetic differentiation (θII= 0.085) and diversity (HS= 0.077, HT= 0.084), which are similar to levels found in other arctic plant species and have been primarily attributed to recent population establishment. Low levels of genetic differentiation among populations of Alaska (θII= 0.072), British Columbia (θII= 0.088), and Washington (θII= 0.058) suggest recent bottleneck or range expansion events. Both the Colorado and Alaska regions showed strong differentiation from each of the other regions, suggesting long-term isolation. The non-association between morphological and genetic variation indicates the effects of phenotypic plasticity or sexual reproduction.
Morphology, molecular characterisation and systematic position of Hemiplectus muscorum Zell, 1991 (Nematoda: Plectida)
Authors: Holovachov Oleksandr , Boström Sven , Mundo-Ocampo Manuel , Tandingan De Ley Irma , Yoder Melissa , Burr A. H. Jay , De Ley Paul 
Published: August 2009

Abstract
Hemiplectus muscorum, the type and single representative of its genus, is
redescribed on the basis of abundant new material collected in the UK,
Canada and the USA using both light and scanning electron microscopy. The
phylogenetic relationships of the species are inferred from morphological as
well as molecular data. Maximum parsimony, neighbour joining and maximum
likelihood analyses of small subunit (SSU) rRNA sequences support a position
nested among the Plectidae. This conflicts with our morphological
assumptions of character polarity, as it implies that the absence of a
valvate bulb in Hemiplectus is a reversal rather than a plesiomorphy. The
excretory system of Hemiplectus is described more precisely. Its structure
is highly reminiscent of the system in Plectus but differs in the presence
of an anterior and posterior pair of pseudocoelomocytes flanking the renette
cell. A pair of lateral somatic setae is identified as possible homologues
of the 'deirids' in Plectus and Rhabditida. Measurements and descriptions
are given of all four juvenile stages.
Selenoprotein N is dynamically expressed during mouse development and detected early in muscle precursors
Authors: Castets Perrine , Maugenre Svetlana , Gartioux Corine , Rederstorff Mathieu , Krol Alain , Lescure Alain , Tajbakhsh Shahragim , Allamand Valérie , Guicheney Pascale 
Published: August 2009

Abstract

Background
In humans, mutations in the SEPN1 gene, encoding selenoprotein N (SelN), are involved in early onset recessive neuromuscular disorders, referred to as SEPN1-related-myopathies. The mechanisms behind these pathologies are poorly understood since the function of SelN remains elusive. However, previous results obtained in humans and more recently in zebrafish pointed to a potential role for SelN during embryogenesis. Using qRT-PCR, Western blot and whole mount in situ hybridization, we characterized in detail the spatio-temporal expression pattern of the murine Sepn1 gene during development, focusing particularly on skeletal muscles.

Results
In whole embryos, Sepn1 transcripts were detected as early as E5.5, with expression levels peaking at E12.5, and then strongly decreasing until birth. In isolated tissues, only mild transcriptional variations were observed during development, whereas a striking reduction of the protein expression was detected during the perinatal period. Furthermore, we demonstrated that Sepn1 is expressed early in somites and restricted to the myotome, the sub-ectodermal mesenchyme and the dorsal root ganglia at mid-gestation stages. Interestingly, Sepn1 deficiency did not alter somitogenesis in embryos, suggesting that SelN is dispensable for these processes in mouse.

Conclusion
We characterized for the first time the expression pattern of Sepn1 during mammalian embryogenesis and we demonstrated that its differential expression is most likely dependent on major post-transcriptional regulations. Overall, our data strongly suggest a potential role for selenoprotein N from mid-gestation stages to the perinatal period. Interestingly, its specific expression pattern could be related to the current hypothesis that selenoprotein N may regulate the activity of the ryanodine receptors.
Hippocampal volumes are important predictors for memory function in elderly women
Authors: Ystad Martin A , Lundervold Astri J , Wehling Eike , Espeseth Thomas , Rootwelt Helge , Westlye Lars Tjelta , Andersson Martin , Adolfsdottir Steinunn , Geitung Jonn Terje , Fjell Anders M , Reinvang Ivar , Lundervold Arvid 
Published: August 2009

Abstract

Background
Normal aging involves a decline in cognitive function that has been shown to correlate with volumetric change in the hippocampus, and with genetic variability in the APOE-gene. In the present study we utilize 3D MR imaging, genetic analysis and assessment of verbal memory function to investigate relationships between these factors in a sample of 170 healthy volunteers (age range 46–77 years).

Methods
Brain morphometric analysis was performed with the automated segmentation work-flow implemented in FreeSurfer. Genetic analysis of the APOE genotype was determined with polymerase chain reaction (PCR) on DNA from whole-blood. All individuals were subjected to extensive neuropsychological testing, including the California Verbal Learning Test-II (CVLT). To obtain robust and easily interpretable relationships between explanatory variables and verbal memory function we applied the recent method of conditional inference trees in addition to scatterplot matrices and simple pairwise linear least-squares regression analysis.

Results
APOE genotype had no significant impact on the CVLT results (scores on long delay free recall, CVLT-LD) or the ICV-normalized hippocampal volumes. Hippocampal volumes were found to decrease with age and a right-larger-than-left hippocampal asymmetry was also found. These findings are in accordance with previous studies. CVLT-LD score was shown to correlate with hippocampal volume. Multivariate conditional inference analysis showed that gender and left hippocampal volume largely dominated predictive values for CVLT-LD scores in our sample. Left hippocampal volume dominated predictive values for females but not for males. APOE genotype did not alter the model significantly, and age was only partly influencing the results.

Conclusion
Gender and left hippocampal volumes are main predictors for verbal memory function in normal aging. APOE genotype did not affect the results in any part of our analysis.
Risk of obesity in immigrants compared with Swedes in two deprived neighbourhoods
Authors: Faskunger Johan , Eriksson Ulf , Johansson Sven-Erik , Sundquist Kristina , Sundquist Jan 
Published: August 2009

Abstract

Background
Despite a strong social gradient in the prevalence of obesity, there is little scientific understanding of obesity in people settled in deprived neighbourhoods. Few studies are actually based on objectively measured data using random sampling of residents in deprived neighbourhoods. In addition, most studies use a crude measure, the body mass index, to estimate obesity. This is of concern because it may cause inaccurate estimations of the true prevalence and give the wrong picture of the factors associated with obesity. The aim of this study was to estimate the prevalence of, and analyse the sociodemographic factors associated with, three indices of obesity in different ethnic groups settled in two deprived neighbourhoods in Sweden.

Methods
Height and weight, waist circumference and body fat percentage were objectively measured in a random sample (n = 289). Sociodemographic data were obtained through a survey. Established cut-offs were used to determine obesity. Country of birth was categorized as Swedish, Other European, and Middle Eastern. Odds ratios were estimated by unconditional logistic regression.

Results
One third of the sample was classified as obese overall, with 39.0% of women being abdominally obese. After adjusting for age, we found higher odds of obesity in Middle Eastern women than in Swedish women regardless of outcome with odds ratios ranging between 2.74 and 5.53. Men of other European origin had higher odds of BMI obesity than Swedish men. Most associations between country of birth and obesity remained in the full model.

Conclusion
This study demonstrates the magnitude of the obesity problem and the need for prevention programmes targeting native and immigrant adults in deprived neighbourhoods in Sweden. The initiatives should also focus on particular groups, e.g. immigrant women and those experiencing economic difficulties. Further studies are needed on behavioural and environmental factors influencing the risk of obesity in residents settled in deprived neighbourhoods.
Multiple sex partner behavior in female undergraduate students in China: A multi-campus survey
Authors: Yan Hong , Chen Weiqi , Wu Haocheng , Bi Yongyi , Zhang Miaoxuan , Li Shiyue , Braun Kathryn L 
Published: August 2009

Abstract

Background
China is realizing increases in women engaged in premarital sex and multiple sex partner behavior. Our aim was to examine prevalence and determinants of multiple sex partner behavior among female undergraduates in China.

Methods
Anonymously completed questionnaires were received from 4,769 unmarried female undergraduates, recruited using randomized cluster sampling by type of university and students' major and grade. Items captured demographic, family, peer and work influence, and student factors (major, academic performance, and sex-related knowledge and attitudes). To examine risk factors for sexual behaviors, we used multi-level logistic regression, yielding odds ratios (OR) and 95% confidence intervals (95% CI).

Results
Of 4,769 female students, 863 (18.10%) reported ever having sexual intercourse, and 5.31% reported having multiple sex partners (29.32% of all women having sexual intercourse). Several demographic, family, peer and work influences, and student factors (including major, performance, knowledge, and attitude toward sex) were risk factors for ever having sex. However, risk factors for multiple sex partners only included working in a place of entertainment, having current close friends that were living with boyfriends, poor academic performance, and positive attitudes toward multiple partners. These women also were more likely to practice masturbation, start having sex at a younger age, have sex with married men and/or men not their "boyfriends" at first coitus, and not use condoms consistently.

Conclusion
A small but important subset of Chinese female undergraduates is engaged in unprotected sex with multiple sex partners. Interventions need to target at risk women, stressing the importance of consistent condom use.
Long-stay in short-stay inpatient facilities: risk factors and barriers to discharge
Authors: Gigantesco Antonella , de Girolamo Giovanni , Santone Giovanni , Miglio Rossella , Picardi Angelo ,   the PROGRES-Acute group
Published: August 2009

Abstract

Background
The aim of the present study was to assess the characteristics of long-stay inpatients in public and private Italian acute inpatient facilities, to identify risk factors and correlates of the long duration of hospital stay in these patients, and to identify possible barriers to alternative placements.

Methods
All patients in 130 Italian public and private psychiatric inpatient units who had been hospitalized for more than 3 months during a specific index period were assessed with standardized assessment instruments and compared to patients discharged during the same index period, but staying in hospital for less than 3 months (short-stay inpatients). Assessed domains included demographic, clinical, and treatment characteristics, as well as process of care. Logistic regression analysis was used to identify specific variables predicting inpatient long-stay status. Reasons for delaying patient discharge, as reported by treatment teams, were also analyzed.

Results
No overall differences between long-stay and short-stay patients emerged in terms of symptom severity or diagnostic status. Admission to a private inpatient facility and display of violent behavior during hospital stay were the most powerful predictors of long-stay. Lack of housing and a shortage of community support were the reasons most commonly cited by treatment teams as barriers to discharge.

Conclusion
Extra-clinical factors are important determinants of prolonged hospitalization in acute inpatient settings.