bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Glutathione Redox Effect on Photosynthetic Membrane Expression in Rhodospirillum rubrum
Authors: Carius Anke Berit , Henkel Marius , Grammel Hartmut 
Published: February 2011

ABSTRACTThe formation of intracytoplasmic photosynthetic membranes by facultative anoxygenic photosynthetic bacteria has become a prime example for exploring redox control of gene expression in response to oxygen and light. Although a number of redox-responsive sensor proteins and transcription factors have been characterized in several species during the last several years in some detail, the overall understanding of the metabolic events that determine the cellular redox environment and initiate redox signaling is still poor. In the present study we demonstrate that inRhodospirillum rubrum, the amount of photosynthetic membranes can be drastically elevated by external supplementation of the growth medium with the low-molecular-weight thiol glutathione. Neither the widely used reductant dithiothreitol nor oxidized glutathione caused the same response, suggesting that the effect was specific for reduced glutathione. By determination of the extracellular and intracellular glutathione levels, we correlate the GSH/GSSG redox potential to the expression level of photosynthetic membranes. Possible regulatory interactions with periplasmic, membrane, and cytosolic proteins are discussed. Furthermore, we found thatR. rubrumcultures excrete substantial amounts of glutathione to the environment.
Expanding the Definition of Class 3 Inteins and Their Proposed Phage Origin
Authors: Tori Kazuo , Perler Francine B. 
Published: February 2011

ABSTRACT

Inteins are the protein equivalent of introns. Their protein splicing activity is essential for the host protein's maturation and function. Inteins are grouped into three classes based on sequence signature and splicing mechanism. The sequence signature of the recently characterized class 3 inteins is a noncontiguous Trp-Cys-Thr (WCT) motif and the absence of the standard class 1 Cys
1
or Ser
1
N-terminal nucleophile. The intein N-terminal Cys
1
or Ser
1
residue is essential for splicing in class 1 inteins. The mycobacteriophage Catera Gp206,
Nocardioides
sp. strain JS614 TOPRIM, and
Thermobifida fusca
YX Tfu2914 inteins have a mixture of class 1 and class 3 motifs. They carry the class 3 Trp-Cys-Thr motif and have the standard class 1 N-terminal Ser
1
or Cys
1
. This study determined which class the mycobacteriophage Catera Gp206 and
Nocardioides
sp. JS614 TOPRIM inteins belong to based on catalytic mechanism. The mycobacteriophage Catera Gp206 intein (starting with Ser
1
) is a class 3 intein, and its Ser
1
residue is not required for splicing. Based on phylogenetic analysis, we propose that class 3 inteins arose from a single mutated intein that was spread by phage into predominantly helicase genes in various phages and their hosts.
Anomalous Spatial Redistribution of Competing Bacteria under Starvation Conditions
Authors: Lambert Guillaume , Liao David , Vyawahare Saurabh , Austin Robert H. 
Published: February 2011

ABSTRACT
Bacterial cells evolved under prolonged stress often have a growth advantage in stationary phase (GASP); we expect GASP cells to maintain a proliferative state and dominate wild-type cells during starvation, especially when nutrients are limited and the medium has been conditioned. However, when we compete GASP mutants against wild-type cells in a chain of microfluidic microhabitat patches (MHPs) with alternating nutrient-rich and nutrient-limited regions, we observe the reverse effect: wild-type cells achieve maximum relative density under nutrient-limited conditions, while GASP cells dominate nutrient-rich regions. We explain this surprising observation in terms of ideal free distributions, where we show that wild-type cells maximize their fitness at high cell density by redistributing themselves to sparsely populated MHPs. At the microscopic level, we describe how biofilm formation also contributes to the population redistribution. We conclude by discussing the implications of these results for social interactions of more complex organisms.
The
sigE
Gene Is Required for Normal Expression of Heterocyst-Specific Genes in Anabaena sp. Strain PCC 7120
Authors: Mella-Herrera Rodrigo A. , Neunuebel M. Ramona , Kumar Krithika , Saha Sushanta K. , Golden James W. 
Published: February 2011

ABSTRACT

The filamentous cyanobacterium
Anabaena
(
Nostoc
) sp. strain PCC 7120 produces specialized cells for nitrogen fixation called heterocysts. Previous work showed that the group 2 sigma factor
sigE
(alr4249; previously called
sigF
) is upregulated in differentiating heterocysts 16 h after nitrogen step-down. We now show that the
sigE
gene is required for normal heterocyst development and normal expression levels of several heterocyst-specific genes. Mobility shift assays showed that the transcription factor NtcA binds to sites in the upstream region of
sigE
and that this binding is enhanced by 2-oxoglutarate (2-OG). Deletions of the region containing the NtcA binding sites in P

sigE
-gfp

reporter plasmids showed that the sites contribute to normal developmental regulation but are not essential for upregulation in heterocysts. Northern RNA blot analysis of
nifH
mRNA revealed delayed and reduced transcript levels during heterocyst differentiation in a
sigE
mutant background. Quantitative reverse transcription-PCR (qRT-PCR) analyses of the
sigE
mutant showed lower levels of transcripts for
nifH
,
fdxH
, and
hglE2
but normal levels for
hupL
. We developed a P

nifHD
-gfp

reporter construct that showed strong heterocyst-specific expression. Time-lapse microscopy of the P

nifHD
-gfp

reporter in a
sigE
mutant background showed delayed development and undetectable green fluorescent protein (GFP) fluorescence. Overexpression of
sigE
caused accelerated heterocyst development, an increased heterocyst frequency, and premature expression of GFP fluorescence from the P

nifHD
-gfp

reporter.
Myogenic mRNA markers in young and old human skeletal muscle prior to and following sequential exercise bouts
Authors: Roberts Michael D. , Dalbo Vincent J. , Sunderland Kyle , Poole Chris , Hassell Scott E. , Kerksick Chad M. 
Published: February 2011

This study examined how multiple bouts of conventional resistance training affected the mRNA expression of transcripts and a protein associated with satellite cell activity in human skeletal muscle. Ten younger men (means ± SE; age, 21.0 ± 0.5 years; body mass, 82.3 ± 4.2 kg; height, 178.4 ± 2.2 cm; percent body fat, 15.4% ± 2.9%) and 10 older men (age, 66.4 ± 1.6 years; body mass, 94.2 ± 3.7 kg; height, 180.9 ± 2.2 cm; percent body fat, 27.4% ± 1.8%) completed 3 lower-body workouts (Monday, Wednesday, Friday; 9 sets of 10 repetitions at 80% 1 repetition maximum). Vastus lateralis muscle biopsies were collected prior to intervention (T1), 48 h following workout 1 (T2), 48 h following workout 2 (T3), and 24 h following workout 3 (T4). Real-time reverse transcription–polymerase chain reaction was performed to assess genes of interest, and muscle proliferating cell nuclear antigen (PCNA) was assessed using Western blotting. The CYCLIN D1 gene was expressed more highly in the older vs. younger men (p < 0.05), whereas the expression of all other genes and muscle PCNA were similar between age groups. MYOD mRNA expression increased at T2 (p < 0.05) and MHCEMB gene expression modestly increased (p < 0.05) at T4 relative to baseline expression values in the younger men. Baseline elevations in CYCLIN D1 mRNA expression in older persons may indicate that a compensatory expression of this transcript is occurring in an attempt to retain the muscle’s proliferative potential. Increases in MYOD and MHCEMB indicate that 1 week of conventional resistance exercise may i\ncrease myogenic activity, including satellite cell proliferation and differentiation, respectively, in younger men.
Regional and relative adiposity patterns in relation to carbohydrate and lipid metabolism in men with spinal cord injury
Authors: Gorgey Ashraf S. , Gater David R. 
Published: February 2011

This study examined the relationship among regional and relative adipose tissue distribution, glucose, and lipid metabolism in men with spinal cord injury (SCI). After overnight fasting, 32 individuals with motor complete tetraplegia (Tetra) (n = 7) and paraplegia (Para) (n = 25) underwent resting energy expenditure and measurement of serum lipid profile, followed by an oral glucose tolerance test to measure plasma glucose and plasma insulin concentrations. Regional fat mass (FM) and fat-free mass were quantified using dual-energy X-ray absorptiometry. Relative adipose tissue was calculated as the ratio of leg FM/trunk FM, leg FM/whole-body FM, and trunk FM/whole-body FM. Individuals with Tetra have greater leg FM/trunk FM (45%) and leg FM/body FM (26%) and lower trunk FM/body FM (29%) ratios than individuals with Para (p < 0.05). Glucose area under the curve (AUC) was positively related to leg FM (r = 0.34, p = 0.05) but not to trunk or body FM. Strong negative relationships were noted between the ratio of trunk FM to body FM and glucose AUC (r = –0.38, p = 0.03) and low-density lipoprotein cholesterol (LDL-C) (r = –0.45, p = 0.001). Whole-body FM was negatively related to high-density lipoprotein cholesterol (r = –0.49, p = 0.007) after controlling for percentage of trunk FM. Both leg and trunk FM may play a pivotal role in determining the metabolic profile in individuals with SCI. Relative to whole-body FM and leg FM, trunk FM may induce a protective effect on glucose homeostasis and the LDL-C profile.
Canadian Sedentary Behaviour Guidelines for Children and Youth
Authors: Tremblay Mark S. , LeBlanc Allana G. , Janssen Ian , Kho Michelle E. , Hicks Audrey , Murumets Kelly , Colley Rachel C. , Duggan Mary 
Published: February 2011

The Canadian Society for Exercise Physiology (CSEP), in partnership with the Healthy Active Living and Obesity Research Group (HALO) at the Children’s Hospital of Eastern Ontario Research Institute, and in collaboration with ParticipACTION, and others, has developed the Canadian Sedentary Behaviour Guidelines for Children (aged 5–11 years) and Youth (aged 12–17 years). The guidelines include a preamble to provide context, followed by the specific recommendations for sedentary behaviour. The entire development process was guided by the Appraisal of Guidelines for Research Evaluation (AGREE) II instrument, which is the international standard for clinical practice guideline development. Thus, the guidelines have gone through a rigorous and transparent developmental process and the recommendations are based on evidence from a systematic review and interpretation of the research evidence. The final guidelines benefitted from an extensive online consultation process with 230 domestic and international stakeholders and key informants. The final guideline recommendations state that for health benefits, children (aged 5–11 years) and youth (aged 12–17 years) should minimize the time that they spend being sedentary each day. This may be achieved by (i) limiting recreational screen time to no more than 2 h per day — lower levels are associated with additional health benefits; and (ii) limiting sedentary (motorized) transport, extended sitting time, and time spent indoors throughout the day. These are the first evidence-based Canadian Sedentary Behaviour Guidelines for Children and Youth and provide important and timely recommendations for the advancement of public health based on a systematic synthesis, interpretation, and application of the current scientific evidence.
Application of anifHmicroarray to assess the impact of environmental factors on free-living diazotrophs in a glacier forefield
Authors: Duc Laurence , Neuenschwander Stefan , Rehrauer Hubert , Zeyer Josef 
Published: February 2011

Glacier forefield environments are exposed to extreme and fluctuating climatic and nutritional conditions. The high diversity of free-living diazotrophic communities found in these environments indicates that nitrogen fixers are able to efficiently cope with such conditions. In this study, a nifH microarray was used to monitor changes in diazotrophic populations in the field over a season, in the presence or absence of plants and in 2 glacier forefields characterized by a different bedrock type (siliceous or calcareous), as well as at different temperatures (10 °C, 15 °C) and under different nitrogen fertilization regimes (0, 10, 40 kg N·ha–1·year–1) in laboratory systems. Population structures responded highly dynamically to environmental changes. Plant presence had the strongest impact, which decreased toward the end of the season and with high amounts of nitrogen fertilization. Temperature and nitrogen fertilization increases indirectly affected diazotrophic communities through their positive impact on plant growth. These results indicate strong carbon limitation in young glacier forefield soils. Phylotypes related to the genus Methylocystis strongly responded to environmental variations. These methanotrophic microorganisms, which are able to retrieve nitrogen and carbon from the atmospheric pool, are particularly adapted to the extreme nutritional conditions found in glacier forefields.
STATUS OF STRANGENESS ELECTRO-PRODUCTION AT MAMI
Authors:   For the A1 Collaboration, Achenbach P. , Achenbach P. , Gayoso C. Ayerbe , Bernauer J. C. , Böhm R. , Bösz M. , Bosnar D. , Debenjak L. , Esser A. , Distler M. O. , Rodríguez M. Gómez , Grießinger K. , Jennewein P. , Makek M. , Merkel H. , Müller U. , Nungesser L. , Pochodzalla J. , Potokar M. , Majos S. Sánchez , Schlimme B. S. , Širca S. , Walcher Th. , Weinriefer M. , Yoon C. J. 
Published: February 2011

At the Institut für Kernphysik in Mainz, Germany, the microtron MAMI has been upgraded to 1.5 GeV electron beam energy and can now be used to study strange hadronic systems. The magnetic spectrometer KAOS from GSI was dismantled and re-installed in the spectrometer facility operated by the A1 collaboration. The spectrometer's primary purpose is to study strangeness electro-production. Its compact design and its capability to detect negative and positive charged particles simultaneously under forward scattering angles complements the existing spectrometers. In 2008, an important milestone has been reached by the successful measurement of kaon production off a liquid hydrogen target. The identification of Λ and Σ0 hyperons in the missing mass spectra has demonstrated the capability of the extended facility to perform strangeness electro-production spectroscopy. To operate KAOS as a double-arm spectrometer under zero degree scattering angle major modifications are needed. A new vacuum chamber was constructed and installed, a new coordinate detector with many thousands of channels was built and tested, a new trigger system for the high rate environment was developed, and a magnetic chicane for the primary electron beam is under construction.
Efficient extraction and analysis of preprocessor-based variability
Authors: Sincero Julio , Tartler Reinhard , Lohmann Daniel , Schröder-Preikschat Wolfgang 
Published: February 2011

The C Preprocessor (CPP) is the tool of choice for the implementation of variability in many large-scale configurable software projects. Linux, probably the most-configurable piece of software ever, employs more than 10,000 preprocessor variables for this purpose. However, this de-facto variability tends to be "hidden in the code"; which on the long term leads to variability defects, such as dead code or inconsistencies with respect to the intended (modeled) variability of the software. This calls for tool support for the efficient extraction of (and reasoning over) CPP-based variability.
We suggest a novel approach to extract CPP-based variability. Our tool transforms CPP-based variability in O(n) complexity into a propositional formula that "mimics" all valid effects of conditional compilation and can be analyzed with standard SAT or BDD packages.
Our evaluation results demonstrate the scalability and practicability of the approach. A dead-block-analysis on the complete Linux source tree takes less than 30 minutes; we thereby have revealed 60 dead blocks, 2 of which meanwhile have been confirmed as new (and long-lasting) bugs; the rest is still under investigation.
Iterative type inference with attribute grammars
Authors: Middelkoop Arie , Dijkstra Atze , Swierstra S. Doaitse 
Published: February 2011

Type inference is the process of constructing a typing derivation while gradually discovering type information. During this process, inference algorithms typically make subtle decisions based on the derivation constructed so far.
Because a typing derivation is a decorated tree we aim to use attribute grammars as the main implementation tool. Unfortunately, we can neither express iteration, nor express decisions based on intermediate derivations in such grammars.
We present the language ruler-front, a conservative extension to ordered attribute grammars, that deals with the aforementioned problems. We show why this extension is suitable for the description of constraint-based inference algorithms.
Modular domain-specific language components in scala
Authors: Hofer Christian , Ostermann Klaus 
Published: February 2011

Programs in domain-­specific embedded languages (DSELs) can be represented in the host language in different ways, for instance implicitly as libraries, or explicitly in the form of abstract syntax trees. Each of these representations has its own strengths and weaknesses. The implicit approach has good composability properties, whereas the explicit approach allows more freedom in making syntactic program transformations.
Traditional designs for DSELs fix the form of representation, which means that it is not possible to choose the best representation for a particular interpretation or transformation. We propose a new design for implementing DSELs in Scala which makes it easy to use different program representations at the same time. It enables the DSL implementor to define modular language components and to compose transformations and interpretations for them.
PTEN Loss Confers BRAF Inhibitor Resistance to Melanoma Cells through the Suppression of BIM Expression
Authors: Paraiso Kim H.T. , Xiang Yun , Rebecca Vito W. , Abel Ethan V. , Chen Y. Ann , Munko A. Cecilia , Wood Elizabeth , Fedorenko Inna V. , Sondak Vernon K. , Anderson Alexander R.A. , Ribas Antoni , Palma Maurizia Dalla , Nathanson Katherine L. , Koomen John M. , Messina Jane L. , Smalley Keiran S.M. 
Published: February 2011

Abstract
This study addresses the role of PTEN loss in intrinsic resistance to the BRAF inhibitor PLX4720. Immunohistochemical staining of a tissue array covering all stages of melanocytic neoplasia (n = 192) revealed PTEN expression to be lost in &gt;10% of all melanoma cases. Although PTEN expression status did not predict for sensitivity to the growth inhibitory effects of PLX4720, it was predictive for apoptosis, with only limited cell death observed in melanomas lacking PTEN expression (PTEN−). Mechanistically, PLX4720 was found to stimulate AKT signaling in the PTEN− but not the PTEN+ cell lines. Liquid chromatography multiple reaction monitoring mass spectrometry (LC-MRM) was performed to identify differences in apoptosis signaling between the two cell line groups. PLX4720 treatment significantly increased BIM expression in the PTEN+ (&gt;14-fold) compared with the PTEN− cell lines (four-fold). A role for PTEN in the regulation of PLX4720-mediated BIM expression was confirmed by siRNA knockdown of PTEN and through reintroduction of PTEN into cells that were PTEN−. Further studies showed that siRNA knockdown of BIM significantly blunted the apoptotic response in PTEN+ melanoma cells. Dual treatment of PTEN− cells with PLX4720 and a PI3K inhibitor enhanced BIM expression at both the mRNA and protein level and increased the level of apoptosis through a mechanism involving AKT3 and the activation of FOXO3a. In conclusion, we have shown for the first time that loss of PTEN contributes to intrinsic BRAF inhibitor resistance via the suppression of BIM-mediated apoptosis. Cancer Res; 71(7); 2750–60. ©2011 AACR.
Cells Lacking IKKα Show Nuclear Cyclin D1 Overexpression and a Neoplastic Phenotype: Role of IKKα as a Tumor Suppressor
Authors: Kwak Youn-Tae , Radaideh Sofyan M. , Ding Lianghao , Li Rui , Frenkel Eugene , Story Michael D. , Girard Luc , Minna John , Verma Udit N. 
Published: February 2011

Abstract
The catalytic subunits of IκB kinase (IKK) complex, IKKα and IKKβ, are involved in activation of NF-κB and in mediating a variety of other biological functions. Though these proteins have a high-sequence homology, IKKα exhibits different functional characteristics as compared with IKKβ. Earlier, we have shown that cyclin D1 is overexpressed and predominantly localized in the nucleus of IKKα−/− cells, indicating that IKKα regulates turnover and subcellular distribution of cyclin D1, which is mediated by IKKα-induced phosphorylation of cyclin D1. Because cyclin D nuclear localization is implicated in tumor development, we examined whether the absence of IKKα leads to tumor development as well. In the current study, we show that IKKα plays a critical role in tumorigenesis. Though IKKα−/− MEF cells show a slower anchorage-dependent growth, they are clonogenic in soft agar. These cells are tumorigenic in nude mice. Microarray analysis of IKKα−/− cells indicates a differential expression of genes involved in proliferation and apoptosis. Furthermore, analysis of microarray data of human lung cancer cell lines revealed decreased IKKα RNA expression level as compared with cell lines derived from normal bronchial epithelium. These results suggest that IKKα may function as a tumor suppressor gene. Absence of IKKα may induce tumorigenicity by nuclear localization of cyclin D1 and modulating the expression of genes involved in neoplastic transformation. Mol Cancer Res; 9(3); 341–9. ©2011 AACR.
Hypertension, White Matter Hyperintensities, and Concurrent Impairments in Mobility, Cognition, and Mood
Authors: Hajjar Ihab , Quach Lien , Yang Frances , Chaves Paulo H.M. , Newman Anne B. , Mukamal Kenneth , Longstreth Will , Inzitari Marco , Lipsitz Lewis A. 
Published: February 2011

Background—
Our objective was to investigate the association between hypertension and concurrent impairments in mobility, cognition, and mood; the role of brain white matter hyperintensities in mediating this association; and the impact of these impairments on disability and mortality in elderly hypertensive individuals.

Methods and Results—

—Blood pressure, gait speed, digit symbol substitution test, and the Center for Epidemiological Studies Depression Scale were measured yearly (1992–1999) on 4700 participants in the Cardiovascular Health Study (age: 74.7, 58% women, 17% blacks, 68% hypertension, 3600 had brain magnetic resonance imaging in 1992–1993, survival data 1992–2005). Using latent profile analysis at baseline, we found that 498 (11%) subjects had concurrent impairments and 3086 (66%) were intact on all 3 measures. Between 1992 and 1999, 651 (21%) became impaired in all 3 domains. Hypertensive individuals were more likely to be impaired at baseline (odds ratio 1.23, 95% confidence interval 1.04 to 1.42,
P
=0.01) and become impaired during the follow-up (hazard ratio=1.3, 95% confidence interval 1.02 to 1.66,
P
=0.037). A greater degree of white matter hyperintensities was associated with impairments in the 3 domains (
P
=0.007) and mediated the association with hypertension (
P
=0.19 for hypertension after adjusting for white matter hyperintensities in the model, 21% hazard ratio change). Impairments in the 3 domains increased subsequent disability with hypertension (
P
<0.0001). Hypertension mortality also was increased in those impaired (compared with unimpaired hypertensive individuals: HR=1.10, 95% confidence interval 1.04 to 1.17,
P
=0.004).

Conclusions—
Hypertension increases the risk of concurrent impairments in mobility, cognition, and mood, which increases disability and mortality. This association is mediated in part by microvascular brain injury.