bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deletion of
PHO13
, Encoding Haloacid Dehalogenase Type IIA Phosphatase, Results in Upregulation of the Pentose Phosphate Pathway in Saccharomyces cerevisiae
Authors: Kim Soo Rin , Xu Haiqing , Lesmana Anastashia , Kuzmanovic Uros , Au Matthew , Florencia Clarissa , Oh Eun Joong , Zhang Guochang , Kim Kyoung Heon , Jin Yong-Su 
Published: December 2014

ABSTRACT

The haloacid dehalogenase (HAD) superfamily is one of the largest enzyme families, consisting mainly of phosphatases. Although intracellular phosphate plays important roles in many cellular activities, the biological functions of HAD enzymes are largely unknown. Pho13 is 1 of 16 putative HAD enzymes in
Saccharomyces cerevisiae
. Pho13 has not been studied extensively, but previous studies have identified
PHO13
to be a deletion target for the generation of industrially attractive phenotypes, namely, efficient xylose fermentation and high tolerance to fermentation inhibitors. In order to understand the molecular mechanisms underlying the improved xylose-fermenting phenotype produced by deletion of
PHO13
(
pho13
Δ), we investigated the response of
S. cerevisiae
to
pho13
Δ at the transcriptomic level when cells were grown on glucose or xylose. Transcriptome sequencing analysis revealed that
pho13
Δ resulted in upregulation of the pentose phosphate (PP) pathway and NADPH-producing enzymes when cells were grown on glucose or xylose. We also found that the transcriptional changes induced by
pho13
Δ required the transcription factor Stb5, which is activated specifically under NADPH-limiting conditions. Thus,
pho13
Δ resulted in the upregulation of the PP pathway and NADPH-producing enzymes as a part of an oxidative stress response mediated by activation of Stb5. Because the PP pathway is the primary pathway for xylose, its upregulation by
pho13
Δ might explain the improved xylose metabolism. These findings will be useful for understanding the biological function of
S. cerevisiae
Pho13 and the HAD superfamily enzymes and for developing
S. cerevisiae
strains with industrially attractive phenotypes.
Transcriptomic Analysis of Xylan Utilization Systems in Paenibacillus sp. Strain JDR-2
Authors: Sawhney Neha , Crooks Casey , St. John Franz , Preston James F. 
Published: December 2014

ABSTRACTXylans, including methylglucuronoxylans (MeGXn) and methylglucuronoarabinoxylans (MeGAXn), are the predominant polysaccharides in hemicellulose fractions of dicots and monocots available for conversion to biofuels and chemicals.Paenibacillussp. strain JDR-2 (Pjdr2) efficiently depolymerizes MeGXnand MeGAXnand assimilates the generated oligosaccharides, resulting in efficient saccharification and subsequent metabolism of these polysaccharides. A xylan utilization regulon encoding a cell-associated GH10 (glycoside hydrolase family 10) endoxylanase, transcriptional regulators, ABC (ATP binding cassette) transporters, an intracellular GH67 α-glucuronidase, and other glycoside hydrolases contributes to complete metabolism. This GH10/GH67 system has been proposed to account for preferential utilization of xylans compared to free oligo- and monosaccharides. To identify additional genes contributing to MeGXnand MeGAXnutilization, the transcriptome of Pjdr2 has been sequenced following growth on each of these substrates as well as xylose and arabinose. Increased expression of genes with different substrates identified pathways common or unique to the utilization of MeGXnor MeGAXn. Coordinate upregulation of genes comprising the GH10/GH67 xylan utilization regulon is accompanied with upregulation of genes encoding a GH11 endoxylanase and a GH115 α-glucuronidase, providing evidence for a novel complementary pathway for processing xylans. Elevated expression of genes encoding a GH43 arabinoxylan arabinofuranohydrolase and an arabinose ABC transporter on MeGAXnbut not on MeGXnsupports a process in which arabinose may be removed extracellularly followed by its rapid assimilation. Further development of Pjdr2 for direct conversion of xylans to targeted products or introduction of these systems into fermentative strains of related bacteria may lead to biocatalysts for consolidated bioprocessing of hemicelluloses released from lignocellulose.
In Situ
Prebiotics for Weaning Piglets:
In Vitro
Production and Fermentation of Potato Galacto-Rhamnogalacturonan
Authors: Strube Mikael Lenz , Ravn Helle Christine , Ingerslev Hans-Christian , Meyer Anne Strunge , Boye Mette 
Published: December 2014

ABSTRACT

Postweaning diarrhea (PWD) in pigs is a leading cause of economic loss in pork production worldwide. The current practice of using antibiotics and zinc to treat PWD is unsustainable due to the potential of antibiotic resistance and ecological disturbance, and novel methods are required. In this study, an
in vitro
model was used to test the possibility of producing prebiotic fiber
in situ
in the gastrointestinal (GI) tract of the piglet and the prebiotic activity of the resulting fiber in the terminal ileum. Soluble fiber was successfully produced from potato pulp, an industrial waste product, with the minimal enzyme dose in a simulated upper GI tract model extracting 26.9% of the initial dry matter. The fiber was rich in galactose and galacturonic acid and was fermented at 2.5, 5, or 10 g/liter in a glucose-free medium inoculated with the gut contents of piglet terminal ileum. Fermentations of 5 g/liter inulin or 5 g/liter of a purified potato fiber were used as controls. The fibers showed high fermentability, evident by a dose-dependent drop in pH and an increase in the organic acid content, with lactate in particular being increased. Deep sequencing showed a significant increase in the numbers of
Lactobacillus
and
Veillonella
organisms and an insignificant increase in the numbers of
Clostridium
organisms as well as a decrease in the numbers of
Streptococcus
organisms. Multivariate analysis showed clustering of the treatment groups, with the group treated with purified potato fiber being clearly separated from the other groups, as the microbiota composition was 60%
Lactobacillus
and almost free of
Clostridium
. For animal studies, a dosage corresponding to the 5-g/liter treatment is suggested.
Genomic Potential for Polysaccharide Deconstruction in Bacteria
Authors: Berlemont Renaud , Martiny Adam C. 
Published: December 2014

ABSTRACT
Glycoside hydrolases are important enzymes that support bacterial growth by enabling the degradation of polysaccharides (e.g., starch, cellulose, xylan, and chitin) in the environment. Presently, little is known about the overall phylogenetic distribution of the genomic potential to degrade these polysaccharides in bacteria. However, knowing the phylogenetic breadth of these traits may help us predict the overall polysaccharide processing in environmental microbial communities. In order to address this, we identified and analyzed the distribution of 392,166 enzyme genes derived from 53 glycoside hydrolase families in 8,133 sequenced bacterial genomes. Enzymes for oligosaccharides and starch/glycogen were observed in most taxonomic groups, whereas glycoside hydrolases for structural polymers (i.e., cellulose, xylan, and chitin) were observed in clusters of relatives at taxonomic levels ranging from species to genus as determined by consenTRAIT. The potential for starch and glycogen processing, as well as oligosaccharide processing, was observed in 85% of the strains, whereas 65% possessed enzymes to degrade some structural polysaccharides (i.e., cellulose, xylan, or chitin). Potential degraders targeting one, two, and three structural polysaccharides accounted for 22.6, 32.9, and 9.3% of genomes analyzed, respectively. Finally, potential degraders targeting multiple structural polysaccharides displayed increased potential for oligosaccharide deconstruction. This study provides a framework for linking the potential for polymer deconstruction with phylogeny in complex microbial assemblages.
A Fungal Sarcolemmal Membrane-Associated Protein (SLMAP) Homolog Plays a Fundamental Role in Development and Localizes to the Nuclear Envelope, Endoplasmic Reticulum, and Mitochondria
Authors: Nordzieke Steffen , Zobel Thomas , Fränzel Benjamin , Wolters Dirk A. , Kück Ulrich , Teichert Ines 
Published: December 2014

ABSTRACT

S
arco
l
emmal
m
embrane-
a
ssociated
p
rotein (SLMAP) is a tail-anchored protein involved in fundamental cellular processes, such as myoblast fusion, cell cycle progression, and chromosomal inheritance. Further,
SLMAP
misexpression is associated with endothelial dysfunctions in diabetes and cancer. SLMAP is part of the conserved
str
iatin-
i
nteracting
p
hosphatase
a
nd
k
inase (STRIPAK) complex required for specific signaling pathways in yeasts, filamentous fungi, insects, and mammals. In filamentous fungi, STRIPAK was initially discovered in
Sordaria macrospora
, a model system for fungal differentiation. Here, we functionally characterize the STRIPAK subunit PRO45, a homolog of human SLMAP. We show that PRO45 is required for sexual propagation and cell-to-cell fusion and that its
f
ork
h
ead-
a
ssociated (FHA) domain is essential for these processes. Protein-protein interaction studies revealed that PRO45 binds to STRIPAK subunits PRO11 and SmMOB3, which are also required for sexual propagation. Superresolution
s
tructured-
i
llumination
m
icroscopy (SIM) further established that PRO45 localizes to the nuclear envelope, endoplasmic reticulum, and mitochondria. SIM also showed that localization to the nuclear envelope requires STRIPAK subunits PRO11 and PRO22, whereas for mitochondria it does not. Taken together, our study provides important insights into fundamental roles of the fungal SLMAP homolog PRO45 and suggests STRIPAK-related and STRIPAK-unrelated functions.
A new screening instrument for disability in low-income and middle-income settings: application at the Iganga-Mayuge Demographic Surveillance System (IM-DSS), Uganda
Authors: Bachani Abdulgafoor M , Galiwango Edward , Kadobera Daniel , Bentley Jacob A , Bishai David , Wegener Stephen , Hyder Adnan A 
Published: December 2014

ObjectiveThe measurement of disability in low-income countries is recognised as a major deficiency in health information systems, especially in Africa. The Iganga and Mayuge Demographic Surveillance System (IM-DSS) in Uganda provides a special opportunity to develop population-based data to inform national health policies and evaluate innovations in assessing the burden of disability in Uganda. In this study, we apply a new instrument to screen for physical disabilities at the IM-DSS. The study utilised a modified version of the short set of questions proposed by the Washington Group on Disability Statistics. The instrument was applied at the household level and information was collected on all individuals over the age of 5, who were residents of the IM-DSS.SettingThe study was based at the IM-DSS, which covers the parts of Iganga and Mayuge districts in Eastern Uganda.Participants57 247 individuals were included in the survey, with 51% of the study population being women.Primary outcomesActivity limitationsResultsThe overall prevalence of physical disability at the IM-DSS was 9.4%, with vision being the most common type of difficulty reported in this population, and communication being least prevalent. Disability was less likely to be observed among males than their female counterparts (OR 0.75; 95% CI 0.71 to 0.81; p<0.001). Statistically significant associations were found between disability and increasing age, as well as disability and decreasing household wealth status.ConclusionsThis study shows that the modified short set of questions can be readily applied in a DSS setting to obtain estimates on the prevalence and types of disability at the population level. This instrument could be adapted for use to screen for disability in other LMIC settings, providing estimates that are comparable across different global regions and populations.
Prevalence of work-related musculoskeletal symptoms of the neck and upper extremity among dentists in China
Authors: Feng Beibei , Liang Qi , Wang Yuling , Andersen Lars L , Szeto Grace 
Published: December 2014

ObjectivesStudies from western countries show that dentists are vulnerable to work-related musculoskeletal disorders (WMSDs) of the neck and upper extremities, but little is known about their epidemiology among members of this rapidly growing profession in China. This study aims to investigate the prevalence of WMSDs and identify potential risk factors associated with their occurrence in the dental profession in China.Setting and participantsA cross-sectional survey was carried out in 52 different hospitals in a large metropolitan city in China. A total of 304 questionnaires were distributed to respondents identified via stratified random sampling and 272 dentists (121 females and 151 males) completed the survey. The response rate was 89.5%.OutcomesVisual analogue score was used to record neck and upper limb musculoskeletal symptoms on a body chart. Work-related risk factors, including physical and psychosocial factors, were accounted for in the regression analysis.Results88% of the dentists reported at least one musculoskeletal disorder and 83.8% suffered from neck pain. In the multivariate analyses, working hours per day were associated with neck pain (OR=1.43; 95% CI 1.03 to 1.98). Inability to select the appropriate size of dental instrument was associated with shoulder (OR=2.07; 95% CI 1.00 to 4.32) and wrist/hand (OR=2.47; 95% CI 1.15 to 5.32) pain. As for psychosocial factors, high job demand was associated with symptoms in the shoulder (OR=1.09; 95% CI 1.00 to 1.18), elbow (OR=1.11; 95% CI 1.03 to 1.19) and wrist/hand (OR=1.09; 95% CI 1.02 to 1.17). Regular physical exercise was associated with decreased neck pain (OR=0.37; 95% CI 0.14 to 1.00).ConclusionsThe prevalence of WMSDs among Chinese dentists is high. Specifically, long working hours, inability to select the appropriate size of dental instrument and high job demand are the most significant risk factors.
The effect of the National Essential Medicines Policy on health expenditures and service delivery in Chinese township health centres: evidence from a longitudinal study
Authors: Zhang Xin , Wu Qunhong , Liu Guoxiang , Li Ye , Gao Lijun , Guo Bin , Fu Wenqi , Hao Yanhua , Cui Yu , Huang Weidong , Coyte Peter C 
Published: December 2014

ObjectivesThe government of China has introduced a National Essential Medicines Policy (NEMP) in the new round of health system reform. The objective of this paper is to analyse whether the NEMP can play a role in curbing the rise of medical expenditures without disrupting the availability of healthcare services at township hospitals in China.DesignThis study adopted a pre–post treatment-control study design. A difference-in-differences method and fixed-effects model for panel data were employed to estimate the effect of the NEMP.SettingChongqing, Jiangsu and Henan Province, in China, in 2009 and 2010.Participants296 township health centres.Outcome measuresOutcomes for health expenditures were average outpatient drug expenses per visit, average inpatient drug expenses per discharged patient, average outpatient expenses per visit and average inpatient expenses per discharged patient. Outcomes for care delivery were the numbers of visits per certified doctor per day and the numbers of hospitalised patients per certified doctor per day.ResultsThe township health centres that were enrolled in the NEMP reported 26% (p<0.01) lower drug expenditures for inpatient care. An 11% (p<0.05) decrease in average inpatient expenditures per discharged patient was found following the implementation of the NEMP. The impacts of the NEMP on average outpatient expenditures and outpatient drug expenditures were not statistically significant at the 5% level. No statistically significant associations were found between the NEMP and reduction in quantity of health service delivery.ConclusionsThe NEMP was significant in its effect in reducing inpatient medication and health service expenditures. This study shows no evidence that the quantity of healthcare service declined significantly after introduction of the NEMP over the study period, which suggests that if appropriate matching policies are introduced, the side effects of the NEMP can be counteracted to some degree. Further research including a long-term follow-up study is needed.
Translation research: ‘Back on Track’, a multiprofessional rehabilitation service for cancer-related fatigue
Authors: Gracey J H , Watson M , Payne C , Rankin J , Dunwoody L 
Published: December 2014

ObjectivesTo assess the effectiveness and acceptability of an individually tailored rehabilitation intervention for patients with cancer-related fatigue (CRF).MethodsEighteen individuals, (16 female, two male, aged 40–83 years), who self-reported CRF (above four on a 10-point Likert scale) took part in an 8 week physical activity intervention weekly review and optional gym-based support. Fifteen participants had a primary diagnosis of breast cancer and along with the other participants had multiple myeloma, colorectal or prostate cancer. All participants took part in a goal-oriented walking and muscle strengthening programme with dietary advice and psychological support based on the Transtheoretical Model (TTM) of behaviour change. Effectiveness was assessed by physical and psychological outcomes. Focus groups with participants and individual interviews with the professionals delivering the intervention explored the feasibility and acceptability of the intervention.ResultsStatistically significant improvements were seen in the primary outcome of fatigue and on the secondary outcomes of physical function, depression and in triceps skin fold thickness reduction. Participants endorsed the intervention as being highly acceptable, holistic and as important as medical treatments for cancer. The importance of team working was highlighted as key to service delivery and success.ConclusionsA multidisciplinary home-based tailored intervention with optional weekly gym attendance is acceptable to people with CRF, improving physical and psychosocial outcomes. Study limitations and suggestions for further research are discussed.
Intravascular versus surface cooling speed and stability after cardiopulmonary resuscitation
Authors: de Waard M C , Banwarie R P , Jewbali L S D , Struijs A , Girbes A R J , Groeneveld A B J 
Published: December 2014

Background and objectiveMild therapeutic hypothermia (MTH) is used to limit neurological injury and improve survival after cardiac arrest (CA) and cardiopulmonary resuscitation, but the optimal mode of cooling is controversial. We therefore compared the effectiveness of MTH using invasive intravascular or non-invasive surface cooling with temperature feedback control.MethodsThis retrospective study in post-CA patients studied the effects of intravascular cooling (CoolGard, Zoll, n=97), applied on the intensive care unit (ICU) in one university hospital compared with those of surface cooling (Medi-Therm, Gaymar, n=76) applied in another university hospital.ResultsTime to reach target temperature and cooling speeds did not differ between groups. During the maintenance phase, mean core temperature was 33.1°C (range 32.7–33.7°C) versus 32.5°C (range 31.7–33.4°C) at targets of 33.0 and 32.5°C in intravascularly versus surface cooled patients, respectively. The variation coefficient for temperature during maintenance was higher in the surface than the intravascular cooling group (mean 0.85% vs 0.35%, p<0.0001). ICU survival was 60% and 50% in the intravascularly and surface cooled groups, respectively (NS). Lower age (OR 0.95; 95% CI 0.93 to 0.98; p<0.0001), ventricular fibrillation/ventricular tachycardia as presenting rhythm (OR 7.6; 95% CI 1.8 to 8.9; p<0.0001) and lower mean temperature during the maintenance phase (OR 0.52; 95% CI 0.25 to 1.08; p=0.081) might be independent determinants of ICU survival, while cooling technique and temperature variability did not contribute.ConclusionsIn post-CA patients, intravascular cooling systems result in equal cooling speed, but less variation in temperature during the maintenance phase, as surface cooling. This may not affect the outcome.
Traumatic Brain Injury Disrupts Cerebrovascular Tone Through Endothelial Inducible Nitric Oxide Synthase Expression and Nitric Oxide Gain of Function
Authors: Villalba Nuria , Sonkusare Swapnil K. , Longden Thomas A. , Tran Tram L. , Sackheim Adrian M. , Nelson Mark T. , Wellman George C. , Freeman Kalev 
Published: December 2014

Background

Traumatic brain injury (
TBI
) has been reported to increase the concentration of nitric oxide (
NO
) in the brain and can lead to loss of cerebrovascular tone; however, the sources, amounts, and consequences of excess
NO
on the cerebral vasculature are unknown. Our objective was to elucidate the mechanism of decreased cerebral artery tone after
TBI
.

Methods and Results

Cerebral arteries were isolated from rats 24 hours after moderate fluid‐percussion
TBI
. Pressure‐induced increases in vasoconstriction (myogenic tone) and smooth muscle Ca
2+
were severely blunted in cerebral arteries after
TBI
. However, myogenic tone and smooth muscle Ca
2+
were restored by inhibition of
NO
synthesis or endothelium removal, suggesting that
TBI
increased endothelial
NO
levels. Live native cell
NO
, indexed by 4,5‐diaminofluorescein (DAF‐2 DA) fluorescence, was increased in endothelium and smooth muscle of cerebral arteries after
TBI
. Clamped concentrations of 20 to 30 nmol/L
NO
were required to simulate the loss of myogenic tone and increased (DAF‐2T) fluorescence observed following
TBI
. In comparison, basal
NO
in control arteries was estimated as 0.4 nmol/L. Consistent with
TBI
causing enhanced
NO
‐mediated vasodilation, inhibitors of guanylyl cyclase, protein kinase G, and large‐conductance Ca
2+
‐activated potassium (
BK
) channel restored function of arteries from animals with TBI. Expression of the inducible isoform of
NO
synthase was upregulated in cerebral arteries isolated from animals with TBI, and the
inducible isoform of NO synthase
inhibitor 1400W restored myogenic responses following
TBI
.

Conclusions

The mechanism of profound cerebral artery vasodilation after
TBI
is a gain of function in vascular
NO
production by 60‐fold over controls, resulting from upregulation of the inducible isoform of NO synthase in the endothelium.
An Intuitive Synthesizer of Continuous-Interaction Sounds: Rubbing, Scratching, and Rolling
Authors: Conan Simon , Thoret Etienne , Aramaki Mitsuko , Derrien Olivier , Gondre Charles , Ystad Sølvi , Kronland-Martinet Richard 
Published: December 2014

AbstractIn this article, we propose a control strategy for synthesized continuous-interaction sounds. The framework of our research is based on the action–object paradigm that describes the sound as the result of an action on an object and that presumes the existence of sound invariants (i.e., perceptually relevant signal morphologies that carry information about the action's or the object's attributes). Auditory cues are investigated here for the evocations of rubbing, scratching, and rolling interactions. A generic sound-synthesis model that simulates these interactions is detailed. We then suggest an intuitive control strategy that enables users to navigate continuously from one interaction to another in an “action space,” thereby offering the possibility to simulate morphed interactions—for instance, ones that morph between rubbing and rolling.