bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancement of Ethanol Fermentation in Saccharomyces cerevisiae Sake Yeast by Disrupting Mitophagy Function
Authors: Shiroma Shodai , Jayakody Lahiru Niroshan , Horie Kenta , Okamoto Koji , Kitagaki Hiroshi 
Published: November 2013

ABSTRACT

Saccharomyces cerevisiae
sake yeast strain Kyokai no. 7 has one of the highest fermentation rates among brewery yeasts used worldwide; therefore, it is assumed that it is not possible to enhance its fermentation rate. However, in this study, we found that fermentation by sake yeast can be enhanced by inhibiting mitophagy. We observed mitophagy in wild-type sake yeast during the brewing of Ginjo sake, but not when the mitophagy gene (
ATG32
) was disrupted. During sake brewing, the maximum rate of CO
2
production and final ethanol concentration generated by the
atg32
Δ laboratory yeast mutant were 7.50% and 2.12% higher than those of the parent strain, respectively. This mutant exhibited an improved fermentation profile when cultured under limiting nutrient concentrations such as those used during Ginjo sake brewing as well as in minimal synthetic medium. The mutant produced ethanol at a concentration that was 2.76% higher than the parent strain, which has significant implications for industrial bioethanol production. The ethanol yield of the
atg32
Δ mutant was increased, and its biomass yield was decreased relative to the parent sake yeast strain, indicating that the
atg32
Δ mutant has acquired a high fermentation capability at the cost of decreasing biomass. Because natural biomass resources often lack sufficient nutrient levels for optimal fermentation, mitophagy may serve as an important target for improving the fermentative capacity of brewery yeasts.
Evaluation of Phytate-Degrading Lactobacillus Culture Administration to Broiler Chickens
Authors: Askelson Tyler E. , Campasino Ashley , Lee Jason T. , Duong Tri 
Published: November 2013

ABSTRACT

Probiotics have been demonstrated to promote growth, stimulate immune responses, and improve food safety of poultry. While widely used, their effectiveness is mixed, and the mechanisms through which they contribute to poultry production are not well understood. Microbial phytases are increasingly supplemented in feed to improve digestibility and reduce antinutritive effects of phytate. The microbial origin of these exogenous enzymes suggests a potentially important mechanism of probiotic functionality. We investigated phytate degradation as a novel probiotic mechanism using recombinant
Lactobacillus
cultures expressing
Bacillus subtilis
phytase.
B. subtilis phyA
was codon optimized for expression in
Lactobacillus
and cloned into the expression vector pTRK882. The resulting plasmid, pTD003, was transformed into
Lactobacillus acidophilus
,
Lactobacillus gallinarum
, and
Lactobacillus gasseri
. SDS-PAGE revealed a protein in the culture supernatants of
Lactobacillus
pTD003 transformants with a molecular weight similar to that of the
B. subtilis
phytase. Expression of
B. subtilis
phytase increased phytate degradation of
L. acidophilus
,
L. gasseri
, and
L. gallinarum
approximately 4-, 10-, and 18-fold over the background activity of empty-vector transformants, respectively. Phytase-expressing
L. gallinarum
and
L. gasseri
were administered to broiler chicks fed a phosphorus-deficient diet. Phytase-expressing
L. gasseri
improved weight gain of broiler chickens to a level comparable to that for chickens fed a control diet adequate in phosphorus, demonstrating proof of principle that administration of phytate-degrading probiotic cultures can improve performance of livestock animals. This will inform future studies investigating whether probiotic cultures are able to provide both the performance benefits of feed enzymes and the animal health and food safety benefits traditionally associated with probiotics.
Engineering the Xylan Utilization System in Bacillus subtilis for Production of Acidic Xylooligosaccharides
Authors: Rhee Mun Su , Wei Lusha , Sawhney Neha , Rice John D. , St. John Franz J. , Hurlbert Jason C. , Preston James F. 
Published: November 2013

ABSTRACT

Xylans are the predominant polysaccharides in hemicelluloses and an important potential source of biofuels and chemicals. The ability of
Bacillus subtilis
subsp.
subtilis
strain 168 to utilize xylans has been ascribed to secreted glycoside hydrolase family 11 (GH11) and GH30 endoxylanases, encoded by the
xynA
and
xynC
genes, respectively. Both of these enzymes have been defined with respect to structure and function. In this study, the effects of deletion of the
xynA
and
xynC
genes, individually and in combination, were evaluated for xylan utilization and formation of acidic xylooligosaccharides. Parent strain 168 depolymerizes methylglucuronoxylans (MeGX

n

), releasing the xylobiose and xylotriose utilized for growth and accumulating the aldouronate methylglucuronoxylotriose (MeGX
3
) with some methylglucuronoxylotetraose (MeGX
4
). The combined GH11 and GH30 activities process the products generated by their respective actions on MeGX

n

to release a maximal amount of neutral xylooligosaccharides for assimilation and growth, at the same time forming MeGX
3
in which the internal xylose is substituted with methylglucuronate (MeG). Deletion of
xynA
results in the accumulation of β-1,4-xylooligosaccharides with degrees of polymerization ranging from 4 to 18 and an average degree of substitution of 1 in 7.2, each with a single MeG linked α-1,2 to the xylose penultimate to the xylose at the reducing terminus. Deletion of the
xynC
gene results in the accumulation of aldouronates comprised of 4 or more xylose residues in which the MeG may be linked α-1,2 to the xylose penultimate to the nonreducing xylose. These
B. subtilis
lines may be used for the production of acidic xylooligosaccharides with applications in human and veterinary medicine.
Investigating the Responses of Cronobacter sakazakii to Garlic-Drived Organosulfur Compounds: a Systematic Study of Pathogenic-Bacterium Injury by Use of High-Throughput Whole-Transcriptome Sequencing and Confocal Micro-Raman Spectroscopy
Authors: Feng Shaolong , Eucker Tyson P. , Holly Mayumi K. , Konkel Michael E. , Lu Xiaonan , Wang Shuo 
Published: November 2013

ABSTRACTWe present the results of a study using high-throughput whole-transcriptome sequencing (RNA-seq) and vibrational spectroscopy to characterize and fingerprint pathogenic-bacterium injury under conditions of unfavorable stress. Two garlic-derived organosulfur compounds were found to be highly effective antimicrobial compounds againstCronobacter sakazakii, a leading pathogen associated with invasive infection of infants and causing meningitis, necrotizing entercolitis, and bacteremia. RNA-seq shows changes in gene expression patterns and transcriptomic response, while confocal micro-Raman spectroscopy characterizes macromolecular changes in the bacterial cell resulting from this chemical stress. RNA-seq analyses showed that the bacterial response to ajoene differed from the response to diallyl sulfide. Specifically, ajoene caused downregulation of motility-related genes, while diallyl sulfide treatment caused an increased expression of cell wall synthesis genes. Confocal micro-Raman spectroscopy revealed that the two compounds appear to have the same phase I antimicrobial mechanism of binding to thiol-containing proteins/enzymes in bacterial cells generating a disulfide stretching band but different phase II antimicrobial mechanisms, showing alterations in the secondary structures of proteins in two different ways. Diallyl sulfide primarily altered the α-helix and β-sheet, as reflected in changes in amide I, while ajoene altered the structures containing phenylalanine and tyrosine. Bayesian probability analysis validated the ability of principal component analysis to differentiate treated and controlC. sakazakiicells. Scanning electron microscopy confirmed cell injury, showing significant morphological variations in cells following treatments by these two compounds. Findings from this study aid in the development of effective intervention strategies to reduce the risk ofC. sakazakiicontamination in the food production environment and on food contact surfaces, reducing the risks to susceptible consumers.
Core Lipopolysaccharide-Specific Phage SSU5 as an Auxiliary Component of a Phage Cocktail for Salmonella Biocontrol
Authors: Kim Minsik , Kim Sujin , Park Bookyung , Ryu Sangryeol 
Published: November 2013

ABSTRACT

Salmonella
spp. are among the major food-borne pathogens that cause mild diarrhea to severe bacteremia. The use of bacteriophages to control various food-borne pathogens, including
Salmonella
, has emerged as a promising alternative to traditional chemotherapy. We isolated the
Siphoviridae
family phage SSU5, which can infect only rough strains of
Salmonella
. The blocking of SSU5 adsorption by periodate treatment of host
Salmonella
cells and spotting and adsorption assays with mutants that contain various truncations in their lipopolysaccharide (LPS) cores revealed that the outer core region of the LPS is a receptor of SSU5. SSU5 could infect O-antigen (O-Ag)-deficient
Salmonella
mutants that developed by challenging of O-Ag-specific phages, and consequently, it delayed the emergence of the phage-resistant
Salmonella
population in broth culture when treated together with phages using O-Ag as a receptor. Therefore, these results suggested that phage SSU5 would be a promising auxiliary component of a phage cocktail to control rough strains of
Salmonella enterica
serovar Typhimurium, which might emerge as resistant mutants upon infection by phages using O-Ag as a receptor.
Biogenesis of YidC Cytoplasmic Membrane Substrates Is Required for Positioning of Autotransporter IcsA at Future Poles
Authors: Gray Andrew N. , Li Zaoping , Henderson-Frost Josephine , Goldberg Marcia B. 
Published: November 2013

ABSTRACTLocalization of proteins to specific sites within bacterial cells is often critical to their function. In rod-shaped bacteria, proteins involved in diverse and important cell processes localize to the cell poles. The molecular mechanisms by which these proteins are targeted to the pole, however, are poorly understood. TheShigellaautotransporter protein IcsA, which is localized to the pole on the surface of the bacterium, is targeted to the pole in the cytoplasm by a mechanism that is conserved across multiple Gram-negative bacterial species and has thus served as an important and informative model for studying polar localization. We present evidence that inEscherichia coli, the establishment of polar positional information recognized by IcsA requires the activity of the cytoplasmic membrane protein insertase YidC. We show that the role of YidC in IcsA localization is independent of the cell septation and cytokinesis proteins FtsQ and FtsEX. FtsQ is required for polar localization of IcsA and, based on cross-linking studies, is inserted in the vicinity of YidC, but, we find, is not dependent on YidC for membrane insertion. FtsEX is a YidC substrate, but we find that it is not required for polar localization of IcsA. These findings indicate that polar positional information recognized by IcsA depends on one or more membrane proteins that require YidC for proper membrane insertion.
Genome-Scale Analyses of Escherichia coli and Salmonella enterica AraC Reveal Noncanonical Targets and an Expanded Core Regulon
Authors: Stringer Anne M. , Currenti Salvatore , Bonocora Richard P. , Baranowski Catherine , Petrone Brianna L. , Palumbo Michael J. , Reilly Andrew A. , Zhang Zhen , Erill Ivan , Wade Joseph T. 
Published: November 2013

ABSTRACT

Escherichia coli
AraC is a well-described transcription activator of genes involved in arabinose metabolism. Using complementary genomic approaches, chromatin immunoprecipitation (ChIP)-chip, and transcription profiling, we identify direct regulatory targets of AraC, including five novel target genes:
ytfQ
,
ydeN
,
ydeM
,
ygeA
, and
polB
. Strikingly, only
ytfQ
has an established connection to arabinose metabolism, suggesting that AraC has a broader function than previously described. We demonstrate arabinose-dependent repression of
ydeNM
by AraC, in contrast to the well-described arabinose-dependent activation of other target genes. We also demonstrate unexpected read-through of transcription at the Rho-independent terminators downstream of
araD
and
araE
, leading to significant increases in the expression of
polB
and
ygeA
, respectively. AraC is highly conserved in the related species
Salmonella enterica
. We use ChIP sequencing (ChIP-seq) and RNA sequencing (RNA-seq) to map the AraC regulon in
S. enterica
. A comparison of the
E. coli
and
S. enterica
AraC regulons, coupled with a bioinformatic analysis of other related species, reveals a conserved regulatory network across the family
Enterobacteriaceae
comprised of 10 genes associated with arabinose transport and metabolism.
Pesticide poisoning in Zhejiang, China: a retrospective analysis of adult cases registration by occupational disease surveillance and reporting systems from 2006 to 2010
Authors: Zhang Meibian , Fang Xinglin , Zhou Lifang , Su Liling , Zheng Jiajia , Jin Minjuan , Zou Hua , Chen Guangdi 
Published: November 2013

ObjectiveDespite the rapid industrialisation and urbanisation over the past 30 years, agriculture is one of the largest economic sectors in China and the unregulated use of pesticides result in extensive pesticide poisoning. The objective of this study was to analyse pesticide poisoning cases registration received by Zhejiang Provincial Center for Disease Control and Prevention, China.DesignRegister-based study.SettingCases registered regarding pesticide poisoning. Data were obtained from the Occupational Disease Surveillance and Reporting Systems in Zhejiang province from 2006 to 2010, which contains anonymous records representing general population of Zhejiang province, China.ParticipantsAll cases registered as pesticide poisoning were identified.Primary outcomeMonthly and age-group pesticide poisoning death rates were calculated.ResultsA total of 20 097 pesticide poisoning cases with 1413 deaths were recorded during the study period. There were 10 513 male pesticide poisoning cases with 782 deaths, and 9584 females with 631 deaths. Pesticide poisoning occurred mostly in non-occupational exposure (79.86%), in which the majority (85.77%) of the cases was of intentional pesticide poisoning. The occupational exposure was most common in men during the farming season. The death rate increased stepwise with age, and the pesticide suicide rate was higher in the older age group.ConclusionsPesticide poisoning remains a major health problem in China, and further recommendations to reduce the pesticide poisoning are required.
The relationship between active ageing and health using longitudinal data from Denmark, France, Italy and England
Authors: Di Gessa Giorgio , Grundy Emily 
Published: November 2013

Background‘Active ageing’ has been promoted as a strategy for extending quality of life and healthy life expectancy. However, there is limited evidence from nationally representative longitudinal studies on whether engagement among older adults is associated with better outcomes and few studies have considered possible bias arising from differential study attrition.MethodsWe investigate associations between the engagement of people aged 50–69 in three types of activity with self-rated health and depression 2 years later using nationally representative longitudinal data from four European countries (Denmark, France, Italy and England). Data were drawn from waves 1 and 2 of the Survey of Health, Ageing and Retirement in Europe and the English Longitudinal Study of Ageing. Multivariable analysis was used to analyse associations between baseline activity and outcomes at follow-up controlling for socioeconomic, demographic and health-related variables at baseline. Multiple imputation techniques and sensitivity analyses were undertaken to investigate possible bias arising from sample attrition.ResultsRespondents in paid work at baseline were less likely to be depressed or to report poor or fair health at follow-up than those who were ‘inactive’, although not in Italy. Engagement in formal and informal activities was not significantly associated with health at follow-up. Sensitivity analyses showed that assuming that those in bad health were over-represented among study attritors weakened the association between work at baseline and health at follow-up.ConclusionsEngagement in paid work may help maintain health in later life, although mechanisms and contextual influences need further investigation.
An early evaluation of clinical and economic costs and benefits of implementing point of care NAAT tests forChlamydia trachomatisandNeisseria gonorrhoeain genitourinary medicine clinics in England
Authors: Turner Katherine M E , Round Jeff , Horner Patrick , Macleod John , Goldenberg Simon , Deol Arminder , Adams Elisabeth J 
Published: November 2013

ObjectivesTo estimate the costs and benefits of clinical pathways incorporating a point of care (POC) nucleic acid amplification test (NAAT) for chlamydia and gonorrhoea in genitourinary medicine (GUM) clinics compared with standard off-site laboratory testing.MethodWe simulated 1.2 million GUM clinic attendees in England. A simulation in Microsoft Excel was developed to compare existing standard pathways of management for chlamydia and gonorrhoea with a POC NAAT. We conducted scenario analyses to evaluate the robustness of the model findings. The primary outcome was the incremental cost-effectiveness ratio. Secondary outcomes included the number of inappropriate treatments, complications and transmissions averted.ResultsThe baseline cost of using the point of POC NAAT was £103.9 million compared with £115.6 million for standard care. The POC NAAT was also associated with a small increase of 46 quality adjusted life years, making the new test both more effective and cheaper. Over 95 000 inappropriate treatments might be avoided by using a POC NAAT. Patients receive diagnosis and treatment on the same day as testing, which may also prevent 189 cases of pelvic inflammatory disease and 17 561 onward transmissions annually.DiscussionReplacing standard laboratory tests for chlamydia and gonorrhoea with a POC test could be cost saving and patients would benefit from more accurate diagnosis and less unnecessary treatment. Overtreatment currently accounts for about a tenth of the reported treatments for chlamydia and gonorrhoea and POC NAATs would effectively eliminate the need for presumptive treatment.
Strain analysis in dilatational shear zones, with examples from Marloes, SW Wales
Authors: Lisle Richard J. 
Published: November 2013

Abstract
New and existing methods for the analysis of finite strains in shear zones involving volume changes are reviewed. By assuming that the wall rocks are undeformed, the position gradients tensor can be determined from data derived from deformed passive markers with or without knowledge of the orientation of cleavage within the shear zone. The new methods are both algebraic and graphical and include those based on off-axis Mohr circles. Application of these methods to deformed sandstones at Marloes Sands reveals important volume changes that would invalidate an approach that assumes simple shear.
Biologic Frontiers in Multiple Myeloma: From Biomarker Identification to Clinical Practice
Authors: Landgren Ola , Morgan Gareth J. 
Published: November 2013

AbstractSince the mid-1990s, the multiple myeloma treatment landscape has evolved considerably, which has led to improved patient outcomes and prolonged survival. In addition to discovering new, targeted agents or treatment regimens, the identification and validation of biomarkers has the potential to further improve patient outcomes. The International Staging System relies on a number of biochemical parameters to stratify patients into risk categories. Other biologically relevant markers that are indicative of inherited genetic variation (e.g., single-nucleotide polymorphisms) or tumor-acquired genetic events (e.g., chromosomal translocations or mutations) have been studied for their prognostic potential. In patients with high-risk cytogenetics, plasma cells (PC) undergo genetic shifts over time, which may partially explain why high-risk patients relapse and are so difficult to treat. Although novel agents have improved treatment outcomes, identification of markers that will enable clinicians to determine which treatment is most appropriate for high-risk patients following initial diagnosis represents an exciting frontier in the clinical management of multiple myeloma. Biomarkers based on quantitating PCs or factors that are secreted from them (e.g., serum free light chain) may also help to risk-stratify patients with asymptomatic multiple myeloma. Eventually, identification of novel biomarkers may lead to the creation of personalized treatment regimens that are optimized to target clonal PCs that express a specific oncogenomic profile. Although the future is exciting, validation will be necessary before these biologic and molecular beacons can inform decision-making processes in a routine clinical setting. Clin Cancer Res; 20(4); 804–13. ©2013 AACR.
BMP Signaling Induces Astrocytic Differentiation of Clinically Derived Oligodendroglioma Propagating Cells
Authors: Srikanth Maya , Kim Juno , Das Sunit , Kessler John A. 
Published: November 2013

Abstract
Oligodendrogliomas are a type of glioma that lack detailed investigation because of an inability to cultivate oligodendroglioma cells that faithfully recapitulate their salient qualities. We have successfully isolated and propagated glioma stem-like cells from multiple clinical oligodendroglioma specimens. These oligodendroglioma-propagating cells (OligPC) are multipotent and form xenografts with oligodendroglioma features. Bone morphogenetic proteins (BMP) are considered potent inhibitors of oligodendrogliogenesis during development; therefore, the effects of BMP signaling in OligPCs were characterized. BMP pathway components are expressed by OligPCs and canonical signaling via Smad proteins is intact. This signaling potently depletes CD133-positive OligPCs, decreasing proliferation, and inducing astrocytic differentiation. Furthermore, analyses revealed that cytoplasmic sequestration of the oligodendrocyte differentiation factors OLIG1/2 by the BMP signaling effectors ID2 and ID4 is a plausible underlying mechanism. These findings elucidate the molecular pathways that underlie the effects of BMP signaling on oligodendroglioma stem-like cells.
Implications: Stem-like cells are capable of propagating oligodendrogliomas, and BMP signaling potently diminishes their stemness by inducing astrocytic differentiation, suggesting that BMP activation may be effective as a cancer stem cell–targeted therapy. Mol Cancer Res; 12(2); 283–94. ©2013 AACR.