bluuebunny/crossref_metadata_2025_split huggingface dataset:
MODELING SOLID–LIQUID EXTRACTION KINETICS OF TRANS‐RESVERATROL AND TRANS‐ε‐VINIFERIN FROM GRAPE CANE
Authors: KARACABEY ERKAN , BAYINDIRLI LEVENT , ARTIK NEVZAT , MAZZA GIUSEPPE 
Published: September 2011

ABSTRACTSolid–liquid extraction of resveratrol and viniferin from grape cane samples was described by using first‐order kinetic model, Peleg's model, two‐site kinetic model and modified Gompertz equation. Goodness of fits of the models were evaluated by comparing the adjusted determination coefficient and root mean square error and mean percentage error values. Although the two‐site kinetic model with four parameters described the data better, Peleg's model, with only two parameters, could explain the data with a slight loss of goodness of fit. The modified Gompertz equation showed the worst performance for describing the solid–liquid extraction of stilbenes.PRACTICAL APPLICATIONSThe present study introduces the comparison of well‐known models applied to explain extraction kinetic of stilbene compounds of grape cane and to determine the best model with its justifications. Mathematical models provide information about the system and/or process to which they are applied. In design and/or process application stages, any information about that process and/or system has crucial importance because in the decision stages, this know‐how helps the designers and researchers find the best design parameters and the most effective process conditions to optimize purposes. Mathematical models are accepted as the most economical ways for these purposes.
Unraveling the Glioma Epigenome—From Molecular Mechanisms to Novel Biomarkers and Therapeutic Targets
Authors: Malzkorn Bastian , Wolter Marietta , Riemenschneider Markus J. , Reifenberger Guido 
Published: September 2011

AbstractEpigenetic regulation of gene expression by DNA methylation and histone modification is frequently altered in human cancers including gliomas, the most common primary brain tumors. In diffuse astrocytic and oligodendroglial gliomas, epigenetic changes often present as aberrant hypermethylation of 5′‐cytosine‐guanine (CpG)‐rich regulatory sequences in a large variety of genes, a phenomenon referred to as glioma CpG island methylator phenotype (G‐CIMP). G‐CIMP is particularly common but not restricted to gliomas with isocitrate dehydrogenase 1 (IDH1) or 2 (IDH2) mutation. Recent studies provided a mechanistic link between these genetic mutations and the associated widespread epigenetic modifications. Specifically, 2‐hydroxyglutarate, the oncometabolite produced by mutant IDH1 and IDH2 proteins, has been shown to function as a competitive inhibitor of various α‐ketoglutarate (α‐KG)‐dependent dioxygenases, including histone demethylases and members of the ten‐eleven‐translocation (TET) family of 5‐methylcytosine (5mC) hydroxylases. In this review article, we briefly address (i) the basic principles of epigenetic control of gene expression; (ii) the most important methods to analyze focal and global epigenetic alterations in cells and tissues; and (iii) the involvement of epigenetic alterations in the molecular pathogenesis of gliomas. Moreover, we discuss the promising roles of epigenetic alterations as molecular diagnostic markers and novel therapeutic targets, and highlight future perspectives toward unraveling the “glioma epigenome.”
Pulsed-Field Gel Electrophoresis Supports the Presence of Host-Adapted Salmonella enterica subsp. enterica Serovar Typhimurium Strains in the British Garden Bird Population
Authors: Lawson Becki , Hughes Laura A. , Peters Tansy , de Pinna Elizabeth , John Shinto K. , Macgregor Shaheed K. , Cunningham Andrew A. 
Published: September 2011

ABSTRACT

Salmonellosis is a frequently diagnosed infectious disease of passerine birds in garden habitats within Great Britain with potential implications for human and domestic animal health. Postmortem examinations were performed on 1,477 garden bird carcasses of circa 50 species from England and Wales, 1999 to 2007 inclusive. Salmonellosis was confirmed in 263 adult birds of 10 passerine species in this 11-year longitudinal study. A subset of 124 fully biotyped
Salmonella enterica
subsp.
enterica
serovar Typhimurium isolates was examined using pulsed-field gel electrophoresis to investigate the hypothesis that these strains are host adapted and to determine whether this molecular technique offers greater resolution in understanding the epidemiology of
Salmonella
Typhimurium infection than phage typing alone. For the two most common phage types, definitive type (DT) 40 and DT56v, which together accounted for 97% (120/124) of isolates, pulsed-field gel electrophoresis groupings closely correlated with phage type with remarkably few exceptions. A high degree of genetic similarity (>90%) was observed within and between the two most common pulsed-field gel electrophoresis groups. No clustering or variation was found in the pulsed-field gel electrophoresis groupings by bird species, year, or geographical region beyond that revealed by phage typing. These findings support the hypothesis that there are currently two host-adapted
Salmonella
phage types,
S
. Typhimurium DT40 and DT56v, circulating widely in British garden birds and that the reservoir of infection is maintained within wild bird populations. Large-scale multilocus sequence typing studies are required to further investigate the epidemiology of this infection.
Isolation and Characterization of a Psychropiezophilic Alphaproteobacterium
Authors: Eloe Emiley A. , Malfatti Francesca , Gutierrez Jennifer , Hardy Kevin , Schmidt Wilford E. , Pogliano Kit , Pogliano Joe , Azam Farooq , Bartlett Douglas H. 
Published: September 2011

ABSTRACT

Cultivated psychropiezophilic (low-temperature- and high-pressure-adapted) bacteria are currently restricted to phylogenetically narrow groupings capable of growth under nutrient-replete conditions, limiting current knowledge of the extant functional attributes and evolutionary constraints of diverse microorganisms inhabiting the cold, deep ocean. This study documents the isolation of a deep-sea bacterium following dilution-to-extinction cultivation using a natural seawater medium at high hydrostatic pressure and low temperature. To our knowledge, this isolate, designated PRT1, is the slowest-growing (minimal doubling time, 36 h) and lowest cell density-producing (maximal densities of 5.0 × 10
6
cells ml
−1
) piezophile yet obtained. Optimal growth was at 80 MPa, correlating with the depth of capture (8,350 m), and 10°C, with average cell sizes of 1.46 μm in length and 0.59 μm in width. Through detailed growth studies, we provide further evidence for the temperature-pressure dependence of the growth rate for deep-ocean bacteria. PRT1 was phylogenetically placed within the
Roseobacter
clade, a bacterial lineage known for widespread geographic distribution and assorted lifestyle strategies in the marine environment. Additionally, the gene transfer agent (GTA)
g5
capsid protein gene was amplified from PRT1, indicating a potential mechanism for increased genetic diversification through horizontal gene transfer within the hadopelagic environment. This study provides a phylogenetically novel isolate for future investigations of high-pressure adaptation, expands the known physiological traits of cultivated members of the
Roseobacter
lineage, and demonstrates the feasibility of cultivating novel microbial members from the deep ocean using natural seawater.
Metabolome Remodeling during the Acidogenic-Solventogenic Transition in Clostridium acetobutylicum
Authors: Amador-Noguez Daniel , Brasg Ian A. , Feng Xiao-Jiang , Roquet Nathaniel , Rabinowitz Joshua D. 
Published: September 2011

ABSTRACT

The fermentation carried out by the biofuel producer
Clostridium acetobutylicum
is characterized by two distinct phases. Acidogenesis occurs during exponential growth and involves the rapid production of acids (acetate and butyrate). Solventogenesis initiates as cell growth slows down and involves the production of solvents (butanol, acetone, and ethanol). Using metabolomics, isotope tracers, and quantitative flux modeling, we have mapped the metabolic changes associated with the acidogenic-solventogenic transition. We observed a remarkably ordered series of metabolite concentration changes, involving almost all of the 114 measured metabolites, as the fermentation progresses from acidogenesis to solventogenesis. The intracellular levels of highly abundant amino acids and upper glycolytic intermediates decrease sharply during this transition. NAD(P)H and nucleotide triphosphates levels also decrease during solventogenesis, while low-energy nucleotides accumulate. These changes in metabolite concentrations are accompanied by large changes in intracellular metabolic fluxes. During solventogenesis, carbon flux into amino acids, as well as flux from pyruvate (the last metabolite in glycolysis) into oxaloacetate, decreases by more than 10-fold. This redirects carbon into acetyl coenzyme A, which cascades into solventogenesis. In addition, the electron-consuming reductive tricarboxylic acid (TCA) cycle is shutdown, while the electron-producing oxidative (clockwise) right side of the TCA cycle remains active. Thus, the solventogenic transition involves global remodeling of metabolism to redirect resources (carbon and reducing power) from biomass production into solvent production.
4,6-α-Glucanotransferase, a Novel Enzyme That Structurally and Functionally Provides an Evolutionary Link between Glycoside Hydrolase Enzyme Families 13 and 70
Authors: Kralj Slavko , Grijpstra Pieter , van Leeuwen Sander S. , Leemhuis Hans , Dobruchowska Justyna M. , van der Kaaij Rachel M. , Malik Amarila , Oetari Ariyanti , Kamerling Johannis P. , Dijkhuizen Lubbert 
Published: September 2011

ABSTRACT

Lactobacillus reuteri
121 uses the glucosyltransferase A (GTFA) enzyme to convert sucrose into large amounts of the α-
d
-glucan reuteran, an exopolysaccharide. Upstream of
gtfA
lies another putative glucansucrase gene, designated
gtfB
. Previously, we have shown that the purified recombinant GTFB protein/enzyme is inactive with sucrose. Various homologs of
gtfB
are present in other
Lactobacillus
strains, including the
L. reuteri
type strain, DSM 20016, the genome sequence of which is available. Here we report that GTFB is a novel α-glucanotransferase enzyme with disproportionating (cleaving α1→4 and synthesizing α1→6 and α1→4 glycosidic linkages) and α1→6 polymerizing types of activity on maltotetraose and larger maltooligosaccharide substrates (in short, it is a 4,6-α-glucanotransferase). Characterization of the types of compounds synthesized from maltoheptaose by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), methylation analysis, and 1-dimensional
1
H nuclear magnetic resonance (NMR) spectroscopy revealed that only linear products were made and that with increasing degrees of polymerization (DP), more α1→6 glycosidic linkages were introduced into the final products, ranging from 18% in the incubation mixture to 33% in an enriched fraction. In view of its primary structure, GTFB clearly is a member of the glycoside hydrolase 70 (GH70) family, comprising enzymes with a permuted (β/α)
8
barrel that use sucrose to synthesize α-
d
-glucan polymers. The GTFB enzyme reaction and product specificities, however, are novel for the GH70 family, resembling those of the GH13 α-amylase type of enzymes in using maltooligosaccharides as substrates but differing in introducing a series of α1→6 glycosidic linkages into linear oligosaccharide products. We conclude that GTFB represents a novel evolutionary intermediate between the GH13 and GH70 enzyme families, and we speculate about its origin.
Gamma-Butyrolactone Regulatory System of Streptomyces chattanoogensis Links Nutrient Utilization, Metabolism, and Development
Authors: Du Yi-Ling , Shen Xue-Ling , Yu Pin , Bai Lin-Quan , Li Yong-Quan 
Published: September 2011

ABSTRACT

Gamma-butyrolactones (GBLs) produced by several
Streptomyces
species have been shown to serve as quorum-sensing signaling molecules for activating antibiotic production. The GBL system of
Streptomyces chattanoogensis
L10, a producer of antifungal agent natamycin, consists of three genes:
scgA
,
scgX
, and
scgR
. Both
scgA
and
scgX
contribute to GBL production, while
scgR
encodes a GBL receptor.
ΔscgA
and
ΔscgX
mutants of
S. chattanoogensis
behaved identically: they had a growth defect in submerged cultures and delayed or abolished the morphological differentiation and secondary metabolites production on solid medium. ScgR could bind to the promoter region of
scgA
and repress its transcription. Moreover,
scgA
seems also to be controlled by a GBL-mediated negative-feedback system. Hence, it is apparent that GBL biosynthesis is tightly controlled to ensure the correct timing for metabolic switch. An additional direct ScgR-target gene
gbdA
was identified by genomic SELEX and transcriptional analysis. Comparative proteomic analysis between L10 and its
ΔscgA
mutant revealed that the GBL system affects the expression of more than 50 proteins, including enzymes involved in carbon uptake system, primary metabolism, and stress response, we thus conclude that
scgR-scgA-scgX
constitute a novel GBL regulatory system involved in nutrient utilization, triggering adaptive responses, and finally dictating the switch from primary to secondary metabolism.
Activity-Based Metagenomic Screening and Biochemical Characterization of Bovine Ruminal Protozoan Glycoside Hydrolases
Authors: Findley Seth D. , Mormile Melanie R. , Sommer-Hurley Andrea , Zhang Xue-Cheng , Tipton Peter , Arnett Krista , Porter James H. , Kerley Monty , Stacey Gary 
Published: September 2011

ABSTRACT
The rumen, the foregut of herbivorous ruminant animals such as cattle, functions as a bioreactor to process complex plant material. Among the numerous and diverse microbes involved in ruminal digestion are the ruminal protozoans, which are single-celled, ciliated eukaryotic organisms. An activity-based screen was executed to identify genes encoding fibrolytic enzymes present in the metatranscriptome of a bovine ruminal protozoan-enriched cDNA expression library. Of the four novel genes identified, two were characterized in biochemical assays. Our results provide evidence for the effective use of functional metagenomics to retrieve novel enzymes from microbial populations that cannot be maintained in axenic cultures.
Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces
Authors: Kim Min-Soo , Park Eun-Jin , Roh Seong Woon , Bae Jin-Woo 
Published: September 2011

ABSTRACT

In this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 10
8
to 10
9
per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of three
Bacteroides
and three
Prevotella
strains, suggesting that
Bacteroides
and
Prevotella
are the sources of infecting microphages in their hosts.
Hemocytes Are Sites of Enteric Virus Persistence within Oysters
Authors: Provost Keleigh , Dancho Brooke A. , Ozbay Gulnihal , Anderson Robert S. , Richards Gary P. , Kingsley David H. 
Published: September 2011

ABSTRACT

The goal of this study was to determine how enteric viruses persist within shellfish tissues. Several lines of novel evidence show that phagocytic blood cells (hemocytes) of Eastern oysters (
Crassostrea virginica
) play an important role in the retention of virus particles. Our results demonstrated an association of virus contamination with hemocytes but not with hemolymph. Live oysters contaminated overnight with hepatitis A virus (HAV) and murine norovirus (MNV) had 56% and 80% of extractable virus associated with hemocytes, respectively. Transfer of HAV-contaminated hemocytes to naï¿½ve (virus-free) oysters resulted in naï¿½ve oyster meat testing HAV positive for up to 3 weeks. Acid tolerance of HAV, MNV, poliovirus (PV), and feline calicivirus (FCV) correlated with the ability of each virus to persist within oysters. Using reverse transcription-PCR (RT-PCR) to evaluate persistence of these viruses in oysters, we showed that HAV persisted the longest (>21 days) and was most acid resistant, MNV and PV were less tolerant of acidic pH, persisting for up to 12 days and 1 day, respectively, and FCV did not persist (<1 day) within oysters and was not acid tolerant. This suggests that the ability of a virus to tolerate the acidic conditions typical of phagolysosomal vesicles within hemocytes plays a role in determining virus persistence in shellfish. Evaluating oyster and hemocyte homogenates and live contaminated oysters as a prelude to developing improved viral RNA extraction methods, we found that viruses were extracted more expediently from hemocytes than from whole shellfish tissues and gave similar RT-PCR detection sensitivities.
Whole-Genome Association Study on Tissue Tropism Phenotypes in Group A Streptococcus
Authors: Bessen Debra E. , Kumar Nikhil , Hall Gerod S. , Riley David R. , Luo Feng , Lizano Sergio , Ford Candace N. , McShan W. Michael , Nguyen Scott V. , Hotopp Julie C. Dunning , Tettelin Hervé 
Published: September 2011

ABSTRACT

Group A
Streptococcus
(GAS) has a rich evolutionary history of horizontal transfer among its core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological phenotypes. To further our understanding of the molecular basis for ecological phenotypes, comparative genomic hybridization of a set of 97 diverse strains to a GAS pangenome microarray was undertaken, and the association of accessory genes with
emm
genotypes that define tissue tropisms for infection was determined. Of the 22 nonprophage accessory gene regions (AGRs) identified, only 3 account for all statistically significant linkage disequilibrium among strains having the genotypic biomarkers for throat versus skin infection specialists. Networked evolution and population structure analyses of loci representing each of the AGRs reveal that most strains with the skin specialist and generalist biomarkers form discrete clusters, whereas strains with the throat specialist biomarker are highly diverse. To identify coinherited and coselected accessory genes, the strength of genetic associations was determined for all possible pairwise combinations of accessory genes among the 97 GAS strains. Accessory genes showing very strong associations provide the basis for an evolutionary model, which reveals that a major transition between many throat and skin specialist haplotypes correlates with the gain or loss of genes encoding fibronectin-binding proteins. This study employs a novel synthesis of tools to help delineate the major genetic changes associated with key adaptive shifts in an extensively recombined bacterial species.
In Rhodobacter sphaeroides, Chemotactic Operon 1 Regulates Rotation of the Flagellar System 2
Authors: Martínez-del Campo Ana , Ballado Teresa , Camarena Laura , Dreyfus Georges 
Published: September 2011

ABSTRACT

Rhodobacter sphaeroides
is able to assemble two different flagella, the subpolar flagellum (Fla1) and the polar flagella (Fla2). In this work, we report the swimming behavior of
R. sphaeroides
Fla2
+
cells lacking each of the proteins encoded by chemotactic operon 1. A model proposing how these proteins control Fla2 rotation is presented.
Role of Sphingomonas sp. Strain Fr1 PhyR-NepR-σ
EcfG
Cascade in General Stress Response and Identification of a Negative Regulator of PhyR
Authors: Kaczmarczyk Andreas , Campagne Sébastien , Danza Francesco , Metzger Lisa C. , Vorholt Julia A. , Francez-Charlot Anne 
Published: September 2011

ABSTRACT

The general stress response in
Alphaproteobacteria
was recently described to depend on the alternative sigma factor σ
EcfG
, whose activity is regulated by its anti-sigma factor NepR. The response regulator PhyR, in turn, regulates NepR activity in a partner-switching mechanism according to which phosphorylation of PhyR triggers sequestration of NepR by the sigma factor-like effector domain of PhyR. Although genes encoding predicted histidine kinases can often be found associated with
phyR
, little is known about their role in modulation of PhyR phosphorylation status. We demonstrate here that the PhyR-NepR-σ
EcfG
cascade is important for multiple stress resistance and competitiveness in the phyllosphere in a naturally abundant plant epiphyte,
Sphingomonas
sp. strain Fr1, and provide evidence that the partner switching mechanism is conserved. We furthermore identify a gene, designated
phyP
, encoding a predicted histidine kinase at the
phyR
locus as essential. Genetic epistasis experiments suggest that PhyP acts upstream of PhyR, keeping PhyR in an unphosphorylated, inactive state in nonstress conditions, strictly depending on the predicted phosphorylatable site of PhyP, His-341.
In vitro
experiments show that
Escherichia coli
inner membrane fractions containing PhyP disrupt the PhyR-P/NepR complex. Together with the fact that PhyP lacks an obvious ATPase domain, these results are in agreement with PhyP functioning as a phosphatase of PhyR, rather than a kinase.
Attitudes regarding ski helmet use among helmet wearers and non-wearers
Authors: Ruedl Gerhard , Kopp Martin , Rumpold Gerhard , Holzner Bernhard , Ledochowski Larissa , Burtscher Martin 
Published: September 2011

ObjectiveThe aim of this study was to compare attitudes regarding ski helmet use in helmet wearers and non-wearers.MethodsIn total, 924 persons ≥18 years (52% men and 48% women) participating in sport programmes at the University Sports Institute Innsbruck/Austria were interviewed about their attitudes regarding ski helmets and scored 14 statements on a five-level Likert Scale. A factor analysis was employed to determine clusters of underlying attitudes that have subsequently been used as predictors of helmet non-use in a conditional logistic regression analysis.ResultsIn total, 65% of participants declared to use a helmet during their preferred winter sport activity while more than 80% of helmet wearers and non-wearers totally agreed that helmets protect from head injuries. According to the factor analysis, attitudes about ski helmets clustered around four major dimensions—subjective disadvantages, safety awareness, comfort/style and risk compensation. Adjusted ORs of regression analysis showed that helmet non-use increased with age and decreased with increasing skill level (beginner: OR 5.4, 95% CI 2.6 to 11.1; intermediate: OR 4.3, 95% CI 2.4 to 7.9; advanced: OR 3.1, 95% CI 1.7 to 5.4). In addition, helmet non-use was associated with subjective disadvantages (OR 2.3, 95% CI 1.8 to 2.9). However, a negative association between helmet non-use and safety awareness (OR 0.3, 95% CI 0.2 to 0.4) was found.ConclusionHelmet use was associated with higher safety awareness, while most arguments against helmet use seem to belong to subjective perception and to represent anticipatory negative cognitions, poorly supported by evidence. Therefore, evidence-based information about wearing a ski helmet should be implemented in preventive helmet campaigns focusing on non-wearers. In addition, health communication programmes should be instituted to get non-helmeted skiers and snowboarders to try out helmets to eliminate their potential prejudices.