bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pour some sugar on it: the expanding world of bacterial protein O‐linked glycosylation
Authors: Iwashkiw Jeremy A. , Vozza Nicolas F. , Kinsella Rachel L. , Feldman Mario F. 
Published: May 2013

SummaryProtein glycosylation was once considered as an eccentricity of a few bacteria. However in the recent years multiple O‐glycosylation mechanisms have been identified in bacterial species from the most diverse genera, including various important human pathogens. This review focuses on summarizing the structural diversity, the various pathways and the physiological roles of this post‐translational protein modification. We propose a classification of O‐glycosylation based on the requirement of an oligosaccharyltransferase (OTase). OTase‐dependent glycosylation utilizes an oligosaccharide synthesized on a lipid carrier that is transferred to proteins en bloc by an OTase. Multiple proteins, including the pilins, are glycosylated using this mechanism. OTase‐independent glycosylation refers to the pathway in which glycosyltransferases sequentially add monosaccharides onto the target proteins. This pathway is employed for glycosylation of flagella and autotransporters. Both systems play key roles in pathogenesis. Exploiting glycosylation machineries it is now possible to generate glycoconjugates made of different proteins attached to polysaccharides derived from LPS or capsule biosynthesis. These recombinant glycoproteins can be exploited for vaccines and diagnostics of bacterial infections. Furthermore, O‐glycosylation systems are promising targets for antibiotic development. Technological advances in MS and NMR will facilitate the discovery of novel glycosylation systems. Likely, the O‐glycosylation pathways we currently know constitute just the tip of the iceberg of a still largely uncharacterized bacterial glycosylation world.
Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly
Authors: Desmarais Samantha M. , De Pedro Miguel A. , Cava Felipe , Huang Kerwyn Casey 
Published: May 2013

SummaryThe peptidoglycan (PG) cell wall is a unique macromolecule responsible for both shape determination and cellular integrity under osmotic stress in virtually all bacteria. A quantitative understanding of the relationships between PG architecture, morphogenesis, immune system activation and pathogenesis can provide molecular‐scale insights into the function of proteins involved in cell wall synthesis and cell growth. High‐performance liquid chromatography (HPLC) has played an important role in our understanding of the structural and chemical complexity of the cell wall by providing an analytical method to quantify differences in chemical composition. Here, we present a primer on the basic chemical features of wall structure that can be revealed through HPLC, along with a description of the applications of HPLC PG analyses for interpreting the effects of genetic and chemical perturbations to a variety of bacterial species in different environments. We describe the physical consequences of different PG compositions on cell shape, and review complementary experimental and computational methodologies for PG analysis. Finally, we present a partial list of future targets of development for HPLC and related techniques.
‘Unlucky’ Gettier Cases
Authors: Stone Jim 
Published: May 2013

AbstractThis article argues that justified true beliefs in Gettier cases often are not true due to luck. I offer two ‘unlucky’ Gettier cases, and it's easy enough to generate more. Hence even attaching a broad ‘anti‐luck’ codicil to the tripartite account of knowledge leaves the Gettier problem intact. Also, two related questions are addressed. First, if epistemic luck isn't distinctive of Gettier cases, what is? Second, what do Gettier cases reveal about knowledge?
Acclimation to humidity modifies the link between leaf size and the density of veins and stomata
Authors: CARINS MURPHY MADELINE R. , JORDAN GREGORY J. , BRODRIBB TIMOTHY J. 
Published: May 2013

AbstractThe coordination of veins and stomata during leaf acclimation to sun and shade can be facilitated by differential epidermal cell expansion so large leaves with low vein and stomatal densities grow in shade, effectively balancing liquid‐ and vapour‐phase conductances. As the difference in vapour pressure between leaf and atmosphere (VPD) determines transpiration at any given stomatal density, we predict that plants grown under high VPD will modify the balance between veins and stomata to accommodate greater maximum transpiration. Thus, we examined the developmental responses of these traits to contrasting VPD in a woody angiosperm (Toona ciliata M. Roem.) and tested whether the relationship between them was altered. High VPD leaves were one‐third the size of low VPD leaves with only marginally greater vein and stomatal density. Transpirational homeostasis was thus maintained by reducing stomatal conductance. VPD acclimation changed leaf size by modifying cell number. Hence, plasticity in vein and stomatal density appears to be generated by plasticity in cell size rather than cell number. Thus, VPD affects cell number and leaf size without changing the relationship between liquid‐ and vapour‐phase conductances. This results in inefficient acclimation to VPD as stomata remain partially closed under high VPD.
Diversity of Phytophthora infestans from Poland
Authors: Chmielarz M. , Sobkowiak S. , Dębski K. , Cooke D. E. L. , Brurberg M. B. , Śliwka J. 
Published: May 2013

A collection of 96 Polish isolates of Phytophthora infestans sampled in the years 2006, 2008 and 2009 were analysed using phenotypic and genotypic markers. Mating type, virulence, resistance to metalaxyl, mitochondrial haplotype and polymorphism at 12 simple sequence repeat (SSR) loci were determined. The majority of isolates were of the A1 mating type, mitochondrial haplotype Ia and sensitive to metalaxyl. Virulence factors against potato R genes R1, R3, R4, R7, R10 and R11 were present in most isolates. Genotyping using SSR markers revealed high genetic diversity within the Polish P. infestans population. Amongst the 96 isolates 66 unique genotypes were identified, 49 of which were observed only in single isolates. Eight isolates of the genotype 13_A2 lineage that has been reported in other parts of Europe were also found in Poland. The implications of these results are discussed.
Holistic Systems Biology Approaches to Molecular Mechanisms of Human Helper T Cell Differentiation to Functionally Distinct Subsets
Authors: Chen Z. , Lönnberg T. , Lahesmaa R. 
Published: May 2013

AbstractCurrent knowledge of helper T cell differentiation largely relies on data generated from mouse studies. To develop therapeutical strategies combating human diseases, understanding the molecular mechanisms how human naïve T cells differentiate to functionally distinct T helper (Th) subsets as well as studies on human differentiated Th cell subsets is particularly valuable. Systems biology approaches provide a holistic view of the processes of T helper differentiation, enable discovery of new factors and pathways involved and generation of new hypotheses to be tested to improve our understanding of human Th cell differentiation and immune‐mediated diseases. Here, we summarize studies where high‐throughput systems biology approaches have been exploited to human primary T cells. These studies reveal new factors and signalling pathways influencing T cell differentiation towards distinct subsets, important for immune regulation. Such information provides new insights into T cell biology and into targeting immune system for therapeutic interventions.
The Antioxidative Effect of Heat‐Shock Protein 70 in Dendritic Cells
Authors: Je J. H. , Kim D. Y. , Roh H. J. , Pak C. , Kim D. H. , Byamba D. , Jee H. , Kim T.‐G. , Park J. M. , Lee S.‐K. , Lee M.‐G. 
Published: May 2013

AbstractReactive oxygen species (ROS) are produced by dendritic cells (DCs) during antigen presentation in contact hypersensitivity (CHS). ROS cause a number of non‐enzymatic protein modifications, such as carbonylation. Carbonylated proteins in DCs in response to hapten have not been fully identified yet. To identify the proteins carbonylated by ROS, murine epidermis‐derived DC line XS106 was challenged with a hapten, 2,4,6‐trinitrobenzene sulphonic acid (TNBS). MALDI‐TOF analysis revealed that heat‐shock protein 70 (HSP70) was one of the carbonylated proteins induced by TNBS. To verify the role of HSP70 in TNBS‐treated XS106 cell, we fused protein transduction domain (PTD) with HSP70 to facilitate protein delivery into the cell. The transfected fusion protein HSP70 within the cell caused transient increase of the cellular level of HSP70. Transient increase of HSP70 level in XS‐106 DCs resulted in inhibition of ROS production, carbonylation of HSP70, p38 MAPK activation and subsequently IL‐12 secretion. To investigate the effects of PTD–HSP70 in vivo, ear‐swelling experiments with 2,4,6‐trinitro‐1‐chlorobenzene (TNCB) were performed in BALB/c mice. Pretreatment of PTD–HSP70 reduced the CHS response to TNCB in vivo. We report here that carbonylation of HSP70 by ROS is associated with the pathogenesis of CHS, suggesting possibility of HSP70‐targeting therapy in CHS.
The Important Role of T Cells and Receptor Expression in Sjögren's Syndrome
Authors: Karabiyik A. , Peck A. B. , Nguyen C. Q. 
Published: May 2013

AbstractSjögren's syndrome (SjS), an autoimmune disease characterized by exocrine gland dysfunction leading to dry mouth and dry eye diseases, is typified by progressive leucocyte infiltrations of the salivary and lacrimal glands. Histologically, these leucocyte infiltrations generally establish periductal aggregates, referred to as lymphocytic foci (LF), which occasionally appear as germinal centre (GC)‐like structures. The formation and organization of these LF suggest an important and dynamic role for helper T cells (TH), specifically TH1, TH2 and the recently discovered TH17, in development and onset of clinical SjS, considered a B cell–mediated hypersensitivity type 2 disease. Despite an ever‐increasing focus on identifying the underlying aetiology of SjS, defining factors that initiate this autoimmune disease remain a mystery. Thus, determining interactions between infiltrating TH cells and exocrine gland tissue (auto‐)antigens represents a fertile research endeavour. This review discusses pathological functions of TH cells in SjS, the current status of TH cell receptor gene rearrangements associated with human and mouse models of SjS and potential future prospects for identifying receptor–autoantigen interactions.
A Multi‐Grid Method of High Accuracy Surface Modeling and Its Validation
Authors: Yue Tian‐Xiang , Zhao Na , Yang Hai , Song Yin‐Jun , Du Zheng‐Ping , Fan Ze‐Meng , Song Dun‐Jiang 
Published: May 2013

AbstractA method of high accuracy surface modeling (HASM) has been constructed to find a solution for error problems that had long troubled surface modeling in geographical information systems (GIS). It is found that when a preconditioned conjugate gradient (PCG) algorithm is used to solve the large sparse linear system, which HASM can be transferred into, HASM performs best in terms of simulation compared with all other algorithms. But its computing speed is not fast enough for all applications. A multi‐grid method is introduced into HASM to try to shorten its computing time. Both numerical and real‐world tests demonstrate that there is a range of stop error (SE). The multi‐grid method of HASM (HASM‐MG) greatly increases computing speed when SEs are within this range, compared with the PCG algorithm of HASM (HASM‐PCG). HASM‐MG is suitable for applications with a need for less accuracy and a shorter computing time. HASM‐PCG is appropriate for issues needing higher accuracy. HASM‐MG performs better than HASM‐PCG in flat areas, while HASM‐PCG does better in complex terrainm in terms of accuracy and computing time.
Genome Sequences of Two Emerging Non-O157 Shiga Toxin-Producing Escherichia coli Strains
Authors: Cao Guojie , Ju Wenting , Rump Lydia , Zhao Shaohua , Zou Likou , Wang Charles , Strain Errol , Luo Yan , Timme Ruth , Allard Marc , Brown Eric , Meng Jianghong 
Published: May 2013

ABSTRACT

Shiga toxin-producing
Escherichia coli
(STEC) causes severe illness in humans, including hemorrhagic colitis and hemolytic uremic syndrome. A parallel evolutionary model was proposed in which
E. coli
strains of distinct phylogenies independently integrate Shiga toxin-encoding genes and evolve into STEC. We report the draft genomes of two emerging non-O157 STEC strains.
Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp.
longum
Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period
Authors: Shkoporov A. N. , Efimov B. A. , Khokhlova E. V. , Chaplin A. V. , Kafarskaya L. I. , Durkin A. S. , McCorrison J. , Torralba M. , Gillis M. , Sutton G. , Weibel D. B. , Nelson K. E. , Smeianov V. V. 
Published: May 2013

ABSTRACT

We report the genome sequences of four isolates of a human gut symbiont,
Bifidobacterium longum
. Strains 44B and 35B were isolated from two 1-year-old infants, while 1-6B and 2-2B were isolated from the same children 5 years later. The sequences permit investigations of factors enabling long-term colonization of bifidobacteria.
Complete Genome Sequence of the γ-Hexachlorocyclohexane-Degrading Bacterium
Sphingomonas
sp. Strain MM-1
Authors: Tabata M. , Ohtsubo Y. , Ohhata S. , Tsuda M. , Nagata Y. 
Published: May 2013

ABSTRACT

γ-Hexachlorocyclohexane (γ-HCH) is a man-made chlorinated insecticide that has caused serious environmental problems. Here, we report the complete genome sequence of the γ-HCH-degrading bacterium
Sphingomonas
sp. strain MM-1, which consists of one chromosome and five plasmids. All the specific
lin
genes that are almost identical to those of
Sphingobium japonicum
UT26 for the conversion of γ-HCH to β-ketoadipate are dispersed on four out of the five plasmids.
Draft Genome Sequence of the Serratia marcescens Strain VGH107, a Taiwanese Clinical Isolate
Authors: Liu Po-Yu , Huang Yao-Ting , Lin Sheng-Yi , Chang Gee-Cheng , Chen Jian-Wei 
Published: May 2013

ABSTRACT

Serratia marcescens
, a member of the family
Enterobacteriaceae
, is the causative agent of various types of wound infections. We report a high-quality draft genome sequence of
S. marcescens
strain VGH107, which was isolated from a patient with an infection from a snakebite wound.
Genome Sequences of Two Morphologically Distinct and Thermophilic Bacillus coagulans Strains, H-1 and XZL9
Authors: Xu Ke , Su Fei , Tao Fei , Li Chao , Ni Jun , Xu Ping 
Published: May 2013

ABSTRACTTwo thermophilicBacillus coagulansstrains, H-1 and XZL9, both of which were isolated from soils, have different morphological properties. Strain XZL9 but not H-1 is an efficient pentose-utilizing producer of important platform compounds, such asl-lactic acid and 2,3-butanediol. Here we announce the 2.86- and 3.43-Mb sequences of their genomes.
Draft Genome Sequence of the Tyramine Producer Enterococcus durans Strain IPLA 655
Authors: Ladero Victor , Linares Daniel M. , del Rio Beatriz , Fernandez Maria , Martin M. Cruz , Alvarez Miguel A. 
Published: May 2013

ABSTRACT

We here report a 3.059-Mbp draft assembly for the genome of
Enterococcus durans
strain IPLA 655. This dairy isolate provides a model for studying the regulation of the biosynthesis of tyramine (a toxic compound). These results should aid our understanding of tyramine production and allow tyramine accumulation in food to be reduced.
Benefits of combining inspiratory muscle with ‘whole muscle’ training in children with cystic fibrosis: a randomised controlled trial
Authors: Santana-Sosa Elena , Gonzalez-Saiz Laura , Groeneveld Iris F , Villa-Asensi José R , Barrio Gómez de Aguero María I , Fleck Steven J , López-Mojares Luis M , Pérez Margarita , Lucia Alejandro 
Published: May 2013

BackgroundThe purpose of this study (randomised controlled trial) was to assess the effects of an 8-week combined ‘whole muscle’ (resistance+aerobic) and inspiratory muscle training (IMT) on lung volume, inspiratory muscle strength (PImax) and cardiorespiratory fitness (VO2peak) (primary outcomes), and dynamic muscle strength, body composition and quality of life in paediatric outpatients with CF (cystic fibrosis, secondary outcomes). We also determined the effects of a detraining period.MethodsParticipants were randomly allocated with a block on gender to a control (standard therapy) or intervention group (initial n=10 (6 boys) in each group; age 10±1 and 11±1 years). The latter group performed a combined programme (IMT (2 sessions/day) and aerobic+strength exercises (3 days/week, in-hospital)) that was followed by a 4-week detraining period. All participants were evaluated at baseline, post-training and detraining.ResultsAdherence to the training programme averaged 97.5%±1.7%. There was a significant interaction (group×time) effect for PImax, VO2peakand five-repetition maximum strength (leg-press, bench-press, seated-row) (all (p<0.001), and also for %fat (p<0.023) and %fat-free mass (p=0.001), with training exerting a significant beneficial effect only in the intervention group, which was maintained after detraining for PImaxand leg-press.ConclusionThe relatively short-term (8-week) training programme used here induced significant benefits in important health phenotypes of paediatric patients with CF. IMT is an easily applicable intervention that could be included, together with supervised exercise training in the standard care of these patients.
The effects on student health of interventions modifying the school environment: systematic review
Authors: Bonell C , Wells H , Harden A , Jamal F , Fletcher A , Thomas J , Campbell R , Petticrew M , Whitehead M , Murphy S , Moore L 
Published: May 2013

BackgroundOwing to the limited effectiveness of traditional health education curricula in schools, there is increasing interest in interventions aiming to promote young people's health by modifying the school environment. Existing systematic reviews cannot determine whether environmental intervention is effective because they examine interventions combining environmental modifications and traditional health education. This gap is significant because school-environment interventions are complex to implement and may be sidelined in underfunded and attainment-focused school systems without evidence to support such an approach. This systematic review examined the effectiveness of school-environment interventions without health-education components on student health and inequalities.MethodsThis was a systematic review of experimental/quasi-experimental studies of school-environment interventions. Sixteen databases were searched, eliciting 62 329 references which were screened, with included studies quality assessed, data extracted and narratively synthesised.ResultsSixteen reports of 10 studies were included, all from the USA and the UK. Five evaluations of interventions aiming to develop a stronger sense of community and/or improve relationships between staff and students suggested potential benefits particularly regarding violence and aggression. Two trials of interventions enabling students to advocate for changes in school catering and physical activity reported benefits for physical activity but not diet. Three evaluations of improvements to school playgrounds offered weak evidence of effects on physical activity.ConclusionsSchool environment interventions show the potential to improve young people's health particularly regarding violence, aggression and physical activity. Further trials are required to provide a stronger and more generalisable evidence base.
RAMAN STUDY OF BENZENE NEAR THE MELTING POINT
Authors: YURTSEVEN H. , ÇETINBAŞ İŞERI E. 
Published: May 2013

We calculate here the Raman frequencies of some lattice modes as a function of pressure at constant temperatures for the solid and liquid phases of benzene. The observed data for the molar volume from literature is used to calculate the Raman frequencies through the mode Grüneisen parameter in benzene. Our calculated frequencies are in good agreement with the observed data when the mode Grüneisen parameter is taken as a constant at one particular pressure in solid benzene. It is shown here that the Raman frequencies can be calculated from the volume data, as demonstrated for benzene here.
Basin fragmentation controlled by tectonic inversion and basement uplift in Sierras Pampeanas and Santa Bárbara System, northwest Argentina
Authors: Iaffa Diego Nicolas , Sàbat F. , Muñoz J. A. , Carrera N. 
Published: May 2013

Abstract
The study area is located within the Central Andes, a complex region composed of different structural styles. The region is characterized by highly elevated basement cored ranges, which abruptly break the foreland plain. These ranges were uplifted mainly by deep detached high-angle faults or by the inversion of former extensional faults of the Cretaceous rift. Palaeozoic orogenies generated crustal scale discontinuities in the basement, some of them reactivated during the Andean orogeny. Sedimentary sequences and layers architecture in the basins bordering ranges recorded the tectonic evolution of the region. Basement, syn–rift, post-rift and three foreland stages were interpreted in the seismic sections according to the arrangement of the horizons and the main outcropping geological units in bordering ranges. Based on seismic data sets and field data, here we document a particular style of activation of basement faults. Thick-skinned structures that are not always related to the tectonic inversion but to the reactivation of older basement anisotropies represent a paradox since they were not active during the rifting stage. A flat slab subduction and a subsequent angle recovery conditioned the structural evolution of the area.
Reconstruction of the early Mesozoic plate margin of Gondwana by U–Pb ages of detrital zircons from northern Victoria Land, Antarctica
Authors: Elsner Martin , Schöner Robert , Gerdes Axel , Gaupp Reinhard 
Published: May 2013

Abstract

Detrital zircons of eight sandstone samples from the Triassic–Early Jurassic Section Peak Formation (Victoria Group, Beacon Supergroup) in northern Victoria Land, Antarctica, were investigated by U–Pb LA–ICPMS dating. The basin was flanked by the East Antarctic craton, and by a magmatic arc at the palaeo-Pacific margin of Gondwana. It accommodated sandstones ranging from quartzo-feldspathic to volcaniclastic in composition. The detrital zircon age spectra yield pronounced concentrations at
c.
190–250 Ma, 500–700 Ma and 800–1200 Ma. The proportion of Triassic–Early Jurassic zircons increases from base to top of the formation, and correlates positively with the abundance of detrital volcanic rock fragments. The youngest zircon ages are close to the stratigraphic age of each sample, indicating contemporaneous magmatic activity along the active margin of Gondwana. Igneous rocks that formed during the Ross Orogeny (
c.
470–545 Ma) were a minor source only, suggesting that the Ross Orogen became progressively covered by sediments as the basin expanded. Pan-African (
c.
500–700 Ma) and Grenville (
c.
800–1200 Ma) age zircons may have been derived from crustal sources currently covered beneath the polar ice sheet, although recycling from Cambro-Ordovician units provides an alternative explanation.

Supplementary material:

The exact results of the age analyses of all samples are presented in Tables A1 to A8 at
www.geolsoc.org.uk/SUP18624