bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Type III Secretion System Effector SptP of Salmonella enterica Serovar Typhi
Authors: Johnson Rebecca , Byrne Alexander , Berger Cedric N. , Klemm Elizabeth , Crepin Valerie F. , Dougan Gordon , Frankel Gad 
Published: December 2016

ABSTRACT

Strains of the various
Salmonella enterica
serovars cause gastroenteritis or typhoid fever in humans, with virulence depending on the action of two type III secretion systems (
Salmonella
pathogenicity island 1 [SPI-1] and SPI-2). SptP is a
Salmonella
SPI-1 effector, involved in mediating recovery of the host cytoskeleton postinfection. SptP requires a chaperone, SicP, for stability and secretion. SptP has 94% identity between
S. enterica
serovar Typhimurium and
S
. Typhi; direct comparison of the protein sequences revealed that
S
. Typhi SptP has numerous amino acid changes within its chaperone-binding domain. Subsequent comparison of Δ
sptP S
. Typhi and
S.
Typhimurium strains demonstrated that, unlike SptP in
S.
Typhimurium, SptP in
S
. Typhi was not involved in invasion or cytoskeletal recovery postinfection. Investigation of whether the observed amino acid changes within SptP of
S
. Typhi affected its function revealed that
S
. Typhi SptP was unable to complement
S.
Typhimurium Δ
sptP
due to an absence of secretion. We further demonstrated that while
S.
Typhimurium SptP is stable intracellularly within
S
. Typhi,
S
. Typhi SptP is unstable, although stability could be recovered following replacement of the chaperone-binding domain with that of
S.
Typhimurium. Direct assessment of the strength of the interaction between SptP and SicP of both serovars via bacterial two-hybrid analysis demonstrated that
S
. Typhi SptP has a significantly weaker interaction with SicP than the equivalent proteins in
S.
Typhimurium. Taken together, our results suggest that changes within the chaperone-binding domain of SptP in
S
. Typhi hinder binding to its chaperone, resulting in instability, preventing translocation, and therefore restricting the intracellular activity of this effector.

IMPORTANCE
Studies investigating
Salmonella
pathogenesis typically rely on
Salmonella
Typhimurium, even though
Salmonella
Typhi causes the more severe disease in humans. As such, an understanding of
S.
Typhi pathogenesis is lacking. Differences within the type III secretion system effector SptP between typhoidal and nontyphoidal serovars led us to characterize this effector within
S
. Typhi. Our results suggest that SptP is not translocated from typhoidal serovars, even though the loss of
sptP
results in virulence defects in
S.
Typhimurium. Although SptP is just one effector, our results exemplify that the behavior of these serovars is significantly different and genes identified to be important for
S.
Typhimurium virulence may not translate to
S
. Typhi.
Malate Synthase and β-Methylmalyl Coenzyme A Lyase Reactions in the Methylaspartate Cycle in Haloarcula hispanica
Authors: Borjian Farshad , Han Jing , Hou Jing , Xiang Hua , Zarzycki Jan , Berg Ivan A. 
Published: December 2016

ABSTRACT

Haloarchaea are extremely halophilic heterotrophic microorganisms belonging to the class
Halobacteria
(
Euryarchaeota
). Almost half of the haloarchaea possesses the genes coding for enzymes of the methylaspartate cycle, a recently discovered anaplerotic acetate assimilation pathway. In this cycle, the enzymes of the tricarboxylic acid cycle together with the dedicated enzymes of the methylaspartate cycle convert two acetyl coenzyme A (acetyl-CoA) molecules to malate. The methylaspartate cycle involves two reactions catalyzed by homologous enzymes belonging to the CitE-like enzyme superfamily, malyl-CoA lyase/thioesterase (haloarchaeal malate synthase [hMS]; Hah_2476 in
Haloarcula hispanica
) and β-methylmalyl-CoA lyase (haloarchaeal β-methylmalyl-CoA lyase [hMCL]; Hah_1341). Although both enzymes catalyze the same reactions, hMS was previously proposed to preferentially catalyze the formation of malate from acetyl-CoA and glyoxylate (malate synthase activity) and hMCL was proposed to primarily cleave β-methylmalyl-CoA to propionyl-CoA and glyoxylate. Here we studied the physiological functions of these enzymes during acetate assimilation in
H. hispanica
by using biochemical assays of the wild type and deletion mutants. Our results reveal that the main physiological function of hMS is malyl-CoA (not malate) formation and that hMCL catalyzes a β-methylmalyl-CoA lyase reaction
in vivo
. The malyl-CoA thioesterase activities of both enzymes appear to be not essential for growth on acetate. Interestingly, despite the different physiological functions of hMS and hMCL, structural comparisons predict that these two proteins have virtually identical active sites, thus highlighting the need for experimental validation of their catalytic functions. Our results provide further proof of the operation of the methylaspartate cycle and indicate the existence of a distinct, yet-to-be-discovered malyl-CoA thioesterase in haloarchaea.

IMPORTANCE
Acetate is one of the most important substances in natural environments. The activated form of acetate, acetyl coenzyme A (acetyl-CoA), is the high-energy intermediate at the crossroads of central metabolism: its oxidation generates energy for the cell, and about a third of all biosynthetic fluxes start directly from acetyl-CoA. Many organic compounds enter the central carbon metabolism via this key molecule. To sustain growth on acetyl-CoA-generating compounds, a dedicated assimilation (anaplerotic) pathway is required. The presence of an anaplerotic pathway is a prerequisite for growth in many environments, being important for environmentally, industrially, and clinically important microorganisms. Here we studied specific reactions of a recently discovered acetate assimilation pathway, the methylaspartate cycle, functioning in extremely halophilic archaea.
Role of the
nifB1
and
nifB2
Promoters in Cell-Type-Specific Expression of Two Mo Nitrogenases in the Cyanobacterium Anabaena variabilis ATCC 29413
Authors: Vernon Susan A. , Pratte Brenda S. , Thiel Teresa 
Published: December 2016

ABSTRACT

Anabaena variabilis
ATCC 29413 has one Mo nitrogenase that is made under oxic growth conditions in specialized cells called heterocysts and a second Mo nitrogenase that is made only under anoxic conditions in vegetative cells. The two large
nif
gene clusters responsible for these two nitrogenases are under the control of the promoter of the first gene in the operon,
nifB1
or
nifB2
. Despite differences in the expression patterns of
nifB1
and
nifB2
, related to oxygen and cell type, the regions upstream of their transcription start sites (tss) show striking homology, including three highly conserved sequences (CS). CS1, CS2, and the region just upstream from the tss were required for optimal expression from the
nifB1
promoter, but CS3 and the 5′ untranslated region (UTR) were not. Hybrid fusions of the
nifB1
and
nifB2
upstream regions revealed that the region including CS1, CS2, and CS3 of
nifB2
could substitute for the similar region of
nifB1
; however, the converse was not true. Expression from the
nifB2
promoter region required the CS1, CS2, and CS3 regions of
nifB2
and also required the
nifB2
5′ UTR. A hybrid promoter that was mostly
nifB2
but that had the region from about position −40 to the tss of
nifB1
was expressed in heterocysts and in anoxic vegetative cells. Thus, addition of the
nifB1
promoter region (from about position −40 to the tss of
nifB1
) in the
nifB
hybrid promoter supported expression in heterocysts but did not prevent the mostly
nifB2
promoter from also functioning in anoxic vegetative cells.

IMPORTANCE
In the filamentous cyanobacterium
Anabaena variabilis
, two Mo nitrogenase gene clusters,
nif1
and
nif2
, function under different environmental conditions in different cell types. Little is known about the regulation of transcription from the promoter upstream of the first gene of the cluster, which drives transcription of each of these two large operons. The similarity in the sequences upstream of the primary promoters for the two
nif
gene clusters belies the differences in their expression patterns. Analysis of these
nif
promoters in strains with mutations in the conserved sequences and in strains with hybrid promoters, comprising parts from
nif1
and
nif2
, provides strong evidence that each promoter has key elements required for cell-type-specific expression of the
nif1
and
nif2
gene clusters.
A Novel Transcriptional Regulator Related to Thiamine Phosphate Synthase Controls Thiamine Metabolism Genes in Archaea
Authors: Rodionov Dmitry A. , Leyn Semen A. , Li Xiaoqing , Rodionova Irina A. 
Published: December 2016

ABSTRACT

Thiamine (vitamin B
1
) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamine biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In
Archaea
, TPP riboswitches are restricted to the
Thermoplasmatales
order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages in the
Crenarchaeota
phylum as well as in the
Halobacteria
and
Thermococci
classes of the
Euryarchaeota
. ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain, which is similar to the archaeal thiamine phosphate synthase ThiN. By using comparative genomics, we predicted ThiR-binding DNA motifs and reconstructed ThiR regulons in 67 genomes representing all above-mentioned lineages. The predicted ThiR-binding motifs are characterized by palindromic symmetry with several distinct lineage-specific consensus sequences. In addition to thiamine biosynthesis genes, the reconstructed ThiR regulons include various transporters for thiamine and its precursors. Bioinformatics predictions were experimentally validated by
in vitro
DNA-binding assays with the recombinant ThiR protein from the hyperthermophilic archaeon
Metallosphaera yellowstonensis
MK1. Thiamine phosphate and, to some extent, TPP and hydroxyethylthiazole phosphate were required for the binding of ThiR to its DNA targets, suggesting that ThiR is derepressed by limitation of thiamine phosphates. The thiamine phosphate-binding residues previously identified in ThiN are highly conserved in ThiR regulators, suggesting a conserved mechanism for effector recognition.

IMPORTANCE
Thiamine pyrophosphate is a cofactor for many essential enzymes for glucose and energy metabolism. Thiamine or vitamin B
1
biosynthesis and its transcriptional regulation in
Archaea
are poorly understood. We applied the comparative genomics approach to identify a novel family of regulators for the transcriptional control of thiamine metabolism genes in
Archaea
and reconstructed the respective regulons. The predicted ThiR regulons in archaeal genomes control the majority of thiamine biosynthesis genes. The reconstructed regulon content suggests that numerous uptake transporters for thiamine and/or its precursors are encoded in archaeal genomes. The ThiR regulon was experimentally validated by DNA-binding assays with
Metallosphaera
spp. These discoveries contribute to our understanding of metabolic and regulatory networks involved in vitamin homeostasis in diverse lineages of
Archaea
.
Contrasting magmatic cannibalism forms evolved phonolitic magmas in the Canary Islands
Authors: Turner S. , Kokfelt T. , Hoernle K. , Johansen T.S. , Hauff F. , Lundstrom C. , van den Bogaard P. , Klügel A. 
Published: December 2016

Abstract
Volcanic sequences on ocean islands record the temporal evolution of underlying magmatic systems and provide insights into how silicic crust is produced away from convergent margins. Assimilation has often been suspected to contribute, but the detection of such a process and its evolving maturity during migration across a mantle plume is less well documented. Here we present new major and trace element and Sr-Nd-Pb-U-Th-Ra-Pa isotope data that facilitate comparison of basanite to phonolite evolution on Tenerife (Canary Islands) with that shown by published data from La Palma. On both islands, (230Th/238U) ratios decrease with differentiation from parental magmas with 230Th excess toward different, silicic contaminants in secular equilibrium. On La Palma, this is inferred to reflect assimilation of small amounts of mafic wall rock. On Tenerife, both (230Th/238U) and (231Pa/235U) ratios decrease toward 1 with increasing differentiation, and this is accompanied by a subtle increase in Pb isotope ratios. At the same time, (226Ra/230Th) ratios change from &gt;1 to &lt;1 (a hitherto unreported magnitude). The Tenerife assimilant is thus constrained to be a partial melt of syenite formed in equilibrium with residual feldspar. The differences reflect a primarily deeper, more mafic magma system beneath La Palma during its late shield-building stage, whereas recent magmatic evolution at Tenerife occurs primarily at lower temperatures in small, shallower magma systems formed during its post–basaltic shield stage. Differentiation takes millennia or less.
Tracing crustal evolution by U-Th-Pb, Sm-Nd, and Lu-Hf isotopes in detrital monazite and zircon from modern rivers
Authors: Liu Xiao-Chi , Wu Yuan-Bao , Fisher Christopher M. , Hanchar John M. , Beranek Luke , Gao Shan , Wang Hao 
Published: December 2016

Abstract
Detrital zircon U-Pb age and Hf isotope studies are useful for identifying the chemical evolution of the continental crust. Zircon, however, is typically a magmatic mineral and thus often fails to document the timing of low-grade metamorphism, and its survival through multiple sedimentary cycles potentially biases the crustal evolution record toward older events. In contrast, monazite typically records metamorphic events and is less likely to survive sedimentary recycling processes, thus providing information not available by zircon. Here, we demonstrate that monazite apparently faithfully records the Sm-Nd isotope composition of the bulk rock and can therefore track the record of crustal evolution and growth, similar to Hf isotopes in zircon. We examine the utility of detrital zircon and monazite for studies of crustal evolution through a comparison of age and tracer isotope information using sediments from two large rivers draining the South China block (SCB). Monazite and zircon grains yield mostly Mesozoic and Paleozoic U-Pb ages and depleted mantle model age peaks at ca. 1900–1300 Ma, indicating that both minerals preserve similar, yet critical, information on the crustal evolution of the catchment area. In contrast, zircon yields abundant Neoproterozoic and older U-Pb ages with a very large spread of model ages, preserving a history strongly skewed to older ages. Based on the lack of known rocks of this age in the catchments, ancient zircon was likely sourced from sedimentary rocks within the catchment area. This combined data set presents a more complete history of crustal evolution and growth in the SCB and demonstrates the advantages of an integrated approach that includes both detrital monazite and zircon.
Doctors' perspectives on PSA testing illuminate established differences in prostate cancer screening rates between Australia and the UK: a qualitative study
Authors: Pickles Kristen , Carter Stacy M , Rychetnik Lucie , Entwistle Vikki A 
Published: December 2016

ObjectivesTo examine how general practitioners (GPs) in the UK and GPs in Australia explain their prostate-specific antigen (PSA) testing practices and to illuminate how these explanations are similar and how they are different.DesignA grounded theory study.SettingPrimary care practices in Australia and the UK.Participants69 GPs in Australia (n=40) and the UK (n=29). We included GPs of varying ages, sex, clinical experience and patient populations. All GPs interested in participating in the study were included.ResultsGPs' accounts revealed fundamental differences in whether and how prostate cancer screening occurred in their practice and in the broader context within which they operate. The history of prostate screening policy, organisational structures and funding models appeared to drive more prostate screening in Australia and less in the UK. In Australia, screening processes and decisions were mostly at the discretion of individual clinicians, and varied considerably, whereas the accounts of UK GPs clearly reflected a consistent, organisationally embedded approach based on local evidence-based recommendations to discourage screening.ConclusionsThe GP accounts suggested that healthcare systems, including historical and current organisational and funding structures and rules, collectively contribute to how and why clinicians use the PSA test and play a significant role in creating the mindlines that GPs employ in their clinic. Australia's recently released consensus guidelines may support more streamlined and consistent care. However, if GP mindlines and thus routine practice in Australia are to shift, to ultimately reduce unnecessary or harmful prostate screening, it is likely that other important drivers at all levels of the screening process will need to be addressed.
The active bacterial assemblages of the upper GI tract in individuals with and without Helicobacter infection
Authors: Schulz Christian , Schütte Kerstin , Koch Nadine , Vilchez-Vargas Ramiro , Wos-Oxley Melissa L , Oxley Andrew P A , Vital Marius , Malfertheiner Peter , Pieper Dietmar H 
Published: December 2016

ObjectivePatients infected with Helicobacter pylori develop chronic gastritis with a subgroup progressing to further complications. The role of microbiota from the oral cavity swallowed with saliva and either transiting the stomach or persisting in the gastric mucosa is uncertain. It is also not known whether the bacterial community differs in luminal and mucosal niches. A key question is whether H. pylori influences the bacterial communities of gastroduodenal niches.DesignSaliva, gastric and duodenal aspirates as well as gastric and duodenal biopsies were collected during oesophagogastroduodenoscopy from 24 patients (m:9, f:15, mean age 52.2±SD 14.5 years). RNA was extracted and the V1–V2 region of the retrotranscribed bacterial 16S rRNA amplified and sequenced on the Illumina MiSeq platform.ResultsOverall, 687 bacterial phylotypes that belonged to 95 genera and 11 phyla were observed. Each individual comprised a unique microbiota composition that was consistent across the different niches. However, the stomach fluid enriched for specific microbiota components. Helicobacter spp were shown to dominate the mucosa-associated community in the stomach, and to significantly influence duodenal and oral communities.ConclusionsThe detailed analysis of the active global bacterial communities from the five distinct sites of the upper GI tract allowed for the first time the differentiation between host effects and the influence of sampling region on the bacterial community. The influence of Helicobacter spp on the global community structures is striking.
Staged carotid artery angioplasty and stenting for patients with high-grade carotid stenosis with high risk of developing hyperperfusion injury: a retrospective analysis of 44 cases
Authors: Mo Dapeng , Luo Gang , Wang Bo , Ma Ning , Gao Feng , Sun Xuan , Xu Xiaotong , Miao Zhongrong 
Published: December 2016

BackgroundHyperperfusion syndrome (HPS) is a rare but potentially a life-threatening complication after carotid artery angioplasty and stenting (CAS). Staged CAS has been an alternative to prevent HPS.Materials and methods44 of 908 patients with high-grade internal carotid artery stenosis or near occlusion were at risk of HPS because of poor collateral flow and impaired cerebral blood flow (CBF). They were treated with first (stage 1), followed by a full CAS (stage 2) 1 month later. Their 30-day outcomes were tabulated and analysed.ResultsDuring follow-up, 1 of the 44 (2.2%) patients developed HPS immediately, 3 (7%) had postprocedural HPS (ie, transcranial Doppler (TCD) >120%) without clinical symptoms and 3 (7%) required stenting at stage 1 for carotid dissections. After stage 1, there were significant improvement between the preprocedural and postprocedural CBF (0.98±0.06 vs 0.85±0.05, p<0.05), mean transit time (MTT; 1.05±0.05 vs 1.15±0.05, p<0.05), time to peak (TTP; 1.04±0.06 vs 1.20±0.06, p<0.05) on CT perfusion (CTP), and CBF (66.41±7.41 vs 44.44±6.43, p<0.05) on TCD. After stage 2, improvement was seen in CBF (1.01±0.07 vs 0.98±0.06, p<0.05), MTT (1.01±0.05 vs 1.05±0.05, p<0.05), TTP (0.99±0.06 vs 1.04±0.06, p<0.05) on CTP and CBF (66.41±7.41 vs 93.78±18.81, p<0.05) on TCD. 2 had postoperative increase of middle cerebral artery mean flow velocity of 120% after stage 2 without clinical symptoms.ConclusionStaged carotid artery stenting probably decreased the chance of developing HPS in this group of selected patients. Although requiring a 2-step intervention, staged CAS may be a safe and effective alternative.
Cosmological consequences of a variable cosmological constant model
Authors: Azri Hemza , Bounames A. 
Published: December 2016

We derive a model of dark energy which evolves with time via the scale factor. The equation-of-state is studied as a function of a parameter [Formula: see text] introduced in this model as [Formula: see text]. In addition to the recent accelerated expansion, the model predicts another decelerated phase. These two phases are studied via the parameter [Formula: see text]. The age of the universe is found to be almost consistent with the observation. In the limiting case, the cosmological constant model, we find that vacuum energy gravitates with a tiny gravitational constant which evolves with the scale factor, rather than with Newton’s constant. This enables degravitation of the vacuum energy which in turn produces the tiny observed curvature, rather than a 120 orders of magnitude larger value.
GPU-Accelerated Generation of Correctly Rounded Elementary Functions
Authors: Fortin Pierre , Gouicem Mourad , Graillat Stef 
Published: December 2016

The IEEE 754-2008 standard recommends the correct rounding of some elementary functions. This requires solving the Table Maker’s Dilemma (TMD), which implies a huge amount of CPU computation time. In this article, we consider accelerating such computations, namely the Lefèvre algorithm on graphics processing units (GPUs), which are massively parallel architectures with a partial single instruction, multiple data execution.
We first propose an analysis of the Lefèvre hard-to-round argument search using the concept of continued fractions. We then propose a new parallel search algorithm that is much more efficient on GPUs thanks to its more regular control flow. We also present an efficient hybrid CPU-GPU deployment of the generation of the polynomial approximations required in the Lefèvre algorithm. In the end, we manage to obtain overall speedups up to 53.4 × on one GPU over a sequential CPU execution and up to 7.1 × over a hex-core CPU, which enable a much faster solution of the TMD for the double-precision format.