bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galactofuranose in Mycoplasma mycoides is important for membrane integrity and conceals adhesins but does not contribute to serum resistance
Authors: Schieck Elise , Lartigue Carole , Frey Joachim , Vozza Nicolas , Hegermann Jan , Miller Rachel A. , Valguarnera Ezequiel , Muriuki Cecilia , Meens Jochen , Nene Vish , Naessens Jan , Weber Johann , Lowary Todd L. , Vashee Sanjay , Feldman Mario F. , Jores Joerg 
Published: September 2015

SummaryMycoplasma mycoides subsp. capri (Mmc) and subsp. mycoides (Mmm) are important ruminant pathogens worldwide causing diseases such as pleuropneumonia, mastitis and septicaemia. They express galactofuranose residues on their surface, but their role in pathogenesis has not yet been determined. The M. mycoides genomes contain up to several copies of the glf gene, which encodes an enzyme catalysing the last step in the synthesis of galactofuranose. We generated a deletion of the glf gene in a strain of Mmc using genome transplantation and tandem repeat endonuclease coupled cleavage (TREC) with yeast as an intermediary host for the genome editing. As expected, the resulting YCp1.1‐Δglf strain did not produce the galactofuranose‐containing glycans as shown by immunoblots and immuno‐electronmicroscopy employing a galactofuranose specific monoclonal antibody. The mutant lacking galactofuranose exhibited a decreased growth rate and a significantly enhanced adhesion to small ruminant cells. The mutant was also ‘leaking’ as revealed by a β‐galactosidase‐based assay employing a membrane impermeable substrate. These findings indicate that galactofuranose‐containing polysaccharides conceal adhesins and are important for membrane integrity. Unexpectedly, the mutant strain showed increased serum resistance.
In vivo recruitment analysis and a mutant strain without any group 2 σ factor reveal roles of different σ factors in cyanobacteria
Authors: Koskinen Satu , Hakkila Kaisa , Gunnelius Liisa , Kurkela Juha , Wada Hajime , Tyystjärvi Taina 
Published: September 2015

SummaryIn eubacteria, replacement of one σ factor in the RNA polymerase (RNAP) holoenzyme by another one changes the transcription pattern. Cyanobacteria are eubacteria characterized by oxygenic photosynthesis, and they typically encode numerous group 2 σ factors that closely resemble the essential primary σ factor. A mutant strain of the model cyanobacterium Synechocystis sp. PCC 6803 without functional group 2 σ factors (named as ΔsigBCDE) could not acclimate to heat, high salt or bright light stress, but in standard conditions ΔsigBCDE grew only 9% slower than the control strain. One‐fifth of the genes in ΔsigBCDE was differently expressed compared with the control strain in standard growth conditions and several physiological changes in photosynthesis, and pigment and lipid compositions were detected. To directly analyze the σ factor content of RNAP holoenzyme in vivo, a His‐tag was added to the γ subunit of RNAP in Synechocystis and RNAPs were collected. The results revealed that all group 2 σ factors were recruited by RNAP in standard conditions, but recruitment of SigB and SigC increased in heat stress, SigD in bright light, SigE in darkness and SigB, SigC and SigE in high salt, explaining the poor acclimation of ΔsigBCDE to these stress conditions.
PepO, a CovRS‐controlled endopeptidase, disrupts Streptococcus pyogenes quorum sensing
Authors: Wilkening Reid V. , Chang Jennifer C. , Federle Michael J. 
Published: September 2015

SummaryGroup A Streptococcus (GAS, Streptococcus pyogenes) is a human‐restricted pathogen with a capacity to both colonize asymptomatically and cause illnesses ranging from pharyngitis to necrotizing fasciitis. An understanding of how and when GAS switches between genetic programs governing these different lifestyles has remained an enduring mystery and likely requires carefully tuned environmental sensors to activate and silence genetic schemes when appropriate. Herein, we describe the relationship between the Control of Virulence (CovRS, CsrRS) two‐component system and the Rgg2/3 quorum‐sensing pathway. We demonstrate that responses of CovRS to the stress signals Mg2+ and a fragment of the antimicrobial peptide LL‐37 result in modulated activity of pheromone signaling of the Rgg2/3 pathway through a means of proteolysis of SHP peptide pheromones. This degradation is mediated by the cytoplasmic endopeptidase PepO, which is the first identified enzymatic silencer of an RRNPP‐type quorum‐sensing pathway. These results suggest that under conditions in which the virulence potential of GAS is elevated (i.e. enhanced virulence gene expression), cellular responses mediated by the Rgg2/3 pathway are abrogated and allow individuals to escape from group behavior. These results also indicate that Rgg2/3 signaling is instead functional during non‐virulent GAS lifestyles.
Genetic dissection of the relationship between plant architecture and yield component traits in soybean (Glycine max) by association analysis across multiple environments
Authors: Zhang Huairen , Hao Derong , Sitoe Hélder Manuel , Yin Zhitong , Hu Zhenbin , Zhang Guozheng , Yu Deyue 
Published: September 2015

AbstractPlant architecture and yield components are critical for the determination of seed yield in soybean. In this study, we performed genetic association analysis to dissect the relationships between plant architecture and yield component traits. Two hundred and nineteen accessions were employed, and eight agronomic traits were evaluated in six environments. Our results revealed strong positive correlations of plant architecture traits with yield components and the significant association of 4 SNPs with plant architecture traits and of 7 SNPs with yield component traits in two or more environments. Eight SNPs were co‐associated with two traits. Based on the phenotypic effects of the alleles of the detected SNPs, the best alleles were mined for twenty‐three distinct SNPs. Fifteen typical carrier materials harbouring the best allele effects were also mined. Twenty parental combinations were proposed by pyramiding possible alleles per SNP in one individual (excluding possible epistatic effects). These proposed combinations with the best alleles and carrier materials will aid in the improvement of targeted traits and marker‐assisted selection (MAS) efficiency in soybean breeding.
A comparative analysis of four internationally traded farmed seafood commodities in China: domestic and international markets as key drivers
Authors: Zhang Wenbo , Murray Francis J. , Liu Liping , Little David C. 
Published: September 2015

AbstractThe historical development, current status and development trends of four internationally traded farmed seafood commodities, tilapia, penaeid shrimp, macrobrachium prawns and catfish in China were reviewed. China is the world's largest producer of tilapia, penaeid shrimp and macrobrachium prawns but, although farming of channel catfish and some indigenous catfish species is well developed, striped catfish failed to become established. In terms of global exports, China ranks first for tilapia and third for shrimp, while macrobrachium prawns and catfish mainly support domestic markets. Endogenous, biological characteristics and market demand explain the different courses of development and the differentiated focus on domestic and international trade. Tilapia and whiteleg shrimp production illustrated rapid growth in both domestic and international markets based on their favourable culture characteristics and well‐developed management systems. Huge production scale and domestic competition have resulted in China attaining a dominant and highly competitive position in the global tilapia market. High value of live freshwater prawns in local markets (and poor processing yield) has limited interest in exports, and local demand is also shifting the emphasis of shrimp production towards domestic markets, and a decline in its international market led to stagnation of channel catfish. Poor tolerance of seasonally low temperatures has restricted tilapia production to south China and completely inhibited the development of striped catfish as a commercial species. Live fish preference and costs of long‐distance transportation have restricted domestic consumption of tilapia. A balance between domestic consumption and export is required to optimise future growth opportunities for the industry.
False memories in Lewy‐body disease
Authors: Algarabel Salvador , Pitarque Alfonso , Sales Alicia , Meléndez Juan Carlos , Escudero Joaquín 
Published: September 2015

Recently, de Boysson, Belleville, Phillips et al. (2011) found that patients with Lewy‐body disease (LBD) showed significantly lower rates of false memories than healthy controls, using the Deese–Roediger–McDermott (DRM) experimental procedure. Given that this result could be explained by the practically null rate of true recognition in the LBD group (0.09), we decided to replicate the study by de Boysson et al. (2011), but including a new condition that would maximize the true recognition rate (and analyze its effect on the rate of false memories). Specifically, in a DRM experiment, we manipulated (within subjects) two study and recognition conditions: in the “immediate” condition, both the LBD patients and the control group of healthy older people received a different recognition test after each study list (containing twelve words associated with a non‐presented critical word), while in the “delayed” condition (similar to the one in de Boysson et al., 2011), the participants received the entire series of study lists and then took only one recognition test. The results showed that, in both samples, the “immediate” condition produced higher corrected rates of both true and false recognition than the “delayed” condition, although they were both lower in the LBD patients, which shows that these patients are capable of encoding and recognizing the general similitude underlying information (gist memory) in the right conditions.
Extent, frequency and rate of water erosion of arable land in Britain – benefits and challenges for modelling
Authors: Evans R. , Collins A. L. , Foster I. D. L. , Rickson R. J. , Anthony S. G. , Brewer T. , Deeks L. , Newell‐Price J. P. , Truckell I. G. , Zhang Y 
Published: September 2015

AbstractSoil erosion on arable land in lowland Britain has been the subject of field‐based surveys, which have assessed the volumes or masses of soil transported in channels across farmers’ fields. These surveys provide a unique database on the extent, frequency and rates of soil loss by water. This study synthesizes the key findings from those surveys and underscores the implications for soil erosion modelling. Rill erosion occurs in a small number of fields (consistently <10%). Over ~5 yr, a considerable proportion of the farmed landscape will suffer from rill erosion, but mostly in fields that erode only once. Mean erosion rates for lowland arable landscapes are much less than mean erosion rates for individual eroded fields within that landscape. These observations pose important challenges for modelling. Rainfall and cropping vary from year to year so that risk of wash or rill erosion in the same field also varies. Due to the infrequent occurrence of rill erosion, loss rates of eroding fields cannot be spatially extrapolated across the landscape, except in the case of wash erosion which takes place a number of times in almost all fields every year. A consistent pattern of increasing wash erosion, in terms of spatial extent, is emerging in lowland Britain. Resulting losses of fine silt and clay‐sized particles are small in amount and possibly insignificant in terms of loss of soil as a resource, but have significant implications for contaminant concentrations and pollution of water courses.
Inferring autogenically induced depositional discontinuities from observations on experimental deltaic shoreline trajectories
Authors: Mikeš Daniel , ten Veen Johan H. , Postma George , Steel Ronald 
Published: September 2015

AbstractPalaeo shoreline is a commonly used proxy for palaeo sea level, but only if deposition is continuous and constant will shoreline trajectory T(l) completely capture sea‐level time‐series E(t). Artificial deltas were generated in the Eurotank flume facility under stepwise tectonic subsidence, periodic sea‐level fluctuation and two periodic water‐discharge scenarios, one in‐phase and the other out‐of‐phase with sea level. Independent input variables tectonic subsidence Y, sea level E and water discharge Q (controlling sediment supply S) were varied and dependent output variable shoreline trajectory T was monitored. These experiments confirm that deposition is discontinuous even for continuous sediment supply, and this hinders the inference of sea‐level curve from shoreline trajectory. These results justify the here‐developed methodology for converting shoreline trajectory from the space domain to the time domain, thereby improving the accuracy of the inferred sea‐level curve.
Validation of new real‐time polymerase chain reaction assays for detection of hepatitis A virus RNA and parvovirus B19 DNA
Authors: Molenaar‐de Backer Marijke W.A. , de Waal Mirjam , Sjerps Margret C. , Koppelman Marco H.G.M. 
Published: September 2015

BACKGROUNDTo meet European guidelines for plasma for fractionation, plasma fractionators have implemented parvovirus B19 (B19V) and hepatitis A virus (HAV) nucleic acid test (NAT) screening on test pools. In this study we evaluate recently developed in‐house NAT assays for B19V DNA and HAV RNA. The B19V NAT was designed to target two different regions of the B19V genome.STUDY DESIGN AND METHODSThe B19V DNA and HAV RNA tests were validated according to commonly used guidelines. The performance of the B19V and HAV assays was evaluated during routine screening of more than 2 × 106 donations.RESULTSThe 95% lower limit of detection (LLD) of the HAV NAT was 1.34 IU/mL. The 95% LLD for B19V was 39.1 IU/mL for the NS1 region and 76.9 IU/mL for the VP2 region. The B19V test showed good accuracy, precision, robustness, and no cross‐contamination was observed. Both assays detected B19V Genotypes 1 to 3 and HAV Genotypes I to III. During routine screening 103 donations showed B19V DNA loads of more than 1.25 × 106 IU/mL and one donation was reactive in the HAV NAT.CONCLUSIONThe dual‐target B19V polymerase chain reaction (PCR) showed good accuracy (<0.1 log IU/mL) at the crucial concentration of 10 IU/µL for the NS1 and the VP2 region of the B19V genome and detected all known genotypes with similar sensitivity for each genotype. In addition, the dual target format reduces the chance that molecular variants of B19V are wrongly quantified. The HAV RNA assay showed high sensitivity for Genotypes I to III. Both new PCR assays have been successfully introduced for plasma screening in test pools of 480 or 96 donations.
Utility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance
Authors: Holmes Anne , Allison Lesley , Ward Melissa , Dallman Timothy J. , Clark Richard , Fawkes Angie , Murphy Lee , Hanson Mary 
Published: September 2015

ABSTRACT

Detailed laboratory characterization of
Escherichia coli
O157 is essential to inform epidemiological investigations. This study assessed the utility of whole-genome sequencing (WGS) for outbreak detection and epidemiological surveillance of
E. coli
O157, and the data were used to identify discernible associations between genotypes and clinical outcomes. One hundred five
E. coli
O157 strains isolated over a 5-year period from human fecal samples in Lothian, Scotland, were sequenced with the Ion Torrent Personal Genome Machine. A total of 8,721 variable sites in the core genome were identified among the 105 isolates; 47% of the single nucleotide polymorphisms (SNPs) were attributable to six “atypical”
E. coli
O157 strains and included recombinant regions. Phylogenetic analyses showed that WGS correlated well with the epidemiological data. Epidemiological links existed between cases whose isolates differed by three or fewer SNPs. WGS also correlated well with multilocus variable-number tandem repeat analysis (MLVA) typing data, with only three discordant results observed, all among isolates from cases not known to be epidemiologically related. WGS produced a better-supported, higher-resolution phylogeny than MLVA, confirming that the method is more suitable for epidemiological surveillance of
E. coli
O157. A combination of
in
silico
analyses (VirulenceFinder, ResFinder, and local BLAST searches) were used to determine
stx
subtypes, multilocus sequence types (15 loci), and the presence of virulence and acquired antimicrobial resistance genes. There was a high level of correlation between the WGS data and our routine typing methods, although some discordant results were observed, mostly related to the limitation of short sequence read assembly. The data were used to identify sublineages and clades of
E. coli
O157, and when they were correlated with the clinical outcome data, they showed that one clade, Ic3, was significantly associated with severe disease. Together, the results show that WGS data can provide higher resolution of the relationships between
E. coli
O157 isolates than that provided by MLVA. The method has the potential to streamline the laboratory workflow and provide detailed information for the clinical management of patients and public health interventions.
Haemophilus influenzae with Non-Beta-Lactamase-Mediated Beta-Lactam Resistance: Easy To Find but Hard To Categorize
Authors: Skaare Dagfinn , Lia Astrid , Hannisdal Anja , Tveten Yngvar , Matuschek Erika , Kahlmeter Gunnar , Kristiansen Bjørn-Erik 
Published: September 2015

ABSTRACT

Haemophilus influenzae
is a major pathogen, and beta-lactams are first-line drugs. Resistance due to altered penicillin-binding protein 3 (rPBP3) is frequent, and susceptibility testing of such strains is challenging. A collection of 154 beta-lactamase-negative isolates with a large proportion of rPBP3 (67.5%) was used to evaluate and compare Etest (
Haemophilus
test medium [HTM]) and disk diffusion (EUCAST method) for categorization of susceptibility to aminopenicillins and cefuroxime, using MICs generated with broth (HTM) microdilution and clinical breakpoints from CLSI and EUCAST as the gold standards. In addition, the proficiency of nine disks in screening for the rPBP3 genotype (N526K positive) was evaluated. By Etest, both essential and categorical agreement were generally poor (<70%), with high very major errors (VME) (CLSI, 13.0%; EUCAST, 34.3%) and falsely susceptible rates (FSR) (CLSI, 87.0%; EUCAST, 88.3%) for ampicillin. Ampicillin (2 μg) with adjusted (+2 mm) zone breakpoints was superior to Etest for categorization of susceptibility to ampicillin (agreement, 74.0%; VME, 11.0%; FSR, 28.3%). Conversely, Etest was superior to 30 μg cefuroxime for categorization of susceptibility to cefuroxime (agreement, 57.1% versus 60.4%; VME, 2.6% versus 9.7%; FSR, 7.1% versus 26.8%). Benzylpenicillin (1 unit) (EUCAST screening disk) and cefuroxime (5 μg) identified rPBP3 isolates with highest accuracies (95.5% and 92.2%, respectively). In conclusion, disk screening reliably detects rPBP3
H. influenzae
, but false ampicillin susceptibility is frequent with routine methods. We suggest adding a comment recommending high-dose aminopenicillin therapy or the use of other agents for severe infections with screening-positive isolates that are susceptible to aminopenicillins by gradient or disk diffusion.
Significance of a Positive Toxoplasma Immunoglobulin M Test Result in the United States
Authors: Dhakal Reshika , Gajurel Kiran , Pomares Christelle , Talucod Jeanne , Press Cynthia J. , Montoya Jose G. 
Published: September 2015

ABSTRACT

A positive
Toxoplasma
immunoglobulin M (IgM) result is often interpreted as a marker of an acute infection. However, IgM can persist for several years, and
Toxoplasma
commercial IgM diagnostic test kits can yield a number of false-positive results. For these reasons, a chronic
Toxoplasma
infection can be erroneously classified as an acute infection, resulting in serious adverse consequences, especially in pregnant women, leading to emotional distress and unnecessary interventions, including termination of pregnancy. Interpretation of
Toxoplasma
serology at a reference laboratory can help differentiate a recently acquired infection from a chronic infection. Serological test results for 451 patients with positive
Toxoplasma
IgM and IgG test results obtained at nonreference laboratories (NRLs) that were referred to Palo Alto Medical Foundation Toxoplasma Serology Laboratory (PAMF-TSL) to determine whether the patient was acutely or chronically infected were retrospectively reviewed. PAMF-TSL results established that of the 451 patients, 335 (74%) had a chronic infection, 100 (22%) had an acute infection, and 7 (2%) were not infected, and for 9 (2%), results were indeterminate. Positive
Toxoplasma
IgM and IgG test results obtained at NRLs cannot accurately distinguish between acute and chronic infections. To do so, testing at reference laboratories is required, as mandated in 1997 in a letter from the Food and Drug Administration (FDA) to clinicians and laboratories in the United States.
Optimal Cutoff Titers for Indirect Immunofluorescence Assay for Diagnosis of Scrub Typhus
Authors: Lim Cherry , Blacksell Stuart D. , Laongnualpanich Achara , Kantipong Pacharee , Day Nicholas P. J. , Paris Daniel H. , Limmathurotsakul Direk 
Published: September 2015

ABSTRACT
We determined the optimal cutoff titers in admission and convalescent-phase samples for scrub typhus indirect immunofluorescence assay using Bayesian latent class models. Cutoff titers of ≥1:3,200 in an admission sample or of a ≥4-fold rise to ≥1:3,200 in a convalescent-phase sample provided the highest accuracy (sensitivity, 81.6%; specificity, 100%).
Comparing Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Phenotypic and Molecular Methods for Identification of Species within the Streptococcus anginosus Group
Authors: Arinto-Garcia Raquel , Pinho Marcos Daniel , Carriço João André , Melo-Cristino José , Ramirez Mário 
Published: September 2015

ABSTRACT

The heterogeneity of members of the
Streptococcus anginosus
group (SAG) has traditionally hampered their correct identification. Recently, the group was subdivided into 6 taxa whose prevalence among human infections is poorly described. We evaluated the accuracy of the Rapid ID32 Strep test, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and a PCR multiplex method to identify 212 SAG isolates recovered from human infections to the species and subspecies level by using multilocus sequence analysis (MLSA) as the gold standard. We also determined the antimicrobial susceptibilities of the isolates. Representatives of all SAG taxa were found among our collection. MALDI-TOF MS and the Rapid ID32 Strep test correctly identified 92% and 68% of the isolates to the species level, respectively, but showed poor performance at the subspecies level, and the latter was responsible for major identification errors. The multiplex PCR method results were in complete agreement with the MLSA identifications but failed to distinguish the subspecies
Streptococcus constellatus
subsp.
pharyngis
and
S. constellatus
subsp.
viborgensis
. A total of 145 MLSA sequence types were present in our collection, indicating that within each taxon a number of different lineages are capable of causing infection. Significant antibiotic resistance was observed only to tetracycline, erythromycin, and clindamycin and was present in most taxa. MALDI-TOF MS is a reliable method for routine SAG species identification, while the need for identification to the subspecies level is not clearly established.