bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”
Authors: Lang Kristina , Schuldes Jörg , Klingl Andreas , Poehlein Anja , Daniel Rolf , Brune Andreas 
Published: December 2014

ABSTRACT

The recently discovered seventh order of methanogens, the
Methanomassiliicoccales
(previously referred to as “
Methanoplasmatales
”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “
Candidatus
Methanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “
Ca
. Methanoplasma termitum” lacks the entire pathway for CO
2
reduction to methyl coenzyme M and produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates that
Methanomassiliicoccales
employ a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophic
Methanosphaera stadtmanae
. Instead, all strains possess a novel complex that is related to the F
420
:methanophenazine oxidoreductase (Fpo) of
Methanosarcinales
but lacks an F
420
-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog in
Methanosaeta thermophila
. Since all
Methanomassiliicoccales
also lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), we propose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin:heterodisulfide oxidoreductase. The dual function of heterodisulfide in
Methanomassiliicoccales
, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.
Individual Predisposition to Staphylococcus aureus Colonization in Pigs on the Basis of Quantification, Carriage Dynamics, and Serological Profiles
Authors: Espinosa-Gongora Carmen , Dahl Jan , Elvstrøm Anders , van Wamel Willem J. , Guardabassi Luca 
Published: December 2014

ABSTRACT

Previous research on
Staphylococcus aureus
in pigs focused on livestock-associated methicillin-resistant
S. aureus
(MRSA) and had a qualitative cross-sectional design. This study aimed to elucidate the frequency, load, and stability of
S. aureus
nasal carriage in pigs over time and investigated possible associations between carriage and immune response. Nasal swabs were collected three times weekly from 480 tagged adult pigs in 20 Danish production farms.
S. aureus
and MRSA were quantified on selective media by the most-probable-number method. The levels of IgG against 10
S. aureus
antigens in serum were quantified in selected pigs by a Luminex assay. All the farms were positive for
S. aureus
and 15 for MRSA, leading to overall prevalences of persistent and intermittent carriers and noncarriers of 24, 52, and 23%, respectively. Carriage frequency and nasal loads were significantly higher on MRSA-positive farms. Logistic-regression modeling revealed the presence of individual pigs characterized by high nasal loads (≥10,000 CFU per swab) and stable carriage regardless of farm- and pen-associated factors. On the other hand, the humoral response was strongly influenced by these environmental factors. The existence of a minority of shedders contributing to maintenance of
S. aureus
within farms opens up new perspectives on the control of MRSA in pig farming.
Novel Phage Group Infecting Lactobacillus delbrueckii subsp. lactis, as Revealed by Genomic and Proteomic Analysis of Bacteriophage Ldl1
Authors: Casey Eoghan , Mahony Jennifer , Neve Horst , Noben Jean-Paul , Dal Bello Fabio , van Sinderen Douwe 
Published: December 2014

ABSTRACT

Ldl1 is a virulent phage infecting the dairy starter
Lactobacillus delbrueckii
subsp.
lactis
LdlS. Electron microscopy analysis revealed that this phage exhibits a large head and a long tail and bears little resemblance to other characterized phages infecting
Lactobacillus delbrueckii
.
In vitro
propagation of this phage revealed a latent period of 30 to 40 min and a burst size of 59.9 ± 1.9 phage particles. Comparative genomic and proteomic analyses showed remarkable similarity between the genome of Ldl1 and that of
Lactobacillus plantarum
phage ATCC 8014-B2. The genomic and proteomic characteristics of Ldl1 demonstrate that this phage does not belong to any of the four previously recognized
L. delbrueckii
phage groups, necessitating the creation of a new group, called group e, thus adding to the knowledge on the diversity of phages targeting strains of this industrially important lactic acid bacterial species.
Transcriptomic Analysis of Temperature Responses of Aspergillus kawachii during Barley Koji Production
Authors: Futagami Taiki , Mori Kazuki , Wada Shotaro , Ida Hiroko , Kajiwara Yasuhiro , Takashita Hideharu , Tashiro Kosuke , Yamada Osamu , Omori Toshiro , Kuhara Satoru , Goto Masatoshi 
Published: December 2014

ABSTRACT

The koji mold
Aspergillus kawachii
is used for making the Japanese distilled spirit shochu. During shochu production,
A. kawachii
is grown in solid-state culture (koji) on steamed grains, such as rice or barley, to convert the grain starch to glucose and produce citric acid. During this process, the cultivation temperature of
A. kawachii
is gradually increased to 40°C and is then lowered to 30°C. This temperature modulation is important for stimulating amylase activity and the accumulation of citric acid. However, the effects of temperature on
A. kawachii
at the gene expression level have not been elucidated. In this study, we investigated the effect of solid-state cultivation temperature on gene expression for
A. kawachii
grown on barley. The results of DNA microarray and gene ontology analyses showed that the expression of genes involved in the glycerol, trehalose, and pentose phosphate metabolic pathways, which function downstream of glycolysis, was downregulated by shifting the cultivation temperature from 40 to 30°C. In addition, significantly reduced expression of genes related to heat shock responses and increased expression of genes related with amino acid transport were also observed. These results suggest that solid-state cultivation at 40°C is stressful for
A. kawachii
and that heat adaptation leads to reduced citric acid accumulation through activation of pathways branching from glycolysis. The gene expression profile of
A. kawachii
elucidated in this study is expected to contribute to the understanding of gene regulation during koji production and optimization of the industrially desirable characteristics of
A. kawachii
.
Detection and Genomic Characterization of Motility in Lactobacillus curvatus: Confirmation of Motility in a Species outside the Lactobacillus salivarius Clade
Authors: Cousin Fabien J. , Lynch Shónagh M. , Harris Hugh M. B. , McCann Angela , Lynch Denise B. , Neville B. Anne , Irisawa Tomohiro , Okada Sanae , Endo Akihito , O'Toole Paul W. 
Published: December 2014

ABSTRACTLactobacillusis the largest genus within the lactic acid bacteria (LAB), with almost 180 species currently identified. Motility has been reported for at least 13Lactobacillusspecies, all belonging to theLactobacillus salivariusclade. Motility in lactobacilli is poorly characterized. It probably confers competitive advantages, such as superior nutrient acquisition and niche colonization, but it could also play an important role in innate immune system activation through flagellin–Toll-like receptor 5 (TLR5) interaction. We now report strong evidence of motility in a species outside theL. salivariusclade,Lactobacillus curvatus(strain NRIC 0822). The motility ofL. curvatusNRIC 0822 was revealed by phase-contrast microscopy and soft-agar motility assays. Strain NRIC 0822 was motile at temperatures between 15°C and 37°C, with a range of different carbohydrates, and under varying atmospheric conditions. We sequenced theL. curvatusNRIC 0822 genome, which revealed that the motility genes are organized in a single operon and that the products are very similar (>98.5% amino acid similarity over >11,000 amino acids) to those encoded by the motility operon ofLactobacillusacidipiscisKCTC 13900 (shown for the first time to be motile also). Moreover, the presence of a large number of mobile genetic elements within and flanking the motility operon ofL. curvatussuggests recent horizontal transfer between members of two distinctLactobacillusclades:L. acidipiscisin theL. salivariusclade andL. curvatusin theL. sakeiclade. This study provides novel phenotypic, genetic, and phylogenetic insights into flagellum-mediated motility in lactobacilli.
Global Transcriptional Response of Clostridium difficile Carrying the ϕCD38-2 Prophage
Authors: Sekulovic Ognjen , Fortier Louis-Charles 
Published: December 2014

ABSTRACT

Clostridium difficile
is one of the most dangerous pathogens in hospital settings. Most strains of
C. difficile
carry one or more prophages, and some of them, like ϕCD38-2 and ϕCD119, can influence the expression of toxin genes. However, little is known about the global host response in the presence of a given prophage. In order to fill this knowledge gap, we used high-throughput RNA sequencing (RNA-seq) to conduct a genome-wide transcriptomic analysis of the epidemic
C. difficile
strain R20291 carrying the ϕCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and phosphotransferase system (PTS) subunits involved in glucose, fructose, and glucitol/sorbitol uptake and metabolism. ϕCD38-2 also upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was that encoding the conserved phase-variable cell wall protein CwpV, which was upregulated ∼20-fold in the lysogen. Quantitative PCR and immunofluorescence showed that the increased
cwpV
expression results from a greater proportion of cells actively transcribing the gene. Indeed, ∼95% of lysogenic cells express
cwpV
, as opposed to only ∼5% of wild-type cells. Furthermore, the higher proportion of cells expressing
cwpV
results from a higher frequency of recombination of the genetic switch controlling phase variation, which we confirmed to be dependent on the host-encoded recombinase RecV. In summary, ϕCD38-2 interferes with phase variation of the surface protein CwpV and the expression of metabolic genes.
Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen
Authors: Dai Xin , Tian Yan , Li Jinting , Su Xiaoyun , Wang Xuewei , Zhao Shengguo , Liu Li , Luo Yingfeng , Liu Di , Zheng Huajun , Wang Jiaqi , Dong Zhiyang , Hu Songnian , Huang Li 
Published: December 2014

ABSTRACT

The bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for ∼1% and ∼0.1% of the total non-rRNAs, respectively. The majority (∼98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by
Ruminococcus
and
Fibrobacter
. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera
Ruminococcus
,
Prevotella
, and
Fibrobacter
. Most (∼82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera
Ruminococcus
,
Fibrobacter
, and
Prevotella
are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.
Emergence Shapes the Structure of the Seed Microbiota
Authors: Barret Matthieu , Briand Martial , Bonneau Sophie , Préveaux Anne , Valière Sophie , Bouchez Olivier , Hunault Gilles , Simoneau Philippe , Jacques Marie-Agnès 
Published: December 2014

ABSTRACTSeeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment ofgyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.
Complex Population Structure of Borrelia burgdorferi in Southeastern and South Central Canada as Revealed by Phylogeographic Analysis
Authors: Mechai S. , Margos G. , Feil E. J. , Lindsay L. R. , Ogden N. H. 
Published: December 2014

ABSTRACT

Lyme disease, caused by the bacterium
Borrelia burgdorferi
sensu stricto
, is an emerging zoonotic disease in Canada and is vectored by the blacklegged tick,
Ixodes scapularis
. Here we used Bayesian analyses of sequence types (STs), determined by multilocus sequence typing (MLST), to investigate the phylogeography of
B. burgdorferi
populations in southern Canada and the United States by analyzing MLST data from 564
B. burgdorferi
-positive samples collected during surveillance. A total of 107 Canadian samples from field sites were characterized as part of this study, and these data were combined with existing MLST data for samples from the United States and Canada. Only 17% of STs were common between both countries, while 49% occurred only in the United States, and 34% occurred only in Canada. However, STs in southeastern Ontario and southwestern Quebec were typically identical to those in the northeastern United States, suggesting a recent introduction into this region from the United States. In contrast, STs in other locations in Canada (the Maritimes; Long Point, Ontario; and southeastern Manitoba) were frequently unique to those locations but were putative descendants of STs previously found in the United States. The picture in Canada is consistent with relatively recent introductions from multiple refugial populations in the United States. These data thus point to a geographic pattern of populations of
B. burgdorferi
in North America that may be more complex than simply comprising northeastern, midwestern, and Californian groups. We speculate that this reflects the complex ecology and spatial distribution of key reservoir hosts.
Influenza Gain-of-Function Experiments: Their Role in Vaccine Virus Recommendation and Pandemic Preparedness
Authors: Schultz-Cherry S. , Webby R. J. , Webster R. G. , Kelso A. , Barr I. G. , McCauley J. W. , Daniels R. S. , Wang D. , Shu Y. , Nobusawa E. , Itamura S. , Tashiro M. , Harada Y. , Watanabe S. , Odagiri T. , Ye Z. , Grohmann G. , Harvey R. , Engelhardt O. , Smith D. , Hamilton K. , Claes F. , Dauphin G. 
Published: December 2014

Abstract
In recent years, controversy has arisen regarding the risks and benefits of certain types of gain-of-function (GOF) studies involving avian influenza viruses. In this article, we provide specific examples of how different types of data, including information garnered from GOF studies, have helped to shape the influenza vaccine production process—from selection of candidate vaccine viruses (CVVs) to the manufacture and stockpiling of safe, high-yield prepandemic vaccines for the global community. The article is not written to support a specific pro- or anti-GOF stance but rather to inform the scientific community about factors involved in vaccine virus selection and the preparation of prepandemic influenza vaccines and the impact that some GOF information has had on this process.
Socioeconomic inequalities in dental caries and their determinants in adolescents in New Delhi, India
Authors: Mathur Manu Raj , Tsakos Georgios , Millett Christopher , Arora Monika , Watt Richard 
Published: December 2014

ObjectivesTo determine whether socioeconomic inequalities are correlated to dental caries experience and decayed teeth of Indian adolescents, and assess whether behavioural and psychosocial factors mediate this association.MethodsCross-sectional study of 1386 adolescents living in three diverse areas of New Delhi. Caries experience and number of decayed teeth were assessed clinically and a questionnaire was used to gather sociodemographic and psychosocial data. Zero Inflated Negative Binomial regression models were used to assess the relationship between the outcomes (caries experience and decayed teeth) and area of residence, adjusting for covariates.ResultsSignificant inequalities in caries experience and number of decayed teeth were observed. Odds of an adolescent being caries free decreased by 66% (OR 0.34, 95% CI 0.23 to 0.49) and 70% (OR 0.30, 95% CI 0.21 to 0.43) in adolescents living in resettlement communities or urban slums, respectively, when compared with the middle class group. No difference was observed among those with caries experience/decayed teeth. Adjusting for covariates did not affect the inequalities.ConclusionsArea of residence appears to be a very strong and significant determinant for an adolescent to be caries/decay free in India. Psychosocial and behavioural factors do not mediate the association between area of residence and oral health.
Cell cycle marker expression in benign and malignant intraductal papillary lesions of the breast
Authors: Loh Seow Foong , Cooper Caroline , Selinger Christina I , Barnes Elizabeth H , Chan Charles , Carmalt Hugh , West Richard , Gluch Laurence , Beith Jane M , Caldon C Elizabeth , O'Toole Sandra 
Published: December 2014

AimsThe diagnosis of intraductal papillary lesions of the breast on core biopsy remains challenging in pathology, with most patients requiring formal surgical excision for a definitive diagnosis. The aim of this study was to determine whether a representative panel of proliferative cell cycle immunohistochemical markers (cyclin A2, cyclin B1 and cyclin D1) could improve the specificity of pathological diagnosis of these lesions.MethodsA series of 68 surgically excised intraductal papillary lesion cases were retrospectively selected, and immunohistochemistry for cyclin A2, cyclin B1 and cyclin D1 was performed.ResultsCyclin B1 (OR 1.80, 95% CI 1.01 to 3.2, p=0.046) and cyclin D1 (OR 1.13, 95% CI 1.05 to 1.22, p=0.002) expression was independently associated with a diagnosis of malignancy in papillary lesions, although expression was frequently heterogeneous and only focal. Cyclin A2 expression (OR 0.76, 95% CI 0.41 to 1.4, p=0.38) was not associated with a malignant diagnosis in multivariable logistic regression models. All three cyclins displayed high sensitivity (80%–95%) for a diagnosis of malignancy, although cyclin B1 showed a superior specificity of 72.7% compared with the low specificity of cyclins A2 and D1.ConclusionsOur study has identified for the first time that the expression of key cell cycle markers differs between benign and malignant papillary breast lesions and identified changes to the mitotic marker, cyclin B1, as particularly significant. However, given the low level and heterogeneous nature of expression of these markers, there remains a significant risk of undersampling in core biopsies and thus they are unlikely to be useful in routine clinical practice.
Changes in referral, treatment and outcomes in patients with systemic lupus erythematosus in Germany in the 1990s and the 2000s
Authors: Albrecht Katinka , Huscher Dörte , Richter Jutta , Backhaus Marina , Bischoff Sascha , Kötter Ina , Thiele Katja , Zink Angela 
Published: December 2014

ObjectiveTo evaluate trends in the referral, treatment and outcome of patients with systemic lupus erythematosus (SLE) in Germany over two decades.MethodsFrom 1993 to 2012, ∼1200 patients with SLE were recorded annually in the national database of the German Collaborative Arthritis Centres. Treatment patterns, healthcare use and outcomes, such as disease activity, function and work participation, were evaluated over time. Furthermore, two distinct cohorts of patients (enrolment 1994–1998, n=467; and 2004–2008, n=376) observed over 5 years were assessed for changes in outcomes.ResultsThe mean disease duration at the first visit to a rheumatologist decreased from 2.6 (1994) to 1.5 (2012) years. Glucocorticoids (69%), antimalarials (56%), azathioprine (22%), non-steroidal anti-inflammatory drugs (23%) and mycophenolate mofetil (15%) were the most frequently used treatments in 2012. A significant increase was observed in the use of antimalarials and mycophenolate mofetil. The use of glucocorticoids at >7.5 mg/day decreased from 27% (1994) to 10% (2012). The average length of sick leave taken due to SLE declined from 9 weeks (1997) to 6 weeks (2012). When comparing the two longitudinal cohorts, in the cohort from the 2000s, the intraindividual decline of disease activity was significantly stronger (p<0.001), and fewer patients retired early (36% vs 46%).ConclusionsThe disease activity and resource use declined considerably over the observation period, and more patients remained in the labour force. Earlier treatment onset, faster modification of the treatment regimen and more intensive use of anti-inflammatory therapy may account for the improved outcomes in patients with SLE across the years.