bluuebunny/crossref_metadata_2025 huggingface dataset:
Metatranscriptomic Evidence for Direct Interspecies Electron Transfer between Geobacter and Methanothrix Species in Methanogenic Rice Paddy Soils
Authors: Holmes Dawn E. , Shrestha Pravin M. , Walker David J. F. , Dang Yan , Nevin Kelly P. , Woodard Trevor L. , Lovley Derek R.
Published: March 2017

The possibility thatMethanothrix(formerlyMethanosaeta) andGeobacterspecies cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) ofGeobacter sulfurreducensaccounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNA sequencing (RNA-seq) libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET. Most of the e-pilin genes and transcripts were affiliated withGeobacterspecies, but sequences most closely related to putative e-pilin genes from genera such asDesulfobacterium,Deferribacter,Geoalkalibacter, andDesulfobacula, were also detected. Approximately 17% of all metagenomic and metatranscriptomic bacterial sequences clustered withGeobacterspecies, and the finding thatGeobacterspp. were actively transcribing growth-related genes indicated that they were metabolically active in the soils. Genes coding for e-pilin were among the most highly transcribedGeobactergenes. In addition, homologs of genes encoding OmcS, ac-type cytochrome associated with the e-pili ofG. sulfurreducensand required for DIET, were also highly expressed in the soils.Methanothrixspecies in the soils highly expressed genes for enzymes involved in the reduction of carbon dioxide to methane. DIET is the only electron donor known to support CO2reduction inMethanothrix. Thus, these results are consistent with a model in whichGeobacterspecies were providing electrons toMethanothrixspecies for methane production through electrical connections of e-pili.

IMPORTANCEMethanothrixspecies are some of the most important microbial contributors to global methane production, but surprisingly little is known about their physiology and ecology. The possibility that DIET is a source of electrons forMethanothrixin methanogenic rice paddy soils is important because it demonstrates that the contribution thatMethanothrixmakes to methane production in terrestrial environments may extend beyond the conversion of acetate to methane. Furthermore, defined coculture studies have suggested that whenMethanothrixspecies receive some of their energy from DIET, they grow faster than when acetate is their sole energy source. Thus,Methanothrixgrowth and metabolism in methanogenic soils may be faster and more robust than generally considered. The results also suggest that the reason thatGeobacterspecies are repeatedly found to be among the most metabolically active microorganisms in methanogenic soils is that they grow syntrophically in cooperation withMethanothrixspp., and possibly other methanogens, via DIET.
Comparison of Fecal Collection Methods for Microbiota Studies in Bangladesh
Authors: Vogtmann Emily , Chen Jun , Kibriya Muhammad G. , Chen Yu , Islam Tariqul , Eunes Mahbubul , Ahmed Alauddin , Naher Jabun , Rahman Anisur , Amir Amnon , Shi Jianxin , Abnet Christian C. , Nelson Heidi , Knight Rob , Chia Nicholas , Ahsan Habibul , Sinha Rashmi
Published: March 2017

To our knowledge, fecal microbiota collection methods have not been evaluated in low- and middle-income countries. Therefore, we evaluated five different fecal sample collection methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from the HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes. Half of the aliquots were frozen immediately at −80°C (day 0) and the remaining samples were left at ambient temperature for 96 h and then frozen (day 4). Intraclass correlation coefficients (ICC) were calculated for the relative abundances of the top three phyla, for two alpha diversity measures, and for four beta diversity measures. The duplicate samples had relatively high ICCs for technical reproducibility at day 0 and day 4 (range, 0.79 to 0.99). The FOBT card and samples preserved in RNAlater and 95% ethanol had the highest ICCs for stability over 4 days. The FIT tube had lower stability measures overall. In comparison to the “gold standard” method using immediately frozen fecal samples with no solution, the ICCs for many of the microbial metrics were low, but the rank order appeared to be preserved as seen by the Spearman correlation. The FOBT cards, 95% ethanol, and RNAlater were effective fecal preservatives. These fecal collection methods are optimal for future cohort studies, particularly in low- and middle-income countries.

IMPORTANCE
The collection of fecal samples in prospective cohort studies is essential to provide the opportunity to study the effect of the human microbiota on numerous health conditions. However, these collection methods have not been adequately tested in low- and middle-income countries. We present estimates of technical reproducibility, stability at ambient temperature for 4 days, and accuracy comparing a “gold standard” for fecal samples in no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test cards, and fecal immunochemical test tubes in a study conducted in Bangladesh. Fecal occult blood test cards and fecal samples stored in 95% ethanol or RNAlater adequately preserve fecal samples in this setting. Therefore, new studies in low- and middle-income countries should include collection of fecal samples using fecal occult blood test cards, 95% ethanol, or RNAlater for prospective cohort studies.
Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity
Authors: Bansal Kanika , Midha Samriti , Kumar Sanjeet , Patil Prabhu B.
Published: March 2017

Citrus canker, caused by
Xanthomonas citri
pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that
X. citri
pv. citri is related to many other pathovars, which can be collectively referred as
Xanthomonas citri
pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of
X. citri
species to rapidly evolve into specialized strains infecting diverse crop plants.

IMPORTANCE
Host specialization is one of the characteristic features of highly evolved pathogens such as the
Xanthomonas
group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of
Xanthomonas
strains pathogenic to diverse plants, including citrus. This group includes the oldest
Xanthomonas
pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a
Xanthomonas
lineage and perhaps will inspire careful study of the host range of the included pathovars.
The Azoarcus anaerobius 1,3-Dihydroxybenzene (Resorcinol) Anaerobic Degradation Pathway Is Controlled by the Coordinated Activity of Two Enhancer-Binding Proteins
Authors: Pacheco-Sánchez Daniel , Molina-Fuentes Águeda , Marín Patricia , Medina-Bellver Javier-I. , González-López Óscar , Marqués Silvia
Published: March 2017

The anaerobic resorcinol degradation pathway in
Azoarcus anaerobius
is unique in that it uses an oxidative rather than a reductive strategy to overcome the aromatic ring stability in degradation of this compound, in a process that is dependent on nitrate respiration. We show that the pathway is organized in five transcriptional units, three of which are inducible by the presence of the substrate. Three σ
54
-dependent promoters located upstream from the three operons coding for the main pathway enzymes were identified, which shared a similar structure with conserved upstream activating sequences (UASs) located at 103 to 111 bp from the transcription start site. Expression of the pathway is controlled by the bacterial enhancer-binding proteins (bEBPs) RedR1 and RedR2, two homologous regulators that, despite their high sequence identity (97%), have nonredundant functions: RedR2, the master regulator which also controls RedR1 expression, is itself able to promote transcription from two of the promoters, while RedR1 activity is strictly dependent on the presence of RedR2. The two regulators were shown to interact with each other, suggesting that the natural mode of activation is by forming heterodimers, which become active in the presence of the substrate after its metabolization to hydroxybenzoquinone through the pathway enzymes. The model structure of the N-terminal domain of the proteins is composed of tandem GAF and PAS motifs; the possible mechanisms controlling the activity of the regulators are discussed.

IMPORTANCE
Azoarcus anaerobius
is a strict anaerobe that is able to use 1,3-dihydroxybenzene as the sole carbon source in a process that is dependent on nitrate respiration. We have shown that expression of the pathway is controlled by two regulators of almost identical sequences: the bEBPs RedR1 and RedR2, which share 97% identity. These regulators control three promoters with similar structure. Despite their sequence identity, the two bEBPs are not redundant and are both required for maximum pathway expression. In fact, the two proteins function as heterodimers and require activation by the pathway intermediate hydroxyhydroquinone. The structure of the domain sensing the activation signal resembles that of regulators that are known to interact with other proteins.
TM0416, a Hyperthermophilic Promiscuous Nonphosphorylated Sugar Isomerase, Catalyzes Various C
5
and C
6
Epimerization Reactions
Authors: Shin Sun-Mi , Cao Thinh-Phat , Choi Jin Myung , Kim Seong-Bo , Lee Sang-Jae , Lee Sung Haeng , Lee Dong-Woo
Published: March 2017

There is currently little information on nonphosphorylated sugar epimerases, which are of potential interest for producing rare sugars. We found a gene (the TM0416 gene) encoding a putative
d
-tagatose-3-epimerase-related protein from the hyperthermophilic bacterium
Thermotoga maritima
. We overexpressed the TM0416 gene in
Escherichia coli
and purified the resulting recombinant protein for detailed characterization. Amino acid sequence alignment and a structural similarity search revealed that TM0416 is a putative nonphosphorylated sugar epimerase. The recombinant enzyme exhibited maximal C-3 epimerization of
l
-ribulose to
l
-xylulose at ∼80°C and pH 7 in the presence of 1 mM Mn
2+
. In addition, this enzyme showed unusually high activity for the epimerization of
d
-tagatose to
d
-sorbose, with a conversion yield of 20% after 6 h at 80°C. Remarkably, the enzyme catalyzed the isomerization of
d
-erythrose or
d
-threose to
d
-erythrulose significantly, with conversion yields of 71% and 54.5%, respectively, after 6 h at 80°C at pH 7. To further investigate the substrate specificity of TM0416, we determined its crystal structures in complex with divalent metal ions and
l
-erythrulose at resolutions of 1.5 and 1.6 Å. Detailed inspection of the structural features and biochemical data clearly demonstrated that this metalloenzyme, with a freely accessible substrate-binding site and neighboring hydrophobic residues, exhibits different and promiscuous substrate preferences, compared with its mesophilic counterparts. Therefore, this study suggests that TM0416 can be functionally classified as a novel type of
l
-ribulose 3-epimerase (R3E) with
d
-erythrose isomerase activity.

IMPORTANCE
Rare sugars, which occur naturally in small amounts, have attracted considerable attention in the food and drug industries. However, there is little information on nonphosphorylated sugar epimerases, which might potentially be applied for the production of rare sugars. This study describes the characterization and functional annotation of a putative nonphosphorylated sugar 3-epimerase from a hyperthermophilic bacterium. Furthermore, we determined its crystal structures in complex with divalent metal ions and
l
-erythrulose, highlighting its metal-dependent, bifunctional, sugar-isomerizing activity. This hyperthermophilic R3E exhibited
d
-erythrose/
d
-threose isomerase activity, with structural features near the substrate-binding site distinct from those of its mesophilic counterparts. Moreover, this metalloenzyme showed unusually high activity for the epimerization of
d
-tagatose to
d
-sorbose at 70°C. Therefore, TM0416 can be functionally classified as a novel type of promiscuous R3E with a potential for the production of rare sugars for the food and pharmaceutical industries.
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem
Authors: Wang Yuanqi , Hatt Janet K. , Tsementzi Despina , Rodriguez-R Luis M. , Ruiz-Pérez Carlos A. , Weigand Michael R. , Kizer Heidi , Maresca Gina , Krishnan Raj , Poretsky Rachel , Spain Jim C. , Konstantinidis Konstantinos T.
Published: March 2017

A single liter of water contains hundreds, if not thousands, of bacterial and archaeal species, each of which typically makes up a very small fraction of the total microbial community (<0.1%), the so-called “rare biosphere.” How often, and via what mechanisms, e.g., clonal amplification versus horizontal gene transfer, the rare taxa and genes contribute to microbial community response to environmental perturbations represent important unanswered questions toward better understanding the value and modeling of microbial diversity. We tested whether rare species frequently responded to changing environmental conditions by establishing 20-liter planktonic mesocosms with water from Lake Lanier (Georgia, USA) and perturbing them with organic compounds that are rarely detected in the lake, including 2,4-dichlorophenoxyacetic acid (2,4-D), 4-nitrophenol (4-NP), and caffeine. The populations of the degraders of these compounds were initially below the detection limit of quantitative PCR (qPCR) or metagenomic sequencing methods, but they increased substantially in abundance after perturbation. Sequencing of several degraders (isolates) and time-series metagenomic data sets revealed distinct cooccurring alleles of degradation genes, frequently carried on transmissible plasmids, especially for the 2,4-D mesocosms, and distinct species dominating the post-enrichment microbial communities from each replicated mesocosm. This diversity of species and genes also underlies distinct degradation profiles among replicated mesocosms. Collectively, these results supported the hypothesis that the rare biosphere can serve as a genetic reservoir, which can be frequently missed by metagenomics but enables community response to changing environmental conditions caused by organic pollutants, and they provided insights into the size of the pool of rare genes and species.

IMPORTANCEA single liter of water or gram of soil contains hundreds of low-abundance bacterial and archaeal species, the so called rare biosphere. The value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants.
Unusual Versatility of the Filamentous, Diazotrophic Cyanobacterium Anabaena torulosa Revealed for Its Survival during Prolonged Uranium Exposure
Authors: Acharya Celin , Chandwadkar Pallavi , Nayak Chandrani
Published: March 2017

Reports on interactions between cyanobacteria and uranyl carbonate are rare. Here, we present an interesting succession of the metabolic responses employed by a marine, filamentous, diazotrophic cyanobacterium,
Anabaena torulosa
for its survival following prolonged exposure to uranyl carbonate extending up to 384 h at pH 7.8 under phosphate-limited conditions. The cells sequestered uranium (U) within polyphosphates on initial exposure to 100 μM uranyl carbonate for 24 to 28 h. Further incubation until 120 h resulted in (i) significant degradation of cellular polyphosphates causing extensive chlorosis and cell lysis, (ii) akinete differentiation followed by (iii) extracellular uranyl precipitation. X-ray diffraction (XRD) analysis, fluorescence spectroscopy, X-ray absorption near edge structure (XANES), and extended X-ray absorption fine structure (EXAFS) spectroscopy established the identity of the bioprecipitated uranium as a U(VI) autunite-type mineral, which settled at the bottom of the vessel. Surprisingly,
A. torulosa
cells resurfaced as small green flakes typical of actively growing colonies on top of the test solutions within 192 to 240 h of U exposure. A consolidated investigation using kinetics, microscopy, and physiological and biochemical analyses suggested a role of inducible alkaline phosphatase activity of cell aggregates/akinetes in facilitating the germination of akinetes leading to substantial regeneration of
A. torulosa
by 384 h of uranyl incubation. The biomineralized uranium appeared to be stable following cell regeneration. Altogether, our results reveal novel insights into the survival mechanism adopted by
A. torulosa
to resist sustained uranium toxicity under phosphate-limited oxic conditions.

IMPORTANCE
Long-term effects of uranyl exposure in cyanobacteria under oxic phosphate-limited conditions have been inadequately explored. We conducted a comprehensive examination of the metabolic responses displayed by a marine cyanobacterium,
Anabaena torulosa
, to cope with prolonged exposure to uranyl carbonate at pH 7.8 under phosphate limitation. Our results highlight distinct adaptive mechanisms harbored by this cyanobacterium that enabled its natural regeneration following extensive cell lysis and uranium biomineralization under sustained uranium exposure. Such complex interactions between environmental microbes such as
Anabaena torulosa
and uranium over a broader time range advance our understanding on the impact of microbial processes on uranium biogeochemistry.
Adaptation of Salmonella enterica Serovar Senftenberg to Linalool and Its Association with Antibiotic Resistance and Environmental Persistence
Authors: Kalily Emmanuel , Hollander Amit , Korin Ben , Cymerman Itamar , Yaron Sima
Published: March 2017

A clinical isolate of
Salmonella enterica
serovar Senftenberg, isolated from an outbreak linked to the herb
Ocimum basilicum
L. (basil), has been shown to be resistant to basil oil and to the terpene alcohol linalool. To better understand how human pathogens might develop resistance to linalool and to investigate the association of this resistance with resistance to different antimicrobial agents, selective pressure was applied to the wild-type strain by sequential exposure to increasing concentrations of linalool. The results demonstrated that
S
. Senftenberg adapted to linalool with a MIC increment of at least 8-fold, which also resulted in better resistance to basil oil and better survival on harvested basil leaves. Adaptation to linalool was shown to confer cross protection against the antibiotics trimethoprim, sulfamethoxazole, piperacillin, chloramphenicol, and tetracycline, increasing their MICs by 2- to 32-fold. The improved resistance was shown to correlate with multiple phenotypes that included changes in membrane fatty acid composition, induced efflux, reduced influx, controlled motility, and the ability to form larger aggregates in the presence of linalool. The adaptation to linalool obtained
in vitro
did not affect survival on the basil phyllosphere
in planta
and even diminished survival in soil, suggesting that development of extreme resistance to linalool may be accompanied by a loss of fitness. Altogether, this report notes the concern regarding the ability of human pathogens to develop resistance to commercial essential oils, a resistance that is also associated with cross-resistance to antibiotics and may endanger public health.

IMPORTANCE
Greater consumer awareness and concern regarding synthetic chemical additives have led producers to control microbial spoilage and hazards by the use of natural preservatives, such as plant essential oils with antimicrobial activity. This report establishes, however, that these compounds may provoke the emergence of resistant human pathogens. Herein, we demonstrate the acquisition of resistance to basil oil by
Salmonella
Senftenberg. Exposure to linalool, a component of basil oil, resulted in adaptation to the basil oil mixture, as well as cross protection against several antibiotics and better survival on harvested basil leaves. Collectively, this work highlights the hazard to public health while using plant essential oils without sufficient knowledge about their influence on pathogens at subinhibitory concentrations.
A Broad-Host-Range Tailocin from Burkholderia cenocepacia
Authors: Yao Guichun W. , Duarte Iris , Le Tram T. , Carmody Lisa , LiPuma John J. , Young Ry , Gonzalez Carlos F.
Published: March 2017

The
Burkholderia cepacia
complex (Bcc) consists of 20 closely related Gram-negative bacterial species that are significant pathogens for persons with cystic fibrosis (CF). Some Bcc strains are highly transmissible and resistant to multiple antibiotics, making infection difficult to treat. A tailocin (phage tail-like bacteriocin), designated BceTMilo, with a broad host range against members of the Bcc, was identified in
B. cenocepacia
strain BC0425. Sixty-eight percent of Bcc representing 10 species and 90% of non-Bcc
Burkholderia
strains tested were sensitive to BceTMilo. BceTMilo also showed killing activity against
Pseudomonas aeruginosa
PAO1 and derivatives. Liquid chromatography-mass spectrometry analysis of the major BceTMilo proteins was used to identify a 23-kb tailocin locus in a draft BC0425 genome. The BceTMilo locus was syntenic and highly similar to a 24.6-kb region on chromosome 1 of
B. cenocepacia
J2315 (BCAL0081 to BCAL0107). A close relationship and synteny were observed between BceTMilo and
Burkholderia
phage KL3 and, by extension, with paradigm temperate myophage P2. Deletion mutants in the gene cluster encoding enzymes for biosynthesis of lipopolysaccharide (LPS) in the indicator strain
B. cenocepacia
K56-2 conferred resistance to BceTMilo. Analysis of the defined mutants in LPS biosynthetic genes indicated that an α-
d
-glucose residue in the core oligosaccharide is the receptor for BceTMilo.

IMPORTANCE
BceTMilo, presented in this study, is a broad-host-range tailocin active against
Burkholderia
spp. As such, BceTMilo and related or modified tailocins have potential as bactericidal therapeutic agents against plant- and human-pathogenic
Burkholderia
.
The patellofemoral pain and osteoarthritis subscale of the KOOS (KOOS-PF): development and validation using the COSMIN checklist
Authors: Crossley Kay M , Macri Erin M , Cowan Sallie M , Collins Natalie J , Roos Ewa M
Published: March 2017

Background

Patellofemoral pain and osteoarthritis are prevalent and associated with substantial pain and functional impairments. Patient-reported outcome measures (PROMs) are recommended for research and clinical use, but no PROMs are specific for patellofemoral osteoarthritis, and existing PROMs for patellofemoral pain have methodological limitations. This study aimed to develop a new subscale of the Knee injury and Osteoarthritis Outcome Score for patellofemoral pain and osteoarthritis (KOOS-PF), and evaluate its measurement properties.

Methods

Items were generated using input from 50 patients with patellofemoral pain and/or osteoarthritis and 14 health and medical clinicians. Item reduction was performed using data from patellofemoral cohorts (n=138). We used the COnsesus-based Standards for the selection of health Measurements INstruments guidelines to evaluate reliability, validity, responsiveness and interpretability of the final version of KOOS-PF and other KOOS subscales.

Results

From an initial 80 generated items, the final subscale included 11 items. KOOS-PF items loaded predominantly on one factor, pain during activities that load the patellofemoral joint. KOOS-PF had good internal consistency (Cronbach’s α 0.86) and adequate test–retest reliability (intraclass correlation coefficient 0.86). Hypothesis testing supported convergent, divergent and known-groups validity. Responsiveness was confirmed, with KOOS-PF demonstrating a moderate correlation with Global Rating of Change scores (r 0.52) and large effect size (Cohen’s d 0.89). Minimal detectable change was 2.3 (groups) and 16 (individuals), while minimal important change was 16.4. There were no floor or ceiling effects.

Conclusions

The 11-item KOOS-PF, developed in consultation with patients and clinicians, demonstrated adequate measurement properties, and is recommended for clinical and research use in patients with patellofemoral pain and osteoarthritis.
Stem cell injections in knee osteoarthritis: a systematic review of the literature
Authors: Pas Haiko IMFL , Winters Marinus , Haisma Hidde J , Koenis Martinus JJ , Tol Johannes L , Moen Maarten H
Published: March 2017

Objective

Stem cell injection for knee osteoarthritis (KOA) is an emerging new therapy, and we aimed to review its evidence of efficacy.

Design

Systematic review.

Eligibility criteria

Criteria for eligibility were randomised controlled trials (RCTs) and non-RCT on the efficacy of stem cell injections in KOA. All references were checked for missed articles.

Data sources

MEDLINE, EMBASE, CINAHL, Web of Science, Cochrane Library, PEDro and SPORTDiscus were searched. A grey literature search was performed. No restrictions were imposed to our search strategy.

Risk of bias and data synthesis

Risk of bias was assessed using the Cochrane risk of bias tool. Descriptive synthesis was performed using the levels of evidence according to the Oxford Levels of Evidence.

Results

Five RCTs and one non-RCT were found. Bone-marrow-derived stem cells, adipose-derived mesenchymal stem cells and peripheral blood stem cells were used. All trials were at high risk of bias, resulting in level-3 evidence. All five RCTs reported superior efficacy for patient-reported outcomes (Visual Analogue Scale, Western Ontario and McMaster Universities Arthritis Index, Tegner, Lysolm, International Knee Documentation Committee, Knee Injury and Osteoarthritis Outcome Score, Lequesne) compared with controls at final follow-up (range 24–48 months). Superior radiological outcomes were found favouring stem cell injection. Superior histological outcomes and/or improved arthroscopically scored healing rates were reported in two trials. No serious adverse events were reported.

Conclusion

Six trials with high risk of bias showed level-3 or level-4 evidence in favour of stem cell injections in KOA. In the absence of high-level evidence, we do not recommend stem cell therapy for KOA.
International criteria for electrocardiographic interpretation in athletes: Consensus statement
Authors: Drezner Jonathan A , Sharma Sanjay , Baggish Aaron , Papadakis Michael , Wilson Mathew G , Prutkin Jordan M , Gerche Andre La , Ackerman Michael J , Borjesson Mats , Salerno Jack C , Asif Irfan M , Owens David S , Chung Eugene H , Emery Michael S , Froelicher Victor F , Heidbuchel Hein , Adamuz Carmen , Asplund Chad A , Cohen Gordon , Harmon Kimberly G , Marek Joseph C , Molossi Silvana , Niebauer Josef , Pelto Hank F , Perez Marco V , Riding Nathan R , Saarel Tess , Schmied Christian M , Shipon David M , Stein Ricardo , Vetter Victoria L , Pelliccia Antonio , Corrado Domenico
Published: March 2017

Sudden cardiac death (SCD) is the leading cause of mortality in athletes during sport. A variety of mostly hereditary, structural or electrical cardiac disorders are associated with SCD in young athletes, the majority of which can be identified or suggested by abnormalities on a resting 12-lead electrocardiogram (ECG). Whether used for diagnostic or screening purposes, physicians responsible for the cardiovascular care of athletes should be knowledgeable and competent in ECG interpretation in athletes. However, in most countries a shortage of physician expertise limits wider application of the ECG in the care of the athlete. A critical need exists for physician education in modern ECG interpretation that distinguishes normal physiological adaptations in athletes from distinctly abnormal findings suggestive of underlying pathology. Since the original 2010 European Society of Cardiology recommendations for ECG interpretation in athletes, ECG standards have evolved quickly, advanced by a growing body of scientific data and investigations that both examine proposed criteria sets and establish new evidence to guide refinements. On 26–27 February 2015, an international group of experts in sports cardiology, inherited cardiac disease, and sports medicine convened in Seattle, Washington (USA), to update contemporary standards for ECG interpretation in athletes. The objective of the meeting was to define and revise ECG interpretation standards based on new and emerging research and to develop a clear guide to the proper evaluation of ECG abnormalities in athletes. This statement represents an international consensus for ECG interpretation in athletes and provides expert opinion-based recommendations linking specific ECG abnormalities and the secondary evaluation for conditions associated with SCD.
Effect of season and sunlight on viral kinetics during hepatitis C virus therapy
Authors: Hernández-Alvarez Noemi , Pascasio Acevedo Juan Manuel , Quintero Enrique , Fernández Vázquez Inmaculada , García-Eliz María , de la Revilla Negro Juan , Crespo García Javier , Hernández-Guerra Manuel
Published: March 2017

Background and aims

Rapid viral response (RVR) during antiviral treatment for hepatitis C virus (HCV) predicts sustained viral response (SVR). Recently, vitamin D levels have been associated with SVR. As sunlight is the most important source of vitamin D and shows seasonal variation, we evaluated the effect of season on viral kinetics during peginterferon/ribavirin-based therapy for HCV.

Methods

Consecutive HCV patients treated with peginterferon/ribavirin and boceprevir/ telaprevir (June 2011–July 2014) were included. Patients were grouped according to season when therapy was initiated (Season A: May–October and Season B: November–April) depending on hours of daily sunlight. Multiple logistic regression analysis included factors known to influence SVR to treatment. The dependent variables were undetectable viral load (VL) or VL ≤15 UI/mL (VL ≤15) at weeks 4, 8 and 12, end of treatment and SVR.

Results

The study included 930 patients (66.8% men; median 54 years) treated with telaprevir (n=537) or boceprevir, without (n=481) or with lead-in therapy of peginterferon/ribavirin. Baseline characteristics of patients in Season A (45.3%, n=421) and Season B groups were similar. Overall, a higher rate of RVR (23.5% vs 16.1%, p=0.005) and VL ≤15 (51.0% vs 38.6%, p≤0.001) was observed in patients starting treatment during Season A versus Season B. By logistic regression analysis, initiating treatment in Season A proved to be an independent predictor of RVR and VL ≤15.

Conclusions

In our setting, seasonality affects viral kinetics in HCV genotype 1 patients treated with peginterferon/ribavirin-based therapy. Our findings support the hypothesis that vitamin D influences viral response to peginterferon/ribavirin-based therapy.
Reducing depressive symptoms after the Great East Japan Earthquake in older survivors through group exercise participation and regular walking: a prospective observational study
Authors: Tsuji Taishi , Sasaki Yuri , Matsuyama Yusuke , Sato Yukihiro , Aida Jun , Kondo Katsunori , Kawachi Ichiro
Published: March 2017

Objectives

Survivors of the 2011 Great East Japan Earthquake have an increased risk of depressive symptoms. We sought to examine whether participation in group exercise and regular walking could mitigate the worsening of depressive symptoms among older survivors.

Design

Prospective observational study.

Setting

Our baseline survey was conducted in August 2010, ∼7 months prior to the Great East Japan Earthquake and tsunami, among people aged 65 or older residing in Iwanuma City, Japan, which suffered significant damage in the disaster. A 3-year follow-up survey was conducted in 2013.

Participants

3567 older survivors responded to the questionnaires predisaster and postdisaster.

Primary outcome measures

Change in depressive symptoms was assessed using the 15-item Geriatric Depression Scale (GDS).

Results

From predisaster to postdisaster, the mean change in GDS score increased by 0.1 point (95% CI −0.003 to 0.207). During the same interval, the frequency of group exercise participation and daily walking time also increased by 1.9 days/year and 1.3 min/day, respectively. After adjusting for all covariates, including personal experiences of disaster, we found that increases in the frequency of group exercise participation (B=−0.139,β=−0.049, p=0.003) and daily walking time (B=−0.087,β=−0.034, p=0.054) were associated with lower GDS scores. Interactions between housing damage and changes in group exercise participation (B=0.103,β=0.034, p=0.063) and changes in walking habit (B=0.095,β=0.033, p=0.070) were marginally significant, meaning that the protective effects tended to be attenuated among survivors reporting more extensive housing damage.

Conclusions

Participation in group exercises or regular walking may mitigate the worsening of depressive symptoms among older survivors who have experienced natural disaster.
In vivo crystalline lens measurements with novel swept-source optical coherent tomography: an investigation on variability of measurement
Authors: Shoji Takuhei , Kato Naoko , Ishikawa Sho , Ibuki Hisashi , Yamada Norihiro , Kimura Itaru , Shinoda Kei
Published: March 2017

Objective

To evaluate the reproducibility of in vivo crystalline lens measurements obtained by novel commercially available swept-source (SS) optical coherence tomography (OCT) specifically designed for anterior segment imaging.

Methods and analysis

One eye from each of 30 healthy subjects was randomly selected using the CASIA2 (Tomey, Nagoya, Japan) in two separate visits within a week. Each eye was imaged twice. After image scanning, the anterior and posterior lens curvatures and lens thickness were calculated automatically by the CASIA2 built-in program at 0 dioptre (D) (static), −1 D, −3 D and −5 D accommodative stress. The intraobserver and intervisit reproducibility coefficient (RC) and intraclass correlation coefficient (ICC) were calculated.

Results

The intraobserver and intervisit RCs ranged from 0.824 to 1.254 mm and 0.789 to 0.911 mm for anterior lens curvature, from 0.276 to 0.299 mm and 0.221 to 0.270 mm for posterior lens curvature and from 0.065 to 0.094 mm and 0.054 to 0.132 mm for lens thickness, respectively. The intraobserver and intervisit ICCs ranged from 0.831 to 0.865 and 0.828 to 0.914 for anterior lens curvature, from 0.832 to 0.898 and 0.840 to 0.933 for posterior lens curvature and from 0.980 to 0.992 and 0.942 to 0.995 for lens thickness. High ICC values were observed for each measurement regardless of accommodative stress. RCs in younger subjects tended to be larger than those in older subjects.

Conclusions

This novel anterior segment SS-OCT instrument produced reliable in vivo crystalline lens measurement with good repeatability and reproducibility regardless of accommodation stress.
Developing a model for embedded palliative care in a cancer clinic
Authors: DeSanto-Madeya Susan , McDermott David , Zerillo Jessica A , Weinstein Nancy , Buss Mary K
Published: March 2017

Objectives

Describe the development and key features of a model for embedded palliative care (PC) for patients with advanced kidney cancer or melanoma seen in a cancer clinic.

Methods

Retrospective chart review of patients following an initial phase and then a prospective review following the implementation of a model for embedded PC.

Results

In the initial phase, 18 patients were seen for a total of 53 visits; 78% were seen more than once, with a mean of three visits per patient. In the model phase, 46 patients were seen for a total of 163 visits; 74% were seen more than once, with a mean of 3.5 visits. Demographics were similar between the two groups. Content of the first PC visit in the initial and model phases was symptom management (61% and 57%), psychosocial support/relationship building (28% and 35%) and advance care planning/decision-making support (11% and 8%), respectively.

Conclusions

The initial phase demonstrated acceptability and feasibility of a model for embedded PC for patients and the oncology team. Establishment of specific eligibility criteria and screening to identify eligible patients in the model phase led to an increased uptake of PC for patients with advanced kidney cancer and melanoma in a cancer clinic.
SENP1 promotes hypoxia-induced cancer stemness by HIF-1α deSUMOylation and SENP1/HIF-1α positive feedback loop
Authors: Cui Chun-Ping , Wong Carmen Chak-Lui , Kai Alan Ka-Lun , Ho Daniel Wai-Hung , Lau Eunice Yuen-Ting , Tsui Yu-Man , Chan Lo-Kong , Cheung Tan-To , Chok Kenneth Siu-Ho , Chan Albert C Y , Lo Regina Cheuk-Lam , Lee Joyce Man-Fong , Lee Terence Kin-Wah , Ng Irene Oi Lin
Published: March 2017

Objective

We investigated the effect and mechanism of hypoxic microenvironment and hypoxia-inducible factors (HIFs) on hepatocellular carcinoma (HCC) cancer stemness.

Design

HCC cancer stemness was analysed by self-renewal ability, chemoresistance, expression of stemness-related genes and cancer stem cell (CSC) marker-positive cell population. Specific small ubiquitin-like modifier (SUMO) proteases 1 (SENP1) mRNA level was examined with quantitative PCR in human paired HCCs. Immunoprecipitation was used to examine the binding of proteins and chromatin immunoprecipitation assay to detect the binding of HIFs with hypoxia response element sequence. In vivo characterisation was performed in immunocompromised mice and stem cell frequency was analysed.

Results

We showed that hypoxia enhanced the stemness of HCC cells and hepatocarcinogenesis through enhancing HIF-1α deSUMOylation by SENP1 and increasing stabilisation and transcriptional activity of HIF-1α. Furthermore, we demonstrated that SENP1 is a direct target of HIF-1/2α and a previously unrecognised positive feedback loop exists between SENP1 and HIF-1α.

Conclusions

Taken together, our findings suggest the significance of this positive feedback loop between HIF-1α and SENP1 in contributing to the increased cancer stemness in HCC and hepatocarcinogenesis under hypoxia. Drugs that specifically target SENP1 may offer a potential novel therapeutic approach for HCC.
Paradigms in Chronic Obstructive Pulmonary Disease: Phenotypes, Immunobiology, and Therapy with a Focus on Vascular Disease
Authors: Schivo Michael , Albertson Timothy E , Haczku Angela , Kenyon Nicholas J , Zeki Amir A , Kuhn Brooks T , Louie Samuel , Avdalovic Mark V
Published: March 2017

Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome that represents a major global health burden. COPD phenotypes have recently emerged based on large cohort studies addressing the need to better characterize the syndrome. Though comprehensive phenotyping is still at an early stage, factors such as ethnicity and radiographic, serum, and exhaled breath biomarkers have shown promise. COPD is also an immunological disease where innate and adaptive immune responses to the environment and tobacco smoke are altered. The frequent overlap between COPD and other systemic diseases, such as cardiovascular disease, has influenced COPD therapy, and treatments for both conditions may lead to improved patient outcomes. Here, we discuss current paradigms that center on improving the definition of COPD, understanding the immunological overlap between COPD and vascular inflammation, and the treatment of COPD—with a focus on comorbid cardiovascular disease.
Bi-allelic variants inCOL3A1encoding the ligand to GPR56 are associated with cobblestone-like cortical malformation, white matter changes and cerebellar cysts
Authors: Vandervore Laura , Stouffs Katrien , Tanyalçin Ibrahim , Vanderhasselt Tim , Roelens Filip , Holder-Espinasse Muriel , Jørgensen Agnete , Pepin Melanie G , Petit Florence , Khau Van Kien Philippe , Bahi-Buisson Nadia , Lissens Willy , Gheldof Alexander , Byers Peter H , Jansen Anna C
Published: March 2017

Background

Collagens are one of the major constituents of the pial membrane, which plays a crucial role in neuronal migration and cortical lamination during brain development. Type III procollagen, the chains of which are encoded byCOL3A1, is the ligand of the G protein-coupled receptor 56 (GPR56), also known as adhesion G protein-coupled receptor G1. Bi-allelic mutations inGPR56give rise to cobblestone-like malformation, white matter changes and cerebellar dysplasia. This report shows that bi-allelic mutations inCOL3A1are associated with a similar phenotype.

Methods

Exome analysis was performed in a family consisting of two affected and two non-affected siblings. Brain imaging studies of this family and of two previously reported individuals with bi-allelic mutations inCOL3A1were reviewed. Functional assays were performed on dermal fibroblasts.

Results

Exome analysis revealed a novel homozygous variant c.145C>G (p.Pro49Ala) in exon 2 ofCOL3A1. Brain MRI in the affected siblings as well as in the two previously reported individuals with bi-allelicCOL3A1mutations showed a brain phenotype similar to that associated with mutations inGPR56.

Conclusion

Homozygous or compound heterozygous mutations inCOL3A1are associated with cobblestone-like malformation in all three families reported to date. The variability of the phenotype across patients suggests that genetic alterations in distinct domains of type III procollagen can lead to different outcomes. The presence of cobblestone-like malformation in patients with bi-allelicCOL3A1mutations emphasises the critical role of the type III collagen–GPR56 axis and the pial membrane in the regulation of brain development and cortical lamination.
Does training respiratory physicians in clinical respiratory physiology and interpretation of pulmonary function tests improve core knowledge?
Authors: Patout M , Sesé L , Gille T , Coiffard B , Korzeniewski S , Lhuillier E , Pradel A , Tardif C , Chambellan A , Straus C , Matecki S , Perez T , Thiberville L , Didier A
Published: March 2017

Lung function tests have a major role in respiratory medicine. Training in lung function tests is variable within the European Union. In this study, we have shown that an internship in a lung function tests laboratory significantly improved the technical and diagnostic skills of French respiratory trainees.
A volcanic centre in Mexico's Pacific continental shelf
Authors: Alvarez Román , Corbo Camargo Fernando , Yutsis Vsevolod V. , Arzate Jorge A.
Published: March 2017

On the continental platform of western Mexico, there is a young island of volcanic origin: Isla Isabel. It is the only volcanic manifestation in the region, contrasting with Islas Tres Marías, which are not volcanic. We aim at characterizing the source of the volcanic activity present in this particular location. Under Isla Isabel there is a bathymetric bulge that rises 60–80 m above the platform, and extends 20 km in the NW–SE direction and 17 km in the perpendicular direction. Isla Isabel is the only emerged portion of the bulge, extending only 1.8 km in the NW–SE direction. The island shows Plio-Pleistocene volcanic activity, including the formation of maars and the presence of mantle xenoliths. Using independent 2D modelling and 3D inversion methods for the gravity and magnetic fields, we analyse the nature of the bulge and its surroundings. A magnetotelluric station yields information about the electrical resistivity under the island, with penetration depths of approximately 20 km. The models are consistent with the presence of dense bodies of varying magnetizations that are interpreted as intrusive bodies. Results support the presence of an intrusion that locally has raised the ocean-floor topography. Volcanic activity projected from the bulge created Isla Isabel; the existence of additional, submerged volcanic centres in the area is most probable. We are inclined to identify the Isabel Bulge as a laccolith.
Geophysical modelling of Isla Isabel: a volcanic island on the Mexican continental margin
Authors: Alvarez Román , Corbo Camargo Fernando , Yutsis Vsevolod V.
Published: March 2017

Isla Isabel is a small island located on top of a 20 km-long bathymetric bulge, part of the continental shelf of Nayarit in the vicinity of the mouth of the Gulf of California; it is of volcanic origin with tuff cones, basaltic flows and Surtseyan-type explosion craters exposed. Geophysical surveys were carried out in order to model the geological bodies associated with the local gravity and magnetic fields. 2D and 3D models are presented, and a 1D inversion model is derived from magnetotelluric data. Analysis of the density models of the upper 1400 m suggests two growth stages for Isla Isabel in this depth range: the first one reaching 800 m in depth and the second one projecting from that depth to the surface. The corresponding magnetic susceptibility models concur with this observation. The bodies projected to the surface appear to correspond to diatremes. The 1D magnetotelluric inversion shows two conductive anomalies within the crust between 3–5 and 8–17 km, followed by a resistive substratum that coincides with the seismically derived limit of the Earth's crust at the island's position.