bluuebunny/crossref_metadata_2025_split huggingface dataset:
Overexpression of
OLE1
Enhances Cytoplasmic Membrane Stability and Confers Resistance to Cadmium in Saccharomyces cerevisiae
Authors: Fang Zhijia , Chen Zhongxiang , Wang Song , Shi Ping , Shen Yuhu , Zhang Youshang , Xiao Junhua , Huang Zhiwei 
Published: October 2016

ABSTRACT

The heavy metal cadmium is widely used and released into the environment, posing a severe threat to crops and humans.
Saccharomyces cerevisiae
is one of the most commonly used organisms in the investigation of environmental metal toxicity. We investigated cadmium stress and the adaptive mechanisms of yeast by screening a genome-wide essential gene overexpression library. A candidate gene,
OLE1
, encodes a delta-9 desaturase and was associated with high anti-cadmium-stress activity. The results demonstrated that the expression of
OLE1
was positively correlated with cadmium stress tolerance and induction was independent of Mga2p and Spt23p (important regulatory factors for
OLE1
). Moreover, in response to cadmium stress, cellular levels of monounsaturated fatty acids were increased. The addition of exogenous unsaturated fatty acids simulated overexpression of
OLE1
, leading to cadmium resistance. Such regulation of
OLE1
in the synthesis of unsaturated fatty acids may serve as a positive feedback mechanism to help cells counter the lipid peroxidation and cytoplasmic membrane damage caused by cadmium.

IMPORTANCE
A
S. cerevisiae
gene encoding a delta-9 desaturase,
OLE1
, was associated with high anti-cadmium-stress activity. The data suggest that the regulation of
OLE1
in the synthesis of unsaturated fatty acids may serve as a positive feedback mechanism to help yeast cells counter the lipid peroxidation and cytoplasmic membrane damage caused by cadmium. The discovery of
OLE1
involvement in membrane stability may indicate a novel defense strategy against cadmium stress.
Pseudo-Second-Order Calcium-Mediated Cryptosporidium parvum Oocyst Attachment to Environmental Biofilms
Authors: Luo Xia , Jedlicka Sabrina , Jellison Kristen 
Published: October 2016

ABSTRACT

Cryptosporidium parvum
oocysts are able to infect a wide range of mammals, including humans, via fecal-oral transmission. The remobilization of biofilm-associated
C. parvum
oocysts back into the water column by biofilm sloughing or bulk erosion poses a threat to public health and may be responsible for waterborne outbreaks; thus, the investigation of
C. parvum
attachment mechanisms to biofilms, particularly the physical and chemical factors controlling oocyst attachment to biofilms, is essential to predict the behavior of oocysts in the environment. In our study, biofilms were grown in rotating annular bioreactors using prefiltered stream water (0.2-μm retention) and rock biofilms (6-μm retention) until the mean biofilm thickness reached steady state. Oocyst deposition followed a calcium-mediated pseudo-second-order kinetic model. Kinetic parameters (i.e., initial oocyst deposition rate constant and total number of oocysts adhered to biofilms at equilibrium) from the model were then used to evaluate the impact of water conductivity on the attachment of oocysts to biofilms. Oocyst deposition was independent of solution ionic strength; instead, the presence of calcium enhanced oocyst attachment, as demonstrated by deposition tests. Calcium was identified as the predominant factor that bridges the carboxylic functional groups on biofilm and oocyst surfaces to cause attachment. The pseudo-second-order kinetic profile fit all experimental conditions, regardless of water chemistry and/or lighting conditions.

IMPORTANCE
The cation bridging model in our study provides new insights into the impact of calcium on the attachment of
C. parvum
oocysts to environmental biofilms. The kinetic parameters derived from the model could be further analyzed to elucidate the behavior of oocysts in commonly encountered complex aquatic systems, which will enable future innovations in parasite detection and treatment technologies to protect public health.
Exploring the Impacts of Postharvest Processing on the Microbiota and Metabolite Profiles during Green Coffee Bean Production
Authors: De Bruyn Florac , Zhang Sophia Jiyuan , Pothakos Vasileios , Torres Julio , Lambot Charles , Moroni Alice V. , Callanan Michael , Sybesma Wilbert , Weckx Stefan , De Vuyst Luc 
Published: October 2016

ABSTRACT

The postharvest treatment and processing of fresh coffee cherries can impact the quality of the unroasted green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through two different wet and dry methods to monitor differences in the microbial community structure and in substrate and metabolite profiles. The changes were followed throughout the postharvest processing chain, from harvest to drying, by implementing up-to-date techniques, encompassing multiple-step metagenomic DNA extraction, high-throughput sequencing, and multiphasic metabolite target analysis. During wet processing, a cohort of lactic acid bacteria (i.e.,
Leuconostoc
,
Lactococcus
, and
Lactobacillus
) was the most commonly identified microbial group, along with enterobacteria and yeasts (
Pichia
and
Starmerella
). Several of the metabolites associated with lactic acid bacterial metabolism (e.g., lactic acid, acetic acid, and mannitol) produced in the mucilage were also found in the endosperm. During dry processing, acetic acid bacteria (i.e.,
Acetobacter
and
Gluconobacter
) were most abundant, along with
Pichia
and non-
Pichia
(
Candida
,
Starmerella
, and
Saccharomycopsis
) yeasts. Accumulation of associated metabolites (e.g., gluconic acid and sugar alcohols) took place in the drying outer layers of the coffee cherries. Consequently, both wet and dry processing methods significantly influenced the microbial community structures and hence the composition of the final green coffee beans. This systematic approach to dissecting the coffee ecosystem contributes to a deeper understanding of coffee processing and might constitute a state-of-the-art framework for the further analysis and subsequent control of this complex biotechnological process.

IMPORTANCE
Coffee production is a long process, starting with the harvest of coffee cherries and the on-farm drying of their beans. In a later stage, the dried green coffee beans are roasted and ground in order to brew a cup of coffee. The on-farm, postharvest processing method applied can impact the quality of the green coffee beans. In the present case study, freshly harvested Arabica coffee cherries were processed through wet and dry processing in four distinct variations. The microorganisms present and the chemical profiles of the coffee beans were analyzed throughout the postharvest processing chain. The up-to-date techniques implemented facilitated the investigation of differences related to the method applied. For instance, different microbial groups were associated with wet and dry processing methods. Additionally, metabolites associated with the respective microorganisms accumulated on the final green coffee beans.
Bacteria as Emerging Indicators of Soil Condition
Authors: Hermans Syrie M. , Buckley Hannah L. , Case Bradley S. , Curran-Cournane Fiona , Taylor Matthew , Lear Gavin 
Published: October 2016

ABSTRACT

Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. We determined, through 16S rRNA gene amplicon sequencing, the composition of bacterial communities in soil samples from 110 natural or human-impacted sites, located up to 300 km apart. Overall, soil bacterial communities varied more in response to changing soil environments than in response to changes in climate or increasing geographic distance. We identified strong correlations between the relative abundances of members of
Pirellulaceae
and soil pH, members of
Gaiellaceae
and carbon-to-nitrogen ratios, members of
Bradyrhizobium
and the levels of Olsen P (a measure of plant available phosphorus), and members of
Chitinophagaceae
and aluminum concentrations. These relationships between specific soil attributes and individual soil taxa not only highlight ecological characteristics of these organisms but also demonstrate the ability of key bacterial taxonomic groups to reflect the impact of specific anthropogenic activities, even in comparisons of samples across large geographic areas and diverse soil types. Overall, we provide strong evidence that there is scope to use relative taxon abundances as biological indicators of soil condition.

IMPORTANCE
The impact of land use change and management on soil microbial community composition remains poorly understood. Therefore, we explored the relationship between a wide range of soil factors and soil bacterial community composition. We included variables related to anthropogenic activity and collected samples across a large spatial scale to interrogate the complex relationships between various bacterial community attributes and soil condition. We provide evidence of strong relationships between individual taxa and specific soil attributes even across large spatial scales and soil and land use types. Collectively, we were able to demonstrate the largely untapped potential of microorganisms to indicate the condition of soil and thereby influence the way that we monitor the effects of anthropogenic activity on soil ecosystems into the future.
Genome Sequence of Paraburkholderia nodosa Strain CNPSo 1341, a N
2
-Fixing Symbiont of the Promiscuous Legume Phaseolus vulgaris
Authors: Dall'Agnol Rebeca Fuzinatto , Costa Maira Rejane , Ribeiro Renan Augusto , Delamuta Jakeline Renata Marçon , Chueire Ligia Maria Oliveira , Hungria Mariangela 
Published: November 2016

ABSTRACT

Paraburkholderia nodosa
CNPSo 1341 is a N
2
-fixing symbiont of
Phaseolus vulgaris
isolated from an undisturbed soil of the Brazilian Cerrado. Its draft genome contains 8,614,032 bp and 8,068 coding sequences (CDSs). Nodulation and N
2
-fixation genes were clustered in the genome that also contains several genes of secretion systems and quorum sensing.
Draft Genome Sequence of a Hospital-Associated Clone of Klebsiella pneumoniae ST340/CC258 Coproducing RmtG and KPC-2 Isolated from a Pediatric Patient
Authors: Cerdeira Louise , Fernandes Miriam R. , Francisco Gabriela R. , Bueno Maria Fernanda C. , Ienne Susan , Souza Tiago A. , de Oliveira Garcia Doroti , Lincopan Nilton 
Published: November 2016

ABSTRACT

We report here the draft genome sequence of a
Klebsiella pneumoniae
strain 1194/11, belonging to the hospital-associated sequence type 340 (ST340; clonal complex CC258), isolated from a catheter tip culture from a pediatric patient. The multidrug-resistant strain coproduced the 16S rRNA methyltransferase rRNA RmtG and β-lactamases KPC-2 and CTX-M-15.
Draft Genome Sequence of the Bacterium Comamonas aquatica CJG
Authors: Dai Wenkui , Zhu Yutong , Wang Xiqian , Sakenova Nazgul , Yang Zhenyu , Wang Hongjuan , Li Guoqiao , He Jiajing , Huang Deyu , Cai Yongfei , Guo Weizheng , Wang Qian , Feng Tingting , Fan Quanshui , Zheng Tianling , Han Aidong 
Published: November 2016

ABSTRACT

A Gram-negative bacterial strain,
Comamonas aquatica
CJG, absorbs low-density lipoprotein but not high-density lipoprotein in serum. Here, we report its draft genomic sequence of 3,764,434 bp, containing total 3,425 genes, 27% of which encode proteins for metabolism and energy conversion, and it is 30% identical to the genome of
Comamonas testosteroni
.
Genome Sequence of a Cynomolgus Macaque Adenovirus (CynAdV-1) Isolate from a Primate Colony in the United Kingdom
Authors: Zeng Zhiwei , Zhang Jing , Jing Shuping , Cheng Zetao , Bofill-Mas Silvia , Maluquer de Motes Carlos , Hundesa Ayalkibet , Girones Rosina , Seto Donald , Zhang Qiwei 
Published: November 2016

ABSTRACT
The genome sequence of a simian adenovirus from a cynomolgus macaque, denoted CynAdV-1, is presented here. Phylogenetic analysis supports CynAdV-1 in an independent clade, comprising a new simian adenovirus (SAdV) species. These genome data are critical for understanding the evolution and relationships of primate adenoviruses, including zoonosis and emergent human pathogens.
Genome Sequence of
Prosthecochloris
sp. Strain CIB 2401 of the Phylum
Chlorobi
Authors: Nabhan Shaza , Bunk Boyke , Spröer Cathrin , Liu Zhenfeng , Bryant Donald A. , Overmann Jörg 
Published: November 2016

ABSTRACT

To date, only 13 genomes of green sulfur bacteria (family
Chlorobiaceae
) have been sequenced. The sequenced strains do not cover the full phylogenetic diversity of the family. We determined the complete genome sequence of
Prosthecochloris
sp. strain CIB 2401, thereby increasing the genome information for the poorly represented marine
Chlorobiaceae
.
Diabetes and diabetic retinopathy in people aged 50 years and older in Hungary
Authors: Tóth Gábor , Szabó Dorottya , Sándor Gábor L , Szalai Irén , Lukács Regina , Pék Anita , Tóth Georgina Z , Papp András , Nagy Zoltán Z , Limburg Hans , Németh János 
Published: October 2016

Background/aimsThe purpose of this study was to estimate the prevalence of diabetes mellitus (DM) and diabetic retinopathy (DR) in the population aged 50 years and older in Hungary, and to assess the coverage of diabetic eye care services.MethodsIn total, 105 clusters of 35 people aged 50 years or older were randomly selected. The standardised rapid assessment of avoidable blindness (RAAB) with the diabetic retinopathy module (DRM) was used. Participants were classified as having DM if they were known to have DM or if their random blood glucose level was ≥200 mg/dL. Dilated fundus examination and Scottish DR grading were performed.ResultsIn total, 3523 (95.9%) out of 3675 eligible subjects were examined. And 705 (20.0%) out of 3523 had known (661) or newly diagnosed DM (44). Twenty per cent of participants with known DM had a blood glucose level ≥200 mg/dL, and 27.4% had never had an ophthalmological examination for DR. Prevalence of DR and/or maculopathy was 20.7% and prevalence of sight-threatening DR (STDR) was 4.3% in one or both eyes among participants with DM.ConclusionsPrevalence of DM was in line with findings of other RAAB+DRM surveys and slightly lower than the unpublished earlier age-matched Hungarian estimate. Prevalence of DR was slightly lower than expected. The prevalence of STDR was low in people aged 50 years and older in Hungary compared with the results of other RAAB with DRM surveys. DR screening coverage was low. To prevent severe complications of DM and possible concomitant visual loss, the coverage of ophthalmic examinations in patients with DM should be increased.
Natural history and effect of therapeutic interventions on subretinal fluid causing foveal detachment in macular telangiectasia type 2
Authors: Mehta Hemal , Müller Simone , Egan Catherine A , Degli Esposti Simona , Tufail Adnan , Sim Dawn A , Holz Frank G , Browning Andrew C , Amoaku Winfried M , Charbel Issa Peter , Gillies Mark C 
Published: October 2016

AimTo report the natural history of subretinal fluid (SRF) causing foveal detachment in macular telangiectasia type 2 (MacTel) and our experience of therapeutic intervention with intravitreal steroids or antivascular endothelial growth factor inhibitor (anti-VEGF) agents in some cases.MethodsRetrospective case series. Three of the MacTel study's largest registries were searched to identify eyes with foveal detachment.ResultsWe identified 7 eyes from 6 exclusively female patients. The prevalence of foveal detachment was low, present in 1.4% of the assessed MacTel population. Age at presentation ranged from 50 to 66 years. Follow-up ranged from 2 to 8 years. There was late-phase leakage on fluorescein angiography from what was presumed to be ectatic capillaries. The SRF fluctuated without a rapid decline in visual acuity in cases that were not treated. When they were, intravitreal anti-VEGF and steroid therapy in general reduced SRF, at least temporarily, but did not halt the gradual long-term decrease in visual acuity. In one case, optical coherence tomography angiography showed significant reduction in the extent of the predominantly deep intraretinal vascular complex 1 month after anti-VEGF therapy.Discussion and conclusionsAs the natural history of this unusual MacTel phenotype is not characterised by rapid visual decline, intervention with intravitreal anti-VEGF or steroid therapy may not be necessary.
Anatomical and functional outcomes following vitrectomy for advanced familial exudative vitreoretinopathy: a single surgeon's experience
Authors: Hocaoglu Mumin , Karacorlu Murat , Sayman Muslubas Isil , Ersoz Mehmet Giray , Arf Serra 
Published: October 2016

PurposeTo assess the anatomical and functional results of vitreoretinal surgery in patients with advanced familial exudative vitreoretinopathy (FEVR).MethodsRetrospective analysis of data for 10 eyes of 9 patients with advanced FEVR who underwent pars plana vitrectomy from March 1997 to May 2015 and had a follow-up of at least 12 months. The primary outcomes were final visual acuity (VA) and anatomical success.ResultsThe average age at the time of the surgery was 10.1±6.5 years (range 2 months–18 years). The mean follow-up period was 58.4±75.1 months. The male-to-female ratio was 7/2. The mean number of vitreoretinal operations was 1.5. At the last visit, 7 (70%) eyes had complete or partial retinal attachment. Preoperatively, the mean Snellen VA was 20/4000 (n=8), and in the remaining 2 (20%) eyes it was recorded as ‘central, steady and maintained’. At final examination, the mean Snellen VA was 20/330 (n=7), and in the remaining 3 (30%) eyes it was recorded as light perception. At the final visit, 5 eyes (50%) had improved VA, 2 eyes (20%) showed stabilisation, and 3 eyes (30%) with total retinal detachment had a decrease in VA. No progression to glaucoma was observed and no enucleation was necessary.ConclusionsAdvanced FEVR in young children tends to be more aggressive, leading to severe complications. These cases are challenging and require special consideration. Despite surgery, disease-related complications remain high. However, surgical intervention for advanced FEVR might be of benefit in helping to preserve vision.
Educating professionals to support self-management in people with asthma or diabetes: protocol for a systematic review and scoping exercise
Authors: McCleary Nicola , Andrews Amanda , Morrow Susan , Wiener-Ogilvie Sharon , Fletcher Monica , Steed Liz , Taylor Stephanie J C , Pinnock Hilary 
Published: October 2016

IntroductionSupported self-management for asthma helps people adjust their treatment in response to symptom changes. This improves day-to-day control and reduces the risk of asthma attacks and the need for emergency healthcare. However, implementation remains poor in routine clinical practice. This systematic review is part of a programme of work developing an intervention to help primary care practice teams embed self-management support into routine asthma care. The aim of the review is to synthesise the evidence regarding the effectiveness of educational interventions for professionals supporting self-management in people with asthma or diabetes (type 1 and type 2). These two conditions have the most robust evidence base for the effectiveness of implementing supported self-management.Methods and analysisElectronic searches will be conducted in CENTRAL, MEDLINE, EMBASE, ISI Web of Science, CINAHL, PsycINFO, AMED, Global Health, WHO Global Health Library, ERIC, BNI, RDRB/CME and Google Scholar. Eligible studies are randomised controlled trials or controlled clinical trials published between 1990 and 2016 which evaluated professional education interventions facilitating asthma or diabetes supported self-management. Further relevant work will be identified from trial registries, citation searching and through contact with authors of included studies. This will be supplemented by scoping potentially relevant educational packages described in English language policy literature or health service websites. Screening, data extraction and risk of bias assessment (using the Cochrane Risk of Bias Tool) will be completed by two independent reviewers, with a third reviewer arbitrating where necessary. We plan a theoretically informed narrative synthesis of the aggregated data as heterogeneity is likely to preclude meta-analysis.Ethics and disseminationEthical approval is not required for this systematic review. The results will be described in a paper submitted for peer-reviewed publication and will inform the development of an implementation intervention.Study registration numberPROSPERO CRD42016032922.
Screening residents for infant lumbar puncture readiness with just-in-time simulation-based assessments
Authors: Kessler David O , Chang Todd P , Auerbach Marc , Fein Daniel M , Lavoie Megan E , Trainor Jennifer , Lee Moon O , Gerard James M , Grossman Devin , Whitfill Travis , Pusic Martin 
Published: October 2016

BackgroundDetermining when to entrust trainees to perform procedures is fundamental to patient safety and competency development.ObjectiveTo determine whether simulation-based readiness assessments of first year residents immediately prior to their first supervised infant lumbar punctures (LPs) are associated with success.MethodsThis prospective cohort study enrolled paediatric and other first year residents who perform LPs at 35 academic hospitals from 2012 to 2014. Within a standardised LP curriculum, a validated 4-point readiness assessment of first year residents was required immediately prior to their first supervised LP. A score ≥3 was required for residents to perform the LP. The proportion of successful LPs (<1000 red blood cells on first attempt) was determined. Process measures included success on any attempt, number of attempts, analgesia usage and use of the early stylet removal technique.ResultsWe analysed 726 LPs reported from 1722 residents (42%). Of the 432 who underwent readiness assessments, 174 (40%, 95% CI 36% to 45%) successfully performed their first LP. Those who were not assessed succeeded in 103/294 (35%, 95% CI 30% to 41%) LPs. Assessed participants reported more frequent direct attending supervision of the LP (diff 16%; 95% CI 8% to 22%), greater use of topical analgesia (diff 6%; 95% CI 1% to 12%) and greater use of the early stylet removal technique (diff 11%; 95% CI 4% to 19%) but no difference in number of attempts or overall procedural success.ConclusionsSimulation-based readiness assessments performed in a point-of-care fashion were associated with several desirable behaviours but were not associated with greater clinical success with LP.