bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of AlkBGT and AlkL from Pseudomonas putida GPo1 for Selective Alkyl Ester ω-Oxyfunctionalization in Escherichia coli
Authors: van Nuland Youri M. , Eggink Gerrit , Weusthuis Ruud A. 
Published: April 2016

ABSTRACT

The enzyme system AlkBGT from
Pseudomonas putida
GPo1 can efficiently ω-functionalize fatty acid methyl esters. Outer membrane protein AlkL boosts this ω-functionalization. In this report, it is shown that whole cells of
Escherichia coli
expressing the AlkBGT system can also ω-oxidize ethyl nonanoate (NAEE). Coexpression of AlkBGT and AlkL resulted in 1.7-fold-higher ω-oxidation activity on NAEE. With this strain, initial activity on NAEE was 70 U/g (dry weight) of cells (g
cdw
), 67% of the initial activity on methyl nonanoate. In time-lapse conversions with 5 mM NAEE the main product was 9-hydroxy NAEE (3.6 mM), but also 9-oxo NAEE (0.1 mM) and 9-carboxy NAEE (0.6 mM) were formed. AlkBGT also ω-oxidized ethyl, propyl, and butyl esters of fatty acids ranging from C
6
to C
10
. Increasing the length of the alkyl chain improved the ω-oxidation activity of AlkBGT on esters of C
6
and C
7
fatty acids. From these esters, application of butyl hexanoate resulted in the highest ω-oxidation activity, 82 U/g
cdw
. Coexpression of AlkL only had a positive effect on ω-functionalization of substrates with a total length of C
11
or longer. These findings indicate that AlkBGT(L) can be applied as a biocatalyst for ω-functionalization of ethyl, propyl, and butyl esters of medium-chain fatty acids.

IMPORTANCE
Fatty acid esters are promising renewable starting materials for the production of ω-hydroxy fatty acid esters (ω-HFAEs). ω-HFAEs can be used to produce sustainable polymers. Chemical conversion of the fatty acid esters to ω-HFAEs is challenging, as it generates by-products and needs harsh reaction conditions. Biocatalytic production is a promising alternative. In this study, biocatalytic conversion of fatty acid esters toward ω-HFAEs was investigated using whole cells. This was achieved with recombinant
Escherichia coli
cells that produce the AlkBGT enzymes. These enzymes can produce ω-HFAEs from a wide variety of fatty acid esters. Medium-chain-length acids (C
6
to C
10
) esterified with ethanol, propanol, or butanol were applied. This is a promising production platform for polymer building blocks that uses renewable substrates and mild reaction conditions.
Use of Redundant Exclusion PCR To Identify a Novel Bacillus thuringiensis Cry8 Toxin Gene from Pooled Genomic DNA
Authors: Zhang Fengjiao , Shu Changlong , Crickmore Neil , Li Yanqiu , Song Fuping , Liu Chunqin , Chen Zhibao , Zhang Jie 
Published: April 2016

ABSTRACT

With the aim of optimizing the cloning of novel genes from a genomic pool containing many previously identified homologous genes, we designed a redundant exclusion PCR (RE-PCR) technique. In RE-PCR, a pair of generic amplification primers are combined with additional primers that are designed to specifically bind to redundant, unwanted genes that are a subset of those copied by the amplification primers. During RE-PCR, the specific primer blocks amplification of the full-length redundant gene. Using this method, we managed to clone a number of
cry8
or
cry9
toxin genes from a pool of
Bacillus thuringiensis
genomic DNA while excluding amplicons for
cry9Da
,
cry9Ea
, and
cry9Eb
. The method proved to be very efficient at increasing the number of rare genes in the resulting library. One such rare (and novel)
cry8
-like gene was expressed, and the encoded toxin was shown to be toxic to
Anomala corpulenta
.

IMPORTANCE
Protein toxins from the bacterium
Bacillus thuringiensis
are being increasingly used as biopesticides against a wide range of insect pests, yet the search for new or improved toxins is becoming more difficult, as traditional methods for gene discovery routinely isolate previously identified clones. This paper describes an approach that we have developed to increase the success rate for novel toxin gene identification through reducing or eliminating the cloning of previously characterized genes.
Motility of Electric Cable Bacteria
Authors: Bjerg Jesper Tataru , Damgaard Lars Riis , Holm Simon Agner , Schramm Andreas , Nielsen Lars Peter 
Published: April 2016

ABSTRACT

Cable bacteria are filamentous bacteria that electrically couple sulfide oxidation and oxygen reduction at centimeter distances, and observations in sediment environments have suggested that they are motile. By time-lapse microscopy, we found that cable bacteria used gliding motility on surfaces with a highly variable speed of 0.5 ± 0.3 μm s
−1
(mean ± standard deviation) and time between reversals of 155 ± 108 s. They frequently moved forward in loops, and formation of twisted loops revealed helical rotation of the filaments. Cable bacteria responded to chemical gradients in their environment, and around the oxic-anoxic interface, they curled and piled up, with straight parts connecting back to the source of sulfide. Thus, it appears that motility serves the cable bacteria in establishing and keeping optimal connections between their distant electron donor and acceptors in a dynamic sediment environment.

IMPORTANCE
This study reports on the motility of cable bacteria, capable of transmitting electrons over centimeter distances. It gives us a new insight into their behavior in sediments and explains previously puzzling findings. Cable bacteria greatly influence their environment, and this article adds significantly to the body of knowledge about this organism.
The Acinetobacter baumannii Two-Component System AdeRS Regulates Genes Required for Multidrug Efflux, Biofilm Formation, and Virulence in a Strain-Specific Manner
Authors: Richmond Grace E. , Evans Laura P. , Anderson Michele J. , Wand Matthew E. , Bonney Laura C. , Ivens Alasdair , Chua Kim Lee , Webber Mark A. , Sutton J. Mark , Peterson Marnie L. , Piddock Laura J. V. 
Published: April 2016

ABSTRACT

The opportunistic pathogen
Acinetobacter baumannii
is able to persist in the environment and is often multidrug resistant (MDR), causing difficulties in the treatment of infections. Here, we show that the two-component system AdeRS, which regulates the production of the AdeABC multidrug resistance efflux pump, is required for the formation of a protective biofilm in an
ex vivo
porcine mucosal model, which mimics a natural infection of the human epithelium. Interestingly, deletion of
adeB
impacted only on the ability of strain AYE to form a biofilm on plastic and only on the virulence of strain Singapore 1 for
Galleria mellonella
. RNA-Seq revealed that loss of AdeRS or AdeB significantly altered the transcriptional landscape, resulting in the changed expression of many genes, notably those associated with antimicrobial resistance and virulence interactions. For example,
A. baumannii
lacking AdeRS displayed decreased expression of
adeABC
,
pil
genes,
com
genes, and a
pgaC
-like gene, whereas loss of AdeB resulted in increased expression of
pil
and
com
genes and decreased expression of ferric acinetobactin transport system genes. These data define the scope of AdeRS-mediated regulation, show that changes in the production of AdeABC mediate important phenotypes controlled by AdeRS, and suggest that AdeABC is a viable target for antimicrobial drug and antibiofilm discovery.

IMPORTANCE
Acinetobacter baumannii
is a nosocomial pathogen and is an increasing problem in hospitals worldwide. This organism is often multidrug resistant, can persist in the environment, and forms a biofilm on environmental surfaces and wounds. Overproduction of efflux pumps can allow specific toxic compounds to be pumped out of the cell and can lead to multidrug resistance. This study demonstrates the role of the
A. baumannii
efflux pump AdeB, and its regulator AdeRS, in multidrug resistance, epithelial cell killing, and biofilm formation. Deletion of the genes encoding these systems led to increased susceptibility to antibiotics, decreased biofilm formation on biotic and abiotic surfaces, and decreased virulence. Our data suggest that inhibition of AdeB could prevent biofilm formation or colonization in patients by
A. baumannii
and provides a good target for drug discovery
.
The Eng1 β-Glucanase EnhancesHistoplasmaVirulence by Reducing β-Glucan Exposure
Authors: Garfoot Andrew L. , Shen Qian , Wüthrich Marcel , Klein Bruce S. , Rappleye Chad A. 
Published: April 2016

ABSTRACTThe fungal pathogenHistoplasma capsulatumparasitizes host phagocytes. To avoid antimicrobial immune responses,Histoplasmayeasts must minimize their detection by host receptors while simultaneously interacting with the phagocyte. PathogenicHistoplasmayeast cells, but not avirulent mycelial cells, secrete the Eng1 protein, which is a member of the glycosylhydrolase 81 (GH81) family. We show thatHistoplasmaEng1 is a glucanase that hydrolyzes β-(1,3)-glycosyl linkages but is not required forHistoplasmagrowthin vitroor for cell separation. However,Histoplasmayeasts lacking Eng1 function have attenuated virulencein vivo, particularly during the cell-mediated immunity stage.Histoplasmayeasts deficient for Eng1 show increased exposure of cell wall β-glucans, which results in enhanced binding to the Dectin-1 β-glucan receptor. Consistent with this, Eng1-deficient yeasts trigger increased tumor necrosis factor alpha (TNF-α) and interleukin-6 (IL-6) cytokine production from macrophages and dendritic cells. While not responsible for large-scale cell wall structure and function, the secreted Eng1 reduces levels of exposed β-glucans at the yeast cell wall, thereby diminishing potential recognition by Dectin-1 and proinflammatory cytokine production by phagocytes. In α-glucan-producingHistoplasmastrains, Eng1 acts in concert with α-glucan to minimize β-glucan exposure: α-glucan provides a masking function by covering the β-glucan-rich cell wall, while Eng1 removes any remaining exposed β-glucans. Thus,HistoplasmaEng1 has evolved a specialized pathogenesis function to remove exposed β-glucans, thereby enhancing the ability of yeasts to escape detection by host phagocytes.IMPORTANCEThe success ofHistoplasma capsulatumas an intracellular pathogen results, in part, from an ability to minimize its detection by receptors on phagocytic cells of the immune system. In this study, we showed thatHistoplasmapathogenic yeast cells, but not avirulent mycelia, secrete a β-glucanase, Eng1, which reduces recognition of fungal cell wall β-glucans. We demonstrated that the Eng1 β-glucanase promotesHistoplasmavirulence by reducing levels of surface-exposed β-glucans on yeast cells, thereby enablingHistoplasmayeasts to escape detection by the host β-glucan receptor, Dectin-1. As a consequence, phagocyte recognition ofHistoplasmayeasts is reduced, leading to less proinflammatory cytokine production by phagocytes and less control ofHistoplasmainfectionin vivo. Thus,Histoplasmayeasts express two mechanisms to avoid phagocyte detection: masking of cell wall β-glucans by α-glucan and enzymatic removal of exposed β-glucans by the Eng1 β-glucanase.
Electroacupuncture and Cognitive Behavioural Therapy for Sub-Syndromal Depression among Undergraduates: A Controlled Clinical Trial
Authors: Guo Tianwei , Guo Zhuo , Zhang Wenyue , Ma Wenhao , Yang Xinjing , Yang Xueqin , Hwang Jiwon , He Xiaotian , Chen Xinyi , Ya Tu 
Published: April 2016

Background Individuals with sub-syndromal depression (SSD) are at increased risk of incident depressive disorders; however, the ideal therapeutic approach to SSD remains unknown. Objective To evaluate the effects of electroacupuncture (EA) and cognitive behavioural therapy (CBT), alone or in combination, on depressive symptoms. Methods Undergraduate students with SSD were recruited and allocated to one of four groups based on their preferences: EA (n=6), CBT (n=10), EA+CBT (n=6), and untreated control (n=11) groups. Six weeks of treatment were provided in the first three groups. Clinical outcomes were measured using the 17-item Hamilton Depression (HAMD-17) rating scale, Center for Epidemiologic Depression (CES-D) scale, WHO Quality of Life-Brief version (WHOQOL-BREF) questionnaire, and clinical remission rate. Results All 33 subjects were included in an intent-to-treat analysis. Statistically significant improvements in HAMD-17, CES-D, and WHOQOL-BREF scores and a higher remission rate were found in the EA, CBT, and EA+CBT intervention groups compared with the control group (all p<0.05). No significant differences were found between the three intervention groups. HAMD-17 factor score analysis revealed that EA reduced sleep disturbance scores more than CBT or EA+CBT (p<0.05), and CBT reduced retardation scores more than EA (p<0.01). EA+CBT reduced anxiety/somatisation scores more than EA or CBT (p<0.05) and retardation scores more than EA (p<0.05). Conclusions Early intervention may alleviate depressive symptoms in SSD. EA and CBT may have differential effects on certain symptoms. Combination therapy targeting both physical and psychological symptoms may represent an ideal strategy for SSD intervention. However, randomised trials with larger sample sizes are needed. Trial Registration Number ChiCTR-TRC-10000889; Results.
Colchicine for children with pericarditis: systematic review of clinical studies
Authors: Alabed Samer , Pérez-Gaxiola Giordano , Burls Amanda 
Published: April 2016

ObjectiveTo review the evidence for the efficacy and safety of colchicine in children with pericarditis.DesignSystematic review.Search strategyThe following databases were searched for studies about colchicine in children with pericarditis (June 2015): Cochrane Central, Medline, EMBASE and LILACS.Eligibility criteriaAll observational and experimental studies on humans with any length of follow-up and no limitations on language or publication status were included. The outcomes studied were recurrences of pericarditis and adverse events.Data extractionTwo authors extracted data and assessed quality of included studies using the Cochrane risk of bias tool for non-randomised trials.ResultsTwo case series and nine case reports reported the use of colchicine in a total of 86 children with pericarditis. Five articles including 74 paediatric patients were in favour of colchicine in preventing further pericarditis recurrences. Six studies including 12 patients showed that colchicine did not prevent recurrences of pericarditis.LimitationsNo randomised controlled trials (RCTs) were found.ConclusionsAlthough colchicine is an established treatment for pericarditis in adults, it is not routinely used in children. There is not enough evidence to support or discourage the use of colchicine in children with pericarditis. Further research in the form of large double-blind RCTs is needed to establish the efficacy of colchicine in children with pericarditis.
Determinants for tuberculosis in HIV-infected adults in Northwest Ethiopia: a multicentre case–control study
Authors: Alemu Yihun Mulugeta , Awoke Worku , Wilder-Smith Annalies 
Published: April 2016

ObjectiveThe objective of this study was to identify determinants for tuberculosis (TB) among HIV-infected adults in Northwest Ethiopia.DesignCase–control study.SettingThree hospitals and 10 health centres in Northwest Ethiopia.ParticipantsA total of 446 individuals consented to participate in the study (150 cases and 296 controls). Cases were HIV-infected adults diagnosed with active TB, and controls were HIV-infected adults without active TB.Main outcome measureThe link between TB and determinants was assessed using logistic regression. Determinants were categorised as sociodemographic, host-related, clinical and environmental.ResultsSmoking (adjusted OR (AOR) 5.47; 95% CI 2.26 to 13.22), presence of a TB patient in the family (AOR 2.66; 95% CI 1.25 to 5.66), alcohol consumption (AOR 2.49; 95% CI 1.29 to 4.80) and chewing khat (AOR 2.22; 95% CI 1.11 to 4.41) were independent determinants for increased occurrence of TB. Highly active antiretroviral therapy (HAART) (AOR 0.25; 95% CI 0.13 to 0.51), isoniazid preventive therapy (IPT) (AOR 0.22; 95% CI 0.11 to 0.41) and cotrimoxazole preventive therapy (AOR 0.32; 95% CI 0.19 to 0.55) had a protective effect against TB.ConclusionsHIV-infected adults with substance abuse (tobacco smoking, khat chewing and alcohol) should be prioritised for TB screening. This study reaffirmed that HAART and IPT are some of the best strategies for reducing TB occurrence in HIV-infected adults. These findings provide impetus to intensify tracing of TB household contacts.
Sex differences in aneurysm morphologies and clinical outcomes in ruptured anterior communicating artery aneurysms: a retrospective study
Authors: Lin Boli , Chen Weijian , Ruan Lei , Chen Yongchun , Zhong Ming , Zhuge Qichuan , Fan Liang Hao , Zhao Bing , Yang Yunjun 
Published: April 2016

ObjectivesRuptured anterior communicating artery (ACoA) aneurysms occur more frequently in men. The purpose of the study was to investigate sex difference in aneurysm morphologies and clinical outcomes in patients with ruptured ACoA aneurysms.SettingA tertiary referral hospital.ParticipantsA total of 574 consecutive patients with ACoA aneurysms were admitted to our hospital from December 2007 to February 2015. In all, 474 patients (257 men and 217 women) with ruptured ACoA aneurysms were included in the study.Main outcome measuresAneurysm morphologies were measured using computed tomographic angiography and clinical outcomes were measured with Glasgow coma score at discharge.ResultsThe aneurysm sizes (p=0.001), aneurysm heights (p=0.011), size ratios (p<0.001), flow angles (p=0.047) and vessel angles (p=0.046) were larger in the male patients than in the females. The female patients more often had larger vessel sizes (p=0.002). Multivariate logistic analysis revealed that significant differences in aneurysm morphologies between men and women were aneurysm size (OR 1.1, 95% CI 1.0 to 1.3; p=0.036), aneurysm height (OR 0.8, 95% CI 0. to 0.9; p=0.006) and size ratio (OR 1.4, 95% CI 0.5 to 1.7; p=0.001). There were no statistically significant differences in the outcomes between men and women (OR 1.0, 95% CI 0.6 to 1.7, p=0.857).ConclusionsThe men were independently associated with larger aneurysm sizes, greater aneurysm heights and larger size ratios. Sex was not a risk factor for poor outcome in patients with ruptured ACoA aneurysms.
Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer
Authors: Hart Steven N , Ellingson Marissa S , Schahl Kim , Vedell Peter T , Carlson Rachel E , Sinnwell Jason P , Barman Poulami , Sicotte Hugues , Eckel-Passow Jeanette E , Wang Liguo , Kalari Krishna R , Qin Rui , Kruisselbrink Teresa M , Jimenez Rafael E , Bryce Alan H , Tan Winston , Weinshilboum Richard , Wang Liewei , Kohli Manish 
Published: April 2016

ObjectivesTo determine the frequency of pathogenic inherited mutations in 157 select genes from patients with metastatic castrate-resistant prostate cancer (mCRPC).DesignObservational.SettingMultisite US-based cohort.ParticipantsSeventy-one adult male patients with histological confirmation of prostate cancer, and had progressive disease while on androgen deprivation therapy.ResultsTwelve patients (17.4%) showed evidence of carrying pathogenic or likely pathogenic germline variants in theATM,ATR,BRCA2,FANCL,MSR1,MUTYH,RB1,TSHRandWRNgenes. All but one patient opted in to receive clinically actionable results at the time of study initiation. We also found that pathogenic germlineBRCA2variants appear to be enriched in mCRPC compared to familial prostate cancers.ConclusionsPathogenic variants in cancer-susceptibility genes are frequently observed in patients with mCRPC. A substantial proportion of patients with mCRPC or their family members would derive clinical utility from mutation screening.Trial registration numberNCT01953640; Results.
National programmes for validating physician competence and fitness for practice: a scoping review
Authors: Horsley Tanya , Lockyer Jocelyn , Cogo Elise , Zeiter Jeanie , Bursey Ford , Campbell Craig 
Published: April 2016

ObjectiveTo explore and categorise the state of existing literature for national programmes designed to affirm or establish the continuing competence of physicians.DesignScoping review.Data sourcesMEDLINE, ERIC, Sociological Abstracts, web/grey literature (2000–2014).SelectionIncluded when a record described a (1) national-level physician validation system, (2) recognised as a system for affirming competence and (3) reported relevant data.Data extractionUsing bibliographic software, title and abstracts were reviewed using an assessment matrix to ensure duplicate, paired screening. Dyads included both a methodologist and content expert on each assessment, reflective of evidence-informed best practices to decrease errors.Results45 reports were included. Publication dates ranged from 2002 to 2014 with the majority of publications occurring in the previous six years (n=35). Country of origin—defined as that of the primary author—included the USA (N=32), the UK (N=8), Canada (N=3), Kuwait (N=1) and Australia (N=1). Three broad themes emerged from this heterogeneous data set: contemporary national programmes, contextual factors and terminological consistency. Four national physician validation systems emerged from the data: the American Board of Medical Specialties Maintenance of Certification Program, the Federation of State Medical Boards Maintenance of Licensure Program, the Canadian Revalidation Program and the UK Revalidation Program. Three contextual factors emerged as stimuli for the implementation of national validation systems: medical regulation, quality of care and professional competence. Finally, great variation among the definitions of key terms was identified.ConclusionsThere is an emerging literature focusing on national physician validation systems. Four major systems have been implemented in recent years and it is anticipated that more will follow. Much of this work is descriptive, and gaps exist for the extent to which systems build on current evidence or theory. Terminology is highly variable across programmes for validating physician competence and fitness for practice.
Epidemiology of road traffic injuries in Nepal, 2001–2013: systematic review and secondary data analysis
Authors: Karkee Rajendra , Lee Andy H 
Published: April 2016

ObjectiveTo investigate the epidemiology of road traffic injury (RTI) in Nepal for the period 2001–2013.Methods2 approaches, secondary data analysis and systematic literature review, were adopted. RTI data were retrieved from traffic police records and analysed for the incidence of RTI. Electronic databases were searched for published articles that described the epidemiology of RTI in Nepal.ResultsA total of 95 902 crashes, 100 499 injuries and 14 512 deaths were recorded by the traffic police over the 12-year period, 2001–2013. The mortality rate increased from 4/100 000 population in 2001–2002 to 7/100 000 population in 2011–2012. There were relatively more reported crashes yet fewer deaths in Kathmandu valley than the rest of the country. Of the 20 articles related to RTI, only 11 articles met the eligibility criteria, but these were mainly descriptive case series or cross-sectional hospital-based studies. The majority of RTI were reported to occur among motorcyclists and pedestrians, in males, and in the age group 20–40 years. The common sites of injury were lower and upper extremities. Only 3 articles mentioned possible causes of accidents that include pedestrian road behaviour, alcohol consumption and improper bus driving.ConclusionsNepal suffers a heavy burden of RTI, with higher fatalities on highways out of Kathmandu valley caused by bus crashes in hilly districts. The majority of published studies on RTI are descriptive and hospital based, indicating the need for more thorough investigation of causes of RTI and systematic recording of crashes for the development of effective interventions.