bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neutral and Phospholipids of the Myxococcus xanthus Lipodome during Fruiting Body Formation and Germination
Authors: Ahrendt Tilman , Wolff Hendrik , Bode Helge B. 
Published: July 2015

ABSTRACT

Myxobacteria are well-known for their complex life cycle, including the formation of spore-filled fruiting bodies. The model organism
Myxococcus xanthus
exhibits a highly complex composition of neutral and phospholipids, including triacylglycerols (TAGs), diacylglycerols (DAGs), phosphatidylethanolamines (PEs), phosphatidylglycerols (PGs), cardiolipins (CLs), and sphingolipids, including ceramides (Cers) and ceramide phosphoinositols (Cer-PIs). In addition, ether lipids have been shown to be involved in development and signaling. In this work, we describe the lipid profile of
M. xanthus
during its entire life cycle, including spore germination. PEs, representing one of the major components of the bacterial membrane, decreased by about 85% during development from vegetative rods to round myxospores, while TAGs first accumulated up to 2-fold before they declined 48 h after the induction of sporulation. Presumably, membrane lipids are incorporated into TAG-containing lipid bodies, serving as an intermediary energy source for myxospore formation. The ceramides Cer(d-19:0/
iso
-17:0) and Cer(d-19:0/16:0) accumulated 6-fold and 3-fold, respectively, after 24 h of development, identifying them to be novel putative biomarkers for
M. xanthus
sporulation. The most abundant ether lipid, 1-
iso
-15:0-alkyl-2,3-di-
iso
-15:0-acyl glycerol (TG1), exhibited a lipid profile different from that of all TAGs during sporulation, reinforcing its signaling character. The absence of all these lipid profile changes in mutants during development supports the importance of lipids in myxobacterial development. During germination of myxospores, only the
de novo
biosynthesis of new cell membrane fatty acids was observed. The unexpected accumulation of TAGs also during germination might indicate a function of TAGs as intermediary storage lipids during this part of the life cycle as well.
A Modified Shuttle Plasmid Facilitates Expression of a Flavin Mononucleotide-Based Fluorescent Protein in Treponema denticola ATCC 35405
Authors: Godovikova Valentina , Goetting-Minesky M. Paula , Shin Jae M. , Kapila Yvonne L. , Rickard Alexander H. , Fenno J. Christopher 
Published: July 2015

ABSTRACT

Oral pathogens, including
Treponema denticola
, initiate the dysregulation of tissue homeostasis that characterizes periodontitis. However, progress of research on the roles of
T. denticola
in microbe-host interactions and signaling, microbial communities, microbial physiology, and molecular evolution has been hampered by limitations in genetic methodologies. This is typified by an extremely low transformation efficiency and inability to transform the most widely studied
T. denticola
strain with shuttle plasmids. Previous studies have suggested that robust restriction-modification (R-M) systems in
T. denticola
contributed to these problems. To facilitate further molecular genetic analysis of
T. denticola
behavior, we optimized existing protocols such that shuttle plasmid transformation efficiency was increased by >100-fold over prior reports. Here, we report routine transformation of
T. denticola
ATCC 35405 with shuttle plasmids, independently of both plasmid methylation status and activity of the type II restriction endonuclease encoded by TDE0911. To validate the utility of this methodological advance, we demonstrated expression and activity in
T. denticola
of a flavin mononucleotide-based fluorescent protein (FbFP) that is active under anoxic conditions. Addition of routine plasmid-based fluorescence labeling to the
Treponema
toolset will enable more-rigorous and -detailed studies of the behavior of this organism.
YvoA and CcpA Repress the Expression of
chiB
in Bacillus thuringiensis
Authors: Jiang Kun , Li Li-na , Pan Jin-hua , Wang Ting-ting , Chen Yue-hua , Cai Jun 
Published: July 2015

ABSTRACT

Bacillus thuringiensis
produces chitinases, which are involved in its antifungal activity and facilitate its insecticidal activity. In our recent work, we found that a 16-bp sequence,

dre
chiB

(AGACTTCGTGATGTCT), downstream of the minimal promoter region of the chitinase B gene (
chiB
) was a critical site for the inducible expression of
chiB
in
B. thuringiensis
Bti75. In this work, we show that a GntR family transcriptional regulator (named YvoA
Bt
), which is homologous to YvoA of
Bacillus subtilis
, can specifically bind to the

dre
chiB

oligonucleotide sequences
in vitro
by using electrophoretic mobility shift assays (EMSAs) and isothermal titration calorimetry (ITC) assays. The results of quantitative real-time reverse transcription-PCR (qRT-PCR) and Western blotting indicated that deletion of
yvoA
caused an ∼7.5-fold increase in the expression level of
chiB
. Furthermore, binding of purified YvoA
Bt
to its target DNA could be abolished by glucosamine-6-phosphate (GlcN-6-P). We also confirmed, in the presence of the phosphoprotein Hpr-Ser
45
-P, that purified CcpA
Bt
bound specifically to the promoter of
chiB
, which contains the “

cre
chiB

” sequence (ATAAAGCGTTTACA). According to the results of qRT-PCR and Western blotting, deletion of
ccpA
resulted in a 39-fold increase in the
chiB
expression level, and glucose no longer influenced the expression of
chiB
. We confirm that
chiB
is negatively controlled by both CcpA
Bt
and YvoA
Bt
in Bti75.
Dual-Color Monitoring Overcomes the Limitations of Single Bioluminescent Reporters in Fast-Growing Microbes and Reveals Phase-Dependent Protein Productivity during the Metabolic Rhythms of Saccharomyces cerevisiae
Authors: Krishnamoorthy Archana , Robertson J. Brian 
Published: July 2015

ABSTRACT

Luciferase is a useful, noninvasive reporter of gene regulation that can be continuously monitored over long periods of time; however, its use is problematic in fast-growing microbes like bacteria and yeast because rapidly changing cell numbers and metabolic states also influence bioluminescence, thereby confounding the reporter's signal. Here we show that these problems can be overcome in the budding yeast
Saccharomyces cerevisiae
by simultaneously monitoring bioluminescence from two different colors of beetle luciferase, where one color (green) reports activity of a gene of interest, while a second color (red) is stably expressed and used to continuously normalize green bioluminescence for fluctuations in signal intensity that are unrelated to gene regulation. We use this dual-luciferase strategy in conjunction with a light-inducible promoter system to test whether different phases of yeast respiratory oscillations are more suitable for heterologous protein production than others. By using pulses of light to activate production of a green luciferase while normalizing signal variation to a red luciferase, we show that the early reductive phase of the yeast metabolic cycle produces more luciferase than other phases.
Unusual Biosynthesis and Structure of Locillomycins from Bacillus subtilis 916
Authors: Luo Chuping , Liu Xuehui , Zhou Xian , Guo Junyao , Truong John , Wang Xiaoyu , Zhou Huafei , Li Xiangqian , Chen Zhiyi 
Published: July 2015

ABSTRACT

Three families of
Bacillus
cyclic lipopeptides—surfactins, iturins, and fengycins—have well-recognized potential uses in biotechnology and biopharmaceutical applications. This study outlines the isolation and characterization of locillomycins, a novel family of cyclic lipopeptides produced by
Bacillus subtilis
916. Elucidation of the locillomycin structure revealed several molecular features not observed in other
Bacillus
lipopeptides, including a unique nonapeptide sequence and macrocyclization. Locillomycins are active against bacteria and viruses. Biochemical analysis and gene deletion studies have supported the assignment of a 38-kb gene cluster as the locillomycin biosynthetic gene cluster. Interestingly, this gene cluster encodes 4 proteins (LocA, LocB, LocC, and LocD) that form a hexamodular nonribosomal peptide synthetase to biosynthesize cyclic nonapeptides. Genome analysis and the chemical structures of the end products indicated that the biosynthetic pathway exhibits two distinct features: (i) a nonlinear hexamodular assembly line, with three modules in the middle utilized twice and the first and last two modules used only once and (ii) several domains that are skipped or optionally selected.
Understanding the Linkage between Elevation and the Activated-Sludge Bacterial Community along a 3,600-Meter Elevation Gradient in China
Authors: Niu Lihua , Li Yi , Wang Peifang , Zhang Wenlong , Wang Chao , Wang Qing 
Published: July 2015

ABSTRACT

To understand the relationship between elevation and bacterial communities in wastewater treatment plants (WWTPs), bacterial communities in 21 municipal WWTPs across China, located 9 to 3,660 m above sea level (masl), were investigated by 454 pyrosequencing. A threshold for the association of elevation with bacterial community richness and evenness was observed at approximately 1,200 masl. At lower elevations, both richness and evenness were not significantly associated with elevation. At higher elevations, significant declines with increased elevations were observed for community richness and evenness. The declining evenness trend at the phylum level was reflected by distinct trends in relative abundance for individual bacterial phyla.
Betaproteobacteria
,
Bacteroidetes
, and
Firmicutes
displayed significant increases, while most other phyla showed declines. Spearman correlation analysis indicated that the community richness and evenness at high elevations were more correlated with elevation than with any other single environmental variable. Redundancy analysis indicated that the contribution of elevation to community composition variances increased from 3% at lower elevations to 11% at higher elevations whereas the community composition variance at higher elevations remained much more explained by operational variables (39.2%) than by elevation. The influent total phosphorus concentration, food/microorganism ratio, and treatment process were the three shared dominant contributors to the community composition variance across the whole elevation gradient, followed by effluent ammonia nitrogen and temperature at higher elevations.
What's Inside That Seed We Brew? A New Approach To Mining the Coffee Microbiome
Authors: Vaughan Michael Joe , Mitchell Thomas , McSpadden Gardener Brian B. 
Published: July 2015

ABSTRACT
Coffee is a critically important agricultural commodity for many tropical states and is a beverage enjoyed by millions of people worldwide. Recent concerns over the sustainability of coffee production have prompted investigations of the coffee microbiome as a tool to improve crop health and bean quality. This review synthesizes literature informing our knowledge of the coffee microbiome, with an emphasis on applications of fruit- and seed-associated microbes in coffee production and processing. A comprehensive inventory of microbial species cited in association with coffee fruits and seeds is presented as reference tool for researchers investigating coffee-microbe associations. It concludes with a discussion of the approaches and techniques that provide a path forward to improve our understanding of the coffee microbiome and its utility, as a whole and as individual components, to help ensure the future sustainability of coffee production.
Focused Directed Evolution of Aryl-Alcohol Oxidase in Saccharomyces cerevisiae by Using Chimeric Signal Peptides
Authors: Viña-Gonzalez Javier , Gonzalez-Perez David , Ferreira Patricia , Martinez Angel T. , Alcalde Miguel 
Published: July 2015

ABSTRACT

Aryl-alcohol oxidase (AAO) is an extracellular flavoprotein that supplies ligninolytic peroxidases with H
2
O
2
during natural wood decay. With a broad substrate specificity and highly stereoselective reaction mechanism, AAO is an attractive candidate for studies into organic synthesis and synthetic biology, and yet the lack of suitable heterologous expression systems has precluded its engineering by directed evolution. In this study, the native signal sequence of AAO from
Pleurotus eryngii
was replaced by those of the mating α-factor and the K
1
killer toxin, as well as different chimeras of both prepro-leaders in order to drive secretion in
Saccharomyces cerevisiae
. The secretion of these AAO constructs increased in the following order: preproα-AAO > preαproK-AAO > preKproα-AAO > preproK-AAO. The chimeric preαproK-AAO was subjected to focused-directed evolution with the aid of a dual screening assay based on the Fenton reaction. Random mutagenesis and DNA recombination was concentrated on two protein segments (Met[α1]-Val109 and Phe392-Gln566), and an array of improved variants was identified, among which the FX7 mutant (harboring the H91N mutation) showed a dramatic 96-fold improvement in total activity with secretion levels of 2 mg/liter. Analysis of the N-terminal sequence of the FX7 variant confirmed the correct processing of the preαproK hybrid peptide by the KEX2 protease. FX7 showed higher stability in terms of pH and temperature, whereas the pH activity profiles and the kinetic parameters were maintained. The Asn91 lies in the flavin attachment loop motif, and it is a highly conserved residue in all members of the GMC superfamily, except for
P. eryngii
and
P. pulmonarius
AAO. The
in vitro
involution of the enzyme by restoring the consensus ancestor Asn91 promoted AAO expression and stability.
Tools for ‘safety netting’ in common paediatric illnesses: a systematic review in emergency care
Authors: de Vos-Kerkhof Evelien , Geurts Dorien HF , Wiggers Mariska , Moll Henriette A , Oostenbrink Rianne 
Published: July 2015

ContextFollow-up strategies after emergency department (ED) discharge, alias safety netting, is often based on the gut feeling of the attending physician.ObjectiveTo systematically identify evaluated safety-netting strategies after ED discharge and to describe determinants of paediatric ED revisits.Data sourcesMEDLINE, Embase, CINAHL, Cochrane central, OvidSP, Web of Science, Google Scholar, PubMed.Study selectionStudies of any design reporting on safety netting/follow-up after ED discharge and/or determinants of ED revisits for the total paediatric population or specifically for children with fever, dyspnoea and/or gastroenteritis. Outcomes included complicated course of disease after initial ED visit (eg, revisits, hospitalisation).Data extractionTwo reviewers independently assessed studies for eligibility and study quality. As meta-analysis was not possible due to heterogeneity of studies, we performed a narrative synthesis of study results. A best-evidence synthesis was used to identify the level of evidence.ResultsWe summarised 58 studies, 36% (21/58) were assessed as having low risk of bias. Limited evidence was observed for different strategies of safety netting, with educational interventions being mostly studied. Young children, a relevant medical history, infectious/respiratory symptoms or seizures and progression/persistence of symptoms were strongly associated with ED revisits. Gender, emergency crowding, physicians’ characteristics and diagnostic tests and/or therapeutic interventions at the index visit were not associated with revisits.ConclusionsWithin the heterogeneous available evidence, we identified a set of strong determinants of revisits that identify high-risk groups in need for safety netting in paediatric emergency care being related to age and clinical symptoms. Gaps remain on intervention studies concerning specific application of a uniform safety-netting strategy and its included time frame.
International comparison of sudden unexpected death in infancy rates using a newly proposed set of cause-of-death codes
Authors: Taylor Barry J , Garstang Joanna , Engelberts Adele , Obonai Toshimasa , Cote Aurore , Freemantle Jane , Vennemann Mechtild , Healey Matt , Sidebotham Peter , Mitchell Edwin A , Moon Rachel Y 
Published: July 2015

BackgroundComparing rates of sudden unexpected death in infancy (SUDI) in different countries and over time is difficult, as these deaths are certified differently in different countries, and, even within the same jurisdiction, changes in this death certification process have occurred over time.AimsTo identify if International Classification of Diseases-10 (ICD-10) codes are being applied differently in different countries, and to develop a more robust tool for international comparison of these types of deaths.MethodsUsage of six ICD-10 codes, which code for the majority of SUDI, was compared for the years 2002–2010 in eight high-income countries.ResultsThere was a great variability in how each country codes SUDI. For example, the proportion of SUDI coded as sudden infant death syndrome (R95) ranged from 32.6% in Japan to 72.5% in Germany. The proportion of deaths coded as accidental suffocation and strangulation in bed (W75) ranged from 1.1% in Germany to 31.7% in New Zealand. Japan was the only country to consistently use the R96 code, with 44.8% of SUDI attributed to that code. The lowest, overall, SUDI rate was seen in the Netherlands (0.19/1000 live births (LB)), and the highest in New Zealand (1.00/1000 LB). SUDI accounted for one-third to half of postneonatal mortality in 2002–2010 for all of the countries except for the Netherlands.ConclusionsThe proposed set of ICD-10 codes encompasses the codes used in different countries for most SUDI cases. Use of these codes will allow for better international comparisons and tracking of trends over time.
Role of probiotics VSL#3 in prevention of suspected sepsis in low birthweight infants in India: a randomised controlled trial
Authors: Sinha Anju , Gupta Subodh S , Chellani Harish , Maliye Chetna , Kumari Vidya , Arya Sugandha , Garg BS , Gaur Sunita Dixit , Gaind Rajni , Deotale Vijayshri , Taywade Manish , Prasad MS , Thavraj Vasantha , Mukherjee Ajit , Roy Malabika 
Published: July 2015

ObjectivesTo assess the effect of the probiotic VSL#3 in prevention of neonatal sepsis in low birthweight (LBW) infants.DesignRandomised, double-blind, placebo-controlled trial.SettingCommunity setting in rural India.ParticipantsLBW infants aged 3–7 days.InterventionsInfants were randomised to receive probiotic (VSL#3, 10 billion colony-forming units (cfu)) or placebo for 30 days, and were followed up for 2 months.Main outcome measurePossible serious bacterial infection (PSBI) as per the Integrated Management of Neonatal Childhood Illnesses algorithm, as diagnosed by fieldworkers/physicians.Results668 infants were randomised to VSL#3 and 672 to placebo. By intention-to-treat analysis, the risk of PSBI among infants in the overall population of LBW infants was not statistically significant (RR 0.79 (95% CI 0.56 to 1.03)). Probiotics reduced median days of hospitalisation (6 days vs 3 days in probiotics) (p=0.018) but not the risk of hospitalisation (RR 0.66 (95% CI 0.42 to 1.04). The onset of PSBI in 10% of infants occurred on the 40th day in the probiotics arm versus the 25th day in the control arm (p=0.063).ConclusionsDaily supplementation of LBW infants with probiotics VSL#3 (10 billion cfu) for 30 days led to a non-significant 21% reduction in risk of neonatal sepsis. A larger study with sufficient power and a more specific primary end point is warranted to confirm the preventive effect of VSL#3 on neonatal sepsis in LBW infants.Trial registration numberThe study is registered at the Clinical Trial Registry of India (CTRI/2008/091/000049).
Effectiveness of a low-intensity telephone counselling intervention on an untreated metabolic syndrome detected by national population screening in Korea: a non-randomised study using regression discontinuity design
Authors: Yi Sang-Wook , Shin Soon-Ae , Lee Youn-Jung 
Published: July 2015

ObjectiveWhether low-intensity telephone-counselling interventions can improve cardiometabolic risk factors in screen-detected people with metabolic syndrome (MetS) is unclear. The aim of this study was to evaluate the effectiveness of a low-intensity, telephone-counselling programme on MetS implemented by the National Health Insurance Service (NHIS) of Korea using regression discontinuity design.DesignA nationwide non-randomised intervention study with a regression discontinuity design. A retrospective analysis using data from NHIS.SettingNHIS, Korea from January 2011 to June 2013.Participants5 378 558 beneficiaries with one or more MetS components by NHIS criteria detected by population screening were enrolled in the NHIS MetS Management Programme in 2012. Of these, 1 147 695 underwent annual follow-up examinations until June 2013 (‘control group’ which received control intervention, n=855 870; ‘eligible group’ which was eligible for counselling, n=291 825; ‘intervention group’ which participated in telephone counselling among eligible groups, n=23 968).Main outcome measuresAbsolute changes in MetS components, weight and body mass index (BMI) were analysed. Multiple regression analyses were applied using the analysis of covariance model (baseline measurements as covariates).ResultsLow-intensity telephone counselling was associated with decreased systolic BP (−0.85 mm Hg, 95% CI −1.02 to −0.68), decreased diastolic BP (−0.63 mm Hg, −95% CI −0.75 to −0.50), decreased triglyceride (−1.57 mg/dL, 95% CI −2.89 to −0.25), reduced waist circumference (−0.09 cm, 95% CI −0.16 to −0.02), reduced weight (−0.19 kg, 95% CI −0.24 to −0.15) and reduced BMI (−0.07 kg/m2, 95% CI −0.09 to −0.05), when comparing the intervention and control groups. When individuals with low high-density lipoprotein cholesterol were analysed, the intervention was also associated with increased HDL cholesterol (0.90 mg/dL, 95% CI 0.51 to 1.29).ConclusionsLow-intensity telephone counselling programmes could yield improvements in the following year on blood pressure, lipid profiles, weight and body mass index in untreated patients detected at the population screening. However, the improvements may be very modest and the clinical relevance of these small improvements may be limited.