bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transposon Mutagenesis Identifies Genes Critical for Growth of Pseudomonas nitroreducens TX1 on Octylphenol Polyethoxylates
Authors: Nguyen Tuan Ngoc , Yeh Chen-Wei , Tsai Po-Chun , Lee Kyoung , Huang Shir-Ly 
Published: September 2016

ABSTRACT

Pseudomonas nitroreducens
TX1 is of special interest because of its ability to utilize 0.05% to 20% octylphenol polyethoxylates (OPEO

n

) as a sole source of carbon. In this study, a library containing 30,000 Tn
5
-insertion mutants of the wild-type strain TX1 was constructed and screened for OPEO

n

utilization, and 93 mutants were found to be unable to grow on OPEO

n

. In total, 42 separate disrupted genes were identified, and the proteins encoded by the genes were then classified into various categories, namely, information storage and processing (14.3%), cellular processes and signaling (28.6%), metabolism (35.7%), and unknown proteins (21.4%). The individual deletion of genes encoding isocitrate lyase (
aceA
), malate synthase (
aceB
), and glycolate dehydrogenase (
glcE
) was carried out, and the requirement for
aceA
and
aceB
but not
glcE
confirmed the role of the glyoxylate cycle in OPEO

n

degradation. Furthermore, acetaldehyde dehydrogenase and acetyl-coenzyme A (acetyl-CoA) synthetase activity levels were 13.2- and 2.1-fold higher in TX1 cells grown on OPEO

n

than in TX1 cells grown on succinate, respectively. Growth of the various mutants on different carbon sources was tested, and based on these findings, a mechanism involving exoscission to liberate acetaldehyde from the end of the OPEO

n

chain during degradation is proposed for the breakdown of OPEO

n

.

IMPORTANCE
Octylphenol polyethoxylates belong to the alkylphenol polyethoxylate (APEO

n

) nonionic surfactant family. Evidence based on the analysis of intermediate metabolites suggested that the primary biodegradation of APEO

n

can be achieved by two possible pathways for the stepwise removal of the C
2
ethoxylate units from the end of the chain. However, direct evidence for these hypotheses is still lacking. In this study, we described the use of transposon mutagenesis to identify genes critical to the catabolism of OPEO

n

by
P. nitroreducens
TX1. The exoscission of the ethoxylate chain leading to the liberation of acetaldehyde is proposed. Isocitrate lyase and malate synthase in glyoxylate cycle are required in the catabolism of ethoxylated surfactants. Our findings also provide many gene candidates that may help elucidate the mechanisms in stress responses to ethoxylated surfactants by bacteria.
Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils
Authors: Pold Grace , Billings Andrew F. , Blanchard Jeff L. , Burkhardt Daniel B. , Frey Serita D. , Melillo Jerry M. , Schnabel Julia , van Diepen Linda T. A. , DeAngelis Kristen M. 
Published: September 2016

ABSTRACTAs Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated withActinobacteriain all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.IMPORTANCEThe massive carbon stocks currently held in soils have been built up over millennia, and while numerous lines of evidence indicate that climate change will accelerate the processing of this carbon, it is unclear whether the genetic repertoire of the microbes responsible for this elevated activity will also change. In this study, we showed that bacteria isolated from plots subject to 20 years of 5°C of warming were more likely to depolymerize the plant polymers xylan and cellulose, but that carbohydrate degradation capacity is not uniformly enriched by warming treatment in the metagenomes of soil microbial communities. This study illustrates the utility of combining culture-dependent and culture-independent surveys of microbial communities to improve our understanding of the role changing microbial communities may play in soil carbon cycling under climate change.
Glycosulfatase-Encoding Gene Cluster in Bifidobacterium breve UCC2003
Authors: Egan Muireann , Jiang Hao , O'Connell Motherway Mary , Oscarson Stefan , van Sinderen Douwe 
Published: September 2016

ABSTRACT

Bifidobacteria constitute a specific group of commensal bacteria typically found in the gastrointestinal tract (GIT) of humans and other mammals.
Bifidobacterium breve
strains are numerically prevalent among the gut microbiota of many healthy breastfed infants. In the present study, we investigated glycosulfatase activity in a bacterial isolate from a nursling stool sample,
B. breve
UCC2003. Two putative sulfatases were identified on the genome of
B. breve
UCC2003. The sulfated monosaccharide
N
-acetylglucosamine-6-sulfate (GlcNAc-6-S) was shown to support the growth of
B. breve
UCC2003, while
N
-acetylglucosamine-3-sulfate,
N
-acetylgalactosamine-3-sulfate, and
N
-acetylgalactosamine-6-sulfate did not support appreciable growth. By using a combination of transcriptomic and functional genomic approaches, a gene cluster designated
ats2
was shown to be specifically required for GlcNAc-6-S metabolism. Transcription of the
ats2
cluster is regulated by a repressor open reading frame kinase (ROK) family transcriptional repressor. This study represents the first description of glycosulfatase activity within the
Bifidobacterium
genus.

IMPORTANCE
Bifidobacteria are saccharolytic organisms naturally found in the digestive tract of mammals and insects.
Bifidobacterium breve
strains utilize a variety of plant- and host-derived carbohydrates that allow them to be present as prominent members of the infant gut microbiota as well as being present in the gastrointestinal tract of adults. In this study, we introduce a previously unexplored area of carbohydrate metabolism in bifidobacteria, namely, the metabolism of sulfated carbohydrates.
B. breve
UCC2003 was shown to metabolize
N
-acetylglucosamine-6-sulfate (GlcNAc-6-S) through one of two sulfatase-encoding gene clusters identified on its genome. GlcNAc-6-S can be found in terminal or branched positions of mucin oligosaccharides, the glycoprotein component of the mucous layer that covers the digestive tract. The results of this study provide further evidence of the ability of this species to utilize mucin-derived sugars, a trait which may provide a competitive advantage in both the infant gut and adult gut.
CYP101J2, CYP101J3, and CYP101J4, 1,8-Cineole-Hydroxylating Cytochrome P450 Monooxygenases from Sphingobium yanoikuyae Strain B2
Authors: Unterweger Birgit , Bulach Dieter M. , Scoble Judith , Midgley David J. , Greenfield Paul , Lyras Dena , Johanesen Priscilla , Dumsday Geoffrey J. 
Published: September 2016

ABSTRACT

We report the isolation and characterization of three new cytochrome P450 monooxygenases: CYP101J2, CYP101J3, and CYP101J4. These P450s were derived from
Sphingobium yanoikuyae
B2, a strain that was isolated from activated sludge based on its ability to fully mineralize 1,8-cineole. Genome sequencing of this strain in combination with purification of native 1,8-cineole-binding proteins enabled identification of 1,8-cineole-binding P450s. The P450 enzymes were cloned, heterologously expressed (N-terminally His
6
tagged) in
Escherichia coli
BL21(DE3), purified, and spectroscopically characterized. Recombinant whole-cell biotransformation in
E. coli
demonstrated that all three P450s hydroxylate 1,8-cineole using electron transport partners from
E. coli
to yield a product putatively identified as (1
S
)-2α-hydroxy-1,8-cineole or (1
R
)-6α-hydroxy-1,8-cineole. The new P450s belong to the CYP101 family and share 47% and 44% identity with other 1,8-cineole-hydroxylating members found in
Novosphingobium aromaticivorans
and
Pseudomonas putida
. Compared to P450
cin
(CYP176A1), a 1,8-cineole-hydroxylating P450 from
Citrobacter braakii
, these enzymes share less than 30% amino acid sequence identity and hydroxylate 1,8-cineole in a different orientation. Expansion of the enzyme toolbox for modification of 1,8-cineole creates a starting point for use of hydroxylated derivatives in a range of industrial applications.

IMPORTANCE
CYP101J2, CYP101J3, and CYP101J4 are cytochrome P450 monooxygenases from
S. yanoikuyae
B2 that hydroxylate the monoterpenoid 1,8-cineole. These enzymes not only play an important role in microbial degradation of this plant-based chemical but also provide an interesting route to synthesize oxygenated 1,8-cineole derivatives for applications as natural flavor and fragrance precursors or incorporation into polymers. The P450 cytochromes also provide an interesting basis from which to compare other enzymes with a similar function and expand the CYP101 family. This could eventually provide enough bacterial parental enzymes with similar amino acid sequences to enable
in vitro
evolution via DNA shuffling.
Cleavage of Rubber by the Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30: Molecular Insights
Authors: Röther Wolf , Austen Stefanie , Birke Jakob , Jendrossek Dieter 
Published: September 2016

ABSTRACT

Gram-positive rubber degraders such as
Streptomyces
sp. strain K30 cleave rubber [poly(
cis
-1,4-isoprene)] to low-molecular-mass oligoisoprenoid products with terminal keto and aldehyde groups by the secretion of a latex clearing protein (Lcp) designated rubber oxygenase. Lcp
K30
is a heme
b
cytochrome and has a domain of unknown function (DUF2236) that is characteristic of orthologous Lcps. Proteins with a DUF2236 domain are characterized by three highly conserved residues (R164, T168, and H198 in Lcp
K30
). Exchange of R164 or T168 by alanine and characterization of the purified Lcp
K30
muteins revealed that both were stable and contained a heme group (red color) but were inactive. This finding identifies both residues as key residues for the cleavage reaction. The purified H198A mutein was also inactive and stable but was colorless due to the absence of heme. We constructed and characterized alanine muteins of four additional histidine residues moderately conserved in 495 Lcp
K30
homologous sequences (H203A, H232A, H259A, H266A). All muteins revealed wild-type properties, excluding any importance for activity and/or heme coordination. Since Lcp
K30
has only eight histidines and the three remaining residues (H103, H184, and H296) were not conserved (<11%), H198 presumably is the only essential histidine, indicating its putative function as a heme ligand. The second axial position of the heme is likely occupied by a not yet identified molecule. Mutational analysis of three strictly conserved arginine residues (R195, R202, R328) showed that R195A and R202A muteins were colorless and instable, suggesting that these residues are important for the protein stability.

IMPORTANCE
Large amounts of rubber waste materials have been permanently released into the environment for more than a century, yet accumulation of rubber particles released, e.g., by abrasion of tires along highways has not been observed. This is indicative of the ubiquitous presence and activity of rubber-degrading microorganisms. Despite increasing research activities on rubber biodegradation during the last 2 decades, the knowledge of the enzymatic cleavage mechanism of rubber by latex clearing protein (Lcp) still is limited. In particular, the catalytic cleavage mechanism and the amino acids of Lcp proteins (Lcps) that are involved have not yet been identified for any Lcp. In this study, we investigated the importance of 10 amino acid residues of Lcp from
Streptomyces
sp. K30 (Lcp
K30
) by mutagenesis, mutein purification, and biochemical characterization. We identified several essential residues, one of which most likely represents an axial heme ligand in Lcp of
Streptomyces
sp. K30.
Essential Genes forIn VitroGrowth of the Endophyte Herbaspirillum seropedicae SmR1 as Revealed by Transposon Insertion Site Sequencing
Authors: Rosconi Federico , de Vries Stefan P. W. , Baig Abiyad , Fabiano Elena , Grant Andrew J. 
Published: September 2016

ABSTRACTThe interior of plants contains microorganisms (referred to as endophytes) that are distinct from those present at the root surface or in the surrounding soil.Herbaspirillum seropedicaestrain SmR1, belonging to the betaproteobacteria, is an endophyte that colonizes crops, including rice, maize, sugarcane, and sorghum. Different approaches have revealed genes and pathways regulated during the interactions ofH. seropedicaewith its plant hosts. However, functional genomic analysis of transposon (Tn) mutants has been hampered by the lack of genetic tools. Here we successfully employed a combination ofin vivohigh-densitymarinerTn mutagenesis and targeted Tn insertion site sequencing (Tn-seq) inH. seropedicaeSmR1. The analysis of multiple gene-saturating Tn libraries revealed that 395 genes are essential for the growth ofH. seropedicaeSmR1 in tryptone-yeast extract medium. A comparative analysis with the Database of Essential Genes (DEG) showed that 25 genes are uniquely essential inH. seropedicaeSmR1. The Tn mutagenesis protocol developed and the gene-saturating Tn libraries generated will facilitate elucidation of the genetic mechanisms of theH. seropedicaeendophytic lifestyle.IMPORTANCEA focal point in the study of endophytes is the development of effective biofertilizers that could help to reduce the input of agrochemicals in croplands. Besides the ability to promote plant growth, a good biofertilizer should be successful in colonizing its host and competing against the native microbiota. By using a systematic Tn-based gene-inactivation strategy and massively parallel sequencing of Tn insertion sites (Tn-seq), it is possible to study the fitness of thousands of Tn mutants in a single experiment. We have applied the combination of these techniques to the plant-growth-promoting endophyteHerbaspirillum seropedicaeSmR1. The Tn mutant libraries generated will enable studies into the genetic mechanisms ofH. seropedicae-plant interactions. The approach that we have taken is applicable to other plant-interacting bacteria.
Onsite midwife-led birth units (OMBUs) for care around the time of childbirth: a systematic review
Authors: Long Qian , Allanson Emma R , Pontre Jennifer , Tunçalp Özge , Hofmeyr George Justus , Gülmezoglu Ahmet Metin 
Published: September 2016

IntroductionTo ensure timely access to comprehensive emergency obstetric care in low- and middle-income countries, a number of interventions have been employed. This systematic review assesses the effects of onsite midwife-led birth units (OMBUs) embedded within hospitals which provide comprehensive emergency obstetric and newborn care.MethodsBoth interventional and observational studies that compared OMBUs with standard medical-led obstetric care were eligible for inclusion. Cochrane Central Register of Controlled Trials, PubMed/Medline, EMBASE, CINAHL, Science Citation and Social Sciences Citation Index, Global Health Library and one Chinese database were searched. Meta-analysis was conducted to synthesise data from randomised controlled trials (RCTs). Findings of observational studies were summarised by forest plots with brief narratives.ResultsThree RCTs, one controlled before-and-after study and six cohort studies were included. There were no or very few maternal and perinatal deaths in either OMBUs or standard obstetric units, with no significant differences between the two. Women giving birth in OMBUs were less likely to use epidural analgesia (risk ratio (RR) 0.67, 95% CI 0.55 to 0.82; three trials, n=2431). The UK national cohort study and two other cohorts in China and Nepal found less oxytocin augmentation, more spontaneous vaginal deliveries, fewer caesarean sections and fewer episiotomies performed in OMBUs than in standard obstetric units. These differences were not statistically significant in RCTs and the remaining cohorts. One study investigated satisfaction with midwife-led birth care among women and midwives, with positive findings in both groups favouring OMBUs. In addition, two studies found that the total cost of birth was lower in OMBUs than in standard obstetric units.ConclusionsOMBUs could be an alternative model for providing safe and cost-effective childbirth care, which may be particularly important in low- and middle-income countries to meet the growing demand for facility-based birth for low-risk women and improve efficiency of health systems.
Is self-monitoring of blood glucose effective in improving glycaemic control in type 2 diabetes without insulin treatment: a meta-analysis of randomised controlled trials
Authors: Zhu Hongmei , Zhu Yanan , Leung Siu-wai 
Published: September 2016

ObjectiveThe present study aimed to verify the effectiveness of self-monitoring of blood glucose (SMBG) in patients with non-insulin-treated type 2 diabetes (T2D).MethodsA comprehensive literature search was conducted in PubMed, Cochrane Library, Web of Science, ScienceDirect and ClinicalTrials.gov from their respective inception dates to 26 October 2015. Eligible randomised controlled trials (RCTs) were included according to prespecified criteria. The quality of the included RCTs was evaluated according to the Cochranerisk ofbiastool, and the evidence quality of meta-analyses was assessed by the Grading of Recommendation, Assessment, Development, and Evaluation (GRADE) criteria. A meta-analysis of primary and secondary outcome measures was performed. Sensitivity and subgroup analyses were carried out to evaluate the robustness and heterogeneity of the findings. Begg's and Egger's tests were used to quantify publication biases.ResultsA total of 15 RCTs, comprising 3383 patients with non-insulin-treated T2D, met the inclusion criteria. The SMBG intervention improved glycated haemoglobin (HbA1c) (mean difference −0.33; 95% CI −0.45 to −0.22; p=3.0730e−8; n=18), body mass index (BMI; −0.65; −1.18 to −0.12; p=0.0164; n=9) and total cholesterol (TC; −0.12; −0.20 to −0.04; p=0.0034; n=8) more effectively than the control in overall effect. The sensitivity analysis revealed little difference in overall effect, indicating the robustness of the results. SMBG moderated HbA1c levels better than the control in all subgroup analyses. Most of the RCTs had high risk of bias in blinding, while the overall quality of evidence for HbA1c was moderate according to the GRADE criteria. Publication bias was moderate for BMI.ConclusionsSMBG improved HbA1c levels in the short term (≤6-month follow-up) and long term (≥12-month follow-up) in patients with T2D who were not using insulin.Trial registration numberCRD42015019099.
Barriers and facilitators to patient and public engagement and recruitment to digital health interventions: protocol of a systematic review of qualitative studies
Authors: O'Connor Siobhan , Hanlon Peter , O'Donnell Catherine A , Garcia Sonia , Glanville Julie , Mair Frances S 
Published: September 2016

IntroductionPatients and the public are beginning to use digital health tools to assist in managing chronic illness, support independent living and self-care, and remain connected to health and care providers. However, engaging with and enrolling in digital health interventions, such as telehealth systems, mobile health applications, patient portals and personal health records, in order to use them varies considerably. Many factors affect people's ability to engage with and sign up to digital health platforms.ObjectivesThe primary aim is to identify the barriers and facilitators patients and the public experience to engagement and recruitment to digital health interventions. The secondary aim is to identify engagement and enrolment strategies, leading if possible to a taxonomy of such approaches, and a conceptual framework of digital health engagement and recruitment processes.MethodsA systematic review of qualitative studies will be conducted by searching six databases: MEDLINE, CINAHL, PubMed, EMBASE, Scopus and the ACM Digital Library for papers published between 2000 and 2015. Titles and abstracts along with full-text papers will be screened by two independent reviewers against predetermined inclusion and exclusion criteria. A data extraction form will be used to provide details of the included studies. Quality assessment will be conducted using the Consolidated Criteria for Reporting Qualitative Research checklist. Any disagreements will be resolved through discussion with an independent third reviewer. Analysis will be guided by framework synthesis and informed by normalization process theory and burden of treatment theory, to aid conceptualisation of digital health engagement and recruitment processes.DiscussionThis systematic review of qualitative studies will explore factors affecting engagement and enrolment in digital health interventions. It will advance our understanding of readiness for digital health by examining the complex factors that affect patients’ and the public's ability to take part.Trial registration numberCRD42015029846.
Cross-sectional study on the relationship between the level of serum cystatin C and blood pressure reverse dipping in hypertensive patients
Authors: Han Jin , Gao Ya , Guo Qi , Su Dan , Yan Bin , Peng Liyuan , Du Yuxing , Li Ke , Wang Gang 
Published: September 2016

ObjectiveTo investigate the relationship between the level of serum cystatin C (s-CC) and reverse-dipper blood pressure (BP) pattern.DesignCross-sectional study.SettingSingle centre.ParticipantsA total of 718 hypertensive patients were eventually recruited from cardiac clinics between 2012 and 2014 in the Second Affiliated Hospital, Xi'an Jiaotong University. They were diagnosed as essential hypertension according to their casual office records of systolic blood pressure (SBP) and/or diastolic blood pressure (DBP). Patients were excluded if they were <18 or >90 years old, under antihypertensive treatment, night workers, suffering from acute stroke or myocardial infarction within the past 6 months, diagnosed as secondary hypertension, sleep apnoea or other sleep disorders, renal failure, cardiac failure, chronic obstructive pulmonary disease, women during pregnancy or intolerant to the ambulatory BP monitoring (ABPM).MeasurementThe selected patients were evaluated with 24 hours ABPM. Peripheral venous blood samples were collected to evaluate the s-CC levels by ELISA.MethodsThe distribution of hypertensive patients with different levels of s-CC among each circadian BP pattern group was analysed using analysis of variance. Multinomial logistic regression analysis was applied to explore the relationship between the relevant variables and ABPM results.ResultsS-CC level in reverse-dipper group (1.19±0.53 mg/L) was increased significantly when compared with dipper group (1.06±0.36 mg/L) (p=0.021). In addition, after multinomial logistic regression analysis, s-CC (OR 1.717; 95% CI 1.033 to 2.854; p=0.037) and diabetes (OR 2.313; 95% CI 1.401 to 3.821; p=0.01) were significantly different between the reverse-dipper group and dipper group. On the other hand, the decline rate of nocturnal SBP (r=−0.117; p=0.002) and DBP (r=−0.089; p=0.018) was negatively correlated with the s-CC level.ConclusionsThe s-CC level was significantly higher in the reverse-dipper group than the dipper group and that s-CC was associated with the reverse-dipper pattern of BP examined with 24 hour ABPM.