bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Subfamily Esterase with a Homoserine Transacetylase-like Fold but No Transferase Activity
Authors: Li Ping-Yi , Yao Qiong-Qiong , Wang Peng , Zhang Yi , Li Yue , Zhang Yan-Qi , Hao Jie , Zhou Bai-Cheng , Chen Xiu-Lan , Shi Mei , Zhang Yu-Zhong , Zhang Xi-Ying 
Published: February 2017

ABSTRACT

Microbial esterases play important roles in deep-sea organic carbon degradation and cycling. Although they have similar catalytic triads and oxyanion holes, esterases are hydrolases and homoserine transacetylases (HTAs) are transferases. Because two HTA homologs were identified as acetyl esterases, the HTA family was recently divided into the
bona fide
acetyltransferase subfamily and the acetyl esterase subfamily. Here, we identified and characterized a novel HTA-like esterase, Est22, from a deep-sea sedimentary metagenomic library. Est22 could efficiently hydrolyze esters with acyl lengths of up to six carbon atoms but had no transacetylase activity, which is different from HTAs and HTA-like acetyl esterases. Phylogenetic analysis also showed that Est22 and its homologs form a separate branch of the HTA family. We solved the structures of Est22 and its L374D mutant and modeled the structure of the L374D mutant with
p
-nitrophenyl butyrate. Based on structural, mutational, and biochemical analyses, Phe
71
and Met
176
in the oxyanion hole and Arg
294
were revealed to be the key substrate-binding residues. A detailed structural comparison indicated that differences in their catalytic tunnels lead to the different substrate specificities of Est22 and the other two HTA subfamilies. Biochemical and sequence analyses suggested that Est22 homologs may have the same substrate recognition and catalysis mechanisms as Est22. Due to the significant differences in sequences, structures, and substrate specificities between Est22 (and its homologs) and the other two HTA subfamilies, we suggest that Est22 and its homologs represent a new subfamily in the HTA family.

IMPORTANCE
Microbial esterases play important roles in the turnover of organic carbon in the deep sea. Esterases and HTAs represent two groups of α/β hydrolases. Esterases catalyze the hydrolysis of simple esters and are widely used in the pharmaceutical and agrochemical industries, while HTAs catalyze the transfer of an acetyl group from acetyl-coenzyme A (CoA) to homoserine and are essential for microbial growth. Here, we report on a novel HTA-like esterase, Est22, from a deep-sea sediment. Because of the significant differences in sequences, structures, and substrate specificities of HTAs and HTA-like acetyl esterases, Est22 and its homologs represent a new subfamily in the HTA family. This study offers new knowledge regarding marine esterases.
Botrytisfragariae, a New Species Causing Gray Mold on Strawberries, Shows High Frequencies of Specific and Efflux-Based Fungicide Resistance
Authors: Rupp Sabrina , Plesken Cecilia , Rumsey Sibylle , Dowling Madeline , Schnabel Guido , Weber Roland W. S. , Hahn Matthias 
Published: February 2017

ABSTRACT

Botrytis cinerea
causes pre- and postharvest decay of many fruit and vegetable crops. A survey of German strawberry fields revealed
Botrytis
strains that differed from
B. cinerea
in diagnostic PCR markers and growth appearance. Phylogenetic analyses showed that these strains belong to an undescribed species in
Botrytis
clade 2, named
Botrytis
fragariae
sp. nov. Isolates of
B
.
fragariae
were detected in strawberry fields throughout Germany, sometimes at frequencies similar to those of
B. cinerea
, and in the southeastern United States.
B
.
fragariae
was isolated from overwintering strawberry tissue but not from freshly infected fruit.
B
.
fragariae
invaded strawberry tissues with an efficiency similar to or lower than that of
B. cinerea
but showed poor colonization of inoculated nonhost plant tissues. These data and the exclusive occurrence of this fungus on strawberry plants indicate that
B
.
fragariae
is host specific and has a tissue preference different from that of
B. cinerea
. Various fungicide resistance patterns were observed in
B
.
fragariae
populations. Many
B
.
fragariae
strains showed resistance to one or several chemical classes of fungicides and an efflux-based multidrug resistance (MDR1) phenotype previously described in
B. cinerea
. Resistance-related mutations in
B
.
fragariae
were identical or similar to those of
B. cinerea
for carbendazim (E198A mutation in
tubA
), azoxystrobin (G143A in
cytB
), iprodione (G367A+V368F in
bos1
), and MDR1 (gain-of-function mutations in the transcription factor
mrr1
gene and overexpression of the drug efflux transporter gene
atrB
). The widespread occurrence of
B
.
fragariae
indicates that this species is adapted to fungicide-treated strawberry fields and may be of local importance as a gray mold pathogen alongside
B. cinerea
.

IMPORTANCE
Gray mold is the most important fruit rot on strawberries worldwide and requires fungicide treatments for control. For a long time, it was believed to be caused only by
Botrytis cinerea
, a ubiquitous pathogen with a broad host range that quickly develops fungicide resistance. We report the discovery and description of a new species, named
Botrytis
fragariae
, that is widely distributed in commercial strawberry fields in Germany and the southeastern United States. It was observed on overwintering tissue but not on freshly infected fruit and seems host specific on the basis of its occurrence and artificial infection tests.
B
.
fragariae
has also developed resistance to several fungicides that is caused by mutations similar to those known in
B. cinerea
, including an efflux-based multidrug resistance. Our data indicate that
B
.
fragariae
could be of practical importance as a strawberry pathogen in some regions where its abundance is similar to that of
B. cinerea
.
Spread from the Sink to the Patient:
In Situ
Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli To Model Bacterial Dispersion from Hand-Washing Sink-Trap Reservoirs
Authors: Kotay Shireen , Chai Weidong , Guilford William , Barry Katie , Mathers Amy J. 
Published: February 2017

ABSTRACT

There have been an increasing number of reports implicating
Gammaproteobacteria
as often carrying genes of drug resistance from colonized sink traps to vulnerable hospitalized patients. However, the mechanism of transmission from the wastewater of the sink P-trap to patients remains poorly understood. Herein we report the use of a designated hand-washing sink lab gallery to model dispersion of green fluorescent protein (GFP)-expressing
Escherichia coli
from sink wastewater to the surrounding environment. We found no dispersion of GFP-expressing
E. coli
directly from the P-trap to the sink basin or surrounding countertop with coincident water flow from a faucet. However, when the GFP-expressing
E. coli
cells were allowed to mature in the P-trap under conditions similar to those in a hospital environment, a GFP-expressing
E. coli
-containing putative biofilm extended upward over 7 days to reach the strainer. This subsequently resulted in droplet dispersion to the surrounding areas (<30 in.) during faucet operation. We also demonstrated that P-trap colonization could occur by retrograde transmission along a common pipe. We postulate that the organisms mobilize up to the strainer from the P-trap, resulting in droplet dispersion rather than dispersion directly from the P-trap. This work helps to further define the mode of transmission of bacteria from a P-trap reservoir to a vulnerable hospitalized patient.

IMPORTANCE
Many recent reports demonstrate that sink drain pipes become colonized with highly consequential multidrug-resistant bacteria, which then results in hospital-acquired infections. However, the mechanism of dispersal of bacteria from the sink to patients has not been fully elucidated. Through establishment of a unique sink gallery, this work found that a staged mode of transmission involving biofilm growth from the lower pipe to the sink strainer and subsequent splatter to the bowl and surrounding area occurs rather than splatter directly from the water in the lower pipe. We have also demonstrated that bacterial transmission can occur via connections in wastewater plumbing to neighboring sinks. This work helps to more clearly define the mechanism and risk of transmission from a wastewater source to hospitalized patients in a world with increasingly antibiotic-resistant bacteria that can thrive in wastewater environments and cause infections in vulnerable patients.
Comparison of Biochemical Properties of the Original and Newly Identified Oleate Hydratases from Stenotrophomonas maltophilia
Authors: Kang Woo-Ri , Seo Min-Ju , Shin Kyung-Chul , Park Jin-Byung , Oh Deok-Kun 
Published: February 2017

ABSTRACT

Oleate hydratases (OhyAs) catalyze the conversion of unsaturated fatty acids to 10-hydroxy fatty acids, which are used as precursors of important industrial compounds, including lactones and ω-hydroxycarboxylic and α,ω-dicarboxylic acids. The genes encoding OhyA and a putative fatty acid hydratase in
Stenotrophomonas maltophilia
were identified by genomic analysis. The putative fatty acid hydratase was purified and identified as an oleate hydratase (OhyA2) based on its substrate specificity. The activity of OhyA2 as a holoenzyme was not affected by adding cofactors, whereas the activity of the original oleate hydratase (OhyA1) showed an increase. Thus, all characterized OhyAs were categorized as either OhyA1 or OhyA2 based on the activities of holoenzymes upon adding cofactors, which were determined by the type of the fourth conserved amino acid of flavin adenine dinucleotide (FAD)-binding motif. The hydration activities of
S. maltophilia
OhyA2 toward unsaturated fatty acids, including oleic acid, palmitoleic acid, linoleic acid, α-linolenic acid, and γ-linolenic acid, were greater than those of OhyA1. Moreover, the specific activity of
S. maltophilia
OhyA2 toward unsaturated fatty acids, with the exception of γ-linolenic acid, was the highest among all reported OhyAs.

IMPORTANCE
All characterized OhyAs were categorized as OhyA1s or OhyA2s based on the different properties of the reported and newly identified holo-OhyAs in
S. maltophilia
upon the addition of cofactors. OhyA2s showed higher activities toward polyunsaturated fatty acids (PUFAs), including linoleic acid, α-linolenic acid, and γ-linolenic acid, than those of OhyA1s. This suggests that OhyA2s can be used more effectively to convert plant oils to 10-hydroxy fatty acids because plant oils contain not only oleic acid but also PUFAs. The hydration activity of the newly identified OhyA2 from
S. maltophilia
toward oleic acid was the highest among the activity levels reported so far. Therefore, this enzyme is an efficient biocatalyst for the conversion of plant oils to 10-hydroxy fatty acids, which can be further converted to important industrial materials.
High-Resolution X-Ray Structures of Two Functionally Distinct Members of the Cyclic Amide Hydrolase Family of Toblerone Fold Enzymes
Authors: Peat Thomas S. , Balotra Sahil , Wilding Matthew , Hartley Carol J. , Newman Janet , Scott Colin 
Published: February 2017

ABSTRACT

The Toblerone fold was discovered recently when the first structure of the cyclic amide hydrolase, AtzD (a cyanuric acid hydrolase), was elucidated. We surveyed the cyclic amide hydrolase family, finding a strong correlation between phylogenetic distribution and specificity for either cyanuric acid or barbituric acid. One of six classes (IV) could not be tested due to a lack of expression of the proteins from it, and another class (V) had neither cyanuric acid nor barbituric acid hydrolase activity. High-resolution X-ray structures were obtained for a class VI barbituric acid hydrolase (1.7 Å) from a
Rhodococcus
species and a class V cyclic amide hydrolase (2.4 Å) from a
Frankia
species for which we were unable to identify a substrate. Both structures were homologous with the tetrameric Toblerone fold enzyme AtzD, demonstrating a high degree of structural conservation within the cyclic amide hydrolase family. The barbituric acid hydrolase structure did not contain zinc, in contrast with early reports of zinc-dependent activity for this enzyme. Instead, each barbituric acid hydrolase monomer contained either Na
+
or Mg
2+
, analogous to the structural metal found in cyanuric acid hydrolase. The
Frankia
cyclic amide hydrolase contained no metal but instead formed unusual, reversible, intermolecular vicinal disulfide bonds that contributed to the thermal stability of the protein. The active sites were largely conserved between the three enzymes, differing at six positions, which likely determine substrate specificity.

IMPORTANCE
The Toblerone fold enzymes catalyze an unusual ring-opening hydrolysis with cyclic amide substrates. A survey of these enzymes shows that there is a good correlation between physiological function and phylogenetic distribution within this family of enzymes and provide insights into the evolutionary relationships between the cyanuric acid and barbituric acid hydrolases. This family of enzymes is structurally and mechanistically distinct from other enzyme families; however, to date the structure of just two, physiologically identical, enzymes from this family has been described. We present two new structures: a barbituric acid hydrolase and an enzyme of unknown function. These structures confirm that members of the CyAH family have the unusual Toblerone fold, albeit with some significant differences.
Systematic review and meta-analysis of dietary carbohydrate restriction in patients with type 2 diabetes
Authors: Snorgaard Ole , Poulsen Grith M , Andersen Henning K , Astrup Arne 
Published: February 2017

ObjectiveNutrition therapy is an integral part of self-management education in patients with type 2 diabetes. Carbohydrates with a low glycemic index are recommended, but the ideal amount of carbohydrate in the diet is unclear. We performed a meta-analysis comparing diets containing low to moderate amounts of carbohydrate (LCD) (energy percentage below 45%) to diets containing high amounts of carbohydrate (HCD) in subjects with type 2 diabetes.Research design and methodsWe systematically reviewed Cochrane library databases, EMBASE, and MEDLINE in the period 2004–2014 for guidelines, meta-analyses, and randomized trials assessing the outcomes HbA1c, BMI, weight, LDL cholesterol, quality of life (QoL), and attrition.ResultsWe identified 10 randomized trials comprising 1376 participants in total. In the first year of intervention, LCD was followed by a 0.34% lower HbA1c (3.7 mmol/mol) compared with HCD (95% CI 0.06 (0.7 mmol/mol), 0.63 (6.9 mmol/mol)). The greater the carbohydrate restriction, the greater the glucose-lowering effect (R=−0.85, p<0.01). At 1 year or later, however, HbA1c was similar in the 2 diet groups. The effect of the 2 types of diet on BMI/body weight, LDL cholesterol, QoL, and attrition rate was similar throughout interventions.LimitationsGlucose-lowering medication, the nutrition therapy, the amount of carbohydrate in the diet, glycemic index, fat and protein intake, baseline HbA1c, and adherence to the prescribed diets could all have affected the outcomes.ConclusionsLow to moderate carbohydrate diets have greater effect on glycemic control in type 2 diabetes compared with high-carbohydrate diets in the first year of intervention. The greater the carbohydrate restriction, the greater glucose lowering, a relationship that has not been demonstrated earlier. Apart from this lowering of HbA1c over the short term, there is no superiority of low-carbohydrate diets in terms of glycemic control, weight, or LDL cholesterol.
Fatigue and its associated factors in liver transplant recipients in Beijing: a cross-sectional study
Authors: Lin Xiao-Hong , Teng Sha , Wang Lu , Zhang Jing , Shang Ya-Bin , Liu Hong-Xia , Zang Yun-Jin 
Published: February 2017

ObjectivesFatigue is a highly prevalent symptom experienced by patients who underwent the liver transplantation. However, the influencing factors of fatigue are poorly understood by healthcare professionals. The aim of this study was to examine the intensity, interference, duration and prevalence of fatigue in liver transplantation recipients and to explore the influencing factors of post-transplantation fatigue.DesignA cross-sectional design was used in this study.MethodsA convenience sample of liver transplant recipients was recruited at an outpatient transplant clinic of a general hospital in Beijing, China. Self-report survey data were provided by liver transplant recipients using the Fatigue Symptom Inventory (FSI), the Hospital Anxiety and Depression Scale (HADS), the Perceived Social Support Scale (PSSS) and the Athens Insomnia Scale (AIS). Demographic, clinical and psychosocial parameters were evaluated as fatigue influencing factors.ResultsParticipants (n=285) included 69 women and 216 men. Fatigue was found in 87.0% of liver transplant recipients. Mean scores of fatigue intensity items were 4.47±2.85, 1.93±1.97, 3.15±2.13 and 2.73±2.42 (most fatigue, least fatigue, average fatigue in the week prior to assessment and fatigue at the point of assessment). The mean score of fatigue interference was 2.27±2.09.The number of days fatigued in the week prior to assessment was 2.26±2.02 and the amount of time fatigued each day was 2.75±2.44. Spearman's correlation analysis showed that fatigue intensity was positively associated with anxiety, depression and insomnia (p<0.001 for all), while fatigue interference was positively associated with gender, anxiety, depression and insomnia (p<0.05 for all). In the multiple linear regression analysis, anxiety and insomnia were positively associated with fatigue intensity (p<0.001), and insomnia, depression and anxiety were positively associated with fatigue interference (p<0.001).ConclusionsFatigue is common in liver transplant recipients, and it is strongly associated with insomnia, anxiety and depression.
How does a physical activity programme in elementary school affect fracture risk? A prospective controlled intervention study in Malmo, Sweden
Authors: Cöster Marcus E , Fritz Jesper , Nilsson Jan-Åke , Karlsson Caroline , Rosengren Björn E , Dencker Magnus , Karlsson Magnus K 
Published: February 2017

ObjectivesRecent evidence from the 7-year follow-up of the Pediatric Osteoporosis Prevention (POP) study indicates an inverse correlation between years of participation in a physical activity (PA) intervention and fracture risk in children. However, we could not see a statistically significant reduction in fracture risk, which urged for an extension of the intervention.SettingThe study was conducted in 4 neighbouring elementary schools, where 1 school functioned as intervention school.ParticipantsWe included all children who began first grade in these 4 schools between 1998 and 2012. This resulted in 1339 children in the intervention group and 2195 children in the control group, all aged 6–8 years at the state of the study.InterventionWe launched an 8-year intervention programme with 40 min of moderate PA per school day, while the controls continued with the Swedish national standard of 60 min of PA per week.Primary outcome measureWe used the regional radiographic archive to register objectively verified fractures and we estimated annual fracture incidences and incidence rate ratios (IRRs).ResultsDuring the first year after initiation of the intervention, the fracture IRR was 1.65 (1.05 to 2.08) (mean 95% CI). For each year of the study, the fracture incidence rate in the control group compared with the intervention group increased by 15.7% (5.6% to 26.8%) (mean 95% CI). After 8 years, the IRR of fractures was 52% lower in the intervention group than in the control group (IRR 0.48 (0.25 to 0.91) (mean 95% CI))].ConclusionsIntroduction of the school-based intervention programme is associated with a higher fracture risk in the intervention group during the first year followed by a gradual reduction, so that during the eighth year, the fracture risk was lower in the intervention group.Trial registration numberNCT00633828.
Electronic nicotine delivery systems and/or electronic non-nicotine delivery systems for tobacco smoking cessation or reduction: a systematic review and meta-analysis
Authors: El Dib Regina , Suzumura Erica A , Akl Elie A , Gomaa Huda , Agarwal Arnav , Chang Yaping , Prasad Manya , Ashoorion Vahid , Heels-Ansdell Diane , Maziak Wasim , Guyatt Gordon 
Published: February 2017

ObjectiveA systematic review and meta-analysis to investigate the impact of electronic nicotine delivery systems (ENDS) and/or electronic non-nicotine delivery systems (ENNDS) versus no smoking cessation aid, or alternative smoking cessation aids, in cigarette smokers on long-term tobacco use.Data sourcesSearches of MEDLINE, EMBASE, PsycInfo, CINAHL, CENTRAL and Web of Science up to December 2015.Study selectionRandomised controlled trials (RCTs) and prospective cohort studies.Data extractionThree pairs of reviewers independently screened potentially eligible articles, extracted data from included studies on populations, interventions and outcomes and assessed their risk of bias. We used the Grading of Recommendations Assessment, Development and Evaluation approach to rate overall certainty of the evidence by outcome.Data synthesisThree randomised trials including 1007 participants and nine cohorts including 13 115 participants proved eligible. Results provided by only two RCTs suggest a possible increase in tobacco smoking cessation with ENDS in comparison with ENNDS (RR 2.03, 95% CI 0.94 to 4.38; p=0.07; I2=0%, risk difference (RD) 64/1000 over 6 to 12 months, low-certainty evidence). Results from cohort studies suggested a possible reduction in quit rates with use of ENDS compared with no use of ENDS (OR 0.74, 95% CI 0.55 to 1.00; p=0.051; I2=56%, very low certainty).ConclusionsThere is very limited evidence regarding the impact of ENDS or ENNDS on tobacco smoking cessation, reduction or adverse effects: data from RCTs are of low certainty and observational studies of very low certainty. The limitations of the cohort studies led us to a rating of very low-certainty evidence from which no credible inferences can be drawn. Lack of usefulness with regard to address the question of e-cigarettes' efficacy on smoking reduction and cessation was largely due to poor reporting. This review underlines the need to conduct well-designed trials measuring biochemically validated outcomes and adverse effects.