bluuebunny/crossref_metadata_2025_split huggingface dataset:
A distinct class of vesicles derived from thetrans‐Golgi mediates secretion of xylogalacturonan in the root border cell
Authors: Wang Pengfei , Chen Xinshi , Goldbeck Cameron , Chung Eric , Kang Byung‐Ho 
Published: September 2017

SummaryRoot border cells lie on the surface of the root cap and secrete massive amounts of mucilage that contains polysaccharides and proteoglycans. Golgi stacks in the border cells have hypertrophied margins, reflecting elevated biosynthetic activity to produce the polysaccharide components of the mucilage. To investigate the three‐dimensional structures and macromolecular compositions of these Golgi stacks, we examined high‐pressure frozen/freeze‐substituted alfalfa root cap cells with electron microscopy/tomography. Golgi stacks in border cells and peripheral cells, precursor cells of border cells, displayed similar morphological features, such as proliferation of transcisternae and swelling of thetranscisternae andtrans‐Golgi network (TGN) compartments. These swollen margins give rise to two types of vesicles larger than other Golgi‐associated vesicles. Margins oftrans‐Golgi cisternae accumulate theLM8 xylogalacturonan (XGA) epitope, and they become darkly stained large vesicles (LVs) after release from the Golgi. Epitopes for xyloglucan (XG), polygalacturonic acid/rhamnogalacturonan‐I (PGA/RG‐I) are detected in thetrans‐most cisternae andTGNcompartments.LVs produced fromTGNcompartments (TGN‐LVs) stained lighter thanLVs and contained the cell wall polysaccharide epitopes seen in theTGN.LVs carrying theXGAepitope fuse with the plasma membrane only in border cells, whereasTGN‐LVs containing theXGandPGA/RG‐I epitopes fuse with the plasma membrane of both peripheral cells and border cells. Taken together, these results indicate thatXGAis secreted by a novel type of secretory vesicles derived fromtrans‐Golgi cisternae. Furthermore, we simulated the collapse in the central domain of thetrans‐cisternae accompanying polysaccharide synthesis with a mathematical model.
CRISPR-Cas9
D10A
Nickase-Assisted Genome Editing in Lactobacillus casei
Authors: Song Xin , Huang He , Xiong Zhiqiang , Ai Lianzhong , Yang Sheng 
Published: September 2017

ABSTRACT

Lactobacillus casei
has drawn increasing attention as a health-promoting probiotic, while effective genetic manipulation tools are often not available, e.g., the single-gene knockout in
L. casei
still depends on the classic homologous recombination-dependent double-crossover strategy, which is quite labor-intensive and time-consuming. In the present study, a rapid and precise genome editing plasmid, pLCNICK, was established for
L. casei
genome engineering based on CRISPR-Cas9
D10A
. In addition to the P
23
-Cas9
D10A
and P
ldh
-sgRNA (single guide RNA) expression cassettes, pLCNICK includes the homologous arms of the target gene as repair templates. The ability and efficiency of chromosomal engineering using pLCNICK were evaluated by in-frame deletions of four independent genes and chromosomal insertion of an enhanced green fluorescent protein (eGFP) expression cassette at the
LC2W_1628
locus. The efficiencies associated with in-frame deletions and chromosomal insertion is 25 to 62%. pLCNICK has been proved to be an effective, rapid, and precise tool for genome editing in
L. casei
, and its potential application in other lactic acid bacteria (LAB) is also discussed in this study.

IMPORTANCE
The lack of efficient genetic tools has limited the investigation and biotechnological application of many LAB. The CRISPR-Cas9
D10A
nickase-based genome editing in
Lactobacillus casei
, an important food industrial microorganism, was demonstrated in this study. This genetic tool allows efficient single-gene deletion and insertion to be accomplished by one-step transformation, and the cycle time is reduced to 9 days. It facilitates a rapid and precise chromosomal manipulation in
L. casei
and overcomes some limitations of previous methods. This editing system can serve as a basic technological platform and offers the possibility to start a comprehensive investigation on
L. casei
. As a broad-host-range plasmid, pLCNICK has the potential to be adapted to other
Lactobacillus
species for genome editing.
Exogenous Polyunsaturated Fatty Acids Impact Membrane Remodeling and Affect Virulence Phenotypes among Pathogenic Vibrio Species
Authors: Moravec Anna R. , Siv Andrew W. , Hobby Chelsea R. , Lindsay Emily N. , Norbash Layla V. , Shults Daniel J. , Symes Steven J. K. , Giles David K. 
Published: September 2017

ABSTRACT

The pathogenic
Vibrio
species (
V. cholerae
,
V. parahaemolyticus
, and
V. vulnificus
) represent a constant threat to human health, causing foodborne and skin wound infections as a result of ingestion of or exposure to contaminated water and seafood. Recent studies have highlighted
Vibrio
's ability to acquire fatty acids from environmental sources and assimilate them into cell membranes. The possession and conservation of such machinery provokes consideration of fatty acids as important factors in the pathogenic lifestyle of
Vibrio
species. The findings here link exogenous fatty acid exposure to changes in bacterial membrane phospholipid structure, permeability, phenotypes associated with virulence, and consequent stress responses that may impact survival and persistence of pathogenic
Vibrio
species. Polyunsaturated fatty acids (PUFAs) (ranging in carbon length and unsaturation) supplied in growth medium were assimilated into bacterial phospholipids, as determined by thin-layer chromatography and liquid chromatography-mass spectrometry. The incorporation of fatty acids variably affected membrane permeability, as judged by uptake of the hydrophobic compound crystal violet. For each species, certain fatty acids were identified as affecting resistance to antimicrobial peptide treatment. Significant fluctuations were observed with regard to both motility and biofilm formation following growth in the presence of individual PUFAs. Our results illustrate the important and complex roles of exogenous fatty acids in the membrane physiology and virulence of a bacterial genus that inhabits aquatic and host environments containing an abundance of diverse fatty acids.

IMPORTANCE
Bacterial responses to fatty acids include, but are not limited to, degradation for metabolic gain, modification of membrane lipids, alteration of protein function, and regulation of gene expression.
Vibrio
species exhibit significant diversity with regard to the machinery known to participate in the uptake and incorporation of fatty acids into their membranes. Both aquatic and host niches occupied by
Vibrio
are rife with various free fatty acids and fatty acid-containing lipids. The roles of fatty acids in the environmental survival and pathogenesis of bacteria have begun to emerge and are expected to expand significantly. The current study demonstrates the responsiveness of
V. cholerae
,
V. parahaemolyticus
, and
V. vulnificus
to exogenous PUFAs. In addition to phospholipid remodeling, PUFA assimilation impacts membrane permeability, motility, biofilm formation, and resistance to polymyxin B.
Chemical Pretreatment-Independent Saccharifications of Xylan and Cellulose of Rice Straw by Bacterial Weak Lignin-Binding Xylanolytic and Cellulolytic Enzymes
Authors: Teeravivattanakit Thitiporn , Baramee Sirilak , Phitsuwan Paripok , Sornyotha Somphit , Waeonukul Rattiya , Pason Patthra , Tachaapaikoon Chakrit , Poomputsa Kanokwan , Kosugi Akihiko , Sakka Kazuo , Ratanakhanokchai Khanok 
Published: September 2017

ABSTRACT

Complete utilization of carbohydrate fractions is one of the prerequisites for obtaining economically favorable lignocellulosic biomass conversion. This study shows that xylan in untreated rice straw was saccharified to xylose in one step without chemical pretreatment, yielding 58.2% of the theoretically maximum value by
Paenibacillus curdlanolyticus
B-6 PcAxy43A, a weak lignin-binding trifunctional xylanolytic enzyme, endoxylanase/β-xylosidase/arabinoxylan arabinofuranohydrolase. Moreover, xylose yield from untreated rice straw was enhanced to 78.9% by adding endoxylanases PcXyn10C and PcXyn11A from the same bacterium, resulting in improvement of cellulose accessibility to cellulolytic enzyme. After autoclaving the xylanolytic enzyme-treated rice straw, it was subjected to subsequent saccharification by a combination of the
Clostridium thermocellum
endoglucanase CtCel9R and
Thermoanaerobacter brockii
β-glucosidase TbCglT, yielding 88.5% of the maximum glucose yield, which was higher than the glucose yield obtained from ammonia-treated rice straw saccharification (59.6%). Moreover, this work presents a new environment-friendly xylanolytic enzyme pretreatment for beneficial hydrolysis of xylan in various agricultural residues, such as rice straw and corn hull. It not only could improve cellulose saccharification but also produced xylose, leading to an improvement of the overall fermentable sugar yields without chemical pretreatment.

IMPORTANCE
Ongoing research is focused on improving “green” pretreatment technologies in order to reduce energy demands and environmental impact and to develop an economically feasible biorefinery. The present study showed that PcAxy43A, a weak lignin-binding trifunctional xylanolytic enzyme, endoxylanase/β-xylosidase/arabinoxylan arabinofuranohydrolase from
P. curdlanolyticus
B-6, was capable of conversion of xylan in lignocellulosic biomass such as untreated rice straw to xylose in one step without chemical pretreatment. It demonstrates efficient synergism with endoxylanases PcXyn10C and PcXyn11A to depolymerize xylan in untreated rice straw and enhanced the xylose production and improved cellulose hydrolysis. Therefore, it can be considered an enzymatic pretreatment. Furthermore, the studies here show that glucose yield released from steam- and xylanolytic enzyme-treated rice straw by the combination of CtCel9R and TbCglT was higher than the glucose yield obtained from ammonia-treated rice straw saccharification. This work presents a novel environment-friendly xylanolytic enzyme pretreatment not only as a green pretreatment but also as an economically feasible biorefinery method.
Cupriavidus necator H16 Uses Flavocytochrome
c
Sulfide Dehydrogenase To Oxidize Self-Produced and Added Sulfide
Authors: Lü Chuanjuan , Xia Yongzhen , Liu Daixi , Zhao Rui , Gao Rui , Liu Honglei , Xun Luying 
Published: September 2017

ABSTRACT

Production of sulfide (H
2
S, HS
−
, and S
2−
) by heterotrophic bacteria during aerobic growth is a common phenomenon. Some bacteria with sulfide:quinone oxidoreductase (SQR) and persulfide dioxygenase (PDO) can oxidize self-produced sulfide to sulfite and thiosulfate, but other bacteria without these enzymes release sulfide into the medium, from which H
2
S can volatilize into the gas phase. Here, we report that
Cupriavidus necator
H16, with the
fccA
and
fccB
genes encoding flavocytochrome
c
sulfide dehydrogenases (FCSDs), also oxidized self-produced H
2
S. A mutant in which
fccA
and
fccB
were deleted accumulated and released H
2
S. When
fccA
and
fccB
were expressed in
Pseudomonas aeruginosa
strain Pa3K with deletions of its
sqr
and
pdo
genes, the recombinant rapidly oxidized sulfide to sulfane sulfur. When PDO was also cloned into the recombinant, the recombinant with both FCSD and PDO oxidized sulfide to sulfite and thiosulfate. Thus, the proposed pathway is similar to the pathway catalyzed by SQR and PDO, in which FCSD oxidizes sulfide to polysulfide, polysulfide spontaneously reacts with reduced glutathione (GSH) to produce glutathione persulfide (GSSH), and PDO oxidizes GSSH to sulfite, which chemically reacts with polysulfide to produce thiosulfate. About 20.6% of sequenced bacterial genomes contain SQR, and only 3.9% contain FCSD. This is not a surprise, since SQR is more efficient in conserving energy because it passes electrons from sulfide oxidation into the electron transport chain at the quinone level, while FCSD passes electrons to cytochrome
c
. The transport of electrons from the latter to O
2
conserves less energy. FCSDs are grouped into three subgroups, well conserved at the taxonomic level. Thus, our data show the diversity in sulfide oxidation by heterotrophic bacteria.

IMPORTANCE
Heterotrophic bacteria with SQR and PDO can oxidize self-produced sulfide and do not release H
2
S into the gas phase.
C. necator
H16 has FCSD but not SQR, and it does not release H
2
S. We confirmed that the bacterium used FCSD for the oxidation of self-produced sulfide. The bacterium also oxidized added sulfide. The common presence of SQRs, FCSDs, and PDOs in heterotrophic bacteria suggests the significant role of heterotrophic bacteria in sulfide oxidation, participating in sulfur biogeochemical cycling. Further, FCSDs have been identified in anaerobic photosynthetic bacteria and chemolithotrophic bacteria, but their physiological roles are unknown. We showed that heterotrophic bacteria use FCSDs to oxidize self-produced sulfide and extraneous sulfide, and they may be used for H
2
S bioremediation.
Correlates of second-line type 2 diabetes medication selection in the USA
Authors: Ackermann Ronald T , Wallia Amisha , O'Brien Matthew J , Kang Raymond , Cooper Andrew , Moran Margaret R , Liss David T 
Published: September 2017

ObjectivePast research provides insufficient evidence to inform second-line diabetes medication prescribing when metformin is no longer sufficient. We evaluated patient, prescriber, and health plan characteristics associated with selection of second-line diabetes medications in the USA.Research design and methodsWe used a multiple case-comparison study design to identify characteristics associated with the probability of starting each of six second-line diabetes medication alternatives within 77 744 adults enrolled in commercial or Medicare Advantage health plans from 2011 to 2015. National administrative data were provided by a large commercial health payer. Multinomial logistic regression models were used to identify characteristics independently associated with selecting each diabetes drug class.ResultsFrom 2011 to 2015, sulfonylureas still represented 47% of all second-line drug starts, with proportionately higher use in patients ≥75 years of age (63% of drug starts). Basal insulin was more likely to be selected when a past A1c test result was >10% (13.0% vs 4.5% for those with A1c <8%; p<0.001). Initiation of a glucagon-like peptide-1 receptor agonist was associated with being female (10.1% vs 6.0% for male; p<0.001) and having a diagnosis code for obesity (10.8% vs 6.9% for no diagnosis; p<0.001). For all drug classes, the recent prescribing behavior of the provider was a strong correlate of subsequent second-line drug selection.ConclusionsSulfonylureas continue to represent almost half of second-line diabetes medication starts in the USA. This could reflect overuse for some groups such as older adults, for whom some alternatives may be safer, although more costly and potentially less effective. Future research should compare outcomes of medication choices and conditions under which particular classes are most effective.
Suicide and all-cause mortality in Swedish deployed military veterans: a population-based matched cohort study
Authors: Pethrus Carl-Martin , Johansson Kari , Neovius Kristian , Reutfors Johan , Sundström Johan , Neovius Martin 
Published: September 2017

ObjectiveTo investigate suicide and mortality risk in deployed military veterans versus non-deployed comparators who had gone through military conscription testing.DesignPopulation-based matched cohort study.SettingSweden.ParticipantsParticipants were identified from the Military Service Conscription Register and deployment status from the Swedish Military Information Personnel Register. Of 1.9 million conscripts, 21 721 had deployed at some time between 1990 and 2013 (deployed military veterans). Non-deployed comparators were matched to deployed military veterans in two ways: (1) by cognitive ability, psychological assessment, mental health, body mass index, sex, birth-year and conscription-year (carefully matched), with further adjustment for exercise capacity and suicide attempt history; and (2) by sex, birth-year and conscription-year (age- and sex-matched).Main outcomeSuicide retrieved from the Swedish National Patient and Causes of Death Register until 31 December 2013.ResultsDuring a median follow-up of 12 years, 39 and 211 deaths by suicide occurred in deployed military veterans (n=21 627) and carefully matched non-deployed comparators (n=107 284), respectively (15 vs 16/100 000 person-years; adjusted HR (aHR) 1.07; 95% CI 0.75 to 1.52; p=0.72) and 329 in age- and sex-matched non-deployed comparators (n=108 140; 25/100 000 person-years; aHR 0.59; 95% CI 0.42 to 0.82; p=0.002). There were 284 and 1444 deaths by suicide or attempted suicides in deployed military veterans and carefully matched non-deployed comparators, respectively (109 vs 112; aHR 0.99; 95% CI 0.88 to 1.13; p=0.93) and 2061 in age- and sex-matched non-deployed comparators (158; aHR 0.69; 95% CI 0.61 to 0.79; p<0.001). The corresponding figures for all-cause mortality for carefully matched non-deployed comparators were 159 and 820 (61 vs 63/100 000 person-years; aHR 0.97; 95% CI 0.82 to 1.15; p=0.71) and 1289 for age- and sex-matched non-deployed comparators (98/100 000 person-years; aHR 0.62; 95% CI 0.52 to 0.73; p<0.001).ConclusionDeployed military veterans had similar suicide and mortality risk as non-deployed comparators after accounting for psychological, psychiatric and physical factors. Studies of mental health in deployed veterans need to adjust for more factors than age and sex for comparisons to be meaningful.
Suicide and self-harm trends in recent immigrant youth in Ontario, 1996-2012: a population-based longitudinal cohort study
Authors: Saunders Natasha Ruth , Lebenbaum Michael , Stukel Therese A , Lu Hong , Urquia Marcelo L , Kurdyak Paul , Guttmann Astrid 
Published: September 2017

ObjectiveTo describe the trends in suicide and emergency department (ED) visits for self-harm in youth by immigration status and immigrant characteristics.DesignPopulation-based longitudinal cohort study from 1996 to 2012 using linked health and administrative datasets.SettingOntario, Canada.ParticipantsYouth 10 to 24 years, living in Ontario, Canada.ExposureThe main exposure was immigrant status (recent immigrant (RI) versus long-term residents (LTR)). Secondary exposures included region of birth, duration or residence, and refugee status.Main outcome measureTrends over time in suicide and ED self-harm were modelled within consecutive 3-year time periods. Rate ratios were estimated using Poisson regression models.Results2.5 to 2.9 million individuals were included per cohort period. LTR suicide rates ranged from 7.4 to 9.4/100 000 male person-years versus 2.2–3.4/100 000 females. RI’s suicide rates were 2.7–7.2/100,000 male versus 1.9–2.7/100 000 female person-years. Suicide rates were lower among RI compared with LTR (adjusted relative rate (aRR)=0.70, 95% CI=0.57 to 0.85) with different mechanisms of suicide. No significant time trend in suicide rates was observed (p=0.40). ED self-harm rates for LTR and RI were highest in females (2.6–3.4/1000 LTR females versus 1.1–1.5/1000 males, 1.2–1.8/1000 RI females versus 0.4–0.6/1000 males). RI had lower rates of self-harm compared with LTR (aRR=0.60, 95% CI=0.56 to 0.65). Stratum-specific rates showed a steeper decline per period in RI compared with LTR (RI: aRR=0.85, 95% CI=0.81 to 0.89; LTR: aRR=0.91, 95% CI=0.90 to 0.93). Observed trends were not universal across region of origin and by refugee status.InterpretationSuicide rates have been stable and ED self-harm rates are declining over time among RI youth. These trends by important subgroups should continue to be monitored to allow for early identification of subpopulations of immigrant youth in need of targeted and culturally appropriate public health interventions.
Efficacy and safety of renal denervation for Chinese patients with resistant hypertension using a microirrigated catheter: study design and protocol for a prospective multicentre randomised controlled trial
Authors: Liu Zongjun , Shen Li , Huang Weijian , Zhao Xianxian , Fang Weiyi , Wang Changqian , Yin Zhaofang , Wang Jianan , Fu Guosheng , Liu Xuebo , Jiang Jianjun , Zhang Zhihui , Li Jingbo , Lu Yingmin , Ge Junbo 
Published: September 2017

IntroductionAvailable data show that approximately 8%–18% of patients with primary hypertension will develop resistant hypertension. In recent years, catheter-based renal denervation (RDN) has emerged as a potential treatment option for resistant hypertension. A number of observational studies and randomised controlled trials among non-Chinese patients have demonstrated its potential safety and efficacy.Methods and analysisThis is a multicentre, randomised, open-label, parallel-group, active controlled trial that will investigate the efficacy and safety of a 5F saline-irrigated radiofrequency ablation (RFA) used for RDN in the treatment of Chinese patients with resistant hypertension. A total of 254 patients who have failed pharmacological therapy will be enrolled. Eligible subjects will be randomised in a 1:1 ratio to undergo RDN using the RFA plus antihypertensive medication or to receive treatment with antihypertensive medication alone. The primary outcome measure is the change in 24 hours average ambulatory systolic blood pressure from baseline to 3 months, comparing the RDN-plus-medication group with the medication-alone group. Important secondary endpoints include the change in office blood pressure from baseline to 6 months after randomisation. Safety endpoints such as changes in renal function will also be evaluated. The full analysis set, according to the intent-to-treat principle, will be established as the primary analysis population.Ethics and disseminationAll participants will provide informed consent; the study protocol has been approved by the Independent Ethics Committee for each site. This study is designed to investigate the efficacy and safety of RDN using a 5F saline microirrigated RFA. Findings will be shared with participating hospitals, policymakers and the academic community to promote the clinical management of resistant hypertension in China.Trial registrationClinicalTrials.gov ID:NCT02900729; pre-results.