bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Regulatory Pathway for K
+
Uptake in the Legume Symbiont Azorhizobium caulinodans in Which TrkJ Represses the
kdpFABC
Operon at High Extracellular K
+
Concentrations
Authors: Siarot Lowela , Toyazaki Hiroki , Hidaka Makoto , Kurumisawa Keigo , Hirakawa Tomoki , Morohashi Kengo , Aono Toshihiro 
Published: August 2017

ABSTRACT

Bacteria have multiple K
+
uptake systems.
Escherichia coli
, for example, has three types of K
+
uptake systems, which include the low-K
+
-inducible KdpFABC system and two constitutive systems, Trk (TrkAG and TrkAH) and Kup.
Azorhizobium caulinodans
ORS571, a rhizobium that forms nitrogen-fixing nodules on the stems and roots of
Sesbania rostrata
, also has three types of K
+
uptake systems. Through phylogenetic analysis, we found that
A. caulinodans
has two genes homologous to
trkG
and
trkH
, designated
trkI
and
trkJ
. We also found that
trkI
is adjacent to
trkA
in the genome and these two genes are transcribed as an operon; however,
trkJ
is present at a distinct locus. Our results demonstrated that
trkAI
,
trkJ
, and
kup
were expressed in the wild-type stem nodules, whereas
kdpFABC
was not. Interestingly, Δ
kup
and Δ
kup
Δ
kdpA
mutants formed Fix
–
nodules, while the Δ
kup
Δ
trkA
Δ
trkI
Δ
trkJ
mutant formed Fix
+
nodules, suggesting that with the additional deletion of Trk system genes in the Δ
kup
mutant, Fix
+
nodule phenotypes were recovered.
kdpFABC
of the Δ
kup
Δ
trkJ
mutant was expressed in stem nodules, but not in the free-living state, under high-K
+
conditions. However,
kdpFABC
of the Δ
kup
Δ
trkA
Δ
trkI
Δ
trkJ
mutant was highly expressed even under high-K
+
conditions. The cytoplasmic K
+
levels in the Δ
kup
Δ
trkA
Δ
trkI
mutant, which did not express
kdpFABC
under high-K
+
conditions, were markedly lower than those in the Δ
kup
Δ
trkA
Δ
trkI
Δ
trkJ
mutant. Taking all these results into consideration, we propose that TrkJ is involved in the repression of
kdpFABC
in response to high external K
+
concentrations and that the TrkAI system is unable to function in stem nodules.

IMPORTANCE
K
+
is a major cytoplasmic cation in prokaryotic and eukaryotic cells. Bacteria have multiple K
+
uptake systems to control the cytoplasmic K
+
levels. In many bacteria, the K
+
uptake system KdpFABC is expressed under low-K
+
conditions. For years, many researchers have argued over how bacteria sense K
+
concentrations. Although KdpD of
Escherichia coli
is known to sense both cytoplasmic and extracellular K
+
concentrations, the detailed mechanism of K
+
sensing is still unclear. In this study, we propose that the transmembrane TrkJ protein of
Azorhizobium caulinodans
acts as a sensor for the extracellular K
+
concentration and that high extracellular K
+
concentrations repress the expression of KdpFABC via TrkJ.
Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing
Authors: Justice N. B. , Sczesnak A. , Hazen T. C. , Arkin A. P. 
Published: August 2017

ABSTRACT
A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA gene amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly.

IMPORTANCE
Through highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.
A Commensal Bifidobacterium longum Strain Prevents Gluten-Related Immunopathology in Mice through Expression of a Serine Protease Inhibitor
Authors: McCarville J. L. , Dong J. , Caminero A. , Bermudez-Brito M. , Jury J. , Murray J. A. , Duboux S. , Steinmann M. , Delley M. , Tangyu M. , Langella P. , Mercenier A. , Bergonzelli G. , Verdu E. F. 
Published: August 2017

ABSTRACT

Microbiota-modulating strategies, including probiotic administration, have been tested for the treatment of chronic gastrointestinal diseases despite limited information regarding their mechanisms of action. We previously demonstrated that patients with active celiac disease have decreased duodenal expression of elafin, a human serine protease inhibitor, and supplementation of elafin by a recombinant
Lactococcus lactis
strain prevents gliadin-induced immunopathology in the NOD/DQ8 mouse model of gluten sensitivity. The commensal probiotic strain
Bifidobacterium longum
NCC2705 produces a serine protease inhibitor (Srp) that exhibits immune-modulating properties. Here, we demonstrate that
B. longum
NCC2705, but not a
srp
knockout mutant, attenuates gliadin-induced immunopathology and impacts intestinal microbial composition in NOD/DQ8 mice. Our results highlight the beneficial effects of a serine protease inhibitor produced by commensal
B. longum
strains.

IMPORTANCE
Probiotic therapies have been widely used to treat gastrointestinal disorders with variable success and poor mechanistic insight. Delivery of specific anti-inflammatory molecules has been limited to the use of genetically modified organisms, which has raised some public and regulatory concerns. By examining a specific microbial product naturally expressed by a commensal bacterial strain, we provide insight into a mechanistic basis for the use of
B. longum
NCC2705 to help treat gluten-related disorders.
Indole Biodegradation in Acinetobacter sp. Strain O153: Genetic and Biochemical Characterization
Authors: Sadauskas Mikas , Vaitekūnas Justas , Gasparavičiūtė Renata , Meškys Rolandas 
Published: August 2017

ABSTRACT

Indole is a molecule of considerable biochemical significance, acting as both an interspecies signal molecule and a building block of biological elements. Bacterial indole degradation has been demonstrated for a number of cases; however, very little is known about genes and proteins involved in this process. This study reports the cloning and initial functional characterization of genes (
iif
and
ant
cluster) responsible for indole biodegradation in
Acinetobacter
sp. strain O153. The catabolic cascade was reconstituted
in vitro
with recombinant proteins, and each protein was assigned an enzymatic function. Degradation starts with oxidation, mediated by the IifC and IifD flavin-dependent two-component oxygenase system. Formation of indigo is prevented by IifB, and the final product, anthranilic acid, is formed by IifA, an enzyme which is both structurally and functionally comparable to cofactor-independent oxygenases. Moreover, the
iif
cluster was identified in the genomes of a wide range of bacteria, suggesting the potential of widespread Iif-mediated indole degradation. This work provides novel insights into the genetic background of microbial indole biodegradation.

IMPORTANCE
The key finding of this research is identification of the genes responsible for microbial biodegradation of indole, a toxic
N
-heterocyclic compound. A large amount of indole is present in urban wastewater and sewage sludge, creating a demand for an efficient and eco-friendly means to eliminate this pollutant. A common strategy of oxidizing indole to indigo has the major drawback of producing insoluble material. Genes and proteins of
Acinetobacter
sp. strain O153 (DSM 103907) reported here pave the way for effective and indigo-free indole removal. In addition, this work suggests possible novel means of indole-mediated bacterial interactions and provides the basis for future research on indole metabolism.
Protocol for a single-centre, randomised controlled study of a preoperative rehabilitation bundle in the frail and elderly undergoing abdominal surgery
Authors: Abdullah Hairil Rizal , Lien Victoria Peixin , Ong Hwee Kuan , Er Pei Ling , Hao Ying , Khan Shariq Ali , Liu Christopher Weiyang 
Published: August 2017

IntroductionFrail patients have decreased physiological reserves and consequently, they are unable to recover as quickly from surgery. Frailty, as an entity, is a risk factor of increased morbidity and mortality. It is also associated with a longer time to discharge. This trial is undertaken to determine if a novel prehabilitation protocol (10-day bundle of interventions—physiotherapy, nutritional supplementation and cognitive training) can reduce the postoperative length of stay of frail patients who are undergoing elective abdominal surgery, compared with standard care.Methods and analysisThis is a prospective, single-centre, randomised controlled trial with two parallel arms. 62 patients who are frail and undergoing elective abdominal surgery will be recruited and randomised to receive either a novel prehabilitation protocol or standard care. Participants will receive telephone reminders preoperatively to encourage protocol compliance. Data will be collected for up to 30 days postoperatively. The primary outcome of the trial will be the postoperative length of stay and the secondary outcomes are the postoperative complications and functional recovery during the hospital admission.Ethics and disseminationThis study has been approved by the Singapore General Hospital Institutional Review Board (CIRB Ref: 2016/2584). The study is also listed on ClinicalTrials.gov (Trial number:NCT02921932). All participants will sign an informed consent form before randomisation and translators will be made available to non-English speaking patients. The results of this study will be published in peer-reviewed journals as well as national and international conferences. The data collected will also be made available in a public data repository.Trial registration numberNCT02921932 (ClinicalTrials.gov)
Use of four asymmetric marks to orient the donor graft during Descemet's membrane endothelial keratoplasty
Authors: Matsuzawa Akiko , Hayashi Takahiko , Oyakawa Itaru , Yuda Kentaro , Shimizu Toshiki , Mizuki Nobuhisa , Yamada Norihiro , Kato Naoko 
Published: August 2017

IntroductionMaintaining the correct orientation of the donor graft is important during Descemet's membrane endothelial keratoplasty (DMEK). We describe a new method of marking the donor graft prior to DMEK.MethodsTwelve eyes of 10 patients with bullous keratopathy who underwent DMEK were retrospectively analysed. Donor discs were created by stripping the endothelium–Descemet's membrane layer from corneoscleral buttons. Four semicircular marks, two 1.0 mm and two 1.5 mm in diameter, were created at the edge of the donor disc. The small and large marks were paired. Each donor graft was inserted into the anterior chamber, unfolded and attached to the posterior corneal stroma with an air bubble.ResultsThe inserted grafts were all appropriately orientated when attached to the back surfaces of the corneas. The two pairs of asymmetric marks afforded valuable guidance. Even when the graft was partially folded or decentred, and one pair of marks was obscured, the other pair was always visible to indicate graft orientation. Best spectacle-corrected visual acuity improved significantly in all patients (p<0.001). Compared with the preoperative endothelial cell density of the donor graft, that of the corneal endothelium had decreased 44.0%±10.0% by 6 months after surgery.ConclusionsTwo pairs of asymmetrical semicircular marks placed on the edge of the donor graft allowed appropriate graft orientation during DMEK.
Comparing the cancer potencies of emissions from vapourised nicotine products including e-cigarettes with those of tobacco smoke
Authors: Stephens William E 
Published: August 2017

BackgroundQuantifying relative harm caused by inhaling the aerosol emissions of vapourised nicotine products compared with smoking combustible tobacco is an important issue for public health.MethodsThe cancer potencies of various nicotine-delivering aerosols are modelled using published chemical analyses of emissions and their associated inhalation unit risks. Potencies are compared using a conversion procedure for expressing smoke and e-cigarette vapours in common units. Lifetime cancer risks are calculated from potencies using daily consumption estimates.ResultsThe aerosols form a spectrum of cancer potencies spanning five orders of magnitude from uncontaminated air to tobacco smoke. E-cigarette emissions span most of this range with the preponderance of products having potencies<1% of tobacco smoke and falling within two orders of magnitude of a medicinal nicotine inhaler; however, a small minority have much higher potencies. These high-risk results tend to be associated with high levels of carbonyls generated when excessive power is delivered to the atomiser coil. Samples of a prototype heat-not-burn device have lower cancer potencies than tobacco smoke by at least one order of magnitude, but higher potencies than most e-cigarettes. Mean lifetime risks decline in the sequence: combustible cigarettes >> heat-not-burn >> e-cigarettes (normal power)≥nicotine inhaler.ConclusionsOptimal combinations of device settings, liquid formulation and vaping behaviour normally result in e-cigarette emissions with much less carcinogenic potency than tobacco smoke, notwithstanding there are circumstances in which the cancer risks of e-cigarette emissions can escalate, sometimes substantially. These circumstances are usually avoidable when the causes are known.
Targeting RNA-Polymerase I in Both Chemosensitive and Chemoresistant Populations in Epithelial Ovarian Cancer
Authors: Cornelison Robert , Dobbin Zachary C. , Katre Ashwini A. , Jeong Dae Hoon , Zhang Yinfeng , Chen Dongquan , Petrova Yuliya , Llaneza Danielle C. , Steg Adam D. , Parsons Laura , Schneider David A. , Landen Charles N. 
Published: August 2017

Abstract
Purpose: A hallmark of neoplasia is increased ribosome biogenesis, and targeting this process with RNA polymerase I (Pol I) inhibitors has shown some efficacy. We examined the contribution and potential targeting of ribosomal machinery in chemotherapy-resistant and -sensitive models of ovarian cancer.
Experimental Design: Pol I machinery expression was examined, and subsequently targeted with the Pol I inhibitor CX-5461, in ovarian cancer cell lines, an immortalized surface epithelial line, and patient-derived xenograft (PDX) models with and without chemotherapy. Effects on viability, Pol I occupancy of rDNA, ribosomal content, and chemosensitivity were examined.
Results: In PDX models, ribosomal machinery components were increased in chemotherapy-treated tumors compared with controls. Thirteen cell lines were sensitive to CX-5461, with IC50s 25 nmol/L–2 μmol/L. Interestingly, two chemoresistant lines were 10.5- and 5.5-fold more sensitive than parental lines. CX-5461 induced DNA damage checkpoint activation and G2–M arrest with increased γH2AX staining. Chemoresistant cells had 2- to 4-fold increased rDNA Pol I occupancy and increased rRNA synthesis, despite having slower proliferation rates, whereas ribosome abundance and translational efficiency were not impaired. In five PDX models treated with CX-5461, one showed a complete response, one a 55% reduction in tumor volume, and one maintained stable disease for 45 days.
Conclusions: Pol I inhibition with CX-5461 shows high activity in ovarian cancer cell lines and PDX models, with an enhanced effect on chemoresistant cells. Effects occur independent of proliferation rates or dormancy. This represents a novel therapeutic approach that may have preferential activity in chemoresistant populations. Clin Cancer Res; 23(21); 6529–40. ©2017 AACR.
Using Antigen-Specific B Cells to Combine Antibody and T Cell–Based Cancer Immunotherapy
Authors: Wennhold Kerstin , Thelen Martin , Schlößer Hans Anton , Haustein Natalie , Reuter Sabrina , Garcia-Marquez Maria , Lechner Axel , Kobold Sebastian , Rataj Felicitas , Utermöhlen Olaf , Chakupurakal Geothy , Theurich Sebastian , Hallek Michael , Abken Hinrich , Shimabukuro-Vornhagen Alexander , von Bergwelt-Baildon Michael 
Published: August 2017

AbstractCancer immunotherapy by therapeutic activation of T cells has demonstrated clinical potential. Approaches include checkpoint inhibitors and chimeric antigen receptor T cells. Here, we report the development of an alternative strategy for cellular immunotherapy that combines induction of a tumor-directed T-cell response and antibody secretion without the need for genetic engineering. CD40 ligand stimulation of murine tumor antigen-specific B cells, isolated by antigen-biotin tetramers, resulted in the development of an antigen-presenting phenotype and the induction of a tumor antigen-specific T-cell response. Differentiation of antigen-specific B cells into antibody-secreting plasma cells was achieved by stimulation with IL21, IL4, anti-CD40, and the specific antigen. Combined treatment of tumor-bearing mice with antigen-specific CD40-activated B cells and antigen-specific plasma cells induced a therapeutic antitumor immune response resulting in remission of established tumors. Human CEA or NY-ESO-1–specific B cells were detected in tumor-draining lymph nodes and were able to induce antigen-specific T-cell responses in vitro, indicating that this approach could be translated into clinical applications. Our results describe a technique for the exploitation of B-cell effector functions and provide the rationale for their use in combinatorial cancer immunotherapy. Cancer Immunol Res; 5(9); 730–43. ©2017 AACR.
Effect of Disclosing Genetic Risk for Coronary Heart Disease on Information Seeking and Sharing
Authors: Brown Sherry-Ann N. , Jouni Hayan , Marroush Tariq S. , Kullo Iftikhar J. 
Published: August 2017

Background—
Whether disclosing genetic risk for coronary heart disease (CHD) to individuals influences information seeking and information sharing is not known. We hypothesized that disclosing genetic risk for CHD to individuals influences information seeking and sharing.

Methods and Results—

The MI-GENES study (Myocardial Infarction Genes) randomized participants (n=203) aged 45 to 65 years who were at intermediate CHD risk based on conventional risk factors and not on statins to receive their conventional risk score alone or also a genetic risk score based on 28 variants. CHD risk was disclosed by a genetic counselor and then discussed with a physician. Surveys assessing information seeking were completed before and after risk disclosure. Information sharing was assessed post-disclosure. Six-month post-disclosure, genetic risk score participants were more likely than conventional risk score participants to visit a website to learn about CHD (odds ratio [OR], 4.88 [confidence interval (CI), 1.55–19.13];
P
=0.01), use the internet for information about how genetic factors affect CHD risk (OR, 2.11 [CI, 1.03–4.47];
P
=0.04), access their CHD risk via a patient portal (OR, 2.99 [CI, 1.35–7.04];
P
=0.01), and discuss their CHD risk with others (OR, 3.13 [CI, 1.41–7.47];
P
=0.01), particularly their siblings (OR, 1.92 [CI, 1.06–3.51];
P
=0.03), extended family (OR, 3.8 [CI, 1.37–12.38];
P=
0.01), coworkers (OR, 2.42 [CI, 1.09–5.76];
P
=0.03), and primary care provider (PCP; OR, 2.00 [CI, 1.08–3.75];
P
=0.03).

Conclusions—
Disclosure of a genetic risk score for CHD increased information seeking and sharing.

Clinical Trial Registration—

URL:
https://clinicaltrials.gov/
. Unique identifier: NCT01936675.
Carotid Plaque Rupture Is Accompanied by an Increase in the Ratio of Serum circR-284 to miR-221 Levels
Authors: Bazan Hernan A. , Hatfield Samuel A. , Brug Aaron , Brooks Ashton J. , Lightell Daniel J. , Woods T. Cooper 
Published: August 2017

Background—
Atherosclerotic plaque rupture is accompanied by an acute decrease in the carotid plaque expression of micro-RNAs (miRs)-221 and miR-222. Circular RNA (circR)-284 is a potential inhibitor of miR-221/miR-222 activity. We aimed to determine whether changes in the serum levels of these noncoding RNAs are observed in patients with asymptomatic high-grade carotid disease versus patients with acutely symptomatic carotid disease and recent ischemic stroke. Additionally, we tested the use of functionally related noncoding RNA pairs to enhance the discriminatory power of noncoding RNAs as circulating biomarkers.

Methods and Results—

Serum levels of miR-221, miR-222, miR-145, and circR-284 were measured in 24 asymptomatic (asymptomatic) and 17 acutely symptomatic patients ([urgent] ischemic cerebrovascular event within the previous 5 days) undergoing carotid endarterectomy. miR-221 was significantly lower, whereas circR-284 was elevated in the serum of the urgent compared with the asymptomatic group. The ratio of serum circR-284:miR-221 was significantly elevated in the urgent group (
P
=0.0002) and exhibited favorable characteristics as a biomarker indicative of carotid plaque rupture and stroke. A validation study in 112 patients (47 asymptomatic, 41 urgent, and 24 patients with a cerebrovascular event between 5 and 180 days of the carotid endarterectomy [symptomatic]) confirmed elevation of serum circR-284:miR-221 uniquely in the urgent group (
P
<0.001) and favorable sensitivity and specificity for detecting plaque rupture and stroke.

Conclusions—
Serum circR-284:miR-221 has potential as a diagnostic biomarker of carotid plaque rupture and stroke. Moreover, we demonstrate the use of functionally related pairs of circulating noncoding RNAs as biomarkers in cardiovascular disease.