bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding
Authors: Ilhan Zehra Esra , DiBaise John K , Isern Nancy G , Hoyt David W , Marcus Andrew K , Kang Dae-Wook , Crowell Michael D , Rittmann Bruce E , Krajmalnik-Brown Rosa 
Published: May 2017

Abstract
Roux-en-Y gastric bypass (RYGB) and laparoscopic adjustable gastric banding (LAGB) are anatomically different bariatric operations. RYGB achieves greater weight loss compared with LAGB. Changes in the gut microbiome have been documented after RYGB, but not LAGB, and the microbial contribution to sustainable surgical weight loss warrants further evaluation. We hypothesized that RYGB imposes greater changes on the microbiota and its metabolism than LAGB, and that the altered microbiota may contribute to greater weight loss. Using multi-omic approaches, we analyzed fecal microbial community structure and metabolites of pre-bariatric surgery morbidly obese (PreB-Ob), normal weight (NW), post-RYGB, and post-LAGB participants. RYGB microbiomes were significantly different from those from NW, LAGB and PreB-Ob. Microbiome differences between RYGB and PreB-Ob populations were mirrored in their metabolomes. Diversity was higher in RYGB compared with LAGB, possibly because of an increase in the abundance of facultative anaerobic, bile-tolerant and acid-sensible microorganisms in the former. Possibly because of lower gastric acid exposure, phylotypes from the oral cavity, such as Escherichia, Veillonella and Streptococcus, were in greater abundance in the RYGB group, and their abundances positively correlated with percent excess weight loss. Many of these post-RYGB microorganisms are capable of amino-acid fermentation. Amino-acid and carbohydrate fermentation products—isovalerate, isobutyrate, butyrate and propionate—were prevalent in RYGB participants, but not in LAGB participants. RYGB resulted in greater alteration of the gut microbiome and metabolome than LAGB, and RYGB group exhibited unique microbiome composed of many amino-acid fermenters, compared with nonsurgical controls.
Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA
Authors: Edwardson Christian F , Hollibaugh James T 
Published: May 2017

Abstract
This study evaluates the transcriptionally active, dissimilatory sulfur- and arsenic-cycling components of the microbial community in alkaline, hypersaline Mono Lake, CA, USA. We sampled five depths spanning the redox gradient (10, 15, 18, 25 and 31 m) during maximum thermal stratification. We used custom databases to identify transcripts of genes encoding complex iron-sulfur molybdoenzyme (CISM) proteins, with a focus on arsenic (arrA, aioA and arxA) and sulfur cycling (dsrA, aprA and soxB), and assigned them to taxonomic bins. We also report on the distribution of transcripts related to the ars arsenic detoxification pathway. Transcripts from detoxification pathways were not abundant in oxic surface waters (10 m). Arsenic cycling in the suboxic and microaerophilic zones of the water column (15 and 18 m) was dominated by arsenite-oxidizing members of the Gammaproteobacteria most closely affiliated with Thioalkalivibrio and Halomonas, transcribing arxA. We observed a transition to arsenate-reducing bacteria belonging to the Deltaproteobacteria and Firmicutes transcribing arsenate reductase (arrA) in anoxic bottom waters of the lake (25 and 31 m). Sulfur cycling at 15 and 18 m was dominated by Gammaproteobacteria (Thioalkalivibrio and Thioalkalimicrobium) oxidizing reduced S species, with a transition to sulfate-reducing Deltaproteobacteria at 25 and 31 m. Genes related to arsenic and sulfur oxidation from Thioalkalivibrio were more highly transcribed at 15 m relative to other depths. Our data highlight the importance of Thioalkalivibrio to arsenic and sulfur biogeochemistry in Mono Lake and identify new taxa that appear capable of transforming arsenic.
The endobacterium of an arbuscular mycorrhizal fungus modulates the expression of its toxin–antitoxin systems during the life cycle of its host
Authors: Salvioli di Fossalunga Alessandra , Lipuma Justine , Venice Francesco , Dupont Laurence , Bonfante Paola 
Published: May 2017

Abstract
Arbuscular mycorrhizal fungi (AMF) are widespread root symbionts that perform important ecological services, such as improving plant nutrient and water acquisition. Some AMF from the Gigasporaceae family host a population of endobacteria, Candidatus Glomeribacter gigasporarum (Cagg). The analysis of the Cagg genome identified six putative toxin–antitoxin modules (TAs), consisting of pairs of stable toxins and unstable antitoxins that affect diverse physiological functions. Sequence analysis suggested that these TA modules were acquired by horizontal transfer. Gene expression patterns of two TAs (yoeB/yefM and chpB/chpS) changed during the fungal life cycle, with the expression during the pre-symbiotic phase higher than during the symbiosis with the plant host. The heterologous expression in Escherichia coli demonstrated the functionality only for the YoeB–YefM pair. On the basis of these observations, we speculate that TA modules might help Cagg adapt to its intracellular habitat, coordinating its proliferation with the physiological state of the AMF host.
Morphometric convergence between Proterozoic and post-vegetation rivers
Authors: Ielpi Alessandro , Rainbird Robert H. , Ventra Dario , Ghinassi Massimiliano 
Published: May 2017

AbstractProterozoic rivers flowed through barren landscapes, and lacked interactions with macroscopic organisms. It is widely held that, in the absence of vegetation, fluvial systems featured barely entrenched channels that promptly widened over floodplains during floods. This hypothesis has never been tested because of an enduring lack of Precambrian fluvial-channel morphometric data. Here we show, through remote sensing and outcrop sedimentology, that deep rivers were developed in the Proterozoic, and that morphometric parameters for large fluvial channels might have remained within a narrow range over almost 2 billion years. Our data set comprises fluvial-channel forms deposited a few tens to thousands of kilometres from their headwaters, likely the record of basin- to craton-scale systems. Large Proterozoic channel forms present width:thickness ranges matching those of Phanerozoic counterparts, suggesting closer parallels between their fluvial dynamics. This outcome may better inform analyses of extraterrestrial planetary surfaces and related comparisons with pre-vegetation Earth landscapes.
Replicating viral vector platform exploits alarmin signals for potent CD8+ T cell-mediated tumour immunotherapy
Authors: Kallert Sandra M. , Darbre Stephanie , Bonilla Weldy V. , Kreutzfeldt Mario , Page Nicolas , Müller Philipp , Kreuzaler Matthias , Lu Min , Favre Stéphanie , Kreppel Florian , Löhning Max , Luther Sanjiv A. , Zippelius Alfred , Merkler Doron , Pinschewer Daniel D. 
Published: May 2017

AbstractViral infections lead to alarmin release and elicit potent cytotoxic effector T lymphocyte (CTLeff) responses. Conversely, the induction of protective tumour-specific CTLeffand their recruitment into the tumour remain challenging tasks. Here we show that lymphocytic choriomeningitis virus (LCMV) can be engineered to serve as a replication competent, stably-attenuated immunotherapy vector (artLCMV). artLCMV delivers tumour-associated antigens to dendritic cells for efficient CTL priming. Unlike replication-deficient vectors, artLCMV targets also lymphoid tissue stroma cells expressing the alarmin interleukin-33. By triggering interleukin-33 signals, artLCMV elicits CTLeffresponses of higher magnitude and functionality than those induced by replication-deficient vectors. Superior anti-tumour efficacy of artLCMV immunotherapy depends on interleukin-33 signalling, and a massive CTLeffinflux triggers an inflammatory conversion of the tumour microenvironment. Our observations suggest that replicating viral delivery systems can release alarmins for improved anti-tumour efficacy. These mechanistic insights may outweigh safety concerns around replicating viral vectors in cancer immunotherapy.
The distinct metabolic phenotype of lung squamous cell carcinoma defines selective vulnerability to glycolytic inhibition
Authors: Goodwin Justin , Neugent Michael L. , Lee Shin Yup , Choe Joshua H. , Choi Hyunsung , Jenkins Dana M. R. , Ruthenborg Robin J. , Robinson Maddox W. , Jeong Ji Yun , Wake Masaki , Abe Hajime , Takeda Norihiko , Endo Hiroko , Inoue Masahiro , Xuan Zhenyu , Yoo Hyuntae , Chen Min , Ahn Jung-Mo , Minna John D. , Helke Kristi L. , Singh Pankaj K. , Shackelford David B. , Kim Jung-whan 
Published: May 2017

AbstractAdenocarcinoma (ADC) and squamous cell carcinoma (SqCC) are the two predominant subtypes of non-small cell lung cancer (NSCLC) and are distinct in their histological, molecular and clinical presentation. However, metabolic signatures specific to individual NSCLC subtypes remain unknown. Here, we perform an integrative analysis of human NSCLC tumour samples, patient-derived xenografts, murine model of NSCLC, NSCLC cell lines and The Cancer Genome Atlas (TCGA) and reveal a markedly elevated expression of the GLUT1 glucose transporter in lung SqCC, which augments glucose uptake and glycolytic flux. We show that a critical reliance on glycolysis renders lung SqCC vulnerable to glycolytic inhibition, while lung ADC exhibits significant glucose independence. Clinically, elevated GLUT1-mediated glycolysis in lung SqCC strongly correlates with high 18F-FDG uptake and poor prognosis. This previously undescribed metabolic heterogeneity of NSCLC subtypes implicates significant potential for the development of diagnostic, prognostic and targeted therapeutic strategies for lung SqCC, a cancer for which existing therapeutic options are clinically insufficient.
Whole genome sequencing identifies a novel homozygous exon deletion in the NT5C2 gene in a family with intellectual disability and spastic paraplegia
Authors: Darvish Hossein , Azcona Luis J. , Tafakhori Abbas , Ahmadi Mona , Ahmadifard Azadeh , Paisán-Ruiz Coro 
Published: May 2017

AbstractHereditary spastic paraplegias are a rare group of clinically and genetically heterogeneous neurodegenerative diseases, with upper motor neuron degeneration and progressive lower limb spasticity as their main phenotypic features. Despite that 76 distinct loci have been reported and some casual genes identified, most of the underlying causes still remain unidentified. Moreover, a wide range of clinical manifestations is present in most hereditary spastic paraplegias subtypes, adding further complexity to their differential clinical diagnoses. Here, we describe the first exon rearrangement reported in the SPG45/SPG65 (NT5C2) loci in a family featuring a complex hereditary spastic paraplegias phenotype. This study expands both the phenotypic and mutational spectra of the NT5C2-associated disease.
The zebrafish ventricle: A hub of cardiac endothelial cells for in vitro cell behavior studies
Authors: Patra Chinmoy , Kontarakis Zacharias , Kaur Harmandeep , Rayrikar Amey , Mukherjee Debanjan , Stainier Didier Y. R. 
Published: May 2017

AbstractDespite our increasing understanding of zebrafish heart development and regeneration, there is limited information about the distribution of endothelial cells (ECs) in the adult zebrafish heart. Here, we investigate and compare the distribution of cardiac ECs (cECs) in adult mouse and zebrafish ventricles. Surprisingly, we find that (i) active coronary vessel growth is present in adult zebrafish, (ii) ~37 and ~39% of cells in the zebrafish heart are ECs and cardiomyocytes, respectively, a composition similar to that seen in mouse. However, we find that in zebrafish, ~36% of the ventricular tissue is covered with ECs, i.e., a substantially larger proportion than in mouse. Capitalising on the high abundance of cECs in zebrafish, we established a protocol to isolate them with high purity using fluorescent transgenic lines. Our approach eliminates side-effects due to antibody utilisation. Moreover, the isolated cECs maintained a high proliferation index even after three passages and were amenable to pharmacological treatments to study cEC migration in vitro. Such primary cultures will be a useful tool for supplementary in vitro studies on the accumulating zebrafish mutant lines as well as the screening of small molecule libraries on cardiac specific endothelial cells.
Confounding factors of ultrafiltration and protein analysis in extracellular vesicle research
Authors: Vergauwen Glenn , Dhondt Bert , Van Deun Jan , De Smedt Eva , Berx Geert , Timmerman Evy , Gevaert Kris , Miinalainen Ilkka , Cocquyt Véronique , Braems Geert , Van den Broecke Rudy , Denys Hannelore , De Wever Olivier , Hendrix An 
Published: May 2017

AbstractIdentification and validation of extracellular vesicle (EV)-associated biomarkers requires robust isolation and characterization protocols. We assessed the impact of some commonly implemented pre-analytical, analytical and post-analytical variables in EV research. Centrifugal filters with different membrane types and pore sizes are used to reduce large volume biofluids prior to EV isolation or to concentrate EVs. We compared five commonly reported filters for their efficiency when using plasma, urine and EV-spiked PBS. Regenerated cellulose membranes with pore size of 10 kDa recovered EVs the most efficient. Less than 40% recovery was achieved with other filters. Next, we analyzed the effect of the type of protein assays to measure EV protein in colorimetric and fluorometric kits. The fluorometric assay Qubit measured low concentration EV and BSA samples the most accurately with the lowest variation among technical and biological replicates. Lastly, we quantified Optiprep remnants in EV samples from density gradient ultracentrifugation and demonstrate that size-exclusion chromatography efficiently removes Optiprep from EVs. In conclusion, choice of centrifugal filters and protein assays confound EV analysis and should be carefully considered to increase efficiency towards biomarker discovery. SEC-based removal of Optiprep remnants from EVs can be considered for downstream applications.
Surface modification of polyvinylidene fluoride (PVDF) membrane via radiation grafting: novel mechanisms underlying the interesting enhanced membrane performance
Authors: Shen Liguo , Feng Shushu , Li Jianxi , Chen Jianrong , Li Fengquan , Lin Hongjun , Yu Genying 
Published: May 2017

AbstractThis study provided the first attempt of grafting hydrophobic polyvinylidene fluoride (PVDF) membrane with hydrophilic hydroxyethyl acrylate (HEA) monomer via a radiation grafting method. This grafted membrane showed an enhanced hydrophilicity (10° decrease of water contact angle), water content ratio, settling ability and wettability compared to the control membrane. Interestingly, filtration tests showed an improved dependence of water flux of the grafted membrane on the solution pH in the acidic stage. Atomic force microscopy (AFM) analysis provided in-situ evidence that the reduced surface pore size of the grafted membrane with the solution pH governed such a dependence. It was proposed that, the reduced surface pore size was caused by the swelling of the grafted chain matrix, with the pH increase due to the chemical potential change. It was found that the grafted membrane showed a lower relative flux decreasing rate than the control membrane. Moreover, flux of the bovine serum albumin (BSA) solution was noticeably larger than that of pure water for the grafted membrane. Higher BSA flux than water flux can be explained by the effects of electric double layer compression on the polymeric swelling. This study not only provided a pH-sensitive PVDF membrane potentially useful for various applications, but also proposed novel mechanisms underlying the enhanced performance of the grafted membrane.
Modulation of Peptide Based Nano-Assemblies with Electric and Magnetic Fields
Authors: Pandey Gaurav , Saikia Jahnu , Sasidharan Sajitha , Joshi Deep C. , Thota Subhash , Nemade Harshal B. , Chaudhary Nitin , Ramakrishnan Vibin 
Published: May 2017

AbstractPeptide based nano-assemblies with their self-organizing ability has shown lot of promise due to their high degree of thermal and chemical stability, for biomaterial fabrication. Developing an effective way to control the organization of these structures is important for fabricating application-oriented materials at the molecular level. The present study reports the impact of electric and magnetic field-mediated perturbation of the self-assembly phenomenon, upon the chemical and structural properties of diphenylalanine assembly. Our studies show that, electric field effectively arrests aggregation and self-assembly formation, while the molecule is allowed to anneal in the presence of applied electric fields of varying magnitudes, both AC and DC. The electric field exposure also modulated the morphology of the self-assembled structures without affecting the overall chemical constitution of the material. Our results on the modulatory effect of the electric field are in good agreement with theoretical studies based on molecular dynamics reported earlier on amyloid forming molecular systems. Furthermore, we demonstrate that the self-assemblies formed post electric-field exposure, showed difference in their crystal habit. Modulation of nano-level architecture of peptide based model systems with external stimulus, points to a potentially rewarding strategy to re-work proven nano-materials to expand their application spectrum.
Expression profiles of cholesterol metabolism-related genes are altered during development of experimental autoimmune encephalomyelitis in the rat spinal cord
Authors: Lavrnja Irena , Smiljanic Kosara , Savic Danijela , Mladenovic-Djordjevic Aleksandra , Tesovic Katarina , Kanazir Selma , Pekovic Sanja 
Published: May 2017

AbstractIncreased evidence suggests that dysregulation of cholesterol metabolism may be a key event contributing to progression of multiple sclerosis (MS). Using an experimental autoimmune encephalomyelitis (EAE) model of MS we revealed specific changes in the mRNA and protein expression of key molecules involved in the maintaining of cholesterol homeostasis in the rat spinal cord: 3-hydroxy-3-methylglutaryl-coenzyme-A reductase (HMGCR), apolipoprotein E (ApoE) and cholesterol 24-hydroxylase (CYP46A1) during the course of disease. The presence of myelin lipid debris was seen only at the peak of EAE in demyelination loci being efficiently removed during the recovery period. Since CYP46A1 is responsible for removal of cholesterol excess, we performed a detailed profiling of CYP46A1 expression and revealed regional and temporal specificities in its distribution. Double immunofluorescence staining demonstrated CYP46A1 localization with neurons, infiltrated macrophages, microglia and astrocytes in the areas of demyelination, suggesting that these cells play a role in cholesterol turnover in EAE. We propose that alterations in the regulation of cholesterol metabolism at the onset and peak of EAE may add to the progression of disease, while during the recovery period may have beneficial effects contributing to the regeneration of myelin sheath and restoration of neuronal function.
An appropriate Wnt/β-catenin expression level during the remodeling phase is required for improved bone fracture healing in mice
Authors: Bao Quanwei , Chen Sixu , Qin Hao , Feng Jianquan , Liu Huayu , Liu Daocheng , Li Ang , Shen Yue , Zhao Yufeng , Li Junfeng , Zong Zhaowen 
Published: May 2017

AbstractAccumulating evidence demonstrates that the Wnt/β-catenin signaling pathway plays a dominant role in bone repair. However, the role of Wnt/β-catenin signaling in the remodeling phase during bone fracture healing is currently unknown. In the present study, β-catenin was activated at different levels or deleted in mice at the late stage of fracture healing, and the effects on healing quality were investigated. Deletion of β-catenin disturbed bone remodeling, as confirmed by increased bone resorption and decreased bone formation, and significantly decreased bone strength compared with wildtype mice. In addition, the constitutive activation of β-catenin significantly increased the bone mass and delayed the bone remodeling process, resulting in slightly impaired bone strength. In contrast, a slight activation of β-catenin significantly increased bone formation and slightly hindered bone resorption. These effects lead to improved bone fracture healing quality compared with wildtype mice. In summary, the present study provides the first demonstration showing that Wnt/β-catenin signaling should be maintained at a slightly activated level during the late stage of fracture healing to ensure better bone fracture repair.
Quantum Phase Transition and Entanglement in Topological Quantum Wires
Authors: Cho Jaeyoon , Kim Kun Woo 
Published: May 2017

AbstractWe investigate the quantum phase transition of the Su-Schrieffer-Heeger (SSH) model by inspecting the two-site entanglements in the ground state. It is shown that the topological phase transition of the SSH model is signified by a nonanalyticity of local entanglement, which becomes discontinuous for finite even system sizes, and that this nonanalyticity has a topological origin. Such a peculiar singularity has a universal nature in one-dimensional topological phase transitions of noninteracting fermions. We make this clearer by pointing out that an analogous quantity in the Kitaev chain exhibiting the identical nonanalyticity is the local electron density. As a byproduct, we show that there exists a different type of phase transition, whereby the pattern of the two-site entanglements undergoes a sudden change. This transition is characterised solely by quantum information theory and does not accompany the closure of the spectral gap. We analyse the scaling behaviours of the entanglement in the vicinities of the transition points.
A high-throughput assay for quantitative measurement of PCR errors
Authors: Shagin Dmitriy A. , Shagina Irina A. , Zaretsky Andrew R. , Barsova Ekaterina V. , Kelmanson Ilya V. , Lukyanov Sergey , Chudakov Dmitriy M. , Shugay Mikhail 
Published: May 2017

AbstractThe accuracy with which DNA polymerase can replicate a template DNA sequence is an extremely important property that can vary by an order of magnitude from one enzyme to another. The rate of nucleotide misincorporation is shaped by multiple factors, including PCR conditions and proofreading capabilities, and proper assessment of polymerase error rate is essential for a wide range of sensitive PCR-based assays. In this paper, we describe a method for studying polymerase errors with exceptional resolution, which combines unique molecular identifier tagging and high-throughput sequencing. Our protocol is less laborious than commonly-used methods, and is also scalable, robust and accurate. In a series of nine PCR assays, we have measured a range of polymerase accuracies that is in line with previous observations. However, we were also able to comprehensively describe individual errors introduced by each polymerase after either 20 PCR cycles or a linear amplification, revealing specific substitution preferences and the diversity of PCR error frequency profiles. We also demonstrate that the detected high-frequency PCR errors are highly recurrent and that the position in the template sequence and polymerase-specific substitution preferences are among the major factors influencing the observed PCR error rate.