bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellulose long fibers fabricated from cellulose nanofibers and its strong and tough characteristics
Authors: Kafy Abdullahil , Kim Hyun Chan , Zhai Lindong , Kim Jung Woong , Hai Le Van , Kang Tae June , kim Jaehwan 
Published: December 2017

AbstractCellulose nanofiber (CNF) with high crystallinity has great mechanical stiffness and strength. However, its length is too short to be used for fibers of environmentally friendly structural composites. This paper presents a fabrication process of cellulose long fiber from CNF suspension by spinning, stretching and drying. Isolation of CNF from the hardwood pulp is done by using (2, 2, 6, 6-tetramethylpiperidine-1-yl) oxidanyl (TEMPO) oxidation. The effect of spinning speed and stretching ratio on mechanical properties of the fabricated fibers are investigated. The modulus of the fabricated fibers increases with the spinning speed as well as the stretching ratio because of the orientation of CNFs. The fabricated long fiber exhibits the maximum tensile modulus of 23.9 GPa with the maximum tensile strength of 383.3 MPa. Moreover, the fabricated long fiber exhibits high strain at break, which indicates high toughness. The results indicate that strong and tough cellulose long fiber can be produced by using ionic crosslinking, controlling spinning speed, stretching and drying.
AICAR suppresses TNF-α-induced complement factor B in RPE cells
Authors: Chung Eun Jee , Efstathiou Nikolaos E. , Konstantinou Eleni K. , Maidana Daniel E. , Miller Joan W. , Young Lucy H. , Vavvas Demetrios G. 
Published: December 2017

AbstractAge related macular degeneration is the leading cause of blindness in the developed world. Although its precise cause remains elusive, dysfunction of the retinal pigment epithelium (RPE) and dysregulation of complement have been implicated in its pathogenesis. The goal of this study was to evaluate the role of an AMP-dependent kinase (AMPK) activator, 5-aminoimidazole-4-carboxamide riboside (AICAR), on tumor necrosis factor alpha (TNF-α) induction of complement factor B (CFB) in RPE cells. We found that AICAR inhibited TNF-α-induced CFB expression in ARPE-19 and human primary RPE cells in a dose-dependent fashion. Treatment of cells with dipyridamole, which blocks AICAR cellular uptake abolished these effects. In contrast, the adenosine kinase inhibitor, 5-iodotubericidin, which inhibits the conversion of AICAR to the direct activator of AMPK, ZMP, did not reverse the effects on TNF-α-induced CFB expression, suggesting AMPK-independent effects. Indeed, knockout of AMPK in RPE cells using Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 did not abolish the inhibitory effects of AICAR on RPE CFB expression. Collectively, our results suggest that AICAR can suppress TNF-α-induced CFB expression in RPE cells in an AMPK-independent mechanism, and could be used as a therapeutic target in certain complement over-activation scenarios.
The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis
Authors: Aguilar-Ayala Diana A. , Tilleman Laurentijn , Van Nieuwerburgh Filip , Deforce Dieter , Palomino Juan Carlos , Vandamme Peter , Gonzalez-Y-Merchand Jorge A. , Martin Anandi 
Published: December 2017

AbstractTuberculosis (TB) is currently the number one killer among infectious diseases worldwide. Lipids are abundant molecules during the infectious cycle of Mycobacterium tuberculosis (Mtb) and studies better mimicking its actual metabolic state during pathogenesis are needed. Though most studies have focused on the mycobacterial lipid metabolism under standard culture conditions, little is known about the transcriptome of Mtb in a lipid environment. Here we determined the transcriptome of Mtb H37Rv in a lipid-rich environment (cholesterol and fatty acid) under aerobic and hypoxic conditions, using RNAseq. Lipids significantly induced the expression of 368 genes. A main core lipid response was observed involving efflux systems, iron caption and sulfur reduction. In co-expression with ncRNAs and other genes discussed below, may act coordinately to prepare the machinery conferring drug tolerance and increasing a persistent population. Our findings could be useful to tag relevant pathways for the development of new drugs, vaccines and new strategies to control TB.
Eco-evolutionary Red Queen dynamics regulate biodiversity in a metabolite-driven microbial system
Authors: Bonachela Juan A. , Wortel Meike T. , Stenseth Nils Chr. 
Published: December 2017

AbstractThe Red Queen Hypothesis proposes that perpetual co-evolution among organisms can result from purely biotic drivers. After more than four decades, there is no satisfactory understanding as to which mechanisms trigger Red Queen dynamics or their implications for ecosystem features such as biodiversity. One reason for such a knowledge gap is that typical models are complicated theories where limit cycles represent an idealized Red Queen, and therefore cannot be used to devise experimental setups. Here, we bridge this gap by introducing a simple model for microbial systems able to show Red Queen dynamics. We explore diverse biotic sources that can drive the emergence of the Red Queen and that have the potential to be found in nature or to be replicated in the laboratory. Our model enables an analytical understanding of how Red Queen dynamics emerge in our setup, and the translation of model terms and phenomenology into general underlying mechanisms. We observe, for example, that in our system the Red Queen offers opportunities for the increase of biodiversity by facilitating challenging conditions for intraspecific dominance, whereas stasis tends to homogenize the system. Our results can be used to design and engineer experimental microbial systems showing Red Queen dynamics.
Genomic footprints of dryland stress adaptation in Egyptian fat-tail sheep and their divergence from East African and western Asia cohorts
Authors: Mwacharo Joram M. , Kim Eui-Soo , Elbeltagy Ahmed R. , Aboul-Naga Adel M. , Rischkowsky Barbara A. , Rothschild Max F. 
Published: December 2017

AbstractAfrican indigenous sheep are classified as fat-tail, thin-tail and fat-rump hair sheep. The fat-tail are well adapted to dryland environments, but little is known on their genome profiles. We analyzed patterns of genomic variation by genotyping, with the Ovine SNP50K microarray, 394 individuals from five populations of fat-tail sheep from a desert environment in Egypt. Comparative inferences with other East African and western Asia fat-tail and European sheep, reveal at least two phylogeographically distinct genepools of fat-tail sheep in Africa that differ from the European genepool, suggesting separate evolutionary and breeding history. We identified 24 candidate selection sweep regions, spanning 172 potentially novel and known genes, which are enriched with genes underpinning dryland adaptation physiology. In particular, we found selection sweeps spanning genes and/or pathways associated with metabolism; response to stress, ultraviolet radiation, oxidative stress and DNA damage repair; activation of immune response; regulation of reproduction, organ function and development, body size and morphology, skin and hair pigmentation, and keratinization. Our findings provide insights on the complexity of genome architecture regarding dryland stress adaptation in the fat-tail sheep and showcase the indigenous stocks as appropriate genotypes for adaptation planning to sustain livestock production and human livelihoods, under future climates.
Elucidating the 16S rRNA 3′ boundaries and defining optimal SD/aSD pairing in Escherichia coli and Bacillus subtilis using RNA-Seq data
Authors: Wei Yulong , Silke Jordan R. , Xia Xuhua 
Published: December 2017

AbstractBacterial translation initiation is influenced by base pairing between the Shine-Dalgarno (SD) sequence in the 5′ UTR of mRNA and the anti-SD (aSD) sequence at the free 3′ end of the 16S rRNA (3′ TAIL) due to: 1) the SD/aSD sequence binding location and 2) SD/aSD binding affinity. In order to understand what makes an SD/aSD interaction optimal, we must define: 1) terminus of the 3′ TAIL and 2) extent of the core aSD sequence within the 3′ TAIL. Our approach to characterize these components in Escherichia coli and Bacillus subtilis involves 1) mapping the 3′ boundary of the mature 16S rRNA using high-throughput RNA sequencing (RNA-Seq), and 2) identifying the segment within the 3′ TAIL that is strongly preferred in SD/aSD pairing. Using RNA-Seq data, we resolve previous discrepancies in the reported 3′ TAIL in B. subtilis and recovered the established 3′ TAIL in E. coli. Furthermore, we extend previous studies to suggest that both highly and lowly expressed genes favor SD sequences with intermediate binding affinity, but this trend is exclusive to SD sequences that complement the core aSD sequences defined herein.
Host species adaptation of TLR5 signalling and flagellin recognition
Authors: Tahoun Amin , Jensen Kirsty , Corripio-Miyar Yolanda , McAteer Sean , Smith David G. E. , McNeilly Tom N. , Gally David L. , Glass Elizabeth J. 
Published: December 2017

AbstractToll-like receptor 5 (TLR5) recognition of flagellin instigates inflammatory signalling. Significant sequence variation in TLR5 exists between animal species but its impact on activity is less well understood. Building on our previous research that bovine TLR5 (bTLR5) is functional, we compared human and bovine TLR5 activity and signalling in cognate cell lines. bTLR5 induced higher levels of CXCL8 when expressed in bovine cells and reciprocal results were found for human TLR5 (hTLR5) in human cells, indicative of host cell specificity in this response. Analysis of Toll/interleukin-1 receptor (TIR) sequences indicated that these differential responses involve cognate MyD88 recognition. siRNA knockdowns and inhibitor experiments demonstrated that there are some host differences in signalling. Although, PI3K activation is required for bTLR5 signalling, mutating bTLR5 F798 to hTLR5 Y798 within a putative PI3K motif resulted in a significantly reduced response. All ruminants have F798 in contrast to most other species, suggesting that TLR5 signalling has evolved differently in ruminants. Evolutionary divergence between bovine and human TLR5 was also apparent in relation to responses measured to diverse bacterial flagellins. Our results underscore the importance of species specific studies and how differences may alter efficacy of TLR-based vaccine adjuvants.
Comparing two remote video survey methods for spatial predictions of the distribution and environmental niche suitability of demersal fishes
Authors: Galaiduk Ronen , Radford Ben T. , Wilson Shaun K. , Harvey Euan S. 
Published: December 2017

AbstractInformation on habitat associations from survey data, combined with spatial modelling, allow the development of more refined species distribution modelling which may identify areas of high conservation/fisheries value and consequentially improve conservation efforts. Generalised additive models were used to model the probability of occurrence of six focal species after surveys that utilised two remote underwater video sampling methods (i.e. baited and towed video). Models developed for the towed video method had consistently better predictive performance for all but one study species although only three models had a good to fair fit, and the rest were poor fits, highlighting the challenges associated with modelling habitat associations of marine species in highly homogenous, low relief environments. Models based on baited video dataset regularly included large-scale measures of structural complexity, suggesting fish attraction to a single focus point by bait. Conversely, models based on the towed video data often incorporated small-scale measures of habitat complexity and were more likely to reflect true species-habitat relationships. The cost associated with use of the towed video systems for surveying low-relief seascapes was also relatively low providing additional support for considering this method for marine spatial ecological modelling.
Ginsenoside Rg3 Decreases Fibrotic and Invasive Nature of Endometriosis by Modulating miRNA-27b: In Vitro and In Vivo Studies
Authors: Kim Min Kyoung , Lee Seung Kyun , Park Ji Hyun , Lee Jae Hoon , Yun Bo Hyon , Park Joo Hyun , Seo Seok Kyo , Cho SiHyun , Choi Young Sik 
Published: December 2017

AbstractThis research aimed to evaluate the potential therapeutic effects of Rg3 on endometriosis and identify target miRNAs. We designed an in vitro study using human endometrial stromal cells (HESCs) obtained from patients with endometriosis and an in vivo study using mouse models. HESCs were treated with Rg3-enhanced red ginseng extract (Rg3E); real-time PCR and microarray profiling, transfection, and western blot were performed. Mouse endometriosis models were developed and supplemented with Rg3E for 8 weeks. Gross lesion size and fibrotic character were analyzed in the mouse models. RNA levels of Ki-67, col-1, CTGF, fibronectin, TGF-β1, MMP2 and MMP9 significantly decreased in HESCs after Rg3E treatment. Microarray analysis revealed downregulation of miR-27b-3p, which is related to fibrosis modulation. Expression of miR-27b-3p was significantly higher in HESCs from patients with endometriosis than that of controls, and Rg3E treatment significantly decreased its expression; the contraction and migration assay revealed significant reductions in both fibrosis and migration potential in Rg3E-treated HESCs from endometriosis patients. A decrease in size and fibrotic character of endometrial lesions from the Rg3E groups was observed in vivo. In conclusion, Rg3 effectively altered fibrotic properties of HESCs from patients with endometriosis, which is likely associated with miR-27b-3p modulation.
Effect of S267F variant of NTCP on the patients with chronic hepatitis B
Authors: Lee Hye Won , Park Hye Jung , Jin Bora , Dezhbord Mehrangiz , Kim Do Young , Han Kwang-Hyub , Ryu Wang-Shick , Kim Seungtaek , Ahn Sang Hoon 
Published: December 2017

AbstractSodium taurocholate cotransporting polypeptide (NTCP) was identified as an entry receptor for hepatitis B virus (HBV) infection. The substitution of serine at position 267 of NTCP with phenylalanine (S267F) is an Asian-specific variation that hampers HBV entry in vitro. In this study, we aimed to evaluate the prevalence of S267F polymorphism in Korean patients with chronic hepatitis B (CHB) and its association with disease progression and potential viral evolution in the preS1 domain of HBV. We found that the frequency of the S267F variant of NTCP in CHB patients and controls was 2.7% and 5.7% (P = 0.031), respectively, and that those who had S267F variant were less susceptible to chronic HBV infection. The frequency of the S267F variant in CHB, cirrhosis and hepatocellular carcinoma (HCC) patients was 3.3%, 0.9%, and 3.5%, respectively. Thus, the S267F variant correlated significantly with a lower risk for cirrhosis (P = 0.036). Sequencing preS1 domain of HBV from the patients who had S267F variant revealed no significant sequence change compared to the wild type. In conclusion, the S267F variant of NTCP is clinically associated with a lower risk of chronic HBV infection and cirrhosis development, which implicates suppressing HBV entry could reduce the disease burden.
Effects of snow properties on humans breathing into an artificial air pocket – an experimental field study
Authors: Strapazzon Giacomo , Paal Peter , Schweizer Jürg , Falk Markus , Reuter Benjamin , Schenk Kai , Gatterer Hannes , Grasegger Katharina , Dal Cappello Tomas , Malacrida Sandro , Riess Lukas , Brugger Hermann 
Published: December 2017

AbstractBreathing under snow, e.g. while buried by a snow avalanche, is possible in the presence of an air pocket, but limited in time as hypoxia and hypercapnia rapidly develop. Snow properties influence levels of hypoxia and hypercapnia, but their effects on ventilation and oxygenation in humans are not fully elucidated yet. We report that in healthy subjects breathing into snow with an artificial air pocket, snow density had a direct influence on ventilation, oxygenation and exhaled CO2. We found that a rapid decline in O2 and increase in CO2 were mainly associated with higher snow densities and led to premature interruption due to critical hypoxia (SpO2 ≤ 75%). However, subjects in the low snow density group demonstrated a higher frequency of test interruptions than expected, due to clinical symptoms related to a rapid CO2 accumulation in the air pocket. Snow properties determine the oxygen support by diffusion from the surrounding snow and the clearance of CO2 by diffusion and absorption. Thus, snow properties are co-responsible for survival during avalanche burial.
Proteasome stress sensitizes malignant pleural mesothelioma cells to bortezomib-induced apoptosis
Authors: Cerruti Fulvia , Jocollè Genny , Salio Chiara , Oliva Laura , Paglietti Luca , Alessandria Beatrice , Mioletti Silvia , Donati Giovanni , Numico Gianmauro , Cenci Simone , Cascio Paolo 
Published: December 2017

AbstractBased on promising results in preclinical models, clinical trials have been performed to evaluate the efficacy of the first-in-class proteasome inhibitor bortezomib towards malignant pleural mesothelioma (MPM), an aggressive cancer arising from the mesothelium of the serous cavities following exposure to asbestos. Unexpectedly, only minimal therapeutic benefits were observed, thus implicating that MPM harbors inherent resistance mechanisms. Identifying the molecular bases of this primary resistance is crucial to develop novel pharmacologic strategies aimed at increasing the vulnerability of MPM to bortezomib. Therefore, we assessed a panel of four human MPM lines with different sensitivity to bortezomib, for functional proteasome activity and levels of free and polymerized ubiquitin. We found that highly sensitive MPM lines display lower proteasome activity than more bortezomib-resistant clones, suggesting that reduced proteasomal capacity might contribute to the intrinsic susceptibility of mesothelioma cells to proteasome inhibitors-induced apoptosis. Moreover, MPM equipped with fewer active proteasomes accumulated polyubiquitinated proteins, at the expense of free ubiquitin, a condition known as proteasome stress, which lowers the cellular apoptotic threshold and sensitizes mesothelioma cells to bortezomib-induced toxicity as shown herein. Taken together, our data suggest that an unfavorable load-versus-capacity balance represents a critical determinant of primary apoptotic sensitivity to bortezomib in MPM.
Extracellular Cyclic GMP Modulates Membrane Expression of The GluA1 and GluA2 Subunits of AMPA Receptor in Cerebellum: Molecular Mechanisms Involved
Authors: Cabrera-Pastor Andrea , Taoro-González Lucas , Cuñat Amparo N. , Canet-López David , Balzano Tiziano , Felipo Vicente 
Published: December 2017

AbstractThere is increasing evidence that extracellular cGMP modulates glutamatergic neurotransmission and some forms of learning. However, the underlying mechanisms remain unknown. We proposed the hypotheses that extracellular cGMP may regulate membrane expression of AMPA receptors. To do this extracellular cGMP should act on a membrane protein and activate signal transduction pathways modulating phosphorylation of the GluA1 and/or GluA2 subunits. It has been shown that extracellular cGMP modulates glycine receptors. The aims of this work were to assess: 1) whether extracellular cGMP modulates membrane expression of GluA1 and GluA2 subunits of AMPA receptors in cerebellum in vivo; 2) whether this is mediated by glycine receptors; 3) the role of GluA1 and GluA2 phosphorylation and 4) identify steps of the intracellular pathways involved. We show that extracellular cGMP modulates membrane expression of GluA1 and GluA2 in cerebellum in vivo and unveil the mechanisms involved. Extracellular cGMP reduced glycine receptor activation, modulating cAMP, protein kinases and phosphatases, and GluA1 and GluA2 phosphorylation, resulting in increased GluA1 and reduced GluA2 membrane expression. Extracellular cGMP therefore modulates membrane expression of AMPA receptors and glutamatergic neurotransmission. The steps identified may be therapeutic targets to improve neurotransmission and neurological function in pathological situations with abnormal glutamatergic neurotransmission.
A next-generation newborn screening pilot study: NGS on dried blood spots detects causal mutations in patients with inherited metabolic diseases
Authors: Boemer F. , Fasquelle C. , d’Otreppe S. , Josse C. , Dideberg V. , Segers K. , Guissard V. , Capraro V. , Debray FG. , Bours V. 
Published: December 2017

AbstractThe range of applications performed on dried blood spots (DBS) widely broadened during the past decades to now include next-generation sequencing (NGS). Previous publications provided a general overview of NGS capacities on DBS-extracted DNA but did not focus on the identification of specific disorders. We thus aimed to demonstrate that NGS was reliable for detecting pathogenic mutations on genomic material extracted from DBS. Assuming the future implementation of NGS technologies into newborn screening (NBS), we conducted a pilot study on fifteen patients with inherited metabolic disorders. Blood was collected from DBS. Whole-exome sequencing was performed, and sequences were analyzed with a specific focus on genes related to NBS. Results were compared to the known pathogenic mutations previously identified by Sanger sequencing. Causal mutations were readily characterized, and multiple polymorphisms have been identified. According to variant database prediction, an unexplained homozygote pathogenic mutation, unrelated to patient’s disorder, was also found in one sample. While amount and quality of DBS-extracted DNA are adequate to identify causal mutations by NGS, bioinformatics analysis revealed critical drawbacks: coverage fluctuations between regions, difficulties in identifying insertions/deletions, and inconsistent reliability of database-referenced variants. Nevertheless, results of this study lead us to consider future perspectives regarding “next-generation” NBS.
Antibacterial activity of ceramide and ceramide analogs against pathogenic Neisseria
Authors: Becam Jérôme , Walter Tim , Burgert Anne , Schlegel Jan , Sauer Markus , Seibel Jürgen , Schubert-Unkmeir Alexandra 
Published: December 2017

AbstractCertain fatty acids and sphingoid bases found at mucosal surfaces are known to have antibacterial activity and are thought to play a more direct role in innate immunity against bacterial infections. Herein, we analysed the antibacterial activity of sphingolipids, including the sphingoid base sphingosine as well as short-chain C6and long-chain C16-ceramides and azido-functionalized ceramide analogs against pathogenicNeisseriae. Determination of the minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) demonstrated that short-chain ceramides and a ω-azido-functionalized C6-ceramide were active againstNeisseria meningitidisandN. gonorrhoeae, whereas they were inactive againstEscherichia coliandStaphylococcus aureus. Kinetic assays showed that killing ofN.meningitidisoccurred within 2 h with ω–azido-C6-ceramide at 1 X the MIC. Of note, at a bactericidal concentration, ω–azido-C6-ceramide had no significant toxic effect on host cells. Moreover, lipid uptake and localization was studied by flow cytometry and confocal laser scanning microscopy (CLSM) and revealed a rapid uptake by bacteria within 5 min. CLSM and super-resolution fluorescence imaging bydirectstochastic optical reconstruction microscopy demonstrated homogeneous distribution of ceramide analogs in the bacterial membrane. Taken together, these data demonstrate the potent bactericidal activity of sphingosine and synthetic short-chain ceramide analogs against pathogenicNeisseriae.