bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional characterization of thermotolerant microbial consortium for lignocellulolytic enzymes with central role of Firmicutes in rice straw depolymerization
Authors: Gavande Parmeshwar V. , Basak Arijita , Sen Subhajit , Lepcha Khusboo , Murmu Nensina , Rai Vijeta , Mazumdar Deepika , Saha Shyama Prasad , Das Vaskar , Ghosh Shilpi 
Published: February 2021

AbstractRice (Oryza sativa L.) straw, an agricultural waste of high yield, is a sustainable source of fermentable sugars for biofuel and other chemicals. However, it shows recalcitrance to microbial catalysed depolymerization. We herein describe development of thermotolerant microbial consortium (RSV) from vermicompost with ability to degrade rice straw and analysis of its metagenome for bacterial diversity, and lignocellulolytic carbohydrate active enzymes (CAZymes) and their phylogenetic affiliations. RSV secretome exhibited cellulases and hemicellulases with higher activity at 60 °C. It catalysed depolymerization of chemical pretreated rice straw as revealed by scanning electron microscopy and saccharification yield of 460 mg g−1 rice straw. Microbial diversity of RSV was distinct from other compost habitats, with predominance of members of phyla Firmicutes, Proteobacteria and Bacteroidetes; and Pseudoclostridium, Thermoanaerobacterium, Chelatococcus and Algoriphagus being most abundant genera. RSV harboured 1389 CAZyme encoding ORFs of glycoside hydrolase, carbohydrate esterase, glycosyl transferase, carbohydrate binding module and auxiliary activity functions. Microorganisms of Firmicutes showed central role in lignocellulose deconstruction with importance in hemicellulose degradation; whereas representatives of Proteobacteria and Bacteroidetes contributed to cellulose and lignin degradation, respectively. RSV consortium could be a resource for mining thermotolerant cellulolytic bacteria or enzymes and studying their synergism in deconstruction of chemically pretreated rice straw.
The effect of multiple interventions to balance healthcare demand for controlling COVID-19 outbreaks: a modelling study
Authors: Yang Po , Yang Geng , Qi Jun , Sheng Bin , Yang Yun , Zhang Shuhao , Bi Gaoshan , Mao Xuxin 
Published: February 2021

AbstractFor controlling recent COVID-19 outbreaks around the world, many countries have implemented suppression and mitigation interventions. This work aims to conduct a feasibility study for accessing the effect of multiple interventions to control the COVID-19 breakouts in the UK and other European countries, accounting for balance of healthcare demand. The model is to infer the impact of mitigation, suppression and multiple rolling interventions for controlling COVID-19 outbreaks in the UK, with two features considered: direct link between exposed and recovered population, and practical healthcare demand by separation of infections. We combined the calibrated model with COVID-19 data in London and non-London regions in the UK during February and April 2020. Our finding suggests that rolling intervention is an optimal strategy to effectively control COVID-19 outbreaks in the UK for balancing healthcare demand and morality ratio. It is better to implement regional based interventions with varied intensities and maintenance periods. We suggest an intervention strategy named as “Besieged and rolling interventions” to the UK that take a consistent suppression in London for 100 days and 3 weeks rolling intervention in other regions. This strategy would reduce the overall infections and deaths of COVID-19 outbreaks, and balance healthcare demand in the UK.
Sensitive mass spectrometric determination of kinin-kallikrein system peptides in light of COVID-19
Authors: Gangnus Tanja , Burckhardt Bjoern B. 
Published: February 2021

AbstractThe outbreak of COVID-19 has raised interest in the kinin–kallikrein system. Viral blockade of the angiotensin-converting enzyme 2 impedes degradation of the active kinin des-Arg(9)-bradykinin, which thus increasingly activates bradykinin receptors known to promote inflammation, cough, and edema—symptoms that are commonly observed in COVID-19. However, lean and reliable investigation of the postulated alterations is currently hindered by non-specific peptide adsorption, lacking sensitivity, and cross-reactivity of applicable assays. Here, an LC–MS/MS method was established to determine the following kinins in respiratory lavage fluids: kallidin, bradykinin, des-Arg(10)-kallidin, des-Arg(9)-bradykinin, bradykinin 1-7, bradykinin 2-9 and bradykinin 1-5. This method was fully validated according to regulatory bioanalytical guidelines of the European Medicine Agency and the US Food and Drug Administration and has a broad calibration curve range (up to a factor of 103), encompassing low quantification limits of 4.4–22.8 pg/mL (depending on the individual kinin). The application of the developed LC–MS/MS method to nasal lavage fluid allowed for the rapid (~ 2 h), comprehensive and low-volume (100 µL) determination of kinins. Hence, this novel assay may support current efforts to investigate the pathophysiology of COVID-19, but can also be extended to other diseases.
The within-host fitness of HIV-1 increases with age in ART-naïve HIV-1 subtype C infected children
Authors: Nagaraja Pradeep , Gopalan Bindu P. , D’Souza Reena R. , Sarkar Debolina , Rajnala Niharika , Dixit Narendra M. , Shet Anita 
Published: February 2021

AbstractAs the immune system develops with age, children combat infections better. HIV-1, however, targets an activated immune system, potentially rendering children increasingly permissive to HIV-1 infection as they grow. How HIV-1 fitness changes with age in children is unknown. Here, we estimated the within-host basic reproductive ratio,R0, a marker of viral fitness, in HIV-1 subtype C-infected children in India, aged between 84 days and 17 years. We measured serial viral load and CD4 T cell counts in 171 children who initiated first-line ART. For 25 children, regular and frequent measurements provided adequate data points for analysis using a mathematical model of viral dynamics to estimateR0. For the rest, we used CD4 counts for approximate estimation ofR0. The viral load decline during therapy was biphasic. The mean lifespans of productively and long-lived infected cells were 1.4 and 27.8 days, respectively. The meanR0was 1.5 in children aged < 5 years, increased with age, and approached 6.0 at 18 years, close to 5.8 estimated previously for adults. The tolerogenic immune environment thus compromises HIV-1 fitness in young children. Early treatment initiation, when theR0is small, will likely improve viral control, in addition to suppressing the latent reservoir.
Mono-ubiquitination of Rabphilin 3A by UBE3A serves a non-degradative function
Authors: Avagliano Trezza Rossella , Punt A. Mattijs , Mientjes Edwin , van den Berg Marlene , Zampeta F. Isabella , de Graaf Ilona J. , van der Weegen Yana , Demmers Jeroen A. A. , Elgersma Ype , Distel Ben 
Published: February 2021

AbstractAngelman syndrome (AS) is a severe neurodevelopmental disorder caused by brain-specific loss of UBE3A, an E3 ubiquitin protein ligase. A substantial number of possible ubiquitination targets of UBE3A have been identified, although evidence of being direct UBE3A substrates is often lacking. Here we identified the synaptic protein Rabphilin-3a (RPH3A), an effector of the RAB3A small GTPase involved in axonal vesicle priming and docking, as a ubiquitination target of UBE3A. We found that the UBE3A and RAB3A binding sites on RPH3A partially overlap, and that RAB3A binding to RPH3A interferes with UBE3A binding. We confirmed previous observations that RPH3A levels are critically dependent on RAB3A binding but, rather surprisingly, we found that the reduced RPH3A levels in the absence of RAB3A are not mediated by UBE3A. Indeed, while we found that RPH3A is ubiquitinated in a UBE3A-dependent manner in mouse brain, UBE3A mono-ubiquitinates RPH3A and does not facilitate RPH3A degradation. Moreover, we found that an AS-linked UBE3A missense mutation in the UBE3A region that interacts with RPH3A, abrogates the interaction with RPH3A. In conclusion, our results identify RPH3A as a novel target of UBE3A and suggest that UBE3A-dependent ubiquitination of RPH3A serves a non-degradative function.
Sequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds
Authors: Vezina Ben , Al-harbi Hulayyil , Ramay Hena R. , Soust Martin , Moore Robert J. , Olchowy Timothy W. J. , Alawneh John I. 
Published: February 2021

AbstractStreptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geographic regions of Australia. All isolates had novel multi locus sequence types (MLST) indicating a highly diverse population of S. uberis. Global clonal complexes (GCC) were more conserved. GCC ST86 and GCC ST143 represented 30% of the total isolates (n = 27) and were clustered within different geographic regions. Core genome phylogeny revealed low phylogenetic clustering by region, isolation source, and MLST. Identification of putative sortase (srtA) substrates and generation of a custom putative virulence factor database revealed genes which may explain the affinity of S. uberis for mammary tissue, evasion of antimicrobial efforts and disease pathogenesis. Of 27 isolates, four contained antibiotic resistance genes including an antimicrobial resistance cluster containing mel/mef(A), mrsE, vatD, lnuD, and transposon-mediated lnuC was also identified. These are novel genes for S. uberis, which suggests interspecies lateral gene transfer. The presence of resistance genes across the two geographic regions tested within one country supports the need for a careful, tailored, implementation and monitoring of antimicrobial stewardship.
Immediate and after effects of transcranial direct-current stimulation in the mouse primary somatosensory cortex
Authors: Sánchez-León Carlos A. , Cordones Isabel , Ammann Claudia , Ausín José M. , Gómez-Climent María A. , Carretero-Guillén Alejandro , Sánchez-Garrido Campos Guillermo , Gruart Agnès , Delgado-García José M. , Cheron Guy , Medina Javier F. , Márquez-Ruiz Javier 
Published: February 2021

AbstractTranscranial direct-current stimulation (tDCS) is a non-invasive brain stimulation technique consisting in the application of weak electric currents on the scalp. Although previous studies have demonstrated the clinical value of tDCS for modulating sensory, motor, and cognitive functions, there are still huge gaps in the knowledge of the underlying physiological mechanisms. To define the immediate impact as well as the after effects of tDCS on sensory processing, we first performed electrophysiological recordings in primary somatosensory cortex (S1) of alert mice during and after administration of S1-tDCS, and followed up with immunohistochemical analysis of the stimulated brain regions. During the application of cathodal and anodal transcranial currents we observed polarity-specific bidirectional changes in the N1 component of the sensory-evoked potentials (SEPs) and associated gamma oscillations. On the other hand, 20 min of cathodal stimulation produced significant after-effects including a decreased SEP amplitude for up to 30 min, a power reduction in the 20–80 Hz range and a decrease in gamma event related synchronization (ERS). In contrast, no significant changes in SEP amplitude or power analysis were observed after anodal stimulation except for a significant increase in gamma ERS after tDCS cessation. The polarity-specific differences of these after effects were corroborated by immunohistochemical analysis, which revealed an unbalance of GAD 65–67 immunoreactivity between the stimulated versus non-stimulated S1 region only after cathodal tDCS. These results highlight the differences between immediate and after effects of tDCS, as well as the asymmetric after effects induced by anodal and cathodal stimulation.
Cytoplasmic vacuolation with endoplasmic reticulum stress directs sorafenib induced non-apoptotic cell death in hepatic stellate cells
Authors: Sharma Sachin , Ghufran Shaikh Maryam , Ghose Sampa , Biswas Subhrajit 
Published: February 2021

AbstractThe activated hepatic stellate cells (HSCs) are the major cells that secrete the ECM proteins and drive the pathogenesis of fibrosis in chronic liver disease. Targeting of HSCs by modulating their activation and proliferation has emerged as a promising approach in the development of anti-fibrotic therapy. Sorafenib, a multi-kinase inhibitor has shown anti-fibrotic properties by inhibiting the survival and proliferation of HSCs. In present study we investigated sorafenib induced cytoplasmic vacuolation mediated decreased cell viability of HSCs in dose and time dependent manner. In this circumstance, sorafenib induces ROS and ER stress in HSCs without involvement of autophagic signals. The protein synthesis inhibitor cycloheximide treatment significantly decreased the sorafenib-induced cytoplasmic vacuolation with increasing cell viability. Antioxidant human serum albumin influences the viability of HSCs by reducing sorafenib induced vacuolation and cell death. However, neither caspase inhibitor Z-VAD-FMK nor autophagy inhibitor chloroquine could rescue the HSCs from sorafenib-induced cytoplasmic vacuolation and cell death. Using TEM and ER organelle tracker, we conclude that the cytoplasmic vacuoles are due to ER dilation. Sorafenib treatment induces calreticulin and GPR78, and activates IRE1α-XBP1s axis of UPR pathway, which eventually trigger the non-apoptotic cell death in HSCs. This study provides a notable mechanistic insight into the ER stress directed non-apoptotic cell death with future directions for the development of efficient anti-fibrotic therapeutic strategies.
Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies
Authors: Sucháčková Bartoňová Alena , Konvička Martin , Marešová Jana , Wiemers Martin , Ignatev Nikolai , Wahlberg Niklas , Schmitt Thomas , Faltýnek Fric Zdeněk 
Published: February 2021

AbstractThe bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host’s mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.
A recombinase polymerase amplification assay for rapid detection of rabies virus
Authors: Faye Martin , Abd El Wahed Ahmed , Faye Oumar , Kissenkötter Jonas , Hoffmann Bernd , Sall Amadou Alpha , Faye Ousmane 
Published: February 2021

AbstractRabies is a generally fatal encephalitis caused by a negative-sense single-stranded RNA lyssavirus transmitted to humans mainly from dog bite. Despite the recommendation by WHO and OIE to use the direct immunofluorescence test as standard method, molecular diagnostic assays like reverse transcription quantitative polymerase chain reaction (RT-qPCR) are increasing as a confirmatory method. However, both technologies are inaccessible in resource-limited settings. Moreover, the available point-of-need molecular assay is of poor detection limit for African strains. Herein, we developed a reverse transcription recombinase polymerase amplification (RT-RPA) assay as potential point-of-need diagnostic tool for rapid detection of various strains of rabies virus including locally isolated African strains. The sensitivity and specificity of the method was evaluated using a molecular RNA standard and different Rabies-related viruses belonging to theRhabdovirideafamily, respectively. The RABV-RPA performances were evaluated on isolates representative of the existing diversity and viral dilutions spiked in non-neural clinical specimen. The results were compared with RT-qPCR as a gold standard. The RABV-RPA detected down to 4 RNA molecules per reaction in 95% of the cases in less than 10 min. The RABV-RPA assay is highly specific as various RABV isolates were identified, but no amplification was observed for other member of theRhabdoviridea family. The sample background did not affect the performance of the RABV-RPA as down to 11 RNA molecules were identified, which is similar to the RT-qPCR results. Our developed assay is suitable for use in low-resource settings as a promising alternative tool forante-mortemrabies diagnosis in humans for facilitating timely control decisions.
Identification of a solo acylhomoserine lactone synthase from the myxobacterium Archangium gephyra
Authors: Albataineh Hanan , Duke Maya , Misra Sandeep K. , Sharp Joshua S. , Stevens D. Cole 
Published: February 2021

AbstractConsidered a key taxon in soil and marine microbial communities, myxobacteria exist as coordinated swarms that utilize a combination of lytic enzymes and specialized metabolites to facilitate predation of microbes. This capacity to produce specialized metabolites and the associated abundance of biosynthetic pathways contained within their genomes have motivated continued drug discovery efforts from myxobacteria. Of all myxobacterial biosynthetic gene clusters deposited in the antiSMASH database, only one putative acylhomoserine lactone (AHL) synthase, agpI, was observed, in genome data from Archangium gephyra. Without an AHL receptor also apparent in the genome of A. gephyra, we sought to determine if AgpI was an uncommon example of an orphaned AHL synthase. Herein we report the bioinformatic assessment of AgpI and discovery of a second AHL synthase from Vitiosangium sp. During axenic cultivation conditions, no detectible AHL metabolites were observed in A. gephyra extracts. However, heterologous expression of each synthase in Escherichia coli provided detectible quantities of 3 AHL signals including 2 known AHLs, C8-AHL and C9-AHL. These results suggest that A. gephyra AHL production is dormant during axenic cultivation. The functional, orphaned AHL synthase, AgpI, is unique to A. gephyra, and its utility to the predatory myxobacterium remains unknown.
Multicenter evaluation of Verigene Enteric Pathogens Nucleic Acid Test for detection of gastrointestinal pathogens
Authors: Kosai Kosuke , Suzuki Hiromichi , Tamai Kiyoko , Okada Yuya , Akamatsu Norihiko , Ueda Atsuo , Notake Shigeyuki , Yaguchi Yuji , Yanagihara Katsunori 
Published: February 2021

AbstractWe investigated the efficiency of the Verigene Enteric Pathogens Nucleic Acid Test (Verigene EP test), which is an automated microarray-based assay system that enables rapid and simultaneous genetic detection of gastrointestinal pathogens and toxins, including those in the Campylobacter Group, Salmonella species, Shigella species, the Vibrio Group, Yersinia enterocolitica, Shiga toxin 1 and 2, norovirus GI/GII, and rotavirus A. Three clinical laboratories evaluated the Verigene EP test, using 268 stool samples for bacterial and toxin genes and 167 samples for viral genes. Culture-based reference methods were used for the detection of bacteria and toxins, while a different molecular assay was used for viral detection. The overall concordance rate between the Verigene EP test and the reference methods for the 1940 assays was 99.0%. The overall sensitivity and specificity of the Verigene EP test were 97.0% and 99.3%, respectively. Of the 19 samples with discordant results, 13 samples were false positives and six were false negatives. The Verigene EP test simultaneously detected two targets in 11 samples; overall, the test demonstrated high efficiency in detecting crucial diarrheagenic pathogens, indicating its suitability for clinical practice.
Cerebellar rTMS and PAS effectively induce cerebellar plasticity
Authors: Pauly Martje G. , Steinmeier Annika , Bolte Christina , Hamami Feline , Tzvi Elinor , Münchau Alexander , Bäumer Tobias , Weissbach Anne 
Published: February 2021

AbstractNon-invasive brain stimulation techniques including repetitive transcranial magnetic stimulation (rTMS), continuous theta-burst stimulation (cTBS), paired associative stimulation (PAS), and transcranial direct current stimulation (tDCS) have been applied over the cerebellum to induce plasticity and gain insights into the interaction of the cerebellum with neo-cortical structures including the motor cortex. We compared the effects of 1 Hz rTMS, cTBS, PAS and tDCS given over the cerebellum on motor cortical excitability and interactions between the cerebellum and dorsal premotor cortex / primary motor cortex in two within subject designs in healthy controls. In experiment 1, rTMS, cTBS, PAS, and tDCS were applied over the cerebellum in 20 healthy subjects. In experiment 2, rTMS and PAS were compared to sham conditions in another group of 20 healthy subjects. In experiment 1, PAS reduced cortical excitability determined by motor evoked potentials (MEP) amplitudes, whereas rTMS increased motor thresholds and facilitated dorsal premotor-motor and cerebellum-motor cortex interactions. TDCS and cTBS had no significant effects. In experiment 2, MEP amplitudes increased after rTMS and motor thresholds following PAS. Analysis of all participants who received rTMS and PAS showed that MEP amplitudes were reduced after PAS and increased following rTMS. rTMS also caused facilitation of dorsal premotor-motor cortex and cerebellum-motor cortex interactions. In summary, cerebellar 1 Hz rTMS and PAS can effectively induce plasticity in cerebello-(premotor)-motor pathways provided larger samples are studied.
Low cost and long-focal-depth metallic axicon for terahertz frequencies based on parallel-plate-waveguides
Authors: Hernandez-Serrano A. I. , Pickwell-MacPherson Emma 
Published: February 2021

AbstractIn this work we demonstrate a triangular surface lens (axicon) operating at frequencies between 350 and 450 GHz using parallel-plate-waveguide technology. The proposed axicon offers longer focal depth characteristics compared to conventional plastic lenses, surpassing common TPX lenses by one order of magnitude. Additionally, due to the triangular surface of the axicon, this device is able to focus THz radiation onto smaller areas than TPX lenses, enhancing the resolution characteristics of THz imaging systems. The frequency range of operation of the proposed axicon can be easily tuned by changing the space between plates, making this approach a very attractive candidate for low-cost, robust and easy to assemble solutions for the next generation of active THz devices.