bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vitro biosynthesis of poly-β-1,4-glucan derivatives using a pro-miscuous glycosyltransferase
Authors: Bulmer Gregory S. , Mattey Ashley P. , Parmeggiani Fabio , Williams Ryan , Ledru Helene , Marchesi Andrea , Seibt Lisa S. , Both Peter , Huang Kun , Galan M. Carmen , Flitsch Sabine L. , Green Anthony P. , van Munster Jolanda M. 
Published: February 2020

AbstractThe β-1,4-glucose linkage of cellulose is the most abundant polymeric linkage on earth and as such is of considerable interest in biology and biotechnology. It remains challenging to synthesize this linkage in vitro due to a lack of suitable biocatalysts; the natural cellulose biosynthetic machinery is a membrane-associated complex with processive activity that cannot be easily manipulated to synthesize tailor-made oligosaccharides and their derivatives. Here we identify a promiscuous activity of a soluble recombinant biocatalyst,Neisseria meningitidisglycosyltransferase LgtB, suitable for the polymerization of glucose from UDP-glucose via the generation of β-1,4-glycosidic linkages. We employed LgtB to synthesize natural and derivatized cello-oligosaccharides and we demonstrate how LgtB can be incorporated in biocatalytic cascades and chemo-enzymatic strategies to synthesize cello-oligosaccharides with tailored functionalities. We also show how the resulting glycan structures can be applied as chemical probes to report on activity and selectivity of plant cell wall degrading enzymes, including lytic polysaccharide monooxygenases. We anticipate that this biocatalytic approach to derivatized cello-oligosaccharides via glucose polymerization will open up new applications in biology and nanobiotechnology.
RanBP2-mediated SUMOylation promotes human DNA polymerase lambda nuclear localization and DNA repair
Authors: Moreno-Oñate M. , Herrero-Ruiz A.M. , García-Dominguez M. , Cortés-Ledesma F. , Ruiz J.F. 
Published: February 2020

AbstractCellular DNA is under constant attack by a wide variety of agents, both endogenous and exogenous. To counteract DNA damage, human cells have a large collection of DNA repair factors. Among them, DNA polymerase lambda (Polλ) stands out for its versatility, as it participates in different DNA repair and damage tolerance pathways in which gap-filling DNA synthesis is required. In this work we show that human Polλ is conjugated with Small Ubiquitin-like MOdifier (SUMO) proteins bothin vitroandin vivo, with Lys27 being the main target of this covalent modification. Polλ SUMOylation takes place in the nuclear pore complex and is mediated by the E3 ligase RanBP2. This post-translational modification promotes Polλ entry into the nucleus, which is required for its recruitment to DNA lesions and stimulated by DNA damage induction. Our work represents an advance in the knowledge of molecular pathways that regulate cellular localization of human Polλ, which are essential to be able to perform its functions during repair of nuclear DNA, and that might constitute an important point for the modulation of its activity in human cells.
“Enteric glia as a source of neural progenitors in adult zebrafish”
Authors: McCallum Sarah , Obata Yuuki , Fourli Evangelia , Boeing Stefan , Peddie Christopher J , Xu Qiling , Horswell Stuart , Kelsh Robert , Collinson Lucy , Wilkinson David , Pin Carmen , Pachnis Vassilis , Heanue Tiffany 
Published: February 2020

AbstractThe presence and identity of neural progenitors in the enteric nervous system (ENS) of vertebrates is a matter of intense debate. Here we demonstrate that the non-neuronal ENS cell compartment of teleosts shares molecular and morphological characteristics with mammalian enteric glia but cannot be identified by the expression of canonical glia markers. However, unlike their mammalian counterparts, which are generally quiescent and do not undergo neuronal differentiation during homeostasis, we show that a relatively high proportion of zebrafish enteric glia proliferate under physiological conditions giving rise to progeny that differentiate into enteric neurons. We also provide evidence that, similar to brain neural stem cells, the activation and neuronal differentiation of enteric glia are regulated by Notch signalling. Our experiments reveal remarkable similarities between enteric glia and brain neural stem cells in teleosts and open new possibilities for use of mammalian enteric glia as a potential source of neurons to restore the activity of intestinal neural circuits compromised by injury or disease.
SingleChlamydomonas reinhardi(C. reinhardtii) cell separation from bacterial cells and auto-fluorescence tracking with a nano-sieve device
Authors: Korensky Grant , Chen Xinye , Bao Mengdi , Miller Abbi , Lapizco-Encinas Blanca , Park Myeongkee , Du Ke 
Published: February 2020

AbstractA planar, transparent, and adaptable nano-sieve device is developed for efficient microalgae/bacteria separation. In our strategy, a sacrificial layer is applied in the dual photolithography patterning to achieve a one-dimensional channel with a very low aspect ratio (1:10,000). Microalgae/bacteria mixture is then introduced into the deformable polydimethylsiloxane (PDMS) nano-channel. The hydrodynamic deformation of the nano-channel is regulated to allow the bacteria cells to pass through while leaving the microalgae cells trapped in the device. At a flow rate of 4 μl/min, ~100% of the microalgae cells are trapped in the device. Additionally, this device is capable of immobilizing single cells in a transparent channel for auto-fluorescence tracking. These microalgae cells demonstrate minimal photo-bleaching over 250 s laser exposure and can be used to monitor hazardous compounds in the sample with a continuous flow fashion. Our method will be valuable to purify microalgae samples containing contaminations and study single cell heterogeneity.
Viral channelrhodopsins: calcium-dependent Na+/K+selective light-gated channels
Authors: Zabelskii D. , Alekseev A. , Kovalev K. , Oliviera A.-S. , Balandin T. , Soloviov D. , Bratanov D. , Volkov D. , Vaganova S. , Astashkin R. , Chizhov I. , Yutin N. , Rulev M. , Popov A. , Rokitskaya T. , Antonenko Y. , Rosselli R. , Rodriguez-Valera F. , Armeev G. , Shaitan K. , Bueldt G. , Vivaudou M. , Kirpichnikov M. , Koonin E. , Bamberg E. , Gordeliy V. 
Published: February 2020

AbstractPhytoplankton is the base of the marine food chain, oxygen, carbon cycle playing a global role in climate and ecology. Nucleocytoplasmic Large DNA Viruses regulating the dynamics of phytoplankton comprise genes of rhodopsins of two distinct families. We present a function-structure characterization of two homologous proteins representatives of family 1 of viral rhodopsins, OLPVR1 and VirChR1. VirChR1 is a highly selective, Ca2+-dependent, Na+/K+- conducting channel and, in contrast to known cation channelrhodopsins (ChRs), is impermeable to Ca2+ions. In human neuroblastoma cells, upon illumination, VirChR1 depolarizes the cell membrane to a level sufficient to fire neurons. It suggests its unique optogenetic potential. 1.4 Å resolution structure of OLPVR1 reveals their remarkable difference from the known channelrhodopsins and a unique ion-conducting pathway. The data suggest that viral channelrhodopsins mediate phototaxis of algae enhancing the host anabolic processes to support virus reproduction, and therefore, their key role in global phytoplankton dynamics.
DeepHE: Accurately Predicting Human Essential Genes based on Deep Learning
Authors: Zhang Xue , Xiao Wangxin , Xiao Weijia 
Published: February 2020

AbstractMotivationAccurately predicting essential genes using computational methods can greatly reduce the effort in finding them via wet experiments at both time and resource scales, and further accelerate the process of drug discovery. Several computational methods have been proposed for predicting essential genes in model organisms by integrating multiple biological data sources either via centrality measures or machine learning based methods. However, the methods aiming to predict human essential genes are still limited and the performance still need improve. In addition, most of the machine learning based essential gene prediction methods are lack of skills to handle the imbalanced learning issue inherent in the essential gene prediction problem, which might be one factor affecting their performance.ResultsWe proposed a deep learning based method, DeepHE, to predict human essential genes by integrating features derived from sequence data and protein-protein interaction (PPI) network. A deep learning based network embedding method was utilized to automatically learn features from PPI network. In addition, 89 sequence features were derived from DNA sequence and protein sequence for each gene. These two types of features were integrated to train a multilayer neural network. A cost-sensitive technique was used to address the imbalanced learning problem when training the deep neural network. The experimental results for predicting human essential genes showed that our proposed method, DeepHE, can accurately predict human gene essentiality with an average AUC higher than 94%, the area under precision-recall curve (AP) higher than 90%, and the accuracy higher than 90%. We also compared DeepHE with several widely used traditional machine learning models (SVM, Naïve Bayes, Random Forest, Adaboost). The experimental results showed that DeepHE greatly outperformed the compared machine learning models.ConclusionsWe demonstrated that human essential genes can be accurately predicted by designing effective machine learning algorithm and integrating representative features captured from available biological data. The proposed deep learning framework is effective for such task.Availability and ImplementationThe python code will be freely available upon the acceptance of this manuscript athttps://github.com/xzhang2016/DeepHE.Contactxue.zhang@tufts.edu
MCT2 Overexpression Rescues Metabolic Vulnerability and Protects Retinal Ganglion Cells in Two Models of Glaucoma
Authors: Harun-Or-Rashid Mohammad , Pappenhagen Nathaniel , Zubricky Ryan , Coughlin Lucy , Jassim Assraa Hassan , Inman Denise M. 
Published: February 2020

AbstractImproving cellular access to energy substrates is one strategy to overcome observed declines in energy production and utilization in the aged and pathologic central nervous system. Monocarboxylate transporters (MCTs), the movers of lactate, pyruvate, and ketone bodies into or out of a cell, are significantly decreased in the DBA/2J mouse model of glaucoma. In order to confirm MCT decreases are disease-associated, we decreased MCT2 in the retinas of MCT2fl/+mice using an injection of AAV2-cre, observing significant decline in ATP production and visual evoked potential. Restoring MCT2 levels in retinal ganglion cells (RGCs) via intraocular injection of AAV2-GFP-MCT2 in two models of glaucoma, the DBA/2J (D2), and a magnetic bead model of ocular hypertension (OHT), preserved RGCs and their function. Viral-mediated overexpression of MCT2 increased RGC density and axon number, reduced energy imbalance, and increased mitochondrial function as measured by cytochrome c oxidase and succinate dehydrogenase activity in both models of glaucoma. Ocular hypertensive mice injected with AAV2:MCT2 had significantly greater P1 amplitude as measured by pattern electroretinogram than mice with OHT alone. These findings indicate overexpression of MCT2 improves energy homeostasis in the glaucomatous visual system, suggesting that expanding energy input options for cells is a viable option to combat neurodegeneration.HighlightsLoss of MCT2 in retina compromises visual function and ATP production in optic nerveMCT2 overexpression preserves RGC soma and axon number in two glaucoma modelsMCT2 overexpression improves energy homeostasis in optic nerve
A meiosis-specific factor C19orf57/4930432K21Rik/BRME1 modulates localization of RAD51 and DMC1 recombinases to DSBs in mouse meiotic recombination
Authors: Takemoto Kazumasa , Tani Naoki , Takada-Horisawa Yuki , Fujimura Sayoko , Tanno Nobuhiro , Yamane Mariko , Okamura Kaho , Sugimoto Michihiko , Araki Kimi , Ishiguro Kei-ichiro 
Published: February 2020

SummaryMeiotic recombination is critical for genetic exchange and generation of chiasmata that ensures faithful chromosome segregation during meiosis I. Meiotic recombination is initiated by DNA double-strand break (DSB) followed by multiple processes of DNA repair. The exact mechanisms how recombinases localize to DSB remained elusive. Here we show that C19orf57/4930432K21Rik/BRME1 is a new player for meiotic recombination in mice. C19orf57/4930432K21Rik/BRME1 associates with ssDNA binding proteins, BRCA2 and MEILB2/HSF2BP, critical recruiters of recombinases onto DSB sites. Disruption of C19orf57/4930432K21Rik/BRME1 shows severe impact on DSB repair and male fertility. Remarkably, removal of single stranded DNA (ssDNA) binding proteins from DSB sites is delayed, and reciprocally the loading of RAD51 and DMC1 onto resected ssDNA is impaired inBrme1KO spermatocytes. We propose that C19orf57/4930432K21Rik/BRME1 modulates localization of recombinases to meiotic DSB sites through the interaction with the BRCA2-MEILB2/HSF2BP complex during meiotic recombination.
Faster and better CRISPR guide RNA design with the Crackling method
Authors: Bradford Jacob , Chappell Timothy , Perrin Dimitri 
Published: February 2020

The design of CRISPR-Cas9 guide RNAs is not trivial, and is a computationally demanding task. Design tools need to identify target sequences that will maximise the likelihood of obtaining the desired cut, whilst minimising off-target risk. There is a need for a tool that can meet both objectives while remaining practical to use on large genomes.Here, we present Crackling, a new method that is more suitable for meeting these objectives. We test its performance on 12 genomes and on data from validation studies. Crackling maximises guide efficiency by combining multiple scoring approaches. On experimental data, the guides it selects are better than those selected by others. It also incorporates Inverted Signature Slice Lists (ISSL) for faster off-target scoring. ISSL provides a gain of an order of magnitude in speed, while preserving the same level of accuracy. Overall, this makes Crackling a faster and better method to design guide RNAs at scale.Crackling is available athttps://github.com/bmds-lab/Cracklingunder the Berkeley Software Distribution (BSD) 3-Clause license.
Revealing Atomic-scale Molecular Diffusion of a Plant Transcription Factor WRKY domain protein along DNA
Authors: Dai Liqiang , Xu Yongping , Du Zhenwei , Su Xiao-dong , Yu Jin 
Published: February 2020

AbstractTranscription factor (TF) target search on genome is highly essential for gene expression and regulation. High-resolution determination of TF diffusion along DNA remains technically challenging. Here we constructed a TF model system of the plant WRKY domain protein in complex with DNA from crystallography and demonstrated microsecond diffusion dynamics of WRKY on the DNA employing all-atom molecular dynamics (MD) simulations. Notably, we found that WRKY preferentially binds to the Crick strand of DNA with significantly stronger energetic association than to the Watson strand. The preferential binding becomes highly prominent from non-specific to specific DNA binding, but less distinct from static binding to diffusive movements of WRKY on the DNA. Remarkably, without employing acceleration forces or bias, we captured a complete one-base pair (bp) stepping cycle of WRKY tracking along major groove of DNA with homogenous (AT)n sequence, as individual protein-DNA contacts break and reform at the binding interface. Continuous tracking of WRKY forward or backward, with occasional sliding as well as strand crossing to the minor groove of DNA, have also been captured in the simulation. The processive diffusion of WRKY had been confirmed by accompanied single-molecule fluorescence assays and coarse-grained (CG) structural simulations. The study thus provides unprecedented structural dynamics details on the TF diffusion, suggests how TF possibly approaches to gene target, and supports further high-precision experimental follow-up. The stochastic movements revealed in the TF diffusion also provide general clues on how other nucleic acid walkers step and slide along DNA.Significance StatementHow transcription factors search for target genes impact on how quickly and accurately the genes are transcribed and expressed. To locate target sufficiently fast, 1D diffusion of the protein along DNA appears essential. Experimentally, it remains challenging to determine diffusional steps of protein on DNA. Here, we report all-atom equilibrium simulations of a WRKY protein binding and diffusing on DNA, revealing structural dynamics details which have not been identified previously. We unprecedently demonstrate a complete stepping cycle of the protein for one base pair on DNA within microseconds, along with stochastic stepping or sliding, directional switching, and strand crossing. Additionally, we have found preferential DNA strand association of WRKY. These suggest how protein factors approach toward target DNA sequences.
Histogenesis of the reticulum of non- descript goat (Capra hircus) of India
Authors: Gupta Varsha , Farooqui Muneer Mohhamad , Sharma Ajay Prakash , Pathak Archana 
Published: February 2020

AbstractThe study was conducted on 36 developing reticulum from healthy and normal embryos/ foeti of Indian goat. Embryos/foeti were assigned into three groups. Histo-differentiation of reticulum of goat stomach took place at 38 days of gestation. The wall of foetal reticulum was made up of three strata i. e. epithelium, pleuripotent blastemic tissue and serosa up to 49 days of fetal age and definite four layersviz.epithelium, propria-submucosa, tunica muscularis and serosa were observed first at 51 days of gestation. Upto 100 days of gestation the reticulum was lined by undifferentiated stratified epithelium and thereafter gradually transformed into stratified squamous epithelium. Keratinization was noticed at term. Primary and secondary reticular crests made their appearance at 60 and 112 days of gestation, respectively. Corial papillae were detected in primary and secondary reticular crests at 121 and 145 days of gestation, respectively. Near term, the core of the reticular crest also contained muscularis mucosae in its proximal 1/3rdregion while core of the corial papillae contained only lamina propria. Reticular, collagen and elastic fibers came into sight at 46, 100 and 134 days of gestation, respectively.Summary statementThe study was conducted on intrauterine reticulum of Indian goat. From this study it can be concluded that the histogenesis of reticulum was almost completed in prenatal life. However, to become functional it still required more time as the relative sizes of reticulum and process of keratinization were yet to be completed.
Seneca Valley virus intercellular transmission mediated by exosomes
Authors: Zhang Keshan , Xu Guowei , Xu Shouxing , Shi Xijuan , Shen Chaochao , hao Junhong , yan Minhao , zhang dajun , Liu Xiangtao , Zheng Haixue 
Published: February 2020

ABSTRACTExosomes are cup-shaped vesicles that are secreted by cells and are involved in the intercellular transport of a variety of substances, including proteins, RNA, and liposomes. Studies have shown that pathogenic microorganisms are contained in exosomes extracted from pathogenic micro-infected cells. The Seneca Valley virus (SVV) is a non-encapsulated single-stranded positive-strand RNA virus that causes ulceration in the pig’s nose, the appearance of blisters, and other clinical symptoms similar to foot-and-mouth disease (FMD). Whether exosomes from SVV-infected cells can mediate SVV intercellular transmission is of great significance. There have been no studies showing whether exosomes can carry SVV in susceptible and non-susceptible cells. Here, we first extracted and identified exosomes from SVV-infected IBRS-2 cells. It was confirmed that replication of SVV can be inhibited when IBRS-2 cells treated with exosomes inbihitor GW4869. Furthermore, laser confocal microscopy and qRT-PCR experiments were performed to investigate whether exosomes can carry SVV and enable the virus to proliferate in susceptible and non-susceptible cells. Finally, exosome-mediated intercellular transmission can not be completely blocked by SVV-specific neutralizing antibodies. Taken together, this study showed that exosomes extracted from the SVV-infected IBRS-2 cells can carry SVV and transmit productive SVV infection between SVV susceptible and non-susceptible cells, this transmit infection is resistant to SVV specific neutralization antibody.IMPORTANCEExosomes participate in intercellular communnication between cells. Exosomes derived from virus-infected cells can mediate virus transmission or/and regulate immune response. However, the function of exosomes that from SVV-infected host cells during SVV transmission is unclear. Here, we demonstrate SVV can utilize host exosomes to establish productive infection in intercellular transmission. Furthermore, exosome-mediated SVV transmission is resistant to SVVV-specific neutralizing antibodies. This discovery sheds light on neutralizing antibodies resistant to SVVV transmission by exosomes as a potential immune evasion mechanism.
mTORC1 induces eukaryotic translation initiation factor 4E interaction with TOS-S6 kinase 1 and its activation
Authors: Majeed Sheikh Tahir , Batool Asiya , Majeed Rabiya , Bhat Nadiem Nazir , Andrabi Khurshid Iqbal 
Published: February 2020

AbstractEukaryotic translation initiation factor 4E was recently shown to be a substrate of mTORC1, suggesting it may be a mediator of mTORC1 signaling. Here, we present evidence that eIF4E phosphorylated at S209 interacts with TOS motif of S6 Kinase1 (S6K1). We also show that this interaction is sufficient to overcome rapamycin sensitivity and mTORC1 dependence of S6K1. Furthermore, we show that eIF4E-TOS interaction relieves S6K1 from auto-inhibition due to carboxy terminal domain (CTD) and primes it for hydrophobic motif (HM) phosphorylation and activation in mTORC1 independent manner. We conclude that the role of mTORC1 is restricted to engaging eIF4E with S6K1-TOS motif to influence its state of HM phosphorylation and inducing its activation.HighlightsPhosphorylated eIF4E interacts with TOS motif of S6 Kinase1eIF4E-TOS interaction relieves S6 Kinase 1 from carboxy terminal domain auto-inhibition and primes it for activation.