bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative proteome and PTMome analysis ofArabidopsis thalianaroot responses to persistent osmotic and salinity stress
Authors: Rodriguez MC. , Mehta D , Tan M , Uhrig RG 
Published: December 2020

ABSTRACTAbiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter, but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h - days) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis ofArabidopsis thalianaroots exposed to 300 mM Mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while PTMs do not. Further, we find significant changes in PTMs and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulphur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
Discovery of TMPRSS2 inhibitors from virtual screening
Authors: Hu Xin , Shrimp Jonathan H. , Guo Hui , Xu Miao , Chen Catherine Z. , Zhu Wei , Zakharov Alexey , Jain Sankalp , Shinn Paul , Simeonov Anton , Hall Matthew D. , Shen Min 
Published: December 2020

AbstractThe SARS-CoV-2 pandemic has prompted researchers to pivot their efforts to finding antiviral compounds and vaccines. In this study, we focused on the human host cell transmembrane protease serine 2 (TMPRSS2), which plays an important role in the viral life cycle by cleaving the spike protein to initiate membrane fusion. TMPRSS2 is an attractive target and has received attention for the development of drugs against SARS and MERS. Starting with comparative structural modeling and binding model analysis, we developed an efficient pharmacophore-based approach and applied a large-scalein silicodatabase screening for small molecule inhibitors against TMPRSS2. The hits were evaluated in the TMPRSS2 biochemical assay and the SARS-CoV-2 pseudotyped particle (PP) entry assay. A number of novel inhibitors were identified, providing starting points for further development of drug candidates for the treatment of COVID-19.
Lentiviral vector-based SARS-CoV-2 pseudovirus enables analysis of neutralizing activity in COVID-19 convalescent plasma
Authors: Pamukcu Cevriye , Celik Elif , Ergun Ebru Zeynep , Karahan Zeynep Sena , Turkoz Gozde , Aras Mertkaya , Eren Canan , Sili Uluhan , Bilgin Huseyin , Suder Ilke , Mandaci Baris Can , Dingiloglu Baran , Tatli Ozge , Doganay Gizem Dinler , Baris Safa , Ozoren Nesrin , Sutlu Tolga 
Published: December 2020

AbstractAs the COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread around the globe, effective vaccination protocols are under deployment. Alternatively, the use of convalescent plasma (CP) therapy relies on the transfer of the immunoglobulin repertoire of a donor that has recovered from the disease as a means of passive vaccination. While the lack of an effective antiviral treatment inadvertently increases the interest in CP products, initial clinical evaluation on COVID-19 patients revealed that critical factors determining the outcome of CP therapy need to be defined clearly if clinical efficacy is to be expected. Measurement of neutralizing activity against SARS-CoV-2 using wildtype virus presents a reliable functional assay but the availability of suitable BSL3 facilities for virus culture restricts its applicability. Instead, the use of pseudovirus particles containing elements from the SARS-CoV-2 virus is widely applied to determine the activity of CP or other neutralizing agents such as monoclonal antibodies.In this study, we present our approach to optimize GFP-encoding lentiviral particles pseudotyped with the SARS-CoV-2 Spike and Membrane proteins for use in neutralization assays. Our results show the feasibility of pseudovirus production using a C-terminal truncated Spike protein which is greatly enhanced by the incorporation of the D614G mutation. Moreover, we report that the use of Sodium Butyrate during lentiviral vector production dramatically increases pseudovirus titers. Analysis of CP neutralizing activity against particles pseudotyped with wildtype or D614G mutant Spike protein in the presence or absence the M protein revealed differential activity in CP samples that did not necessarily correlate with the amount of anti-SARS-CoV-2 antibodies.Our results indicate that the extent of neutralizing activity in CP samples depends on the quality rather than the quantity of the humoral immune responses and varies greatly between donors. Functional screening of neutralizing activity using pseudovirus-based neutralization assays must be accepted as a critical tool for choosing CP donors if clinical efficacy is to be maximized.
Modular deep learning enables automated identification of monoclonal cell lines
Authors: Fischbacher Brodie , Hedaya Sarita , Hartley Brigham J. , Wang Zhongwei , Lallos Gregory , Hutson Dillion , Zimmer Matthew , Brammer Jacob ,   The NYSCF Global Stem Cell Array® Team, Paull Daniel 
Published: December 2020

AbstractMonoclonalization refers to the isolation and expansion of a single cell derived from a cultured population. This is a valuable step in cell culture so as to minimize a cell line’s technical variability downstream of cell-altering events, such as reprogramming or gene editing, as well as for processes such as monoclonal antibody development. However, traditional methods for verifying clonality do not scale well, posing a critical obstacle to studies involving large cohorts. Without automated, standardized methods for assessing clonalitypost-hoc, methods involving monoclonalization cannot be reliably upscaled without exacerbating the technical variability of cell lines. We report the design of a deep learning workflow that automatically detects colony presence and identifies clonality from cellular imaging. The workflow, termed Monoqlo, integrates multiple convolutional neural networks and, critically, leverages the chronological directionality of the cell culturing process. Our algorithm design provides a fully scalable, highly interpretable framework, capable of analyzing industrial data volumes in under an hour using commodity hardware. In the present study, we focus on monoclonalization of human induced pluripotent stem cells (HiPSCs) as a case example. Monoqlo standardizes the monoclonalization process, enabling colony selection protocols to be infinitely upscaled while minimizing technical variability.
Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients
Authors: Xiang Haitao , Zhao Yingze , Li Xinyang , Liu Peipei , Wang Longlong , Wang Meiniang , Tian Lei , Sun Haixi , Zhang Wei , Xu Ziqian , Ye Beiwei , Yuan Xiaoju , Wang Pengyan , Zhang Ning , Gong Yuhuan , Bian Chengrong , Wang Zhaohai , Yu Linxiang , Yan Jin , Meng Fanping , Bai Changqing , Wang Xiaoshan , Liu Xiaopan , Gao Kai , Wu Liang , Liu Longqi , Gu Ying , Bi Yuhai , Shi Yi , Zhang Shaogeng , Zhu Chen , Xu Xun , Wu Guizhen , Gao George F. , Yang Naibo , Liu William J. , Yang Penghui 
Published: December 2020

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patient’s immunological status, and found dramatic changes in the IGH within the patients’ immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.
Serotonin 2A receptor signaling coordinates central metabolic processes to modulate aging in response to nutrient choice
Authors: Lyu Yang , Weaver Kristina J. , Shaukat Humza A. , Plumhoff Marta L. , Tjilos Maria , Promislow Daniel E.L. , Pletcher Scott D. 
Published: December 2020

AbstractIt has been recognized for nearly a century that diet modulates aging. Despite early experiments suggesting that reduced caloric intake augmented lifespan, accumulating evidence indicates that other characteristics of the diet may be equally or more influential in modulating aging. We demonstrate that behavior, metabolism, and lifespan inDrosophilaare affected by whether flies are provided a choice of different nutrients or a single, complete medium, largely independent of the amount of nutrients that are consumed. Meal choice elicits a rapid metabolic reprogramming that indicates a potentiation of TCA cycle and amino acid metabolism, which requires serotonin 2A receptor. Knockdown ofglutamate dehydrogenase, a key TCA pathway component, abrogates the effect of dietary choice on lifespan. Our results reveal a mechanism of aging that applies in natural conditions, including our own, in which organisms continuously perceive and evaluate nutrient availability to promote fitness and well-being.
Host’s Specific SARS-CoV-2 Mutations: Insertion of the Phenylalanine in the NSP6 Linked to the United Kingdom and Premature Termination of the ORF-8 Associated with the European and the United States of America Derived Samples
Authors: Khalid Mohammad , Al-ebini Yousef , Murphy David , Shoai Maryam 
Published: December 2020

AbstractThe coronavirus belongs to the order Nidovirales, which is known for the longest RNA genome virus. The polymerase enzyme of SARS-CoV-2 has proofreading functions, but still, the RNA viruses have a higher mutation rate than DNA viruses. The mutations in the viral genome provide a replication advantage in any population/geographical location and that may have profound consequences in the outcome and pathogenesis, diagnosis and patient management of the viral infection. In the present study, we have analysed full-length SARS-CoV-2 genome sequences, derived from symptomatic/asymptomatic COVID-19 patients from all six continents to investigate the common mutations globally. Our results revealed that SARS-CoV-2 is mutating independently, we identified total 313 mutations and some (21 mutations) of them are prevailing over time irrespective of geographical location. Another important finding, we are reporting here is, the mutation rate of the virus varies in different geographical locations suggesting the virus is adapting different strategies in the infected populations, having different genetic backgrounds across the globe. We have identified 11085TTT insertion (insertion of the Phenylalanine in NSP6 at position 38) mutation, which is mainly linked to the UK derived SARS-CoV-2 samples, we have also discovered non-sense mutation in ORF-8 after 17 amino acid is linked to the European and the USA derived SARS-CoV-2 samples.
LazySampling and LinearSampling: Fast Stochastic Sampling of RNA Secondary Structure with Applications to SARS-CoV-2
Authors: Zhang He , Zhang Liang , Li Sizhen , Mathews David H. , Huang Liang 
Published: December 2020

Many RNAs fold into multiple structures at equilibrium. The classical stochastic sampling algorithm can sample secondary structures according to their probabilities in the Boltzmann ensemble, and is widely used. However, this algorithm, consisting of a bottom-up partition function phase followed by a top-down sampling phase, suffers from three limitations: (a) the formulation and implementation of the sampling phase are unnecessarily complicated; (b) the sampling phase repeatedly recalculates many redundant recursions already done during the partition function phase; (c) the partition function runtime scales cubically with the sequence length. These issues prevent stochastic sampling from being used for very long RNAs such as the full genomes of SARS-CoV-2. To address these problems, we first adopt a hypergraph framework under which the sampling algorithm can be greatly simplified. We then present three sampling algorithms under this framework, among which the LazySampling algorithm is the fastest by eliminating redundant work in the sampling phase via on-demand caching. Based on LazySampling, we further replace the cubic-time partition function by a linear-time approximate one, and derive LinearSampling, an end-to-end linear-time sampling algorithm that is orders of magnitude faster than the standard one. For instance, LinearSampling is 176× faster (38.9s vs. 1.9h) than Vienna RNAsubopt on the full genome of Ebola virus (18,959nt). More importantly, LinearSampling is the first RNA structure sampling algorithm to scale up to the full-genome of SARS-CoV-2 without local window constraints, taking only 69.2 seconds on its reference sequence (29,903nt). The resulting sample correlates well with the experimentally-guided structures. On the SARS-CoV-2 genome, LinearSampling finds 23 regions of 15ntwith high accessibilities, which are potential targets for COVID-19 diagnostics and drug design.See code:https://github.com/LinearFold/LinearSampling
Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution
Authors: Trevino Alexandro E. , Müller Fabian , Andersen Jimena , Sundaram Laksshman , Kathiria Arwa , Shcherbina Anna , Farh Kyle , Chang Howard Y. , Paşca Anca M. , Kundaje Anshul , Paşca Sergiu P. , Greenleaf William J. 
Published: December 2020

ABSTRACTGenetic perturbations of cerebral cortical development can lead to neurodevelopmental disease, including autism spectrum disorder (ASD). To identify genomic regions crucial to corticogenesis, we mapped the activity of gene-regulatory elements generating a single-cell atlas of gene expression and chromatin accessibility both independently and jointly. This revealed waves of gene regulation by key transcription factors (TFs) across a nearly continuous differentiation trajectory into glutamatergic neurons, distinguished the expression programs of glial lineages, and identified lineage-determining TFs that exhibited strong correlation between linked gene-regulatory elements and expression levels. These highly connected genes adopted an active chromatin state in early differentiating cells, consistent with lineage commitment. Basepair-resolution neural network models identified strong cell-type specific enrichment of noncoding mutations predicted to be disruptive in a cohort of ASD subjects and identified frequently disrupted TF binding sites. This approach illustrates how cell-type specific mapping can provide insights into the programs governing human development and disease.
Environmental Dependence of the Structure of the C-terminal Domain of the SARS-CoV-2 Envelope Protein
Authors: Gadhave Kundlik , Kumar Ankur , Kumar Prateek , Kapuganti Shivani K. , Garg Neha , Vendruscolo Michele , Giri Rajanish 
Published: December 2020

AbstractThe SARS-CoV-2 envelope protein (E) is involved in a broad spectrum of functions in the cycle of the virus, including assembly, budding, envelope formation, and pathogenesis. To enable these activities, E is likely to be capable of changing its conformation depending on environmental cues. To investigate this issue, here we characterised the structural properties of the C-terminal domain of E (E-CTD), which has been reported to interact with host cell membranes. We first studied the conformation of the E-CTD in solution, finding characteristic features of a disordered protein. By contrast, in the presence of large unilamellar vesicles and micelles, which mimic cell membranes, the E-CTD was observed to become structured. The E-CTD was also found to display conformational changes with osmolytes. Furthermore, prolonged incubation of the E-CTD under physiological conditions resulted in amyloid-like fibril formation. Taken together, these findings indicate that the E-CTD can change its conformation depending on its environment, ranging from a disordered state, to a membrane-bound folded state, and an amyloid state. Our results thus provide insight into the structural basis of the role of E in the viral infection process.HighlightsThe E-CTD of SARS-CoV-2 is intrinsically disordered in solutionThe E-CTD folds into an ordered structure in presence of membrane mimeticsThe E-CTD displays conformational changes in the presence of osmolytesProlonged incubation of the E-CTD leads to its self-assembly into amyloid-like fibrilsGraphical AbstractStructural heterogeneity of the E-CTD.The E-CTD shows a disordered secondary structure in an aqueous solution and converts into an ordered structure in the presence of membrane mimetics (neutral and negative lipids) and natural osmolytes (TMAO). Incubation at physiological condition shows typical amyloid-like fibrils. The yellow-colored structure represents a predicted structure of the E-CTD by PEP-FOLD.
C1q/CTRP1 exerts neuroprotective effects in TBI rats by regulating inflammation and autophagy
Authors: Pei Ming , Wang Chaoqun , Li Zhengdong , Zhang Jianhua , Huang Ping , Wang Jiawen , Huang Jiang , Zou Donghua , Chen Yijiu 
Published: December 2020

AbstractObjectiveC1q/CTRP1 is a newly discovered adiponectin protein, which is highly expressed in adipose and heart tissues. Recent studies have revealed that C1q/CTRP1 can regulate metabolism and inhibit inflammation. CTRP1 is also expressed in brain tissues and vascular cells of human and rat, and research on cerebral hemorrhage and cerebral ischemia-reperfusion injury demonstrates that the CTRP family can attenuate secondary brain injury and exert neuroprotective effects. Thus, this study was designed to explore the role of CTRP1 in traumatic brain injury (TBI) and the underlying mechanism.Main methodsRats were assigned into rCTRP1 group, vehicle group, and sham group. Modified Feeney’s method was used to establish a closed traumatic brain injury model. Morris water maze was used for directional navigation, reverse searching and space exploration tests in rats. In addition, Golgi-Cox staining was utilized to visualize neurons, dendrites and dendritic spines. ELISA was conducted to detect the levels of inflammatory factors (IL-6 and TNF-α). Finally, Western blot was adopted to detect the relative expression ofp-mTOR and autophagy-related proteins (Beclin-1 and LC3-II).ResultsCTRP1 improved the behavioral and histopathological outcomes, inhibited the inflammatory response, activated mTOR and decreased autophagy-associated protein synthesis in TBI rats.ConclusionCTRP1 exerts neuroprotective effects in TBI rats by regulating inflammation and autophagy and has potential therapeutic properties after TBI.
Heterologous expression of methylxanthine synthesis enzymes in mammalian cells and their use as reporter proteins
Authors: Cisneros Brandon T. , Devaraj Neal K. 
Published: December 2020

AbstractThis work demonstrates the reconstitution of active methylxanthine synthesis enzymes in human cells and their potential use as inducible reporter enzymes. A variety of plant enzymes involved in caffeine synthesis have been characterizedin vitroand several of these methylxanthine synthesis enzymes have been heterologously-expressed in yeast or bacteria. In this work, enzymes fromCoffea arabica, Camellia sinensis, andPaullinia cupanahave been heterologously-expressed in human cells. We demonstrate that the enzymes tested exhibit similar patterns of activity with a set of xanthine substrates in human cells when compared to previous reports ofin vitroactivity. We demonstrate that the activity of these enzymes can be used as a reporter for juxtacrine signaling using synNotch-induced expression in the presence of an appropriate substrate. When used in combination with synthetic caffeine receptors, this work has potential for use as anin vivoreporter (e.g. enabling non-invasive monitoring of cell-cell interactions after a cellular transplant) or in synthetic intercellular signaling a methylxanthine, such as caffeine, acting as a synthetic paracrine hormone.
A Sequential Niche Multimodal Conformation Sampling Algorithm for Protein Structure Prediction
Authors: Xia Yu-Hao , Peng Chun-Xiang , Zhou Xiao-Gen , Zhang Gui-Jun 
Published: December 2020

AbstractMotivationMassive local minima on the protein energy surface often causes traditional conformation sampling algorithms to be easily trapped in local basin regions, because they are difficult to stride over high-energy barriers. Also, the lowest energy conformation may not correspond to the native structure due to the inaccuracy of energy models. This study investigates whether these two problems can be alleviated by a sequential niche technique without loss of accuracy.ResultsA sequential niche multimodal conformation sampling algorithm for protein structure prediction (SNfold) is proposed in this study. In SNfold, a derating function is designed based on the knowledge learned from the previous sampling and used to construct a series of sampling-guided energy functions. These functions then help the sampling algorithm stride over high-energy barriers and avoid the re-sampling of the explored regions. In inaccurate protein energy models, the high- energy conformation that may correspond to the native structure can be sampled with successively updated sampling-guided energy functions. The proposed SNfold is tested on 300 benchmark proteins and 24 CASP13 FM targets. Results show that SNfold is comparable with Rosetta restrained by distance (Rosetta-dist) and C-QUARK. SNfold correctly folds (TM-score ≥ 0.5) 231 out of 300 proteins. In particular, compared with Rosetta-dist protocol, SNfold achieves higher average TM- score and improves the sampling efficiency by more than 100 times. On the 24 CASP13 FM targets, SNfold is also comparable with four state-of-the-art methods in the CASP13 server group. As a plugin conformation sampling algorithm, SNfold can be extended to other protein structure prediction methods.AvailabilityThe source code and executable versions are freely available athttps://github.com/iobio-zjut/SNfold.Contactzgj@zjut.edu.cn