bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulating Multiple Substrate Binding Events by γ-Glutamyltransferase using Accelerated Molecular Dynamics
Authors: Oliva Francesco , Flores-Canales Jose C. , Pieraccini Stefano , Morelli Carlo F. , Sironi Maurizio , Schiøtt Birgit 
Published: April 2020

Abstractγ-glutamyltransferase (GGT) is an enzyme that uses γ-glutamyl compounds as substrate and catalyzes their transfer into a water molecule or an acceptor substrate with varied physiological-function in bacteria, plants and animals. Crystal structures of GGT are known for different species and in different states of the chemical reaction; however, structural dynamics of the substrate binding to the catalytic site of GGT is unknown. Here, we modeledEscherichia ColiGGT’s glutamine binding by using a swarm of accelerated molecular dynamics (aMD) simulations. Characterization of multiple binding events identified three structural binding motifs composed of polar residues in the binding pocket that govern glutamine binding into the active site. Simulated open and closed conformations of a lid-loop protecting the binding cavity suggests its role as a gating element by allowing or blocking substrates entry into the binding pocket. Partially open states of the lid-loop are accessible within thermal fluctuations, while the estimated free energy cost of a complete open state is 2.4 kcal/mol. Our results suggest that both specific electrostatic interactions and GGT conformational dynamics dictate the molecular recognition of substrate-GGT complexes.
Time-resolved cryoEM using Spotiton
Authors: Dandey Venkata P. , Budell William C. , Wei Hui , Bobe Daija , Maruthi Kashyap , Kopylov Mykhailo , Eng Edward , Kahn Peter A. , Hinshaw Jenny E. , Kundu Nidhi , Nimigean Crina M. , Fan Chen , Sukomon Nattakan , Darst Seth , Saecker Ruth , Chen James , Malone Brandon , Potter Clinton S. , Carragher Bridget 
Published: April 2020

AbstractWe present an approach for preparing cryoEM grids to study short-lived molecular states. Using piezo electric dispensing, two independent streams of ~50 pL sample drops are deposited within 10 ms of each other onto a nanowire EM grid surface, and the mixing reaction stops when the grid is vitrified in liquid ethane, on the order of ~100 ms later. We demonstrate the utility of this approach for four biological systems where short-lived states are of high interest.
Functional Interrogation ofHOXA9Regulome in MLLr Leukemia via Reporter-based CRISPR/Cas9 screen
Authors: Zhang Hao , Zhang Yang , Wright Shaela , Hyle Judith , Zhao Lianzhong , An Jie , Zhou Xinyue , Zhao Xujie , Shao Ying , Lee Hyeong-Min , Chen Taosheng , Zhou Yang , Lu Rui , Li Chunliang 
Published: April 2020

ABSTRACTAberrantHOXA9expression is a hallmark of most aggressive acute leukemias, including human acute myeloid leukemia (AML) and subtypes of acute lymphoblastic leukemia (ALL).HOXA9overexpression not only predicts poor diagnosis and outcome but also plays a critical role in leukemia transformation and maintenance. However, our current understanding ofHOXA9regulation in leukemia is limited, hindering development of therapeutic strategies to treatHOXA9-driven leukemia. To mitigate these challenges, we generated the firstHOXA9-mCherryknock-in reporter in an MLL-rearranged (MLLr) B-ALL cell line to dissectHOXA9regulation. By utilizing the reporter and CRISPR/Cas9 mediated screens, we identified transcription factors controllingHOXA9expression, including a novel regulator, USF2 and its homolog USF1. USF1/USF2 depletion significantly down-regulatedHOXA9expression and impaired MLLr leukemia cell proliferation. Ectopic expression of HOXA9-MEIS1 fusion protein rescued the impaired leukemia cell proliferation upon USF2 loss. Cut&Run analysis revealed the direct occupancy of USF2 ontoHOXA9promoter in MLLr leukemia cells. Collectively, theHOXA9reporter facilitated the functional interrogation of theHOXA9regulome and has advanced our understanding of the molecular regulation network inHOXA9-driven leukemia.
A CRISPR-Cas9–engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions
Authors: de los Santos Miguel Rodríguez , Rivalan Marion , David Friederike S. , Stumpf Alexander , Pitsch Julika , Tsortouktzidis Despina , Velasquez Laura Moreno , Voigt Anne , Schilling Karl , Mattei Daniele , Long Melissa , Vogt Guido , Knaus Alexej , Fischer-Zirnsak Björn , Wittler Lars , Timmermann Bernd , Robinson Peter N. , Horn Denise , Mundlos Stefan , Kornak Uwe , Becker Albert J. , Schmitz Dietmar , Winter York , Krawitz Peter M. 
Published: April 2020

Pathogenic germline mutations inPIGVlead to glycosylphosphatidylinositol biosynthesis deficiency (GPIBD). Individuals with pathogenic biallelic mutations in genes of the glycosylphosphatidylinositol (GPI) anchor pathway exhibit cognitive impairments, motor delay, and often epilepsy. Thus far, the pathophysiology underlying the disease remains unclear, and suitable rodent models that mirror all symptoms observed in human patients have not been available. Therefore, we used CRISPR-Cas9 to introduce the most prevalent hypomorphic missense mutation in European patients,Pigv:c.1022C>A (p.A341E), at a site that is conserved in mice. Mirroring the human pathology, mutantPigv341Emice exhibited deficits in motor coordination, cognitive impairments, and alterations in sociability and sleep patterns, as well as increased seizure susceptibility. Furthermore, immunohistochemistry revealed reduced synaptophysin immunoreactivity inPigv341Emice, and electrophysiology recordings showed decreased hippocampal synaptic transmission that could underlie impaired memory formation. In single-cell RNA sequencing,Pigv341E-hippocampal cells exhibited changes in gene expression, most prominently in a subtype of microglia and subicular neurons. A significant reduction inAbl1transcript levels in several cell clusters suggested a link to the signaling pathway of GPI-anchored ephrins. We also observed elevated levels ofHdctranscripts, which might affect histamine metabolism with consequences for circadian rhythm. This new mouse model will not only open the doors to further investigation into the pathophysiology of GPIBD, but will also deepen our understanding of the role of GPI-anchor–related pathways in brain development.Significance statementInherited GPI-anchor biosynthesis deficiencies (IGDs) explain many cases of syndromic intellectual disability. Although diagnostic methods are improving, the pathophysiology underlying the disease remains unclear. Furthermore, we lack rodent models suitable for characterizing cognitive and social disabilities. To address this issue, we generated the first viable mouse model for an IGD that mirrors the condition in human patients with a behavioral phenotype and susceptibility to epilepsy. Using the new model, we obtained neurological insights such as deficits in synaptic transmission that will facilitate understanding of the pathophysiology of IGDs.
Digestive parameters during gestation of Holstein heifers
Authors: Vieira Pereira Jéssica Marcela , Marcondes Marcos Inácio , de Campos Valadares Filho Sebastião , Caton Joel , Lacerda Sguizzato Anna Luiza , Silva Alex Lopes , da Silva Julia Travassos , Lima Moraes Valber Carlos , Gomes Lucas Faria , Rotta Polyana Pizzi 
Published: April 2020

AbstractOur objective was to estimate nutrient intake, ruminal flow, total apparent and ruminal digestibility, rates of passage and digestion, ruminal and omasal pH, blood metabolite concentrations, and body measurements during gestation of Holstein heifers. Eleven pregnant Holstein heifers, 8 of which fitted with a rumen cannula (450 ± 27.6 kg of body weight and 20 ± 3.5 months of initial age) were used. All heifers received the same diet composed of corn silage, soybean meal, corn meal, minerals and vitamins, with a corn silage:concentrate ratio of 50:50 (on a dry matter basis), aiming an average daily gain of approximately 1.0 kg. The sampling periods were established according to the days of gestation: 145, 200, and 255 with a duration of 10 days per period. Total fecal samples were collected to estimate dry matter, organic matter, crude protein, and neutral detergent fiber digestibility. Blood samples were collected to analyze metabolites (non-esterified fatty acids, β-hydroxybutyrate, urea, and glucose). Data were analyzed as a repeated measurements scheme, using MIXED procedure, with differences declared whenP< 0.05. Dry matter intake expressed in kg/day increased from d-145 to d-200, and remaining stable until d-255 of gestation. The same results were observed for organic matter and crude protein intake, increasing 15.0 and 35.8% respectively. In contrast, when dry matter intake was evaluated as % body weight, we observed a decrease of 16.7% from d-200 to d-255. Days of gestation did not influence ruminal flow of dry matter, organic matter, crude protein, and neutral detergent fiber. We observed an increase in the ruminal digestibility of neutral detergent fiber by 20.5%. The apparent total-tract digestibility of dry matter, organic matter, and crude protein changed over days of gestation, with an increase of 11.9, 8.5, and 9.8%, respectively, when comparing d-145 with d-200. The rate of digestion of neutral detergent fiber increased from 2.0 to 3.5% h-1. Glucose levels decreased, while β-hydroxybutirate and non-esterified fatty acids increased from d-145 to d-255. In conclusion, our results demonstrate a reduction in dry matter intake in % body weight due to pregnancy. It also shows an increase in total apparent digestibility through gestation, which imply a greater efficiency of use of nutrients by pregnant animals. Thus, further research is still needed to consolidate such results and to elucidate the mechanism about nutrient usage during the final third of gestation in heifers.
Targeted immuno-antiretroviral HIV therapeutic approach to provide dual protection and boosts cellular immunity: A proof-of-concept study
Authors: Mandal Subhra , Sunagawa Shawnalyn W. , Prathipati Pavan Kumar , Belshan Michael , Shibata Annemarie , Destache Christopher J. 
Published: April 2020

AbstractHuman immunodeficiency virus (HIV)-infected active and latent CCR5 expressing long-lived T-cells are the primary barrier to HIV/AIDS eradication. Broadly neutralizing antibodies and latency-reversing agents are the two most promising strategies emerging to achieve ‘functional cure’ against HIV infection. Antiretrovirals (ARVs) have shown to suppress plasma viral loads to non-detectable levels and above strategies have demonstrated a ‘functional cure’ against HIV infection is achievable. Both the above strategies are effective at inducing direct or immune-mediated cell death of latent HIV+ T-cells but have shown respective limitations. In this study, we designed a novel targeted ARVs-loaded nanoformulation that combines the CCR5 monoclonal antibody and antiretroviral drugs (ARV) as a dual protection strategy to promote HIV ‘functional cure’. The modified CCR5 monoclonal antibody (xfR5 mAb) surface-coated dolutegravir (DTG) and tenofovir alafenamide (TAF) loaded nanoformulation (xfR5-D+T NPs) were uniformly sized <250 nm, with 6.5 times enhanced antigen-binding affinity compared to naïve xfR5 mAb, and provided prolonged DTG and TAF intracellular retention (t1/2). The multivalent and sustained drug release properties of xfR5-D+T NPs enhance the protection efficiency against HIV by approximately 12, 3, and 5 times compared to naïve xfR5 mAb, D+T NP alone, and xfR5 NPs, respectively. Further, the nanoformulation demonstrated high binding-affinity to CCR5 expressing CD4+ cells, monocytes, and other HIV prone/latent T-cells by 25, 2, and 2 times, respectively. Further, the xfR5-D+T NPs during short-term pre-exposure prophylaxis induced a protective immunophenotype, i.e., boosted T-helper (Th), temporary memory (TM), and effector (E) sub-population. Moreover, treatment with xfR5-D+T NPs to HIV-infected T-cells induced a defensive/activated immunophenotype i.e., boosted naïve, Th, boosted central memory, TM, EM, E, and activated cytotoxic T-cells population. Therefore, this dual-action targeted mAb-ARV loaded nanoformulation could potentially become a multifactorial/multilayered solution to achieve a “functional cure.”
Schistosoma mansoniinfection reprograms the metabolic potential of the myeloid lineage in a mouse model of metabolic syndrome
Authors: Cortes-Selva Diana , Gibbs Lisa , Maschek J. Alan , Van Ry Tyler , Rajwa Bartek , Cox James E. , Amiel Eyal , Fairfax Keke C. 
Published: April 2020

SummaryDespite evidence that helminths protect from metabolic disease, a major gap exists in understanding the underlying mechanism(s). Here we demonstrate that bone marrow derived macrophages (BMDM) fromS. mansoniinfected male ApoE-/-mice have dramatically increased mitochondrial respiration compared to those from uninfected mice. This change associates with increased glucose and palmitate shuttling into TCA cycle intermediates and decreased accumulation of cellular cholesterol esters. Moreover, systemic metabolic modulation by schistosomes is a function of biological sex, where infection protects ApoE-/-male, but not female, mice from obesity and glucose intolerance. Sex-dependence extends to myeloid cells, where reprogramming leads to opposite cholesterol phenotypes in BMDM from females and males. Finally, the metabolic reprogramming of male myeloid cells is transferrable via bone marrow transplantation to an uninfected host, indicating maintenance of reprogramming in the absence of sustained antigen exposure. This work reveals thatS. mansonisystemic reprograming of myeloid metabolism is sex-dependent.
Cadherin-6 mediates thrombosisin vivo
Authors: Bouck Emma G. , de la Fuente Maria , Zunica Elizabeth R. , Li Wei , Mumaw Michele M. , Nieman Marvin T. 
Published: April 2020

AbstractBackgroundPlatelet adhesion is the critical process mediating stable thrombus formation. Previous reports of cadherin-6 on human platelets have demonstrated its role in platelet aggregation and thrombus formation.ObjectivesWe aimed to further characterize the importance of cadherin-6 in thrombosisin vivo.MethodsCadherin-6 platelet expression was evaluated by western blotting, flow cytometry and immunoprecipitation. Thrombosis was evaluated using the FeCl3and Rose Bengal carotid artery models in C57Bl6 mice treated with anti-cadherin-6 or IgG and wild-type orCdh6-/-mice. Platelet function was compared in wild type andCdh6-/-mice using tail-clip assays and aggregometry.ResultsHuman platelet expression of cadherin-6 was confirmed at ~3,000 copies per platelet.Cdh6-/-mice or those treated with anti-Cadherin-6 antibody showed an increased time to occlusion in both thrombosis models. Cadherin-6 was not expressed on mouse platelets, and there were no differences in tail bleeding times or platelet aggregation in wild-type versusCdh6-/-mice.ConclusionsCadherin-6 plays an essential role in thrombosisin vivo. However, cadherin-6 is not expressed on murine platelets. These data are in contrast to human platelets, which express a functional cadherin-6/catenin complex. The essential, platelet-independent role for cadherin-6 in hemostasis may allow it to be an effective and safe therapeutic target.EssentialsCadherin-6 function in thrombus formation was investigated in vivo using two murine models of thrombosis.Blocking or deleting cadherin-6 significantly delayed time to occlusionHuman platelets express cadherin-6, but murine platelets do not.
Dendrites decrease the synaptic weight resolution necessary to implement linearly separable computations
Authors: Cazé Romain , Stimberg Marcel 
Published: April 2020

AbstractIn theory, neurons modelled as single layer perceptrons can implement all linearly separable computations. In practice, however, these computations may require arbitrarily precise synaptic weights. This is a strong constraint since both, biological neurons and their artificial counterparts, have to cope with limited precision. Here, we explore how the non-linear processing in dendrites helps overcoming this constraint. We start by finding a class of computations which requires increasing precision with the number of inputs in a perceptron and show that it can be implemented without this constraint in a neuron with sub-linear subunits. Then, we complement this analytical study by a simulation of a biophysical neuron model with two passive dendrites and a soma, and show that it can implement this computation. This works demonstrates a new role of dendrites in neural computation: by distributing the computation across independent subunits, the same computation can be performed more efficiently with less precise tuning of the synaptic weights. We hope that this works not only offers new insight into the importance of dendrites for biological neurons, but also paves the way for new, more efficient architectures of artificial neuromorphic chips.Author SummaryIn theory, we know how much neurons can compute, in practice, the number of possible synaptic weights values limits their computation capacity. Such a limitation holds true for artificial and synthetic neurons. We introduce here a computation where the required means evolve significantly with the number of inputs, this poses a problem as neurons receive multiple thousands of inputs. We study here how the neurons’ receptive element-called dendrites-can mitigate such a problem. We show that, without dendrites, the largest synaptic weight need to be multiple orders of magnitude larger than the smallest to implement the computation. Yet a neuron with dendrites implements the same computation with constant synaptic weights whatever the number of inputs. This study paves the way for the use of dendritic neurons in a new generation of artificial neural network and neuromorphic chips with a considerably better cost-benefit balance.
The microtubule-associated protein CLASP is translationally-regulated in light-dependent root apical meristem growth
Authors: Halat Laryssa , Gyte Katherine , Wasteneys Geoffrey 
Published: April 2020

ABSTRACTThe ability for plant growth to be optimized, either in the light or dark, depends on the intricate balance between cell division and differentiation in specialized regions called meristems. WhenArabidopsis thalianaseedlings are grown in the dark, hypocotyl elongation is promoted, whereas root growth is greatly reduced as a result of changes in hormone transport and a reduction in meristematic cell proliferation. Previous work showed that the microtubule-associated protein CLASP sustains root apical meristem (RAM) size by influencing microtubule (MT) organization and by modulating the brassinosteroid (BR) signalling pathway. Here, we investigated whether CLASP is involved in light-dependent root growth promotion, since dark-grown seedlings have reduced RAM activity that is observed in theclasp-1null mutant. We showed that CLASP protein levels were greatly reduced in the root tips of dark-grown seedlings, which could be reversed by exposing plants to light. We confirmed that removing seedlings from the light led to a discernible shift in MT organization from bundled arrays, which are prominent in dividing cells, to transverse orientations typically observed in cells that have exited the meristem. BR receptors and auxin transporters, both of which are sustained by CLASP, were largely degraded in the dark. Interestingly, we found that despite the lack of protein,CLASPtranscript levels were higher in dark-grown root tips. Together, these findings uncover a mechanism that sustains meristem homeostasis through CLASP, and advances our understanding of how roots modulate their growth according to the amount of light and nutrients perceived by the plant.One Sentence SummaryThe microtubule-associated protein CLASP is regulated at the translational level when root meristem growth is inhibited in dark-grown plants.
Time-resolved transcriptome of barley anthers and meiocytes reveals robust and largely stable gene expression changes at meiosis entry
Authors: Barakate Abdellah , Orr Jamie , Schreiber Miriam , Colas Isabelle , Lewandowska Dominika , McCallum Nicola , Macaulay Malcolm , Morris Jenny , Arrieta Mikel , Hedley Pete E. , Ramsay Luke , Waugh Robbie 
Published: April 2020

ABSTRACTIn flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialised reproductive development programme we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes occur at the transition from pre-meiosis to leptotene–zygotene, which is followed by largely stable transcript abundance throughout prophase I. Our analysis reveals that the developing anthers and meiocytes are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologues showed differential transcript abundance in at least one stage or tissue comparison. Changes in the abundance of numerous transcription factors, representatives of the small RNA processing machinery, and post-translational modification pathways highlight the complexity of the regulatory networks involved. These developmental, time-resolved, and dynamic transcriptomes increase our understanding of anther and meiocyte development and will help guide future research.One sentence summaryAnalysis of RNA-seq data from meiotically staged barley anthers and meiocytes highlights the role of lncRNAs within a complex network of transcriptional and post-transcriptional regulation accompanied by a hiatus in differential gene expression during prophase I.The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Robbie Waugh (robbie.waugh@hutton.ac.uk)
Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: An in silico analysis
Authors: Yazdani Zahra , Rafiei Alireza , Yazdani Mohammadreza , Valadan Reza 
Published: April 2020

AbstractBackgroundTo date, no specific vaccine or drug has been proven to be effective for SARS-CoV-2 infection. Therefore, we implemented immunoinformatics approach to design an efficient multi-epitopes vaccine against SARS-CoV-2.ResultsThe designed vaccine construct has several immunodominant epitopes from structural proteins of Spike, Nucleocapsid, Membrane and Envelope. These peptides promote cellular and humoral immunity and Interferon gamma responses. In addition, these epitopes have antigenicity ability and no allergenicity probability. To enhance the vaccine immunogenicity, we used three potent adjuvants; Flagellin, a driven peptide from high mobility group box 1 as HP-91 and human beta defensin 3 protein. The physicochemical and immunological properties of the vaccine structure were evaluated. Tertiary structure of the vaccine protein was predicted and refined by I-Tasser and galaxi refine and validated using Rampage and ERRAT. Results of Ellipro showed 242 residues from vaccine might be conformational B cell epitopes. Docking of vaccine with Toll-Like Receptors 3, 5 and 8 proved an appropriate interaction between the vaccine and receptor proteins. In silico cloning demonstrated that the vaccine can be efficiently expressed inEscherichia coli.ConclusionsThe designed multi epitope vaccine is potentially antigenic in nature and has the ability to induce humoral and cellular immune responses against SARS-CoV-2. This vaccine can interact appropriately with the TLR3, 5, and 8. Also, this vaccine has high quality structure and suitable characteristics such as high stability and potential for expression inEscherichia coli.