bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic spectrum and distinct evolution patterns of SARS-CoV-2
Authors: Liu Sheng , Shen Jikui , Fang Shuyi , Li Kailing , Liu Juli , Yang Lei , Hu Chang-Deng , Wan Jun
Published: June 2020

Four signature groups of frequently occurred single-nucleotide variants (SNVs) were identified in over twenty-eight thousand high-quality and high-coverage SARS-CoV-2 complete genome sequences, representing different viral strains. Some SNVs predominated but were mutually exclusively presented in patients from different countries and areas. These major SNV signatures exhibited distinguishable evolution patterns over time. A few hundred patients were detected with multiple viral strain-representing mutations simultaneously, which may stand for possible co-infection or potential homogenous recombination of SARS-CoV-2 in environment or within the viral host. Interestingly nucleotide substitutions among SARS-CoV-2 genomes tended to switch between bat RaTG13 coronavirus sequence and Wuhan-Hu-1 genome, indicating the higher genetic instability or tolerance of mutations on those sites or suggesting that major viral strains might exist between Wuhan-Hu-1 and RaTG13 coronavirus.
Estimation of the incubation period of COVID-19 using viral load data
Authors: Ejima Keisuke , Kim Kwang Su , Ludema Christina , Bento Ana I. , Iwanami Shoya , Fujita Yasuhisa , Ohashi Hirofumi , Koizumi Yoshiki , Watashi Koichi , Aihara Kazuyuki , Nishiura Hiroshi , Iwami Shingo
Published: June 2020

The incubation period, or the time from infection to symptom onset of COVID-19 has been usually estimated using data collected through interviews with cases and their contacts. However, this estimation is influenced by uncertainty in recalling effort of exposure time. We propose a novel method that uses viral load data collected over time since hospitalization, hindcasting the timing of infection with a mathematical model for viral dynamics. As an example, we used the reported viral load data from multiple countries (Singapore, China, Germany, France, and Korea) and estimated the incubation period. The median, 2.5, and 97.5 percentiles of the incubation period were 5.23 days (95% CI: 5.17, 5.25), 3.29 days (3.25, 3.37), and 8.22 days (8.02, 8.46), respectively, which are comparable to the values estimated in previous studies. Using viral load to estimate the incubation period might be a useful approach especially when impractical to directly observe the infection event.
Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis
Authors: Bakhit Mina , Krzyzaniak Natalia , Scott Anna Mae , Clark Justin , Glasziou Paul , Del Mar Chris
Published: June 2020

Objective

To identify, appraise, and synthesise studies evaluating the downsides of wearing facemasks in any setting. We also discuss potential strategies to mitigate these downsides.

Methods

PubMed, Embase, CENTRAL, EuropePMC were searched (inception-18/5/2020), and clinical registries were searched via CENTRAL. We also did forward-backward citation search of the included studies. We included randomised controlled trials and observational studies comparing facemask use to any active intervention or to control. Two author pairs independently screened articles for inclusion, extracted data and assessed the quality of included studies. The primary outcomes were compliance, discomforts, harms, and adverse events of wearing facemasks.

Findings

We screened 5471 articles, including 37 (40 references); 11 were meta-analysed. For mask wear adherence, 47% more people wore facemasks in the facemask group compared to control; adherence was significantly higher (26%) in the surgical/medical mask group than in N95/P2 group. The largest number of studies reported on the discomfort and irritation outcome (20-studies); fewest reported on the misuse of masks, and none reported on mask contamination or risk compensation behaviour. Risk of bias was generally high for blinding of participants and personnel and low for attrition and reporting biases.

Conclusion

There are insufficient data to quantify all of the adverse effects that might reduce the acceptability, adherence, and effectiveness of face masks. New research on facemasks should assess and report the harms and downsides. Urgent research is also needed on methods and designs to mitigate the downsides of facemask wearing, particularly the assessment of alternatives such as face shields.
Laser-activated drug implant for controlled release to the posterior segment of the eye
Authors: He Xingyu , Yuan Zheng , Gaeke Samantha , Kao Winston W.-Y. , Li S. Kevin , Miller Daniel , Williams Basil , Park Yoonjee C.
Published: June 2020

The current standard of care for posterior segment eye diseases, such as age-related macular degeneration and diabetic macular edema, is frequent intravitreal injections or sustained-release drug implants. Drug implants have side effects due to the burst release of the drugs, and their release cannot be easily controlled after implantation. Present study attempts to develop a dosage-controllable drug delivery implant which consists of a nanoporous biodegradable PLGA capsule and light-activated liposomes. Controllable drug release from the implant was achieved by using pulsed near-infrared (NIR) laser both in vitro and in vivo. The in vitro drug release kinetics from two different initial dose implants, 1000 μg and 500 μg, was analyzed by fitting zero order and first order kinetics, as well as the Korsmeyer-Peppas and Higuchi models. The 1000 μg and 500 μg implants fit the first-order and zero-order kinetics model, respectively, the best. The multiple drug releases in the vitreous was determined by in vivo fluorimeter, which was consistent with the in vitro data. The dose released was also clinically relevant. Histology and optical and ultrasound imaging data showed no abnormality in the eyes received implant treatment suggesting that the drug delivery system was safe to the retina. This on-demand dose-controllable drug delivery system could be potentially used for long-term posterior eye disease treatment.
Neuronal Variability Reflects Probabilistic Inference Tuned to Natural Image Statistics
Authors: Festa Dylan , Aschner Amir , Davila Aida , Kohn Adam , Coen-Cagli Ruben
Published: June 2020

Neuronal activity in sensory cortex fluctuates over time and across repetitions of the same input. This variability is often considered detrimental to neural coding. The theory of neural sampling proposes instead that variability encodes the uncertainty of perceptual inferences. In primary visual cortex (V1), modulation of variability by sensory and non-sensory factors supports this view. However, it is unknown whether V1 variability reflects the statistical structure of visual inputs, as would be required for inferences correctly tuned to the statistics of the natural environment. Here we combine analysis of image statistics and recordings in macaque V1 to show that probabilistic inference tuned to natural image statistics explains the widely observed dependence between spike-count variance and mean, and the modulation of V1 activity and variability by spatial context in images. Our results show that the properties of a basic aspect of cortical responses — their variability — can be explained by a probabilistic representation tuned to naturalistic inputs.
A program to automate the discovery of drugs for West Nile and Dengue virus – programmatic screening of over a billion compounds on PubChem, generation of drug leads and automatedIn Silicomodelling
Authors: Ben Geoffrey A S , Sanker Akhil , Madaj Rafal , Valdés Tresanco Mario Sergio , Upadhyay Manish , Gracia Judith
Published: June 2020

Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning based AutoQSAR algorithm to generate drug leads for the flaviviruses – Dengue and West Nile. The drug leads generated by the program are feed as programmatic inputs to AutoDock Vina package for automatedIn Silicomodelling of interaction between the compounds generated as drug leads by the program and the chosen Dengue and West Nile drug target methyltransferase, whose inhibition leads to the control of viral replication. The machine learning based AutoQSAR algorithm involves feature selection, QSAR modelling, validation and prediction. The drug leads generated each time the program is run is reflective of the constantly growing PubChem database is an important dynamic feature of the program which facilitates fast and dynamic drug lead generation against the West Nile and Dengue virus in way which is reflective of the constantly growing PubChem database. The program prints out the top drug leads after screening PubChem library which is over a billion compounds. The leads generated by the program are fed as programmatic inputs to anIn Silicomodelling package. The interaction of top drug lead compounds generated by the program and drug targets of West Nile and Dengue virus, was modelled in an automated way through programmatic commands. Thus our program ushers in a new age of automatic ease in the virtual drug screening and drug identification through programmatic data mining of chemical data libraries and drug lead generation through machine learning based AutoQSAR algorithm and an automatedIn Silicomodelling run through the program to study the interaction between the drug lead compounds and the drug target protein of West Nile and Dengue virus
Endogenization from diverse viral ancestors is common and widespread in parasitoid wasps
Authors: Burke Gaelen R. , Hines Heather M. , Sharanowski Barbara J.
Published: June 2020

The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral generaBracovirus(in Braconidae) andIchnovirus(in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now heritable viral integration events in wasp genomes. Here, new genome sequence assemblies for eleven species and six publicly available genomes from the Ichneumonoidea were screened with the goal of identifying novel EVEs and characterizing the breadth of species in lineages with known EVEs. Exhaustive similarity searches combined with the identification of ancient core genes revealed sequences from both known and novel EVEs. Two species harbored novel, independently derived EVEs related to a divergent large double-stranded DNA (dsDNA) virus that manipulates behavior in other hymenopteran species. While bracovirus or ichnovirus EVEs were identified as expected in three species, the absence of ichnoviruses in several species suggests that they are independently derived and present in two younger, less widespread lineages than previously thought. Overall, this study presents a novel bioinformatic approach for EVE discovery in genomes and shows that three divergent virus families (nudiviruses, the ancestors of ichnoviruses, and LbFV-like viruses) are recurrently acquired as EVEs in parasitoid wasps. Virus acquisition in the parasitoid wasps is a common process that has occurred in many more than two lineages from a diverse range of arthropod-infecting dsDNA viruses.

Significance

Parasitoid wasps are an extremely diverse group of animals that are known to harbor Endogenous Virus Elements (EVEs) that produce virions or virus-like particles of key importance in wasps’ parasitism success. However, the prevalence and diversity of independently acquired EVEs in parasitoid wasp lineages has remained largely uncharacterized on a widespread scale. This study represents an important first step and hints at the massive, untapped diversity of EVEs in parasitoid wasps via the identification of several novel virus co-option events from diverse groups of double-stranded DNA virus pathogens.
Infinity Flow: High-throughput single-cell quantification of 100s of proteins using conventional flow cytometry and machine learning
Authors: Becht Etienne , Tolstrup Daniel , Dutertre Charles-Antoine , Ginhoux Florent , Newell Evan W. , Gottardo Raphael , Headley Mark B.
Published: June 2020

Modern immunologic research increasingly requires high-dimensional analyses in order to understand the complex milieu of cell-types that comprise the tissue microenvironments of disease. To achieve this, we developed Infinity Flow combining hundreds of overlapping flow cytometry panels using machine learning to enable the simultaneous analysis of the co-expression patterns of 100s of surface-expressed proteins across millions of individual cells. In this study, we demonstrate that this approach allows the comprehensive analysis of the cellular constituency of the steady-state murine lung and to identify novel cellular heterogeneity in the lungs of melanoma metastasis bearing mice. We show that by using supervised machine learning, Infinity Flow enhances the accuracy and depth of clustering or dimensionality reduction algorithms. Infinity Flow is a highly scalable, low-cost and accessible solution to single cell proteomics in complex tissues.
Norepinephrine, olfactory bulb and memory stability
Authors: Linster Christiane , Midroit Maellie , Forest Jeremy , Thenaisie Yohann , Cho Christina , Richard Marion , Didier Anne , Mandairon Nathalie
Published: June 2020

Memory stability is essential for animal survival when environment and behavioral state change over short or long time spans. The stability of a memory can be expressed by its duration, its perseverance when conditions change as well as its specificity to the learned stimulus. Using optogenetic and pharmacological manipulations, we show that stability of an odor-reward association can be modulated by noradrenergic inputs to the first olfactory network, the olfactory bulb. We show that while manipulations of noradrenaline during an odor-reward acquisition have no acute effects, they impact learning flexibility as well as the duration and the specificity of the memory. We use a computational approach to propose a proof of concept model showing that a single, simple network effect of noradrenaline on olfactory bulb dynamics can underlie these seemingly different behavioral effects. Our results show how acute changes in network dynamics can have long term effects that extend beyond the network that was manipulated.
Exogenous Nitro-Oleic Acid inhibits primary root growth by reducing the mitosis in the meristem inArabidopsis thaliana
Authors: Di Fino Luciano M. , Cerrudo Ignacio , Salvatore Sonia R. , Schopfer Francisco J. , García-Mata Carlos , Laxalt Ana M.
Published: June 2020

Nitric oxide (NO) is a second messenger that regulates a broad range of physiological processes in plants. NO-derived molecules called reactive nitrogen species (RNS) can react with unsaturated fatty acids generating nitrated fatty acids (NO2-FA). NO2-FA work as signaling molecules in mammals where production and targets have been described under different stress conditions. Recently, NO2-FAs were detected in plants, however their role(s) on plant physiological processes is still poorly known. Here we show that exogenous application of nitro-oleic acid (NO2-OA) inhibits Arabidopsis primary root growth; this inhibition is not likely due to nitric oxide (NO) production or impaired auxin or cytokinin root responses. Deep analyses showed that roots incubated with NO2-OA had a lower cell number in the division area. Although this NO2-FA did not affect the signaling mechanisms maintaining the stem cell niche, plants incubated with NO2-OA showed a reduction of cell division in the meristematic area. Therefore, this work shows that NO2-OA inhibits mitotic processes subsequently reducing primary root growth.
Multiple epigenetic layers accompany the spatial distribution of ribosomal genes in Arabidopsis
Authors: Kutashev Konstantin O. , Franek Michal , Diamanti Klev , Komorowski Jan , Olšinová Marie , Dvořáčková Martina
Published: June 2020

45S ribosomal genes in A. thaliana (rDNA) are located in tandem arrays on termini of chromosomes 2 and 4 (NOR2 and NOR4) and encode rRNA, crucial structural elements of the ribosome. Inactive rDNA genes accumulate in the condensed chromocenters in the nucleus and at the nucleolar periphery, while nucleolus delimits the active genes. We show that a subset of nucleolar rDNA assembles into condensed foci marked by H3.1 and H3.3 histones and that progressive rDNA condensation is connected with rDNA transcriptional activity, cell ploidy and rDNA copy number. Interestingly, some nucleolar foci are reminiscent of perinucleolar chromocenters, containing the NOR4 region. We further demonstrate that rDNA promoter is a key regulatory region of the rDNA repeat and describe large involvement of repressive epigenetic mark H3K9me2 and H2A.W histone variant in rDNA activity regulation. In addition, we found euchromatic H3.3 histone enrichment at the rDNA transcription start site in actively dividing tissues, despite its accumulation in nucleolar foci containing condensed rDNA repeats.
Electrophysiological validation of premotor interneurons monosynaptically connected to the aCC motoneuron in theDrosophilalarval CNS
Authors: Giachello Carlo N. G. , Zarin Aref Arzan , Kohsaka Hiroshi , Fan Yuen Ngan , Nose Akinao , Landgraf Matthias , Baines Richard A.
Published: June 2020

Mapping the wired connectivity of a nervous system is a prerequisite for full understanding of function. In this respect, such endeavours can be likened to genome sequencing projects. These projects similarly produce impressive amounts of data which, whilst a technicaltour-de-force, remain under-utilised without validation. Validation of neuron synaptic connectivity requires electrophysiology which has the necessary temporal and spatial resolution to map synaptic connectivity. However, this technique is not common and requires extensive equipment and training to master, particularly when applied to the small CNS of theDrosophilalarva. Thus, validation of connectivity in this CNS has been more reliant on behavioural analyses and, in particular, activity imaging using the calcium-sensor GCaMP. Whilst both techniques are powerful, they each have significant limitations for this purpose. Here we use electrophysiology to validate an array of driver lines reported to label specific premotor interneurons that theDrosophilaconnectome project suggests are monosynaptically connected to an identified motoneuron termed the anterior corner cell (aCC). Our results validate this proposition for four selected lines. Thus, in addition to validating the connectome with respect to these four premotor interneurons, our study highlights the need to functionally validate driver lines prior to use.
Single cell RNA sequence analysis of human bone marrow samples reveals new targets for isolation of skeletal stem cells using DNA-coated gold nanoparticles
Authors: Matthews Elloise , Lanham Stuart , White Kate , Kyriazi Maria-Eleni , Alexaki Konstantina , El-Sagheer Afaf H. , Brown Tom , Kanaras Antonios G. , West Jonathan , MacArthur Ben D. , Stumpf Patrick S. , Oreffo Richard O.C.
Published: June 2020

There is a wealth of data indicating human bone marrow derived stromal cells (HBMSCs) contain the skeletal stem cell (SSC) with the potential to differentiate along the stromal osteogenic, adipogenic and chondrogenic lineages. However, despite these advances, current methods to isolate skeletal stem cells (SSCs) from human tissues have proved challenging as no single specific marker has been identified limiting understanding of SSC fate, immunophenotype and the widespread clinical application of these cells. While a number of cell surface markers can enrich for SSCs, none of the proposed markers, alone, provide a platform to isolate single cells with the ability to form bone, cartilage, and adipose tissue in humans. The current study details the application of oligonucleotide-coated nanoparticles, spherical nucleic acids (SNAs), to rapidly isolate human cells using mRNAs signatures detected in SSCs in real time, to identify stem and progenitor skeletal populations using single cell RNA sequencing. Based on scRNA-seq of samples from 11 patients, this method was able to identify novel targets for SSC enrichment, which were assessed in a total of 80 patients. This methodology was able to isolate potential SSCs found at a frequency of <1 in 1,000,000 in human bone marrow, with a capacity for tri-lineage differentiationin vitro. The current approach provides new targets and a platform to advance SSC isolation, enrichment with significant therapeutic impact therein.
Chromatin potential identified by shared single cell profiling of RNA and chromatin
Authors: Ma Sai , Zhang Bing , LaFave Lindsay , Chiang Zachary , Hu Yan , Ding Jiarui , Brack Alison , Kartha Vinay K. , Law Travis , Lareau Caleb , Hsu Ya-Chieh , Regev Aviv , Buenrostro Jason D.
Published: June 2020

Cell differentiation and function are regulated across multiple layers of gene regulation, including the modulation of gene expression by changes in chromatin accessibility. However, differentiation is an asynchronous process precluding a temporal understanding of the regulatory events leading to cell fate commitment. Here, we developed SHARE-seq, a highly scalable approach for measurement of chromatin accessibility and gene expression within the same single cell. Using 34,774 joint profiles from mouse skin, we develop a computational strategy to identifycis-regulatory interactions and define Domains of Regulatory Chromatin (DORCs), which significantly overlap with super-enhancers. We show that during lineage commitment, chromatin accessibility at DORCs precedes gene expression, suggesting changes in chromatin accessibility may prime cells for lineage commitment. We therefore develop a computational strategy (chromatin potential) to quantify chromatin lineage-priming and predict cell fate outcomes. Together, SHARE-seq provides an extensible platform to study regulatory circuitry across diverse cells within tissues.
WNT inhibition creates a BRCA-like state in Wnt-addicted cancer
Authors: Kaur Amanpreet , Sepramaniam Sugunavathi , Lim Jun Yi Stanley , Patnaik Siddhi , Harmston Nathan , Lee May Ann , Petretto Enrico , Virshup David M. , Madan Babita
Published: June 2020

Wnt signaling maintains diverse adult stem cell compartments and is implicated in chemotherapy resistance in cancer. PORCN inhibitors that block Wnt secretion have proven effective in Wnt-addicted preclinical cancer models and are in clinical trials. In a survey for potential combination therapies, we found that Wnt inhibition synergizes with the PARP inhibitor olaparib in Wnt-addicted cancers. Mechanistically, we find that multiple genes in the homologous recombination and Fanconi anemia repair pathways, includingBRCA1,FANCD2, andRAD51are dependent on Wnt/β-catenin signaling in Wnt-high cancers, and treatment with a PORCN inhibitor creates a BRCA-like state. This coherent regulation of DNA repair genes occurs via a Wnt/β-catenin/MYBL2 axis. Importantly, this pathway also functions in intestinal crypts, where high expression of BRCA and Fanconi anemia genes is seen in intestinal stem cells, with further upregulation in Wnt high APCminmutant polyps. Our findings suggest a general paradigm that Wnt/β-catenin signaling enhances DNA repair in stem cells and cancers to maintain genomic integrity. Conversely, interventions that block Wnt signaling may sensitize cancers to radiation and other DNA damaging agents.
Model of intracellular ATP production reproduces common electrophysiological signatures of anesthesia
Authors: Joo Pangyu , Lee Heonsoo , Wang Shiyong , Kim Seunghwan , Hudetz Anthony G.
Published: June 2020

Accumulating evidence suggest that general anesthetics with diverse chemical structure reduce cerebral metabolism with consequent reduction of intracellular adenosine triphosphate (ATP) levels. How cerebral hypometabolism is associated with the typical electroencephalographic (EEG) changes under general anesthesia remains largely unknown.,. We hypothesized that the deficit in ATP production would reduce high-frequency activity, increase low-frequency activity, and cause burst suppression, which are common dose-dependent anesthetic effects on the EEG. To test the hypothesis, we developed a novel neural network model consisting of leaky integrate-and-fire neurons with additional dependency on ATP dynamics. The effect of varying rate of ATP production on neuronal and population activity patterns was simulated under various excitatory/inhibitory balance conditions. A decrease of ATP production suppressed neuronal spiking and enhanced synchronization of neurons over a range of excitatory/inhibitory synaptic strength ratios. As anticipated, the initially asynchronous fast activity was replaced by globally desynchronized slow oscillation and, on further decrease of ATP production, changed into burst suppression with enhanced global synchronization. This study substantiates a novel biophysical mechanism for anesthetic-induced EEG changes through a relationship between energy production and synchronization of neural network.
Comparative analysis of the molecular mechanism of heat shock proteins from pathogenic and non-pathogenicE.coli
Authors: Bhattacharjee Sanchari , Saha Mohana , Dasgupta Rakhi , Bagchi Angshuman
Published: June 2020

Cells can withstand the effects of temperature stress by activating small heat shock proteins IbpA and IbpB. Lon protease employing Ser679 – Lys722 catalytic dyad proteolyze IbpA and IbpB in their free forms, at physiological temperature i.e. without any temperature stress. However, the proteolytic activity of IbpA and IbpB is affected when the catalytic dyad residue of Lon protease is mutated. The mutation S679A in Lon protease brings about some changes so that the proteolytic interactions between the small heat shock proteins with that of the mutant Lon protease are lost which makes a difference in the interaction pattern of mutant Lon protease with their substrates. In the present study, we made an attempt through in-silico approach to figure out the underlying aspects of the interactions between the small heat shock proteins IbpA and IbpB with mutant Lon protease inEscherichia coli. We have tried to decipher the molecular details of the mechanism of interaction of proteolytic machinery of small heat shock proteins and mutant Lon protease with S679A mutation at physiological temperature in absence cellular temperature stress. Our study may therefore be helpful to decode the mechanistic details of the correlation with IbpA, IbpB and S679A mutant Lon protease inE. coli.
A designed high-affinity peptide that hijacks microtubule-based transport
Authors: Cross Jessica A. , Chegkazi Magda S. , Steiner Roberto A. , Woolfson Derek N. , Dodding Mark P.
Published: June 2020

Technologies that manipulate and augment the transport of vesicles and organelles by motor proteins along microtubules offer new routes to understanding its mechanistic basis, and could lead to therapeutics. Many cargoes for the kinesin-1 family of microtubule motors utilize adaptor proteins that harbor linear peptide motifs that are recognized by the tetratricopeptide repeats of kinesin light chains (KLCTPRs). These motifs bind with micromolar affinities at independent but overlapping sites. Here, we employ a fragment-linking peptide design strategy to generate an extended synthetic ligand (KinTag) with low nanomolar affinity for KLCTPRs. The X-ray crystal structure of the KLCTPR:KinTag complex demonstrates interactions as designed. Moreover, KinTag functions in cells to promote the transport of lysosomes with a high efficiency that correlates with its enhanced affinity. Together, these data demonstrate a new strategy for peptide design and its application to reveal that the more tightly a motor holds its cargo, the greater is the extent of cargo transport.
Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale
Authors: Li Chenghan , Yue Zhi , Espinoza-Fonseca L. Michel , Voth Gregory A.
Published: June 2020

The sarcoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ions from the cytoplasm to the reticulum lumen at the expense of ATP hydrolysis. In addition to transporting Ca2+, SERCA facilitates bidirectional proton transport across the sarcoplasmic reticulum to maintain the charge balance of the transport sites and to balance the charge deficit generated by the exchange of Ca2+. Previous studies have shown the existence of a transient water-filled pore in SERCA that connects the Ca2+-binding sites with the lumen, but the capacity of this pathway to sustain passive proton transport has remained unknown. In this study, we used the multiscale reactive molecular dynamics (MS-RMD) method and free energy sampling to quantify the free energy profile and timescale of the proton transport across this pathway while also explicitly accounting for the dynamically coupled hydration changes of the pore. We find that proton transport from the central binding site to the lumen has a microsecond timescale, revealing a novel passive cytoplasm-to-lumen proton flow beside the well-known inverse proton countertransport occurring in active Ca2+transport. We propose that this proton transport mechanism is operational and serves as a functional conduit for passive proton transport across the sarcoplasmic reticulum.

SIGNIFICANCE

Multiscale reactive molecular dynamics combined with free energy sampling was applied to study proton transport through a transient water pore connecting the Ca2+-binding site to the lumen in SERCA. This is the first computational study of this large biomolecular system that treats the hydrated excess proton and its transport through water structures and amino acids explicitly. When also correctly accounting for the hydration fluctuations of the pore, it is found that a transiently hydrated channel can transport protons on a microsecond timescale. These results quantitatively support the hypothesis of the proton intake into the sarcoplasm via SERCA, in addition to the well-known proton pumping by SERCA to the cytoplasm along with Ca2+transport.
Skeletal Muscle Remodeling in Immobilized Patients: Determined Using a Parameter Estimation Histomorphometric Approach
Authors: Formosa Brent , Liyanaarachchi Asiri , Silvers Samantha , Gatti Domenico L. , Larsson Lars , Arslanturk Suzan , Jena Bhanu P.
Published: June 2020

Skeletal muscle biopsy commonly used for light microscopic, electron microscopic and biochemical and transcriptional evaluation remains the gold standard for establishing the etiology of a myopathy. While most myopathies exhibit one or more phenotypes, early stages or several metabolic myopathies often exhibit normal muscle morphology, making diagnosis difficult. In such cases where standard staining techniques fail to offer definitive diagnostic information, a combination of expensive and time-consuming electron microscopy and biochemical testing is required to provide definitive diagnosis. As a step toward overcoming these limitations in diagnostic pathology of skeletal muscle tissue, here we report the application of parameter estimation machine learning approaches on immunofluorescent images of human skeletal muscle tissue acquired using fluorescent microscopy. The machine learning morphometric approach enables the recognition of fine cellular changes in skeletal muscle tissue, allowing determination of skeletal muscle remodeling as a consequence of immobilization.
Wild emmer introgressions alter root-to-shoot growth dynamics in response to water stress
Authors: Bacher Harel , Zhu Feiyu , Gao Tian , Liu Kan , Dhatt Balpreet K , Awada Tala , Zhang Chi , Distelfeld Assaf , Yu Hongfeng , Peleg Zvi , Walia Harkamal
Published: June 2020

Water deficit is a major limiting factor for wheat (Triticumsp.) development and productivity. One approach to increase water stress adaptation in wheat is incorporating novel alleles from the drought-adapted wheat progenitor, wild emmer (T. turgidumssp.dicoccoides). We explored this idea in the context of vegetative growth by examining the phenotypic consequence of a series of wild emmer (acc. Zavitan) introgressions into elite durum wheat (cv. Svevo) under water-limited conditions. Using image-based phenotyping we cataloged divergent (from Svevo) growth responses to water stress ranging from high plasticity to high stability among the introgression lines. We identified an introgression line (IL20) that exhibits a highly plastic response to water stress by shifting its root-to-shoot biomass ratio for detailed characterization. By combining genotypic information with root transcriptome analysis, we propose several candidate genes (including a root-specific kinase) that can confer the shoot-to-root carbon resource allocation in IL20 under water stress. Discovery of high plasticity trait in IL20 in response to water stress highlights the potential of wild introgressions for enhancing stress adaptation via mechanisms that may be absent or rare in elite breeding material.
Optimizing spectral quality with quantum dots to enhance crop yield in controlled environments
Authors: Parrish Charles H. , Hebert Damon , Jackson Aaron , Ramasamy Karthik , McDaniel Hunter , Giacomelli Gene A. , Bergren Matthew R.
Published: June 2020

Bioregenerative life-support systems (BLSS) involving plants will be required to realize self-sustaining human settlements beyond Earth. To improve plant photosynthetic efficiency in BLSS, the quality of the solar spectrum can be modified by lightweight, luminescent films. CuInS2/ZnS quantum dot (QD) films with peak emissions at 600 and 660 nm were used to redshift ultraviolet and blue photons to increase biomass accumulation in red romaine lettuce. Plant growth parameters, except spectral quality, were held constant among three equivalent production environments. Lettuce grown under the 600 and 660 nm-emitting QD films respectively increased edible dry mass (13% and 9%), edible fresh mass (11% each), and total leaf area (8% and 13%) compared to under a control film that contained no QDs. Spectral modifications by the luminescent QD films improved photosynthetic efficiency in lettuce and could enhance crop productivity in greenhouses on Earth or in space, where further improvements are expected from greater availability of ultraviolet photons for conversion.
TBK1 interacts with tau and enhances neurodegeneration in tauopathy
Authors: Abreha Measho H. , Ojelade Shamsideen , Dammer Eric B. , McEachin Zachary T. , Duong Duc M. , Gearing Marla , Bassell Gary J. , Lah James J. , Levey Allan I. , Shulman Joshua M. , Seyfried Nicholas T.
Published: June 2020

One of the defining pathological features of Alzheimer’s Disease (AD) is the deposition of neurofibrillary tangles (NFTs) composed of hyperphosphorylated tau in the brain. Aberrant activation of kinases in AD has been suggested to enhance phosphorylation and toxicity of tau, making the responsible tau-directed kinases attractive therapeutic targets. The full complement of tau interacting kinases in AD brain and their activity in disease remains incompletely defined. Here, immunoaffinity enrichment coupled with mass spectrometry (MS) identified TANK-binding kinase 1 (TBK1) as a tau-interacting partner in human AD cortical brain tissues. We validated this interaction in both human AD and familial frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) caused by mutations inMAPT(R406W) postmortem brain tissues as well as human cell lines. Further, we document increased TBK1 activity in both AD and FTDP-17 and map the predominant TBK1 phosphorylation sites on tau based onin vitrokinase assays coupled to MS. Lastly, in aDrosophilatauopathy model, activating expression of a conserved TBK1 ortholog triggers tau hyperphosphorylation and enhanced neurodegeneration, whereas knockdown had the reciprocal effect, suppressing tau toxicity. Collectively, our findings suggest that increased TBK1 activity may promote tau hyperphosphorylation and neuronal loss in AD and related tauopathies.
Quantitative differences between intra-host HCV populations from persons with recently established and persistent infections
Authors: Baykal Pelin Icer , Lara James , Zelikovsky Alex , Khudyakov Yury , Skums Pavel
Published: June 2020

Background

Detection of incident hepatitis C virus (HCV) infections is crucial for identification of outbreaks and development of public health interventions. However, there is no single diagnostic assay for distinguishing recent and persistent HCV infections. HCV exists in each infected host as a heterogeneous population of genomic variants, whose evolutionary dynamics remain incompletely understood. Genetic analysis of such viral populations can be applied to the detection of incident HCV infections and used to understand intra-host viral evolution.

Methods

We studied intra-host HCV populations sampled using next-generation sequencing from 98 recently and 256 persistently infected individuals. Genetic structure of the populations was evaluated using 245,878 viral sequences from these individuals and a set of selected parameters measuring their diversity, topological structure, complexity, strength of selection, epistasis, evolutionary dynamics, and physico-chemical properties.

Findings

Distributions of the viral population parameters differ significantly between recent and persistent infections. A general increase in viral genetic diversity from recent to persistent infections is frequently accompanied by decline in genomic complexity and increase in structuredness of the HCV population, likely reflecting a high level of intra-host adaptation at later stages of infection. Using these findings, we developed a Machine Learning classifier for the infection staging, which yielded a detection accuracy of 95.22%, thus providing a higher accuracy than other genomic-based models.

Interpretation

The detection of a strong association between several HCV genetic factors and stages of infection suggests that intra-host HCV population develops in a complex but regular and predictable manner in the course of infection. The proposed models may serve as a foundation of cyber-molecular assays for staging infection, that could potentially complement and/or substitute standard laboratory assays.

Funding

AZ and PS were supported by NIH grant 1R01EB025022. PIB was supported by GSU MBD fellowship.
Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase
Authors: Matos Jason O. , Kumar Ramasamy P. , Ma Alison C. , Patterson MacKenzie , Krauss Isaac J. , Oprian Daniel D.
Published: June 2020

Most terpene synthase reactions follow Markovnikov rules for formation of high energy carbenium ion intermediates. However, there are notable exceptions. For example, pentalenene synthase (PS) undergoes an initial anti-Markovnikov cyclization reaction followed by a 1,2-hydride shift to form an intermediate humulyl cation with positive charge on the secondary carbon C9 of the farnesyl diphosphate substrate. The mechanism by which these enzymes stabilize and guide regioselectivity of secondary carbocations has not heretofore been elucidated. In an effort to better understand these reactions, we grew crystals of apo-PS, soaked them with the non-reactive substrate analog 12,13-difluorofarnesyl diphosphate, and solved the x-ray structure of the resulting complex at 2.2 Å resolution. The most striking feature of the active site structure is that C9 is positioned 3.5 Å above the center of the side chain benzene ring of residue F76, perfectly poised for stabilization of the charge through a cation-π interaction. In addition, the main chain carbonyl of I177 and neighboring intramolecular C6,C7-double bond are positioned to stabilize the carbocation by interaction with the face opposite that of F76. Mutagenesis experiments also support a role for residue 76 in cation-π interactions. Most interesting is the F76W mutant which gives a mixture of products that likely result from stabilizing a positive charge on the adjacent secondary carbon C10 in addition to C9 as in the wild-type enzyme. The crystal structure of the F76W mutant clearly shows carbons C9 and C10 centered above the fused benzene and pyrrole rings of the indole side chain, respectively, such that a carbocation at either position could be stabilized in this complex, and two anti-Markovnikov products, pentalenene and humulene, are formed. Finally, we show that there is a rough correlation (although not absolute) of an aromatic side chain (F or Y) at position 76 in related terpene synthases fromStreptomycesthat catalyze similar anti-Markovnikov addition reactions.
Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil
Authors: Resende Paola Cristina , Delatorre Edson , Gräf Tiago , Mir Daiana , Motta Fernando do Couto , Appolinario Luciana Reis , da Paixão Anna Carolina Dias , Ogrzewalska Maria , Caetano Braulia , dos Santos Mirleide Cordeiro , de Almeida Ferreira Jessylene , Santos Junior Edivaldo Costa , da Silva Sandro Patroca , Fernandes Sandra Bianchini , Vianna Lucas A , da Costa Souza Larissa , Ferro Jean F G , Nardy Vanessa B , Croda Júlio , Oliveira Wanderson K , Abreu André , Bello Gonzalo , Siqueira Marilda M
Published: June 2020

Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil.
The projections of ipRGCs and conventional RGCs to retinorecipient brain nuclei
Authors: Beier Corinne , Zhang Ze , Yurgel Maria , Hattar Samer
Published: June 2020

Retinal ganglion cells (RGCs), the output neurons of the retina, allow us to perceive our visual environment. RGCs respond to rod/cone input through the retinal circuitry, however, a small population of RGCs are in addition intrinsically photosensitive (ipRGCs) and project to unique targets in the brain to modulate a broad range of subconscious visual behaviors such as pupil constriction and circadian photoentrainment. Despite the discovery of ipRGCs nearly two decades ago, there is still little information about how or if conventional RGCs (non-ipRGCs) target ipRGC-recipient nuclei to influence subconscious visual behavior. Using a dual recombinase color strategy, we showed that conventional RGCs innervate many subconscious ipRGC-recipient nuclei, apart from the suprachiasmatic nucleus. We revealed previously unrecognized stratification patterns of retinal innervation from ipRGCs and conventional RGCs in the ventral portion of the lateral geniculate nucleus. Further, we found that the percent innervation of ipRGCs and conventional RGCs across ipsi- and contralateral nuclei differ. Our data provide a blueprint to understand how conventional RGCs and ipRGCs innervate different brain regions to influence subconscious visual behaviors.
Herbivore-induced activation of viral phosphatase disarms plant antiviral immunities for pathogen transmission
Authors: Zhao Pingzhi , Wang Ning , Yao Xiangmei , Zhu Changxiang , Hogenhout Saskia A. , Liu Shu-sheng , Zhou Xueping , Fang Rongxiang , Ye Jian
Published: June 2020

The survival of pathogens depends on their ability to overcome host immunity, especially arthropod-borne viruses (arboviruses) which must withstand the immune responses of both the host and the arthropod vector. Successful arboviruses often modify host immunity to accelerate pathogen transmission; however, few studies have explored the underlying mechanism. Here we report attracted herbivore infestation on the virus-infected plants promote transmission by the associated vector herbivore. This herbivore-induced defense suppression underpins a subversive mechanism used byBegomovirus, the largest genus of plant viruses, to compromise host defense for pathogen transmission. Begomovirus-infected plants accumulated βC1 proteins in the phloem where they were bound to host defense regulators, transcription factor WRKY20 and two mitogen-activated protein kinases MPK3 and MPK6. Once perceiving whitefly herbivory or endogenous secreted peptide PEP1, the plants started dephosphorylation on serine33and stimulated βC1 protein as a phosphatase. βC1 dephosphorylated MPK3/6 and WRKY20, the latter negatively regulated salicylic acid signaling and vascular callose deposition. This viral hijacking of WRKY20 accumulated more vascular callose by which enforced whitefly prolonged salivation and phloem sap ingestion, therefore impelling more virus transmission among plants. We present a scenario in which viruses dynamically respond to the presence of their vectors, suppressing host immunity and promoting pathogen transmission only when needed.
Computational Model of G2-M DNA Damage Checkpoint Regulation in Normal and p53-null Cancer Cells
Authors: Jung Yongwoon , Kraikivski Pavel
Published: June 2020

The authors have withdrawn their manuscript due to authorship disputes. Therefore, they do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
The genome assembly and annotation ofMagnolia biondiiPamp., a phylogenetically, economically, and medicinally important ornamental tree species
Authors: Dong Shanshan , Liu Min , Liu Yang , Chen Fei , Yang Ting , Chen Lu , Zhang Xingtan , Guo Xing , Fang Dongming , Li Linzhou , Deng Tian , Yao Zhangxiu , Lang Xiaoan , Gong Yiqing , Wu Ernest , Wang Yaling , Shen Yamei , Gong Xun , Liu Huan , Zhang Shouzhou
Published: June 2020

Magnolia biondiiPamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Contributing a genome sequence forM. biondiiwill help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution inMagnolia. We assembled a chromosome-level reference genome ofM. biondiiusing ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ⍰2.22 Gb with a contig N50 of 269.11 Kb and a BUSCO complete gene ratio of 91.90%. About 89.17% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 48,319 protein-coding genes, accounting for 22.97% of the genome length, in contrast to 66.48% of the genome length for the repetitive elements. We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae. Functional enrichment of theMagnoliaspecific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage. Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence ofM. biondiicould empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms.