bluuebunny/crossref_metadata_2025 huggingface dataset:
A Unified Probabilistic Modeling Framework for Eukaryotic Transcription Based on Nascent RNA Sequencing Data
Authors: Siepel Adam
Published: January 2021

Nascent RNA sequencing protocols, such as PRO-seq and NET-seq, are now widely used in the study of eukaryotic transcription, and these experimental techniques have given rise to a variety of statistical and machine-learning methods for data analysis. These computational methods, however, are generally designed to address specialized signal-processing or prediction tasks, rather than directly describing the dynamics of RNA polymerases as they move along the DNA template. Here, I introduce a general probabilistic model that describes the kinetics of transcription initiation, elongation, pause release, and termination, as well as the generation of sequencing read counts. I show that this generative model enables estimation of separate pause-release rates, termination rates, and the initiation/elongation rate ratio up to a proportionality constant. Furthermore, if applied to time-course data in a nonequilibrium setting, the model can be used to estimate elongation rates. This model leads naturally to likelihood ratio tests for differences between genes, conditions, or species in various rates of interest. If read counts are assumed to be Poisson-distributed, convenient, closed-form solutions are available for both parameter estimates and likelihood-ratio-test statistics. Straightforward extensions of the model accommodate variability in the pause site and steric hindrance of initiation by paused polymerases. Additional extensions address Bayesian inference under the Poisson model and a generalized linear model that can be used to discover genomic features associated with rates of elongation. Finally, I address technicalities concerning estimation of library size, normalization and sequencing replicates. Altogether, this modeling framework enables a unified treatment of many common tasks in the analysis of nascent RNA sequencing data.
DNA looping by protamine follows a nonuniform spatial distribution
Authors: McMillan Ryan B. , Kuntz Victoria D. , Devenica Luka M. , Bediako Hilary , Carter Ashley R.
Published: January 2021

DNA looping plays an important role in cells in both regulating and protecting the genome. Often, studies of looping focus on looping by prokaryotic transcription factors likelacrepressor or by structural maintenance of chromosomes (SMC) proteins such as condensin. Here, however, we are interested in a different looping method whereby multivalent cations (charge≥+3), such as protamine proteins, neutralize the DNA, causing it to form loops and toroids. We considered two previously proposed mechanisms for DNA looping by protamine. In the first mechanism, protamine stabilizes spontaneous DNA fluctuations, forming randomly distributed loops along the DNA. In the second mechanism, protamine binds and bends the DNA to form a loop, creating a distribution of loops that is biased by protamine binding. To differentiate between these mechanisms, we imaged both spontaneous and protamine-induced loops on short-length (≤ 1μm) DNA fragments using atomic force microscopy (AFM). We then compared the spatial distribution of the loops to several model distributions. A random looping model, which describes the mechanism of spontaneous DNA folding, fit the distribution of spontaneous loops, but it did not fit the distribution of protamine-induced loops. Specifically, it overestimated the number of loops that form at the ends of the molecule and failed to predict a peak in the spatial distribution of loops at an intermediate location along the DNA. An electrostatic multibinding model, which was created to mimic the bind-and-bend mechanism of protamine, was a better fit of the distribution of protamine-induced loops. In this model, multiple protamines bind to the DNA electrostatically within a particular region along the DNA to coordinate the formation of a loop. We speculate that these findings will impact our understanding of protamine’sin vivorole for looping DNA into toroids and the mechanism of DNA condensation by multivalent cations more broadly.

SIGNIFICANCE

DNA looping is important in a variety of bothin vivofunctions (e.g. gene regulation) andin vitroapplications (e.g. DNA origami). Here, we sought a mechanistic understanding of DNA looping by multivalent cations (≥+3), which condense DNA into loops and toroids. One such multivalent cation is the protein protamine, which condenses DNA in sperm. We investigated the mechanism for loop formation by protamine and found that the experimental data was consistent with an electrostatic multibinding model in which two protamines bind electrostatically to the DNA within a 50-nm region to form a loop. This model is likely general to all multivalent cations and may be helpful in applications involving toroid formation or DNA nanoengineering.
An Open-Source Pipeline for Analyzing Changes In Microglial Morphology
Authors: Clarke Devin , Crombag Hans S. , Hall Catherine N.
Published: January 2021

Changes in microglial morphology are powerful indicators of the inflammatory state of the brain. Here we provide an open-source microglia morphology analysis pipeline that first cleans and registers images of microglia, before extracting 62 parameters describing microglial morphology. It then compares control and “inflammation” training data and uses dimensionality reduction to generate a single metric of morphological change (an ‘inflammation index’). This index can then be calculated for test data to assess inflammation, as we demonstrate by investigating the effect of short-term high fat diet consumption in heterozygous Cx3CR1-GFP mice, finding no significant effects of diet. Our pipeline represents the first open-source microglia morphology pipeline combining semi-automated image processing and dimensionality reduction. It uses free software (ImageJ and R) and can be applied to a wide variety of experimental paradigms. We anticipate it will enable others to more easily take advantage of the powerful insights microglial morphology analysis provides.
NeurotoxKb: compilation, curation and exploration of a knowledgebase of environmental neurotoxicants specific to mammals
Authors: Ravichandran Janani , Karthikeyan Bagavathy Shanmugam , Singla Palak , Aparna S. R. , Samal Areejit
Published: January 2021

Exposure to environmental neurotoxicants is a significant concern due to their potential to cause permanent or irreversible damage to the human nervous system. Here, we present the first dedicated knowledgebase, NeurotoxKb, on environmental neurotoxicants specific to mammals. Using a detailed workflow, we have compiled 475 potential non-biogenic neurotoxicants from 835 published studies with evidence of neurotoxicity specific to mammals. A unique feature of NeurotoxKb is the manual curation effort to compile and standardize the observed neurotoxic effects for the potential neurotoxicants from 835 published studies. For the 475 potential neurotoxicants, we have compiled diverse information such as chemical structures, environmental sources, chemical classification, physicochemical properties, molecular descriptors, predicted ADMET properties, and target human genes. To better understand the prospect of human exposure, we have explored the presence of potential neurotoxicants in external exposomes via two different analyses. By analyzing 55 chemical lists representing global regulations and guidelines, we reveal potential neurotoxicants both in regular use and produced in high volume. By analyzing human biospecimens, we reveal potential neurotoxicants detected in them. Lastly, a construction of the chemical similarity network and ensuing analysis revealed the diversity of the toxicological space of 475 potential neurotoxicants. NeurotoxKb is accessible online at:https://cb.imsc.res.in/neurotoxkb/.
DISMIR: a deep learning-based cancer-detection method by integrating DNA sequence and methylation information of individual cell-free DNA reads
Authors: Li Jiaqi , Wei Lei , Zhang Xianglin , Zhang Wei , Wang Haochen , Zhong Bixi , Xie Zhen , Lv Hairong , Wang Xiaowo
Published: January 2021

Detecting cancer signals in cell-free DNA (cfDNA) high-throughput sequencing data is emerging as a novel non-invasive cancer detection method. Due to the high cost of sequencing, it is crucial to make robust and precise prediction with low-depth cfDNA sequencing data. Here we propose a novel approach named DISMIR, which can provide ultrasensitive and robust cancer detection by integrating DNA sequence and methylation information in plasma cfDNA whole genome bisulfite sequencing (WGBS) data. DISMIR introduces a new feature termed as “switching region” to define cancer-specific differentially methylated regions, which can enrich the cancer-related signal at read-resolution. DISMIR applies a deep learning model to predict the source of every single read based on its DNA sequence and methylation state, and then predicts the risk that the plasma donor is suffering from cancer. DISMIR exhibited high accuracy and robustness on hepatocellular carcinoma detection by plasma cfDNA WGBS data even at ultra-low sequencing depths. Analysis showed that DISMIR tends to be insensitive to alterations of single CpG sites’ methylation states, which suggests DISMIR could resist to technical noise of WGBS. All these results showed DISMIR with the potential to be a precise and robust method for low-cost early cancer detection.
Pre-metastatic niche drives breast cancer invasion by modulating MSC homing and CAF differentiation
Authors: Saxena Neha , Bhardwaj Garvit , Jadhav Sameer , Zafar Hamim , Sen Shamik
Published: January 2021

The extent to which cancer-associated alterations in extracellular matrix stiffness influences the crosstalk between cancer cells and mesenchymal stem cells (MSCs) remains unclear. By analyzing multiple singlecell RNA sequencing datasets, we establish the existence of a cell sub-population co-expressing MSC and cancer associated fibroblast (CAF) markers in highly aggressive triple-negative breast cancers in primary tumor, secondary sites, and in circulatory tumor cell clusters. Using hydrogels of varying stiffness corresponding to different stages of cancer progression, we show that on pre-metastatic stroma mimetic 2 kPa gels, MDA-MB-231 breast cancer cell secreted conditioned media drives efficient MSC chemotaxis and induces stable CAF differentiation in a TGFβ/contractility-dependent manner. In addition to enhancing cancer cell proliferation, 2 kPa CAFs maximally boost local invasion and confer resistance to flow-induced shear stresses. Together, our results suggest that homing of MSCs at the pre-metastatic stage and their differentiation into CAFs actively drives breast cancer invasion and metastasis.
Endogenous feline leukemia virus siRNA transcription may interfere with exogenous FeLV infection
Authors: Chiu Elliott S. , VandeWoude Sue
Published: January 2021

Endogenous retroviruses (ERVs) are increasingly recognized for biological impacts on host cell function and susceptibility to infectious agents, particularly in relation to interactions with exogenous retroviral progenitors (XRVs). ERVs can simultaneously promote and restrict XRV infections using different mechanisms that are virus- and host-specific. The majority of endogenous-exogenous retroviral interactions have been evaluated in experimental mouse or chicken systems which are limited in their ability to extend findings to naturally infected outbred animals. Feline leukemia virus (FeLV) has a relatively well-characterized endogenous retrovirus with a coexisting virulent exogenous counterpart and is endemic worldwide in domestic cats. We have previously documented an association between endogenous FeLV LTR copy number and abrogated exogenous FeLV in naturally infected cats and experimental infections in tissue culture. Analyses described here examine limited FeLV replication in experimentally infected peripheral blood mononuclear cells. We further examine NCBI Sequence Read Archive RNA transcripts to evaluate enFeLV transcripts and RNA interference precursors. We find that lymphoid-derived tissues, which are experimentally less permissive to exogenous FeLV infection, transcribe higher levels of enFeLV under basal conditions. Transcription of enFeLV-LTR segments is significantly greater than other enFeLV genes. We documented transcription of a 21-nt miRNA just 3′ to the enFeLV 5′-LTR in the feline miRNAome of all datasets evaluated (n=27). Our findings point to important biological functions of enFeLV transcription linked to solo LTRs distributed within the domestic cat genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis.

Importance

Endogenous retroviruses (ERVs) are increasingly implicated in host cellular processes and susceptibility to infectious agents, specifically regarding interactions with exogenous retroviral progenitors (XRVs). Exogenous feline leukemia virus (FeLV) and its endogenous counterpart (enFeLV) represent a well characterized, naturally occurring XRV-ERV dyad. We have previously documented an abrogated FeLV infection in both naturally infected cats and experimental fibroblast infections that harbor higher enFeLV proviral loads. Using anin silicoapproach, we provide evidence of miRNA-transcription that are produced in tissues most important for FeLV infection, replication, and transmission. Our findings point to important biological functions of enFeLV transcription linked to solo-LTRs distributed within the feline genome, with potential impacts on domestic cat exogenous FeLV susceptibility and pathogenesis. This body of work provides additional evidence of RNAi as a mechanism of viral interference and is a demonstration of ERV exaptation by the host to defend against related XRVs.
Nasopharyngeal and serological anti SARS-CoV-2 IgG/IgA responses in COVID-19 patients
Authors: Crescenzo-Chaigne Bernadette , Behillil Sylvie , Enouf Vincent , Escriou Nicolas , Petres Stephane , Ungeheuer Marie Noelle , Ghosn Jade , Tubiana Sarah , Bouadma Lila , van der Werf Sylvie , Demeret Caroline ,   for the French COVID cohort study group
Published: January 2021

Background

The systemic antibody responses to SARS-CoV-2 in COVID-19 patients has been extensively studied. However, much less is known about the mucosal responses in the upper airways at the site of initial SARS-CoV-2 replication. Local antibody responses in the nasopharyngeal epithelium, that are likely to determine the course of infection, have not been analysed so far nor their correlation with antibody responses in serum.

Methods

The IgG and IgA antibody responses were analysed in the plasma as well as in nasopharyngeal swabs (NPS) from the first four COVID-19 patients confirmed by RT-qPCR in France. Two were pauci-symptomatic while two developed severe disease. Taking advantage of a comprehensive series of plasma and nasopharyngeal samples, we characterized their antibody profiles from the second week post symptoms onset, by using an in-house ELISA to detect anti-SARS-CoV-2 Nucleoprotein (N) IgG and IgA.

Results

Anti-N IgG and IgA antibodies were detected in the NPS of severe patients. Overall, the levels of IgA and IgG antibodies in plasma and NPS appeared specific to each patient.

Conclusions

Anti-N IgG and IgA antibodies are detected in NPS, and their levels are related to antibody levels in plasma. The two patients with severe disease exhibited different antibody profiles that may reflect different disease outcome. For the pauci-symptomatic patients, one showed a low anti-N IgG and IgA response in the plasma only, while the other one did not exhibit overt serological response.
Epidemiology of the early COVID-19 epidemic in Orange County, California: comparison of predictors of test positivity, mortality, and seropositivity
Authors: Parker Daniel M. , Bruckner Tim , Vieira Veronica M. , Medina Catalina , Minin Vladimir N. , Felgner Philip L. , Dratch Alissa , Zahn Matthew , Bartell Scott M. , Boden-Albala Bernadette
Published: January 2021

COVID-19 is one of the largest public health emergencies in modern history. Here we present a detailed analysis from a large population center in Southern California (Orange County, population of 3.2 million) to understand heterogeneity in risks of infection, test positivity, and death. We used a combination of datasets, including a population-representative seroprevalence survey, to assess the true burden of disease as well as COVID-19 testing intensity, test positivity, and mortality. In the first month of the local epidemic, case incidence clustered in high income areas. This pattern quickly shifted, with cases next clustering in much higher rates in the north-central area which has a lower socio-economic status. Since April, a concentration of reported cases, test positivity, testing intensity, and seropositivity in a north-central area persisted. At the individual level, several factors (e.g., age, race/ethnicity, zip codes with low educational attainment) strongly affected risk of seropositivity and death.
A Vital Sign-based Prediction Algorithm for Differentiating COVID-19 Versus Seasonal Influenza in Hospitalized Patients
Authors: Yanamala Naveena , Krishna Nanda H. , Hathaway Quincy A. , Radhakrishnan Aditya , Sunkara Srinidhi , Patel Heenaben , Farjo Peter , Patel Brijesh , Sengupta Partho P
Published: January 2021

Patients with influenza and SARS-CoV2/Coronavirus disease 2019 (COVID-19) infections have different clinical course and outcomes. We developed and validated a supervised machine learning pipeline to distinguish the two viral infections using the available vital signs and demographic dataset from the first hospital/emergency room encounters of 3,883 patients who had confirmed diagnoses of influenza A/B, COVID-19 or negative laboratory test results. The models were able to achieve an area under the receiver operating characteristic curve (ROC AUC) of at least 97% using our multiclass classifier. The predictive models were externally validated on 15,697 encounters in 3,125 patients available on TrinetX database that contains patient-level data from different healthcare organizations. The influenza vs. COVID-19-positive model had an AUC of 98%, and 92% on the internal and external test sets, respectively. Our study illustrates the potentials of machine-learning models for accurately distinguishing the two viral infections. The code is made available at https://github.com/ynaveena/COVID-19-vs-Influenza and may be have utility as a frontline diagnostic tool to aid healthcare workers in triaging patients once the two viral infections start cocirculating in the communities.
Impact of training modules on physicians’ perspective of COVID-19: An online survey
Authors: Umar Badar Uddin , Alam Nazmun Nahar , Alam Tanbira , Mannan Mahmudul , Rahman S M Niazur
Published: January 2021

Background

The outbreak of COVID-19 has remained a massive challenge for healthcare workers specially physicians. Effective professional training has a crucial role in preparing doctors for responding to pandemics.

Objective

To assess the effectiveness of existing training modules on enhancing knowledge, ensuring safe practice, and improving behavior on COVID-19 among physicians.

Methods

This is a descriptive, cross-sectional, online survey; where a virtual questionnaire was used to collect data through online professional platforms. A pre-tested survey tool was employed to assess the impact of professional training on infection prevention and control.

Results

Total 161 physicians participated in this survey from 15 different countries. Most of the respondents (72%) received training from various sources like the workplace (60%) and international agencies (21%), through the in-person or online format. Knowledge assessment revealed advanced (43%) and competent (40%) understanding by the participants. Improving knowledge progression was displayed by the cohort who received professional training (p<0.00). Physicians’ positive behavior and good practices were observed with the training modules.

Conclusion

It became evident from this study, that professional training is effective in enhancing knowledge, improving behavior, and ensuring safe practices. Hence, designing such training modules for the physicians is warranted to tackle ongoing and future pandemics.
Unsupervised clustering reveals a unique Treg profile in slow progressors to type 1 diabetes
Authors: Boldison Joanne , Long Anna E , Aitken Rachel J , Wilson Isabel V , Megson Claire , Hanna Stephanie J , Wong F. Susan , Gillespie Kathleen M
Published: January 2021

Objective

To profile CD4+ regulatory T cells (Tregs) in a well-characterised cohort of slow progressors to type 1 diabetes, individuals positive for multiple islet autoantibodies who remain diabetes-free for at least 10 years.

Research Design and Methods

Peripheral blood samples were obtained from extreme slow progressor individuals (n=8), with up to 32 years follow-up, and age and gender-matched to healthy donors. One participant in this study was identified with a raised HbA1c at the time of assessment, and was individually evaluated in the data analysis. PBMCs were isolated, from donors, and to assess frequency, phenotype and function of Tregs, multi-parameter flow cytometry and T cell suppression assays were performed. Unsupervised clustering analysis, FlowSOM and CITRUS, was used to evaluate Treg phenotypes.

Results

Treg mediated suppression of CD4+ effector T cells, from slow progressors was significantly impaired, compared to healthy donors (P<0.05). Effector CD4 T cells, from slow progressors, were more responsive to Treg suppression, compared to healthy donors, demonstrated by increased suppression of CD25 expression on effector CD4 T cells (P<0.05). Unsupervised clustering on memory CD4 T cells, from slow progressors, showed an increased frequency of activated-memory CD4 Tregs associated with increased expression of GITR, compared to healthy donors (P<0.05). The participant with a raised HbA1c had a different Treg profile, compared to slow progressors and the matched controls.

Conclusions

CD4+ Tregs from slow progressor individuals have a unique Treg signature. This report highlights the need for further study of Treg heterogeneity in individuals at-risk of developing type 1 diabetes.
Epidemiology and antibiotic resistance profile of Helicobacter pylori infection in Cameroon: a systematic review with meta-analysis
Authors: Ngnameko Corinne Raïssa , Noubiap Jean Jacques , Simo Nemg Freddy Brice , Galdima Mohamadou Abdou , Takuissu-Nguemto Guy Roussel , Ngo-Boumso Sophie , Njayou Frederic Nico , Moundipa Paul F. , Bigna Jean Joel
Published: January 2021

Objectives

Although global epidemiology of Helicobacter pylori (HP) infection is well characterized, country-specific figure is more accurate for context-specific tailored interventions. The aim was to determine the prevalence, factors associated with infection, antibiotic resistance profile, and genotypes of HP in Cameroon.

Design

A systematic review with meta-analysis.

Participants

People living in Cameroon regardless of their clinical profile.

Data sources and synthesis

Observational studies published in PubMed, EMBASE, African Index Medicus, African Journals Online, and Health Sciences and Diseases up to October 12th, 2020. Study selection, data extraction, and methodological quality assessment were done by two independent authors. Random-effect meta-analysis served to pool prevalence data.

Results

Fifteen studies were included. None investigated the genotypes of HP. Among symptomatic patients, the most common used test, urea breath test on gastric biopsy, yielded a prevalence 57.8% (95% confidence interval (CI): 34.3-79.5) of HP infection. This prevalence significantly varied between 47.0% (95%CI: 43.0-51.0) for antigen test in stool samples and 71.2% (95%CI: 59.1-81.9) for Giemsa on gastric biopsy; p = 0.0006. One study in asymptomatic children reported the prevalence of 52.3% (95%CI: 44.9-59.6) using antigen test for stool samples. Among the six studies investigating factors associated with HP infection, one performed a multivariable model and identified being student as protective factor compared to being employed (Odds ratio: 0.09; 95%CI: 0.02–0.49). For antibiotics used for first line treatment, HP was resistant to amoxicillin (85.6-97.1%), metronidazole (93.2-97.9%), and clarithromycin (13.6-44.7%) as reported in two studies.

Limitation

Data were from six of the ten regions of Cameroon, hindering the generalizability of the findings to the country.

Conclusion

This study depicted a high prevalence of HP infection and a worrying resistance profile to first-line antibiotics. When waiting for well-conducted studies, updated guidelines are needed for clinical practice for first-line antibiotic treatment.

Registration

PROSPERO, CRD42020220084.

Strengths and limitations of this study

Not all the 10 regions of the country were represented in this study, hindering the generalizability of the findings.

We were not able to substantially investigate sources of heterogeneity in the prevalence of Helicobacter pylori infection due to scarcity of data.

Evidence investigating factors associated with Helicobacter pylori infection are weak and there was scarcity on data exploring antibiotic resistance profile of Helicobacter pylori.

This study is the first to provide an estimate of the epidemiology and resistance profile of Helicobacter pylori in Cameroon.
Automated Bias Reduction in Deep Learning Based Melanoma Diagnosis using a Semi-Supervised Algorithm
Authors: Das Sauman
Published: January 2021

Melanoma is one of the most fatal forms of skin cancer and is often very difficult to differentiate from other benign skin lesions. However, if detected at its early stages, it can almost always be cured. Researchers and data scientists have studied this disease in-depth with the help of large datasets containing high-quality dermascopic images, such as those assembled by the International Skin Imaging Collaboration (ISIC). However, these images often lack diversity and over-represent patients with very common skin features such as light skin and having no visible body hair. In this study, we introduce a novel architecture called LatentNet which automatically detects over-represented features and reduces their weights during training. We tested our model on four distinct categories - three skin color levels corresponding to Type I, II, and III on the Fitzpatrick Scale, and images containing visible hair. We then compared the accuracy against the conventional Deep Convolutional Neural Network (DCNN) model trained using the standard approach (i.e. without detecting over-represented features) and containing the same hyper-parameters as the LatentNet. LatentNet showed significant performance improvement over the standard DCNN model with accuracy of 89.52%, 79.05%, 64.31%, and 64.35% compared to the DCNN accuracy of 90.41%, 70.82%, 45.28%, 56.52% in the corresponding categories, respectively. Differences in the average performance between the models were statistically significant (p < 0.05), suggesting that the proposed model successfully reduced bias amongst the tested categories. LatentNet is the first architecture that addresses racial bias (and other sources of bias) in deep-learning based Melanoma diagnosis.
Astrocyte-derived ApoE is Required for the Maturation of Injury-induced Hippocampal Neurons and Regulates Cognitive Recovery After Traumatic Brain Injury
Authors: Yu Tzong-Shiue , Tensaouti Yacine , Stephanz Elizabeth P. , Rafikian Elizabeth E. , Yang Mu , Kernie Steven G.
Published: January 2021

Polymorphisms in the apolipoprotein E (ApoE) gene confer a major genetic risk for the development of late-onset Alzheimer’s disease (AD) and are predictive of outcome following traumatic brain injury (TBI). Alterations in adult hippocampal neurogenesis have long been associated with both the development of AD and recovery following TBI, and ApoE is known to play a role in this process. In order to determine how ApoE might influence hippocampal injury-induced neurogenesis, we developed a novel conditional system whereby functional ApoE from astrocytes was ablated just prior to injury. While successfully ablating 90% of astrocytic ApoE just prior to a closed cortical impact injury in mice, we observed an attenuation in the development of newly born neurons using a GFP-expressing retrovirus, but not in existing hippocampal neurons visualized with a Golgi stain. Intriguingly, animals with a “double-hit”, i.e. injury and ApoE conditionally inactivated in astrocytes, demonstrated the most pronounced impairments in the hippocampal-dependent Morris water maze test, failing to exhibit spatial memory after both acquisition and reversal training trials. In comparison, conditional knockout mice without injury displayed impairments but only in the reversal phase of the test, suggesting accumulative effects of astrocytic ApoE deficiency and traumatic brain injury on AD-like phenotypes. Together, these findings demonstrate that astrocytic ApoE is required for functional injury-induced neurogenesis following traumatic brain injury.

Significance Statement

ApoE has long been implicated in the development of Alzheimer’s disease and recovery from traumatic brain injury via unknown mechanisms. Using a novel conditional ablation model of mouse ApoE and subsequent tracing of individual hippocampal neurons, we demonstrate its requirement in injury-induced neurogenesis for proper dendritic arborization and cognitive function in hippocampal-dependent learning and memory tasks.
Nanobody Mediated Macromolecular Crowding Induces Membrane Fission and Remodeling in the African Trypanosome
Authors: Hempelmann Alexander , Hartleb Laura , van Straaten Monique , Hashemi Hamidreza , Zeelen Johan P. , Papavasiliou F. Nina , Engstler Markus , Stebbins C. Erec , Jones Nicola G.
Published: January 2021

The dense Variant Surface Glycoprotein (VSG) coat of African trypanosomes represents the primary host-pathogen interface. Antigenic variation prevents clearing of the pathogen by employing a large repertoire of antigenically distinct VSG genes, thus neutralizing the host’s antibody response. To explore the epitope space of VSGs, we generated anti-VSG nanobodies and combined high-resolution structural analysis of VSG-nanobody complexes with binding assays on living cells, revealing that these camelid antibodies bind deeply inside the coat. One nanobody caused rapid loss of cellular motility, possibly due to blockage of VSG mobility on the coat, whose rapid endo-and exocytosis is mechanistically linked toT. bruceipropulsion and whose density is required for survival. Electron microscopy studies demonstrated that this loss of motility was accompanied by rapid formation and shedding of nanovesicles and nanotubes, suggesting that increased protein crowding on the dense membrane can be a driving force for membrane fission in living cells.
Colletotrichum higginsianumeffectors exhibit cell to cell hypermobility in plant tissues and modulate intercellular connectivity amongst a variety of cellular processes
Authors: Ohtsu Mina , Jennings Joanna , Johnston Matthew , Liu Xiaokun , Hughes Aoife , Stark Kara , Morris Richard J. , de Keijzer Jeroen , Faulkner Christine
Published: January 2021

Multicellular organisms exchange information and resources between cells to co-ordinate growth and responses. In plants, plasmodesmata establish cytoplasmic continuity between cells to allow for communication and resource exchange across the cell wall. Some plant pathogens use plasmodesmata as a pathway for both molecular and physical invasion. However, the benefits of molecular invasion (cell-to-cell movement of pathogen effectors) are poorly understood. To begin to investigate this and identify which effectors are cell-to-cell mobile, we performed a live imaging-based screen and identified 15 cell-to-cell mobile effectors of the fungal pathogenColletotrichum higginsianum. Of these, 6 are “hypermobile”, showing cell-to-cell mobility greater than expected for a protein of its size. We further identified 3 effectors that can indirectly modify plasmodesmal aperture. Transcriptional profiling of plants expressing hypermobile effectors implicate them in a variety of processes including senescence, glucosinolate production, cell wall integrity, growth and iron metabolism. However, not all effectors had an independent effect on virulence. This suggests a wide range of benefits to infection gained by the mobility ofC. higginsianumeffectors that likely interact in a complex way during infection.
Anti-CoVid19 plasmid DNA vaccine induces a potent immune response in rodents by Pyro-drive Jet Injector intradermal inoculation
Authors: Nishikawa Tomoyuki , Chang Chin Yang , Tai Jiayu A , Hayashi Hiroki , Sun Jiao , Torii Shiho , Ono Chikako , Matsuura Yoshiharu , Ide Ryoko , Mineno Junichi , Sasai Miwa , Yamamoto Masahiro , Nakagami Hironori , Yamashita Kunihiko
Published: January 2021

There is an urgent need to limit and stop the worldwide coronavirus disease 2019 (COVID-19) pandemic via quick development of efficient and safe vaccination methods. Plasmid DNA vaccines are one of the most remarkable vaccines that can be developed in a short term. pVAX1-SARS-CoV2-co, which is a plasmid DNA vaccine, was designed to express severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein. The produced antibodies lead to Immunoreactions against S protein, anti-receptor-binding-domain, and neutralizing action of pVAX1-SARS-CoV2-co, as confirmed in a previous study. To promote the efficacy of the pVAX1-SARS-CoV2-co vaccine, a pyro-drive jet injector (PJI) was employed. PJI is an injection device that can adjust the injection pressure depending on various target tissues. Intradermally-adjusted PJI demonstrated that pVAX1-SARS-CoV2-co vaccine injection caused a strong production of anti-S protein antibodies, triggered immunoreactions and neutralizing actions against SARS-CoV-2. Moreover, a high dose of pVAX1-SARS-CoV2-co intradermal injection via PJI did not cause any serious disorders in the rat model. Finally, virus infection challenge in mice, confirmed that intradermally immunized (via PJI) mice were potently protected from COVID-19 infection. Thus, pVAX1-SARS-CoV2-co intradermal injection via PJI is a safe and promising vaccination method to overcome the COVID-19 pandemic.
Differential Conditioning Produces Merged Long-term Memory inDrosophila
Authors: Zhao Bohan , Sun Jiameng , Li Qian , Zhong Yi
Published: January 2021

Multiple spaced trials of aversive differential conditioning can produce two independent long-term memories (LTMs) of opposite valence. One is an aversive memory for avoiding the conditioned stimulus (CS+), and the other is a safety memory for approaching the non-conditioned stimulus (CS–). Here, we show that a single trial of aversive differential conditioning yields one merged LTM (mLTM) for avoiding both CS+ and CS–. Such mLTM can be detected after sequential exposures to the shock-paired CS+ and unpaired CS–, and be retrieved by either CS+ or CS–. The formation of mLTM relies on triggering aversive-reinforcing dopaminergic neurons and subsequent new protein synthesis. Expressing mLTM involves αβ Kenyon cells and corresponding approach-directing mushroom body output neurons (MBONs), in which similar-amplitude long-term depression of responses to CS+ and CS– seems to signal the mLTM. Our results suggest that animals can develop distinct strategies for occasional and repeated threatening experiences.
Functional and multiscale 3D structural investigation of brain tissue through correlativein vivophysiology, synchrotron micro-tomography and volume electron microscopy
Authors: Bosch Carles , Ackels Tobias , Pacureanu Alexandra , Zhang Yuxin , Peddie Christopher J , Berning Manuel , Rzepka Norman , Zdora Marie-Christine , Whiteley Isabell , Storm Malte , Bonnin Anne , Rau Christoph , Margrie Troy , Collinson Lucy , Schaefer Andreas T
Published: January 2021

Attributingin vivoneurophysiology to the brains’ ultrastructure requires a large field of view containing contextual anatomy. Electron microscopy (EM) is the gold standard technique to identify ultrastructure, yet acquiring volumes containing full mammalian neural circuits is challenging and time consuming using EM. Here, we show that synchrotron X-ray computed tomography (SXRT) provides rapid imaging of EM-prepared tissue volumes of several cubic millimetres. Resolution was sufficient for distinguishing cell bodies as well as for tracing apical dendrites in olfactory bulb and hippocampus, for up to 350 μm. Correlating EM with SXRT allowed us to associate dendritic spines on pyramidal cell apical dendrites in the stratum radiatum to their corresponding soma locations. Superficial pyramidal neurons had larger spine apparatus density compared to deeper ones, implying differential synaptic plasticity for superficial and deeper cells. Finally, we show that X-ray tomography and volume EM can be reliably correlated to priorin vivoimaging. Thus, combining functional measurements with multiscale X-ray microscopy and volume EM establishes a correlative workflow that enables functional and structural investigation of subcellular features in the context of cellular morphologies, tissues and ultimately whole organs.
Activity and stress during a critical period regulate olfactory sensory neuron differentiation
Authors: Jafari Shadi , Henriksson Johan , Yan Hua , Alenius Mattias
Published: January 2021

Here, we reveal that the regulation ofDrosophilaodorant receptor (OR) expression during the pupal stage is permissive and imprecise. We found that olfactory sensory neuron activity directly after hatching both directs and refines OR expression. We demonstrate that, as in mice,dLsd1andSu(var)3-9balance heterochromatin formation to direct OR expression. Neuronal activity induces dLsd1andSu(var)3-9expression, linking neuronal activity to OR expression. OR expression refinement shows a restricted duration, suggesting a gene regulatory critical period brings olfactory sensory neuron differentiation to an end. Consistent with a change in differentiation, stress during the critical period repressesdLsd1andSu(var)3-9expression and makes the early permissive OR expression permanent. This induced permissive gene regulatory state makes OR expression resilient to stress later in life. Hence, during a critical period, OR activity feedback similar to in mouse OR selection, defines adult OR expression inDrosophila.
Modality-specific tracking of attention and sensory statistics in the human electrophysiological spectral exponent
Authors: Waschke Leonhard , Donoghue Thomas , Fiedler Lorenz , Smith Sydney , Garrett Douglas D. , Voytek Bradley , Obleser Jonas
Published: January 2021

A hallmark of electrophysiological brain activity is its 1/f-like spectrum – power decreases with increasing frequency. The steepness of this “roll-off” is approximated by the spectral exponent, which in invasively recorded neural populations reflects the balance of excitatory to inhibitory neural activity (E:I balance). Here, we first establish that the spectral exponent of non-invasive electroencephalography (EEG) recordings is highly sensitive to general (i.e., anaesthesia-driven) changes in E:I balance. Building on the EEG spectral exponent as a viable marker of E:I, we then demonstrate its sensitivity to the focus of selective attention in an EEG experiment during which participants detected targets in simultaneous audio-visual noise. In addition to these endogenous changes in E:I balance, EEG spectral exponents over auditory and visual sensory cortices also tracked auditory and visual stimulus spectral exponents, respectively. Individuals’ degree of this selective stimulus–brain coupling in spectral exponents predicted behavioural performance. Our results highlight the rich information contained in 1/f-like neural activity, providing a window into diverse neural processes previously thought to be inaccessible in non-invasive human recordings.
Simple and Rapid High-Throughput Assay to Identify HSV-1 ICP0 Transactivation Inhibitors
Authors: Ly Cindy Y. , Yu Chunmiao , McDonald Peter , Roy Anuradha , Johnson David , Davido David J.
Published: January 2021

Herpes simplex virus 1 (HSV-1) is a ubiquitous virus that results in lifelong infections due to it’s ability to cycle between lytic replication and latency. As an obligate intracellular pathogen, HSV-1 exploits host cellular factors to replicate and aid in its life cycle. HSV-1 expresses infected cell protein 0 (ICP0), an immediate-early regulator, to stimulate the transcription of all classes of viral genes via its E3 ubiquitin ligase activity. Mechanisms by which ICP0 activates viral gene expression and the cellular factors involved are largely unknown. Here we report an automated, inexpensive, and rapid high-throughput approach to examine the effects of small molecule compounds on ICP0 transactivator function in cells. Two HSV-1 reporter viruses, KOS6β (wt) anddlx3.1-6β (ICP0-null mutant), were used to monitor ICP0 transactivation activity through the HSV-1 ICP6 promoter::laczexpression cassette. A ≥10-fold difference in β-galactosidase activity was observed in cells infected with KOS6β compared todlx3.1-6β, demonstrating that ICP0 potently transactivates the ICP6 promoter. We established the robustness and reproducibility with a Z′- factor score of ≥0.69, an important criterium for high-throughput analyses. Approximately 19,000 structurally diverse compounds were screened and 76 potential inhibitors of the HSV-1 transactivator ICP0 were identified. We expect this assay will aid in the discovery of novel inhibitors and tools against HSV-1 ICP0. Using well-annotated compounds could identify potential novel factors and pathways that interact with ICP0 to promote HSV-1 gene expression.
Effects of arsenic on the topology and solubility of promyelocytic leukemia (PML)-nuclear bodies
Authors: Hirano Seishiro , Udagawa Osamu
Published: January 2021

Promyelocytic leukemia (PML) proteins are involved in the pathogenesis of acute promyelocytic leukemia (APL). Trivalent arsenic (As3+) is known to cure APL by binding to cysteine residues of PML and enhance the degradation of PML-retinoic acid receptor α (RARα), a t(15;17) gene translocation product in APL cells, and restore PML-nuclear bodies (NBs). The size, number, and shape of PML-NBs vary among cell types and during cell division. However, topological changes of PML-NBs in As3+-exposed cells have not been well-documented. We report that As3+-induced solubility shift underlies rapid SUMOylation of PML and late aggregation of PML-NBs. Most PML-NBs were toroidal and irregular-shaped inGFPPML-transduced CHO-K1 and HEK293 cells, respectively. The annular PML-NBs appeared unstable and dissipated into small PML-NBs in HEK cells. Exposure to As3+and antimony (Sb3+) greatly reduced the solubility of PML and enhanced SUMOylation within 2 h, and prolonged exposure resulted in PML-NB agglomeration. Exposure to bismuth (Bi3+), another Group 15 element, did not induce any of these changes. ML792, a SUMO activation inhibitor, reduced the number of PML-NBs and increased the size of the NBs, but had little effect on the As3+-induced solubility change of PML. The results show that SUMOylation regulates the dynamics of PML-NBs but does not contribute to the As3+-induced solubility change of PML.
Distinct lung-homing receptor expression and activation profiles on NK cell and T cell subsets in COVID-19 and influenza
Authors: Brownlie Demi , Rødahl Inga , Varnaite Renata , Asgeirsson Hilmir , Glans Hedvig , Falck-Jones Sara , Vangeti Sindhu , Buggert Marcus , Ljunggren Hans-Gustaf , Michaëlsson Jakob , Gredmark-Russ Sara , Smed-Sörensen Anna , Marquardt Nicole
Published: January 2021

Respiratory viral infections with SARS-CoV-2 or influenza viruses commonly induce a strong infiltration of immune cells into the lung, with potential detrimental effects on the integrity of the lung tissue. Despite comprising the largest fractions of circulating lymphocytes in the lung, little is known about how blood natural killer (NK) cells and T cell subsets are equipped for lung-homing in COVID-19 and influenza. Using 28-colour flow cytometry and re-analysis of published RNA-seq datasets, we provide a detailed comparative analysis of NK cells and T cells in peripheral blood from moderately sick COVID-19 and influenza patients, focusing on the expression of chemokine receptors known to be involved in leukocyte recruitment to the lung. The results reveal a predominant role for CXCR3, CXCR6, and CCR5 in COVID-19 and influenza patients, mirrored by scRNA-seq signatures in peripheral blood and bronchoalveolar lavage from publicly available datasets. NK cells and T cells expressing lung-homing receptors displayed stronger phenotypic signs of activation as compared to cells lacking lung-homing receptors, and activation was overall stronger in influenza as compared to COVID-19. Together, our results indicate migration of functionally competent CXCR3+, CXCR6+, and/or CCR5+NK cells and T cells to the lungs in moderate COVID-19 and influenza patients, identifying potential common targets for future therapeutic interventions in respiratory viral infections.

Author summary

The composition of in particular CXCR3+and/or CXCR6+NK cells and T cells is altered in peripheral blood upon infection with SARS-CoV-2 or influenza virus in patients with moderate disease. Lung-homing receptor-expression is biased towards phenotypically activated NK cells and T cells, suggesting a functional role for these cells co-expressing in particular CXCR3 and/or CXCR6 upon homing towards the lung.
An advanced lentil backcross population developed from a cross betweenLens culinaris×L. ervoidesfor future disease resistance and genomic studies
Authors: Gela Tadesse S , Adobor Stanley , Khazaei Hamid , Vandenberg Albert
Published: January 2021

Genetically accessible variation to some of the abiotic and biotic stresses are limited in the cultivated lentil (Lens culinarisMedik.) germplasm. Introgression of novel alleles from its wild relative species might be required for enhancing the genetic improvement of the crop.L. ervoides, one of the wild relatives of lentil, is a proven source of disease resistance for the crop. Here we introduce a lentil advanced backcross population (LABC-01) developed in cultivar CDC Redberry background, based onL. ervoidesalleles derived from an interspecific recombinant inbred population, LR-59-81. Two-hundred and seventeen individuals of the LABC-01 population at BC2F3:4generation were screened for the race 0 of anthracnose (Colletotrichum lentis) and stemphylium blight (Stemphylium botryosum) under controlled conditions. The population showed significant variations for both diseases and transfer of resistance alleles into the elite cultivar was evident. It also segregated for other traits such as days to flowering, seed coat colour, seed coat pattern and flower colour. Overall, we showed that LABC-01 population can be used in breeding programs worldwide to improve disease resistance and will be available as a valuable genetic resource for future genetic analysis of desired loci introgressed fromL. ervoides.