bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza
Authors: Abbott Timothy R. , Dhamdhere Girija , Liu Yanxia , Lin Xueqiu , Goudy Laine , Zeng Leiping , Chemparathy Augustine , Chmura Stephen , Heaton Nicholas S. , Debs Robert , Pande Tara , Endy Drew , La Russa Marie , Lewis David B. , Qi Lei S.
Published: March 2020

The outbreak of the coronavirus disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), has infected more than 100,000 people worldwide with over 3,000 deaths since December 2019. There is no cure for COVID-19 and the vaccine development is estimated to require 12-18 months. Here we demonstrate a CRISPR-Cas13-based strategy, PAC-MAN (ProphylacticAntiviralCRISPR in huMAN cells), for viral inhibition that can effectively degrade SARS-CoV-2 sequences and live influenza A virus (IAV) genome in human lung epithelial cells. We designed and screened a group of CRISPR RNAs (crRNAs) targeting conserved viral regions and identified functional crRNAs for cleaving SARS-CoV-2. The approach is effective in reducing respiratory cell viral replication for H1N1 IAV. Our bioinformatic analysis showed a group of only six crRNAs can target more than 90% of all coronaviruses. The PAC-MAN approach is potentially a rapidly implementable pan-coronavirus strategy to deal with emerging pandemic strains.
The Mitochondrial Permeability Transition Phenomenon Elucidated by Cryo-EM Reveals the Genuine Impact of Calcium Overload on Mitochondrial Structure and Function
Authors: Strubbe-Rivera Jasiel O. , Schrad Jason R. , Pavlov Evgeny V. , Conway James F. , Parent Kristin N. , Bazil Jason N.
Published: March 2020

Mitochondria have a remarkable ability to uptake and store massive amounts of calcium. However, the consequences of massive calcium accumulation remain enigmatic. In the present study, we analyzed a series of time-course experiments to identify the sequence of events that occur in a population of guinea pig cardiac mitochondria exposed to excessive calcium overload that cause mitochondrial permeability transition (MPT). By analyzing coincident structural and functional data, we determined that excessive calcium overload is associated with large calcium phosphate granules and inner membrane fragmentation, which explains the extent of mitochondrial dysfunction. This data also reveals a novel mechanism for cyclosporin A, an inhibitor of MPT, in which it preserves inner membrane architecture despite the presence of massive calcium phosphate granules in the matrix. Overall, these findings establish a mechanism of calcium-induced mitochondrial dysfunction and the impact of calcium regulation on mitochondrial structure and function.
AGO HITS-CLIP in Adipose Tissue Reveals miR-29 as a Post-Transcriptional Regulator of Leptin
Authors: O’Connor Sean , Murphy Elisabeth , Szwed Sarah K. , Kanke Matt , Marchildon François , Darnell Robert B. , Sethupathy Praveen , Cohen Paul
Published: March 2020

MicroRNAs (miRNAs) are short, non-coding RNAs that associate with Argonaute (AGO) to regulate mRNA stability and translation. While individual miRNAs have been shown to play important roles in white and brown adipose tissue in normal physiology and disease1,2,3, a comprehensive analysis of miRNA activity in these tissues has not been performed. We used high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) to comprehensively characterize the network of high-confidence,in vivomRNA:miRNA interactions across white and brown fat, revealing over 100,000 unique miRNA binding sites. Targets for each miRNA were ranked to generate a catalog of miRNA binding activity, and the miR-29 family emerged as a top regulator of adipose tissue gene expression. Among the top targets of miR-29 was leptin, an adipocyte-derived hormone that acts on the brain to regulate food intake and energy expenditure4. Two independent miR-29 binding sites in the leptin 3’-UTR were validated using luciferase assays, and miR-29 gain and loss-of-function modulated leptin mRNA and protein secretion in primary adipocytes. In mice, miR-29 abundance inversely correlated with leptin levels in two independent models of obesity. This work represents the only experimentally generated miRNA targetome in adipose tissue and identifies the first known post-transcriptional regulator of leptin. Future work aimed at manipulating miR-29:leptin binding may provide a therapeutic opportunity to treat obesity and its sequelae.
SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a transient secretory cell type in subsegmental bronchial branches
Authors: Lukassen Soeren , Chua Robert Lorenz , Trefzer Timo , Kahn Nicolas C. , Schneider Marc A. , Muley Thomas , Winter Hauke , Meister Michael , Veith Carmen , Boots Agnes W. , Hennig Bianca P. , Kreuter Michael , Conrad Christian , Eils Roland
Published: March 2020

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigateACE2andTMPRSS2expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. WhileTMPRSS2is expressed in both tissues, in the subsegmental bronchial branchesACE2is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.
A Self-Supervised Workflow for Particle Picking in Cryo-EM
Authors: McSweeney Donal M. , McSweeney Sean M. , Liu Qun
Published: March 2020

High-resolution single-particle cryo-EM data analysis relies on accurate particle picking. To facilitate the particle picking process, we have developed a self-supervised workflow. Our workflow includes an iterative strategy to use the 2D class average to improve training particles and a progressively improved convolutional neural network (CNN) for particle picking. To automate the selection of particles, we define a threshold (%/Res) using the ratio of percentage class distribution and resolution as a cutoff. Our workflow has been tested using six publicly available data sets with different particle sizes and shapes, and is able to automatically pick particles with minimal user input. The picked particles support high-resolution reconstructions at 3.0 Å or better. Our workflow offers a way toward automated single-particle Cryo-EM data analysis at the stage of particle picking. The workflow may be used in conjunction with commonly used single-particle analysis packages such as Relion, cryoSPARC, cisTEM, SPHIRE, and EMAN2.
All small things considered: the diversity of fungi, bacteria and oomycota isolated from the seagrass,Zostera marina
Authors: Ettinger Cassandra L. , Eisen Jonathan A.
Published: March 2020

Fungi in the marine environment are often neglected as a research topic, despite that fungi having critical roles on land as decomposers, pathogens or beneficial endophytes. Here we used culture-dependent methods to survey the fungi associated with the seagrass,Zostera marina, also obtaining bacteria and oomycete isolates in the process. A total of 108 fungi, 41 bacteria and 2 oomycetes were isolated. These isolates were then taxonomically identified using a combination of molecular and phylogenetic methods. The majority of the fungal isolates were classified as belonging to the classes Eurotiomycetes, Dothideomycetes, and Sordariomycetes. Most fungal isolates were habitat generalists likePenicillium sp.andCladosporium sp., but we also cultured a diverse set of rare taxa including possible habitat specialists likeColletotrichum sp.which may preferentially associate withZ. marinaleaf tissue. Although the bulk of bacterial isolates were identified as being from known ubiquitous marine lineages, we also obtained several Actinomycetes isolates which might produce interesting secondary metabolites and aPhyllobacterium sp. which may be involved in nitrogen cycling in the seagrass ecosystem. We identified two oomycetes, another understudied group of marine microbial eukaryotes, asHalophytophthora sp. which may be opportunistic pathogens ofZ. marina. Overall, this study generates a culture collection of fungi, bacteria and oomycetes which expands knowledge of the diversity ofZ. marinaassociated microbes and highlights a need for more investigation into the functional and evolutionary roles of microbial eukaryotes associated with seagrasses.
Increased Ethanol Intake is Associated with Social Anxiety in Offspring Exposed to Ethanol on Gestational Day 12
Authors: Diaz Marvin R. , Johnson Julia M. , Varlinskaya Elena I.
Published: March 2020

Prenatal alcohol exposure (PAE) can result in physical, cognitive, and neurological deficits termed Fetal Alcohol Spectrum Disorder (FASD). Deficits in social functioning associated with PAE are frequently observed and persist throughout the lifespan. Social impairments, such as social anxiety, are associated with increased alcohol abuse, which is also highly pervasive following PAE. Yet, the relationship between PAE-induced social alterations and alcohol intake later in life is not well understood. In order to test this relationship, we exposed pregnant female Sprague Dawley rats to a single instance of PAE on gestational day 12 and tested offspring in adulthood (postnatal day 63) in a modified social interaction test followed by alternating alone and social ethanol intake sessions. Consistent with our previous findings, we found that, in general, PAE reduced social preference (measure of social anxiety-like behavior) in female but not male adults. However, ethanol intake was significantly higher in the PAE group regardless of sex. When dividing subjects according to level of social anxiety-like behavior (low, medium, or high), PAE males (under both drinking contexts) and control females (under the social drinking context) with a high social anxiety phenotype showed the highest level of ethanol intake. Taken together, these data indicate that PAE differentially affects the interactions between social anxiety, ethanol intake, and drinking context in males and females. These findings extend our understanding of the complexity and persistence of PAE’s sex-dependent effects into adulthood.
A highly conserved cryptic epitope in the receptor-binding domains of SARS-CoV-2 and SARS-CoV
Authors: Yuan Meng , Wu Nicholas C. , Zhu Xueyong , Lee Chang-Chun D. , So Ray T. Y. , Lv Huibin , Mok Chris K. P. , Wilson Ian A.
Published: March 2020

The outbreak of COVID-19, which is caused by SARS-CoV-2 virus, continues to spread globally, but there is currently very little understanding of the epitopes on the virus. In this study, we have determined the crystal structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein in complex with CR3022, a neutralizing antibody previously isolated from a convalescent SARS patient. CR3022 targets a highly conserved epitope that enables cross-reactive binding between SARS-CoV-2 and SARS-CoV. Structural modeling further demonstrates that the binding site can only be accessed when at least two RBDs on the trimeric S protein are in the “up” conformation. Overall, this study provides structural and molecular insight into the antigenicity of SARS-CoV-2.

ONE SENTENCE SUMMARY

Structural study of a cross-reactive SARS antibody reveals a conserved epitope on the SARS-CoV-2 receptor-binding domain.
A molecular map of lymph node blood vascular endothelium at single cell resolution
Authors: Brulois Kevin , Rajaraman Anusha , Szade Agata , Nordling Sofia , Bogoslowski Ania , Dermadi Denis , Rahman Milladur , Kiefel Helena , O’Hara Edward , Koning Jasper J , Kawashima Hiroto , Zhou Bin , Vestweber Dietmar , Red-Horse Kristy , Mebius Reina , Adams Ralf H. , Kubes Paul , Pan Junliang , Butcher Eugene C
Published: March 2020

Blood vascular endothelial cells (BECs) control the immune response by regulating immune cell recruitment, metabolite exchange and blood flow in lymphoid tissues. However, the diversity of BEC and their origins during immune angiogenesis remain poorly understood. Here we profile transcriptomes of BEC from mouse peripheral lymph nodes and map key phenotypes to the vasculature. Our analysis identifies multiple novel subsets including a venous population whose gene signature predicts an unexpectedly selective role in myeloid cell (vs lymphocyte) recruitment to the medulla, confirmed by 2 photon videomicroscopy. We define five phenotypes of capillary lining BEC including a capillary resident regenerative population (CRP) that displays stem cell and migratory gene signatures and contributes to homeostatic BEC turnover and to vascular neogenesis after immunization. Trajectory analyses reveal retention of developmental programs along a progression of cellular phenotypes from CRP to mature venous and arterial BEC subsets. Overall, our single cell atlas provides a molecular blueprint of the lymph node blood vasculature and defines subset specialization for immune cell recruitment and vascular homeostasis.
HCFC1R1 Deficiency Blocks Herpes Simplex Virus-1 Infection by Inhibiting Nuclear Translocation of HCFC1 and VP16
Authors: Shen Yangkun , Ye Zhoujie , Zhao Xiangqian , Feng Zhihua , Chen Jinfeng , Yang Lei , Chen Qi
Published: March 2020

Upon HSV-1 infection, viral protein 16 (VP16), supported by Host Cell Factor C1 (HCFC1), is rapidly transported into the nucleus, and help to express a series of HSV-1 immediate-early proteins to begin its lytic replication. However, no direct evidence has shown if the HCFC1 deficiency can affect the proliferation of HSV-1 so far. Here, we showed that the HCFC1 deficiency led to a strong resistance to HSV-1 infection. Moreover, we identified Host Cell Factor C1 Regulator 1 (HCFC1R1) as a new host factor acting early in HSV infection for the transport of the HSV-1 capsid to the nucleus. The HCFC1R1 deficiency also led to a strong resistance to HSV-1 infection. The HCFC1R1 deficiency did not affect the attachment of HSV-1 to host cells but act early in HSV-1 infection by perturbing the formation of HCFC1/VP16 complex. Remarkably, in addition to wild-type HSV-1 infection, the host cells in the absence of either HCFC1 or HCFC1R1 showed strong resistant to the infection of TK-deficient HSV-1, which strain can course severe symptoms and tolerate to the current anti-HSV drug Acyclovir. Our data suggest that HCFC1 or HCFC1R1 may be used as the novel target for developing anti-HSV-1 therapies.

IMPORTANCE

Herpes simplex virus-1 (HSV-1) is widely spread in the human population and can cause a variety of herpetic diseases. Acyclovir, a guanosine analogue that targets the TK protein of HSV-1, is the first specific and selective anti-HSV-1 drug. However, the rapid emergence of resistant HSV-1 strains is occurring worldwide, endangering the efficacy of Acyclovir. Alternatively, targeting host factors is another strategy to stop HSV-1 infection. Unfortunately, although the HSV-1’s receptor, Nectin-1, was discovered in 1998, no effective antiviral drug to date has been developed by targeting Nectin-1. Targeting multiple pathways is the ultimate choice to prevent HSV-1 infection. Here we demonstrated that the deletion of HCFC1 or HCFC1R1 exhibits a strong inhibitory effect on both wild-type and TK-deficient HSV-1. Overall, we present evidence that HCFC1 or HCFC1R1 may be used as the novel target for developing anti-HSV-1 therapies with a defined mechanism of action.
Cell Type Development inChlamydia trachomatisFollows a Program Intrinsic to the Reticulate Body
Authors: Chiarelli Travis J , Grieshaber Nicole A , Omsland Anders , Remien Christopher H , Grieshaber Scott S
Published: March 2020

The obligate intracellular bacterial pathogenChlamydia trachomatis(Ctr) is reliant on an unusual developmental cycle consisting of two cell forms termed the elementary body (EB) and the reticulate body (RB). The EB is infectious and utilizes a type III secretion system and preformed effector proteins during invasion, but does not replicate. The RB replicates in the host cell but is non-infectious. This developmental cycle is central to chlamydial pathogenesis. In this study we developed mathematical models of the chlamydial developmental cycle that account for potential factors influencing the timing of RB to EB cell type switching during infection. Our models predicted that two broad categories of regulatory signals for RB to EB development could be differentiated experimentally; an “intrinsic” cell autonomous program inherent to each RB or an “extrinsic” environmental signal to which RBs respond. To experimentally differentiate between these hypotheses, we tracked the expression ofCtrdevelopmental specific promoters using fluorescent reporters and live cell imaging. These experiments indicated that EB production was not influenced by increased MOI or by superinfection, suggesting the cycle follows an intrinsic program that is not influenced by environmental factors. Additionally, live cell imaging of these promoter constructs revealed that EB development is a multistep process linked to RB growth rate and cell division. The formation of EBs followed a cell type gene expression progression with the promoters foreuoandihtAactive in RBs, while the promoter forhctAwas active in early EBs/intermediate cells and finally the promoters for the true late genes,hctB, scc2, andtarpactive in the maturing EB.

Importance

Chlamydia trachomatisis an obligate intracellular bacteria that can cause trachoma, cervicitis, urethritis, salpingitis, and pelvic inflammatory disease. To establish infection in host cellsChlamydiamust complete a multi cell type developmental cycle. The developmental cycle consists of two specialized cells; the EB which mediates infection of new cells and the RB which replicates and eventually produces more EB cells to mediate the next round of infection. By developing and testing mathematical models to discriminate between two competing hypotheses for the nature of the signal controlling RB to EB cell type switching. We demonstrate that RB to EB development follows a cell autonomous program that does not respond to environmental cues. Additionally, we show that RB to EB development is a function of cell growth and cell division. This study serves to further our understanding of the chlamydial developmental cycle that is central to the bacterium’s pathogenesis.
Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR
Authors: Dong Lianhua , Zhou Junbo , Niu Chunyan , Wang Quanyi , Pan Yang , Sheng Sitong , Wang Xia , Zhang Yongzhuo , Yang Jiayi , Liu Manqing , Zhao Yang , Zhang Xiaoying , Zhu Tao , Peng Tao , Xie Jie , Gao Yunhua , Wang Di , Zhao Yun , Dai Xinhua , Fang Xiang
Published: March 2020

BACKGROUND

The outbreak of COVID-19 caused by a novel Coronavirus (termed SARS-CoV-2) has spread to over 140 countries around the world. Currently, reverse transcription quantitative qPCR (RT-qPCR) is used as the gold standard for diagnostics of SARS-CoV-2. However, the positive rate of RT-qPCR assay of pharyngeal swab samples are reported to vary from 30∼60%. More accurate and sensitive methods are urgently needed to support the quality assurance of the RT-qPCR or as an alternative diagnostic approach.

METHODS

We established a reverse transcription digital PCR (RT-dPCR) protocol to detect SARS-CoV-2 on 194 clinical pharyngeal swab samples, including 103 suspected patients, 75 close contacts and 16 supposed convalescents.

RESULTS

The limit of blanks (LoBs) of the RT-dPCR assays were ∼1.6, ∼1.6 and ∼0.8 copies/reaction for ORF 1ab, N and E genes, respectively. The limit of detection (LoD) was 2 copies/reaction. For the 103 fever suspected patients, the sensitivity of SARS-CoV-2 detection was significantly improved from 28.2% by RT-qPCR to 87.4% by RT-dPCR. For close contacts, the suspect rate was greatly decreased from 21% down to 1%. The overall sensitivity, specificity and diagnostic accuracy of RT-dPCR were 90%, 100% and 93 %, respectively. In addition, quantification of the viral load for convalescents by RT-dPCR showed that a longer observation period was needed in the hospital for elderly patients.

CONCLUSION

RT-dPCR could be a confirmatory method for suspected patients diagnosed by RT-qPCR. Furthermore, RT-dPCR was more sensitive and suitable for low viral load specimens from the both patients under isolation and those under observation who may not be exhibiting clinical symptoms.
ATM-mediated DNA damage response in macrophages primes phagocytosis and immune checkpoint regulation
Authors: Bansal Aakanksha , Neuhaus René , Izquierdo-Alvarez Elena , Vorholt Daniela , Feldkötter Henning , Nolte Hendrik , Lohneis Philipp , Büttner Reinhard , Krüger Markus , Pallasch Christian P. , Schumacher Björn
Published: March 2020

Genotoxin-based cancer therapies trigger a DNA damage response (DDR) to eliminate cancer cells but similarly exert profound alterations to the immune cell compartment. Macrophages in the tumor microenvironment are important and multifaceted components in actively sustaining tumor progression but also in clearance of tumor cells and play an important role in the outcome of chemotherapy. Here, we report that post neo-adjuvant chemotherapy macrophages in tumor samples display elevated expression of the immune checkpoint PD-L1. We determined that chemotherapy or direct application of DNA damage to macrophagesin vitrotriggers a specific MDDRpolarization phenotype characterized by increased phagocytic activity, elevated PD-L1 expression, and induction of endotoxin tolerance. Phospho-proteomics analysis revealed epigenetic alterations and ATM-dependent induction of senescence in macrophages upon DNA damage. We propose that ATM-induced senescence and PD-L1 immune checkpoint induction mediate a specific MDDRmacrophage polarization that might contribute to chemotherapy responses. Furthermore, our results clarify the functional role of tumor associated macrophages in the context of DNA damage and combination therapies including checkpoint inhibition.
SARS-CoV-2 invades host cells via a novel route: CD147-spike protein
Authors: Wang Ke , Chen Wei , Zhou Yu-Sen , Lian Jian-Qi , Zhang Zheng , Du Peng , Gong Li , Zhang Yang , Cui Hong-Yong , Geng Jie-Jie , Wang Bin , Sun Xiu-Xuan , Wang Chun-Fu , Yang Xu , Lin Peng , Deng Yong-Qiang , Wei Ding , Yang Xiang-Min , Zhu Yu-Meng , Zhang Kui , Zheng Zhao-Hui , Miao Jin-Lin , Guo Ting , Shi Ying , Zhang Jun , Fu Ling , Wang Qing-Yi , Bian Huijie , Zhu Ping , Chen Zhi-Nan
Published: March 2020

Currently, COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely spread around the world; nevertheless, so far there exist no specific antiviral drugs for treatment of the disease, which poses great challenge to control and contain the virus. Here, we reported a research finding that SARS-CoV-2 invaded host cells via a novel route of CD147-spike protein (SP). SP bound to CD147, a receptor on the host cells, thereby mediating the viral invasion. Our further research confirmed this finding. First, in vitro antiviral tests indicated Meplazumab, an anti-CD147 humanized antibody, significantly inhibited the viruses from invading host cells, with an EC50of 24.86 μg/mL and IC50of 15.16 μg/mL. Second, we validated the interaction between CD147 and SP, with an affinity constant of 1.85×10−7M. Co-Immunoprecipitation and ELISA also confirmed the binding of the two proteins. Finally, the localization of CD147 and SP was observed in SARS-CoV-2 infected Vero E6 cells by immuno-electron microscope. Therefore, the discovery of the new route CD147-SP for SARS-CoV-2 invading host cells provides a critical target for development of specific antiviral drugs.
Self-antigen driven affinity maturation is required for pathogenic monovalent IgG4 autoantibody development
Authors: Fichtner Miriam L. , Vieni Casey , Redler Rachel L. , Kolich Ljuvica , Jiang Ruoyi , Takata Kazushiro , Stathopoulos Panos , Suarez Pablo , Nowak Richard J. , Burden Steven J. , Ekiert Damian C. , O’Connor Kevin C.
Published: March 2020

Pathogenic IgG4 autoantibodies in autoimmune myasthenia gravis (MG) are functionally monovalent as a result of Fab-arm exchange. The origin and development of these unique autoantibodies are not well understood. We examined MG patient-derived monoclonal autoantibodies (mAbs), their corresponding germline-encoded unmutated common ancestors (UCA) and monovalent antigen-binding fragments (Fabs) to investigate how antigen-driven affinity maturation contributes to both binding and immunopathology. Mature mAbs, their UCA counterparts and mature monovalent Fabs bound to the autoantigen and retained their pathogenic capacity. However, monovalent UCA Fabs still bound the autoantigen but lost their pathogenic capacity. The mature Fabs were characterized by very high affinity (sub-nanomolar) driven by a rapid on-rate and slow off-rate. However, the UCA affinity was approximately 100-fold less than that of the mature Fabs, which was driven by a rapid off-rate. Crystal structures of two Fabs shed light on how mutations acquired during affinity maturation may contribute to increased MuSK binding affinity. These collective findings indicate that the autoantigen initiates the autoimmune response in MuSK MG and drives autoimmunity through the accumulation of somatic hypermutation such that monovalent IgG4 Fab-arm exchanged MG autoantibodies reach a high affinity threshold required for pathogenic capacity.

IgG4 autoantibodies in autoimmune myasthenia gravis are functionally monovalent, requiring a high affinity threshold featuring fast on/slow off rates, to reach pathogenic capacity. This capacity is dependent on self-antigen initiated and driven maturation, which includes the accumulation of indispensable somatic hypermutations that may alter electrostatic interactions with the antigen.
Differential encoding in prefrontal cortex projection neuron classes across cognitive tasks
Authors: Lui Jan H. , Nguyen Nghia D. , Grutzner Sophie M. , Darmanis Spyros , Peixoto Diogo , Wagner Mark J. , Allen William E. , Kebschull Justus M. , Richman Ethan B. , Ren Jing , Newsome William T. , Quake Stephen R. , Luo Liqun
Published: March 2020

Single-cell transcriptomics has been widely applied to classify neurons in the mammalian brain, while systems neuroscience has historically analyzed the encoding properties of cortical neurons without considering cell types. Here we examine how specific transcriptomic types of mouse prefrontal cortex (PFC) projection neurons relate to axonal projections and encoding properties across multiple cognitive tasks. We found that most types projected to multiple targets, and most targets received projections from multiple types, except PFC→PAG (periaqueductal gray). By comparing Ca2+-activity of the molecularly homogeneous PFC→PAG type against two heterogeneous classes in several two-alternative choice tasks in freely-moving mice, we found that all task-related signals assayed were qualitatively present in all examined classes. However, PAG-projecting neurons most potently encoded choice in cued tasks, whereas contralateral PFC-projecting neurons most potently encoded reward context in an uncued task. Thus, task signals are organized redundantly, but with clear quantitative biases across cells of specific molecular-anatomical characteristics.
Dynamic changes in tRNA modifications and abundance during T-cell activation
Authors: Rak Roni , Polonsky Michal , Eizenberg-Magar Inbal , Mo Yufeng , Sakaguchi Yuriko , Mizrahi Orel , Nachshon Aharon , Reich-Zeliger Shlomit , Stern-Ginossar Noam , Dahan Orna , Suzuki Tsutomu , Friedman Nir , Pilpel Yitzhak
Published: March 2020

The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observe a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode “slippery codons”, that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with a HIV gag-pol frameshifting site reporter. These results may explain HIV’s specific tropism towards proliferating T-Cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity.

Significance statement

The tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation- T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which are relaxed when cells reduce back their proliferation rate and differentiate into memory cells. We found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication.

Classification

BIOLOGICAL SCIENCES; cell biology
New gene association measures by joint network embedding of multiple gene expression datasets
Authors: Wu Guiying , Li Xiangyu , Guo Wenbo , Wei Zheng , Hu Tao , Gu Jin
Published: March 2020

Large number of samples are required to construct a reliable gene co-expression network, the samples from a single gene expression dataset are obviously not enough. However, batch effect may widely exist among datasets due to different experimental conditions. We proposed JEBIN (Joint Embedding of multiple BIpartite Networks) algorithm, it can learn a low-dimensional representation vector for each gene by integrating multiple bipartite networks, and each network corresponds to one dataset. JEBIN owns many inherent advantages, such as it is a nonlinear, global model, has linear time complexity with the number of genes, dataset or samples, and can integrate datasets with different distribution. We verified the effectiveness and scalability of JEBIN through a series of simulation experiments, and proved better performance on real biological data than commonly used integration algorithms. In addition, we conducted a differential co-expression analysis of hepatocellular carcinoma between the single-cell and bulk RNA-seq data, and also a contrast between the hepatocellular carcinoma and its adjacency samples using the bulk RNA-seq data. Analysis results prove that JEBIN can obtain comprehensive and stable gene co-expression networks through integrating multiple datasets and has wide prospect in the functional annotation of unknown genes and the regulatory mechanism inference of target genes.
Brain network motifs are markers of loss and recovery of consciousness
Authors: Duclos Catherine , Nadin Danielle , Mahdid Yacine , Tarnal Vijay , Picton Paul , Vanini Giancarlo , Golmirzaie Goodarz , Janke Ellen , Avidan Michael S. , Kelz Max B. , Mashour George A. , Blain-Moraes Stefanie
Published: March 2020

Motifs are patterns of inter-connections between nodes of a network, and have been investigated as building blocks of directed networks. This study explored the re-organization of 3-node motifs during loss and recovery of consciousness. Nine healthy subjects underwent a 3-hour anesthetic protocol while 128-channel electroencephalography (EEG) was recorded. In the alpha (8–13 Hz) band, five-minute epochs of EEG were extracted for: baseline; induction; unconscious; 30-, 10- and 5-minutes pre-recovery of responsiveness; 30- and 180-minutes post-recovery of responsiveness. We constructed a functional brain network using the weighted and directed phase lag index, on which we calculated the frequency and topology of 3-node motifs. Three motifs (motifs 1, 2 and 5) were significantly present across participants and epochs, when compared to random networks (p<0.05). The topology of motifs 1 and 5 changed significantly between responsive and unresponsive epochs (p<0.01). Motif 1 was constituted by long-range chain-like connections, while motif 5 was constituted by short-range, loop-like connections. Our results suggest that anesthetic-induced unconsciousness is associated with a topological re-organization of network motifs. As motif topological re-organization may precede (motif 5) or accompany (motif 1) the return of responsiveness, motifs could contribute to the understanding of the neural correlates of consciousness.
IsOculudentavisa bird or even archosaur?
Authors: Li Zhiheng , Wang Wei , Hu Han , Wang Min , Yi Hongyu , Lu Jing
Published: March 2020

Recent finding of a fossil –Oculudentavis khaungraaeXing et al. 2020, entombed in a Late Cretaceous amber – was claimed to represent a humming bird-sized dinosaur1. Regardless of the intriguing evolutionary hypotheses about the bauplan of Mesozoic dinosaurs (including birds) posited therein, this enigmatic animal demonstrates various morphologies resembling lizards. IfOculudentaviswas a bird, it challenges several fundamental morphological differences between Lepidosauria and Archosauria. Here we reanalyze the original computed tomography scan data ofOculudentavis. Morphological evidences demonstrated here highly contradict the avian or even archosaurian phylogenetic placement ofOculudentavis. In contrast, our analysis revealed multiple synapomorphies of the Squamata in this taxon, including pleurodont marginal teeth and an open infratemporal fenestra, which suggests a squamate rather than avian or dinosaurian affinity ofOculudentavis.
Negative effects characterization and comparative transcriptomics elucidation on the lag phase of an industrialS. cerevisiaeunder the corn stover hydrolysate stress
Authors: Kuang Xiaolin , Guo Yaping , Zhang Zhengyue , Hu Xiangdong , Han Xuebing , Ouyang Yidan , Xiao Difan , Li Qian , Wang Hanyu , Li Xi , Chen Qiang , Ma Menggen
Published: March 2020

During biofuels fermentation from pretreated lignocellulosic biomass, the strong toxicity of the lignocellulose hydrolysate is resulted from the synergistic effect of multiple lignocellulosic inhibitors, which far exceeds the sum of effects caused by every single inhibitor. Meanwhile, the synergistic effect is unclear and the underlying response mechanism of the industrial yeast towards the actual pretreated lignocellulose hydrolysate is still under exploration. Here, we employed an industrialS. cerevisiaefor the transcriptomic analysis in two time points (early and late) of the lag phase under the corn stover hydrolysate stress. As investigation, the corn stover hydrolysate caused the accumulation of reactive oxygen species (ROS), damages of mitochondrial membrane and endoplasmic reticulum (ER) membrane in the industrialS. cerevisiaeYBA_08 during the lag phase, especially these negative effects were more significant at the early lag phase. Based on the transcriptome profile, the industrialS. cerevisiaeYBA_08 might recruit stress-related transcription factors (MSN4,STE12,SFL1,CIN5,COM2,MIG3, etc.) through the mitogen-activated protein kinase (MAPK)-signaling pathway to induce a transient G1/G2 arrest, and to activate defense bioprocesses like protectants metabolism, sulfur metabolism, glutaredoxin system, thioredoxin system, heat shock proteins chaperone and oxidoreductase detoxification, resisting those compounded stresses including oxidative stress, osmotic stress and structural stress. Surprisingly, this defense system might be accompanied with the transient repression of several bioprocesses like fatty acid metabolism, purinede novobiosynthesis and ergosterol biosynthesis.

Importance

This research systematically demonstrated the lag phase response of an industrial yeast to the lignocellulosic hydrolysate in transcriptional level, providing a molecular fundament for understanding the synergistic effect of various lignocellulosic inhibitors and the regulatory mechanism of tolerance for industrial yeasts under this stress.
Depression of heart rate in fish at critically high temperatures is due to atrioventricular block
Authors: Haverinen Jaakko , Vornanen Matti
Published: March 2020

At critically high temperature, cardiac output in fish collapses due to depression of heart rate (bradycardia). However, the cause of bradycardia remains unresolved. Here we provide a mechanistic explanation for the temperature induced bradycardia. To this end rainbow trout (Oncorhynchus mykiss; acclimated at +12°C) were exposed to acute warming, while cardiac function was followed from electrocardiograms. From +12°C to +25.3°C, electrical excitation between different parts of the heart was coordinated but above +25.3°C atrial and ventricular beating rates became partly dissociated due to 2:1 atrioventricular (AV) block. With further warming atrial rate increased to the peak value of 188 ± 22 bpm at +27°C, while the rate of the ventricle reached the peak value of 124 ± 10 bpm at +25.3°C and thereafter dropped to 111 ± 15 bpm at +27°C. In single ventricular myocytes, warming from +12°C to +25°C attenuated electrical excitability as evidenced by increases in rheobase current and critical depolarization required to trigger action potential. The depression of excitability was caused by temperature induced decrease in input resistance (sarcolemmal K+leak via the outward IK1current) of resting myocytes and decrease in inward charge transfer by the Na+current (INa) of active myocytes. Collectively these findings show that at critically high temperatures AV block causes ventricular bradycardia which is an outcome from the increased excitation threshold of the ventricle due to changes in passive (resting ion leak) and active (inward charge movement) electrical properties of ventricular myocytes. The sequence of events from the level of ion channels to the cardiac functionin vivoprovides a mechanistic explanation for the depression of cardiac output in fish at critically high temperature.
Highly Sensitive Identification of Lymphatic and Hematogenous Metastasis Routes of Novel Radiolabeled Exosomes Using Non-invasive PET Imaging
Authors: Jung Kyung Oh , Kim Young-Hwa , Chung Seock-Jin , Kang Keon Wook , Rhee Siyeon , Pratx Guillem , Chung June-Key , Youn Hyewon
Published: March 2020

Clinically, there has been significant interest in the use of exosomes for diagnostic applications as promising biomarkers and therapeutic applications as therapeutic vehicles. However, knowledge ofin vivophysiological biodistribution of exosomes was difficult to assess until now. Physiological distribution of exosomes in the body must be elucidated for clinical application. In this study, we aimed to develop reliable and novel methods to monitor biodistribution of exosomes usingin vivoPET and optical imaging.

Methods

Exosomes were isolated from cultured medium of 4T1, mouse breast cancer cells. Exosomes were labeled with Cy7 and64Cu (or68Ga). In mice, radio/fluorescent dye-labeled exosomes were injected through the lymphatic routes (footpad injection) and hematogenous metastatic routes (tail vein injection). Fluorescence and PET images were obtained and quantified. Radio-activity ofex vivoorgans was measured by gamma counter.

Results

PET signals from exosomes in the lymphatic metastatic route were observed in the draining lymph nodes, which are not distinguishable with optical imaging. Immunohistochemistry revealed greater uptake of exosomes in brachial and axillary lymph nodes than inguinal lymph node. After administration through the hematogenous metastasis pathway, accumulation of exosomes was clearly observed in PET images in the lungs, liver, and spleen, showing results similar toex vivogamma counter data.

Conclusion

Exosomes from tumor cells were successfully labeled with64Cu (or68Ga) and visualized by PET imaging. These results suggest that this cell type-independent, quick, and easy exosome labeling method using PET isotopes could provide valuable information for further application of exosomes in the clinic.
Delivering equitable distance library services to off-campus users at the University of the Free State in South Africa
Authors: Coetzer Lianda , Mapulanga Patrick
Published: March 2020

Purpose

The purpose of this study is to assess the perceived satisfaction of Advanced Certificate in Teaching students and facilitators regarding online library services offered by the University of the Free State (UFS) in South Africa.

Design/methodology/approach

The study adopted a quantitative approach with open-ended questions that generated some qualitative data. Data has been presented using descriptive statistics in the form of tables, graphs and charts and thematic content analysis for some qualitative data.

Findings

All learners in this study were adults between 45 and 55 years of age. Of the respondents, 13% lacked online experience, while about 85% had never used online library services and 35% indicated that Google was their primary source of information. The majority of respondents indicated information literacy as a core function of the academic library. High data cost in South Africa came out as one of the major issues affecting distance learners as well as login and password frustrations. The study confirmed computer anxiety, physical discomfort, information overflow and prompt response as some of the perceived challenges and levels of satisfaction respectively of Advanced Certificate in Teaching students and facilitators regarding online library services offered by the University of the Free State (UFS) in South Africa.

Practical implications

The study revealed that a distance learning library policy is of the essence because it helps to put in place rules and regulations that guide the delivery of distance library services.

Originality/value

The offering of online and distance library services is a fairly new concept to the UFS library. This study bridges the gap between theory and practice regarding the perceived satisfaction of distance users on online library services and how to improve the current practice.
Attractive and facilitating store atmospheric stimuli
Authors: Bhatt Gaurav , Sarkar Abhigyan , Sarkar Juhi Gahlot
Published: March 2020

Purpose

The majority of past studies on the physical store environment have focused on the impacts of distinct store environmental cues like music, crowding and décor on consumers' responses. However, recent research posits that consumer is more likely to experience several cues in a combination, rather than in isolation, i.e. different categories of store environmental cues are likely to impact consumer psychology holistically. Hence, our study aims to identify the relevant factors of store atmospheric cues impacting consumer's attitude in physical retail store context and validate scales to measure such factors.

Design/methodology/approach

This research develops and validates psychometrically reliable scales to measure two broad store stimuli factors namely: attractive and facilitating store stimuli, following the scale development method suggested by Churchill (1979).

Findings

The study shows that attractive store stimuli predict affective and sensory store brand experiences. The facilitating store stimuli moderate the effects of attractive store stimuli on affective and sensory store brand experiences. Affective and sensory store brand experiences predict store satisfaction.

Originality/value

This research contributes to the existing body of store ambience research by empirically understanding the psychological mechanism through which customers perceive different store cues holistically leading to the elicitation of store satisfaction.
Modelling Twitter conversations in #favela towards the conceptualization of the eVoice of the unheard
Authors: Inversini Alessandro , Williams Nigel L. , Rega Isabella , Samakovlis Ioanna
Published: March 2020

Purpose

The purpose of this study to shed light on the importance of social media hosted content related to socially-motivated discussions. Moving from the field of communication for development, the research leverages social media as a powerful tool for collecting and analyse peer-to-peer communication towards the conceptualization of eVoices of Unheard. The deep understanding of these conversation can generate recommendations for organizations and governments designing and providing interventions fostering local socio-economic development.

Design/methodology/approach

The study presents a large-scale analysis of social media interactions on the topic “#favela” to generate insights into a social network structure, narrative contents and meaning generated.

Findings

Structurally, the analysed networks are comparable with those presented in current academic literature; automatic text analysis confirmed the promise of the inner value of communication for development opening the floor to conceptualization of the “eVoices of unheard”, which is the collective and conscious use of social media to mediate community discussions about tangible and intangible issues related to socio-economic development.

Originality/value

Framed within the rise of interactive communication for development this research show that social media an support the notion of voice proposed by Couldry (2010) moving from process (i.e. the recording of the voice) towards value (i.e. the possibility of giving an account of one’s life and its conditions to have an impact on human life and resources) thereby understanding intangible issues related with socio-economic development.
Navigating the campus past: college yearbook controversies
Authors: Batchelor Oliver
Published: March 2020

Purpose

This paper is about the controversies stemming from digitized college and university yearbook photos and the professional values of librarians and archivists in helping higher education communities to confront their unsettling pasts. The actions taken by college librarians and archivists reveal their dedication to core values.

Design/methodology/approach

The approach taken in this concept paper includes a review of various college yearbook controversies in higher education and the strategies used by librarians to address the controversy.

Findings

My findings revealed that librarians and archivists play a crucial role in assisting higher education institutions in coming to terms with their histories.

Originality/value

Although various news outlets have reported on college yearbook controversies, very few (if any) library publications have addressed this issue. This document will serve as a comprehensive evaluation of the controversies and how librarians have taken action.