bluuebunny/crossref_metadata_2025 huggingface dataset:
Birth weight is associated with brain tissue volumes seven decades later, but not with age-associated changes to brain structure
Authors: Wheater Emily N. W. , Shenkin Susan D. , Maniega Susana Muñoz , Hernández Maria Valdés , Wardlaw Joanna M. , Deary Ian J. , Bastin Mark E. , Boardman James P. , Cox Simon R.
Published: August 2020

Birth weight, an indicator of fetal growth, is associated with cognitive outcomes in early life and risk of metabolic and cardiovascular disease across the life course. Cognitive ability in early life is predictive of cognitive ability in later life. Brain health in older age, defined by MRI features, is associated with cognitive performance. However, little is known about how variation in normal birth weight impacts on brain structure in later life. In a community dwelling cohort of participants in their early seventies we tested the hypothesis that birthweight is associated with the following MRI features: total brain (TB), grey matter (GM) and normal appearing white matter (NAWM) volumes; whiter matter hyperintensity (WMH) volume; a general factor of fractional anisotropy (gFA) and peak width skeletonised mean diffusivity (PSMD) across the white matter skeleton. We also investigated the associations of birthweight with cortical surface area, volume and thickness. Birthweight was positively associated with TB, GM and NAWM volumes in later life (β ≥ 0.194), and with regional cortical surface area but not gFA, PSMD, WMH volume, or cortical volume or thickness. These positive relationships appear to be explained by larger intracranial volume rather than by age-related tissue atrophy, and are independent of body height and weight in adulthood. This suggests that larger birthweight is linked to increased brain tissue reserve in older life, rather than a resilience to age-related changes in brain structure, such as tissue atrophy or WMH volume.

Significance Statement

Cognitive brain ageing carries a high personal, societal and financial cost and understanding its developmental origins is important for identifying possible preventative strategies. In a sample of older participants from the Lothian Birth Cohort 1936 we were able to explore the neurobiological correlates of birth weight, which is indicative of the fetal experience. We find that higher birth weight is related to larger brain tissue volumes in later life, but does not modify the trajectory of age-related change. This suggests that early life growth confers preserved differentiation, rather than differential preservation with regards to brain reserve. That these effects are detectable into later life indicates that this variable may be valuable biomarker in the epidemiology of ageing.
Hyperbolic geometry of gene expression
Authors: Zhou Yuansheng , Sharpee Tatyana
Published: August 2020

Understanding the patterns of gene expression is key to elucidating the differences between cell types and across disease conditions. The overwhelmingly large number of genes involved generally makes this problem intractable. Yet, we find that gene expression patterns in five different data datasets can all be described using a small number of variables. These variables describe differences between cells according to a hyperbolic metric. We reach this conclusion by developing methods that, starting with an initial assumption of a Euclidean geometry, can detect the presence of other geometries in the data. The Euclidean metric is used in most of current studies of gene expression, primarily because it is difficult to use other non-linear metrics in high dimensional spaces. The hyperbolic metric is much more suitable for describing data produced by a hierarchically organized network, which is relevant for many biological processes. We find that the hyperbolic effects, but not the space dimensionality, increase with the number of genes that are taken into account. The hyperbolic curvature was the smallest for mouse embryonic stem cells, stronger for mouse kidney, lung and brain cells, and reached the largest value in a set of human cells integrated from multiple sources. We show that taking into account hyperbolic geometry strongly improves the visualization of gene expression data compared to leading visualization methods. These results demonstrate the advantages of knowing the underlying geometry when analyzing high-dimensional data.
PIEZO ion channel is required for root mechanotransduction inArabidopsis thaliana
Authors: Mousavi Seyed A. R. , Dubin Adrienne E , Zeng Wei-Zheng , Coombs Adam M. , Do Khai , Ghadiri Darian A. , Ge Chennan , Zhao Yunde , Patapoutian Ardem
Published: August 2020

Plant roots adapt to the mechanical constraints of the soil to grow and absorb water and nutrients. As in animal species, mechanosensitive ion channels in plants are proposed to transduce external mechanical forces into biological signals. However, the identity of these plant root ion channels remains unknown. Here, we show thatArabidopsis thalianaPIEZO (AtPIEZO) has preserved the function of its animal relatives and acts as an ion channel. We present evidence that plant PIEZO is highly expressed in the columella and lateral root cap cells of the root tip which experience robust mechanical strain during root growth. Deleting PIEZO from the whole plant significantly reduced the ability of its roots to penetrate denser barriers compared to wild type plants.piezomutant root tips exhibited diminished calcium transients in response to mechanical stimulation, supporting a role of AtPIEZO in root mechanotransduction. Finally, a chimeric PIEZO channel that includes the C-terminal half of AtPIEZO containing the putative pore region was functional and mechanosensitive when expressed in naive mammalian cells. Collectively, our data suggest thatArabidopsisPIEZO plays an important role in root mechanotransduction and establishes PIEZOs as physiologically relevant mechanosensitive ion channels across animal and plant kingdoms.
Transcriptomic response during wasp parasitism in theDrosophila-Spiroplasmainteraction
Authors: Higareda-Alvear Victor M. , Mateos Mariana , Quezada Diego Cortez , Tamborindeguy Cecilia , Martínez-Romero Esperanza
Published: August 2020

Several facultative bacterial symbionts of insects protect their hosts against natural enemies.Spiroplasma poulsoniistrainsMel, a male-killing heritable symbiont ofDrosophila melanogaster, confers protection against some species of parasitic wasps. Several lines of evidence suggest thatSpiroplasma-encoded ribosome inactivating proteins (RIPs) are involved in the protection mechanism, but the potential contribution of the fly-encoded functions has not been deeply explored. Here we used RNA-seq to evaluate the response ofD. melanogasterto infection bySpiroplasmaand parasitism by theSpiroplasma-susceptible waspLeptopilina heterotoma, and theSpiroplasma-resistant waspGanaspis hookeri. In the absence ofSpiroplasmainfection, we found evidence ofDrosophilaimmune activation byG. hookeri, but not byL. heterotoma, which in turn negatively influenced functions associated with male gonad development. As expected for a symbiont that kills males, we detected extensive downregulation in theSpiroplasma-infected treatments of genes known to have male-biased expression. We detected very few genes whose expression was influenced by theSpiroplasma-L. heterotomainteraction, and they do not appear to be related to immune response. For most of them, parasitism byL. heterotoma(in the absence ofSpiroplasma) caused an expression change that was at least partly reversed whenSpiroplasmawas also present. It is unclear whether such genes are involved in theSpiroplasma-mediated mechanism that leads to wasp death or fly rescue. Nonetheless, the expression pattern of some of these genes, which reportedly undergo expression shifts during the larva-to-pupa transition, is suggestive of an influence ofSpiroplasmaon the development time ofL. heterotoma-parasitized flies. In addition, we used the RNAseq data and quantitative (q)PCR to evaluate the transcript levels of theSpiroplasma-encoded RIP genes. One of the five RIP genes (RIP2) was consistently highly expressed independently of wasp parasitism, in two substrains ofsMel. Finally, the RNAseq data revealed evidence consistent with RIP-induced damage in the ribosomal (r)RNA of theSpiroplasma-susceptible, but not theSpiroplasma-resistant, wasp. We conclude that immune priming is unlikely to contribute to theSpiroplasma-mediated protection against wasps, and that the mechanism by whichG. hookeriresists/toleratesSpiroplasmadoes not involve inhibition of RIP transcription.
Using protein interaction networks to identify cancer dependencies from tumor genome data
Authors: Horn Heiko , Fagre Christian , Gupta Anika , Tsafou Kalliopi , Fornelos Nadine , Neal James T , Lage Kasper
Published: August 2020

Genes required for tumor proliferation and survival (dependencies) are challenging to predict from cancer genome data, but are of high therapeutic value. We developed an algorithm (network purifying selection [NPS]) that aggregates weak signals of purifying selection across a gene’s first order protein-protein interaction network. We applied NPS to 4,742 tumor genomes to show that a gene’s NPS score is predictive of whether it is a dependency and validated 58 NPS-predicted dependencies in six cancer cell lines. Importantly, we demonstrate that leveraging NPS predictions to execute targeted CRISPR screens is a powerful, highly cost-efficient approach for identifying and validating dependencies quickly, because it eliminates the substantial experimental overhead required for whole-genome screening.
Twin studies with unmet assumptions are biased towards genetic heritability
Authors: Dalmaijer Edwin S.
Published: August 2020

For a century [1,2], studies of monozygotic and dizygotic twins have yielded estimates of trait heritability. The clever logic behind them is that while both types of twins share environments, their genetic overlap is different. Hence, larger trait correlations between monozygotic compared to dizygotic twins indicate heritability (nature), whereas similar correlations indicate shared environmental influences (nurture), and low correlations indicate shaping through non-shared environments (external influences and measurement error). While many have written on the assumptions that both types of twins share equal environments [3–5], and that parental genetics and environment are independent [6,7]; fewer have put their data where their mouth is. Here, the impacts of unmet assumptions were investigated using a generative mixture model of twin phenotypes. The results indicated that violations of the equal environments assumption yielded large overestimations of heritability and underestimations of shared environmental influences. On the other hand, when parental genetics shaped twins’ shared environments, only minor non-linear biases against heritability emerged. Finally, realistic levels of measurement error uniformly depressed estimates for genetic and shared environmental factors. In sum, twin studies are particularly susceptible to overestimation of genetic and non-shared environmental influences. This bias could explain why some traits, such as attitudes towards property taxes [8], show suspiciously high heritability without a biologically plausible mechanism. Particularly in the context of traits with convincing mechanisms of cultural transmission [9–11] and complex gene-environment interactions [6], researchers should not allow biases in twin studies to overestimate heritability.
The high-affinity immunoglobulin receptor FcγRI potentiates HIV-1 neutralization via antibodies against the gp41 N-heptad repeat
Authors: Montefiori David C. , Filsinger Interrante Maria V. , Bell Benjamin N. , Rubio Adonis A. , Joyce Joseph G. , Shiver John W. , LaBranche Celia C. , Kim Peter S.
Published: August 2020

The HIV-1 gp41 N-heptad repeat (NHR) region of the pre-hairpin intermediate, which is transiently exposed during HIV-1 viral membrane fusion, is a validated clinical target in humans and is inhibited by the FDA-approved drug enfuvirtide. However, vaccine candidates targeting the NHR have yielded only modest neutralization activities in animals; this inhibition has been largely restricted to tier-1 viruses, which are most sensitive to neutralization by sera from HIV-1-infected individuals. Here, we show that the neutralization activity of the well-characterized NHR-targeting antibody D5 is potentiated >5,000-fold in TZM-bl cells expressing FcγRI compared to those without, resulting in neutralization of many tier-2 viruses (which are less susceptible to neutralization by sera from HIV-1-infected individuals and are the target of current antibody-based vaccine efforts). Further, antisera from guinea pigs immunized with the NHR-based vaccine candidate (ccIZN36)3neutralized tier-2 viruses from multiple clades in an FcγRI-dependent manner. As FcγRI is expressed on macrophages and dendritic cells, which are present at mucosal surfaces and are implicated in the early establishment of HIV-1 infection following sexual transmission, these results may be important in the development of a prophylactic HIV-1 vaccine.
Long Period Modeling SARS-CoV-2 Infection of in Vitro Cultured Polarized Human Airway Epithelium
Authors: Hao Siyuan , Ning Kang , Kuz Cagla Aksu , Vorhies Kai , Yan Ziying , Qiu Jianming
Published: August 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replicates throughout human airways. The polarized human airway epithelium (HAE) cultured at an airway-liquid interface (HAE-ALI) is an in vitro model mimicking the in vivo human mucociliary airway epithelium and supports the replication of SARS-CoV-2. However, previous studies only characterized short-period SARS-CoV-2 infection in HAE. In this study, continuously monitoring the SARS-CoV-2 infection in HAE-ALI cultures for a long period of up to 51 days revealed that SARS-CoV-2 infection was long lasting with recurrent replication peaks appearing between an interval of approximately 7-10 days, which was consistent in all the tested HAE-ALI cultures derived from 4 lung bronchi of independent donors. We also identified that SARS-CoV-2 does not infect HAE from the basolateral side, and the dominant SARS-CoV-2 permissive epithelial cells are ciliated cells and goblet cells, whereas virus replication in basal cells and club cells was not detectable. Notably, virus infection immediately damaged the HAE, which is demonstrated by dispersed Zonula occludens-1 (ZO-1) expression without clear tight junctions and partial loss of cilia. Importantly, we identified that SARS-CoV-2 productive infection of HAE requires a high viral load of 2.5 × 105virions per cm2of epithelium. Thus, our studies highlight the importance of a high viral load and that epithelial renewal initiates and maintains a recurrent infection of HAE with SARS-CoV-2.
Immune response to vaccine candidates based on different types of nanoscaffolded RBD domain of the SARS-CoV-2 spike protein
Authors: Lainšček Duško , Fink Tina , Forstnerič Vida , Hafner-Bratkovič Iva , Orehek Sara , Strmšek Žiga , Manček-Keber Mateja , Pečan Peter , Esih Hana , Malenšek Špela , Aupič Jana , Dekleva Petra , Plaper Tjaša , Vidmar Sara , Kadunc Lucija , Benčina Mojca , Omersa Neža , Anderluh Gregor , Pojer Florence , Lau Kelvin , Hacker David , Correia Bruno , Peterhoff David , Wagner Ralf , Jerala Roman
Published: August 2020

Effective and safe vaccines against SARS-CoV-2 are highly desirable to prevent casualties and societal cost caused by Covid-19 pandemic. The receptor binding domain (RBD) of the surface-exposed spike protein of SARS-CoV-2 represents a suitable target for the induction of neutralizing antibodies upon vaccination. Small protein antigens typically induce weak immune response while particles measuring tens of nanometers are efficiently presented to B cell follicles and subsequently to follicular germinal center B cells in draining lymph nodes, where B cell proliferation and affinity maturation occurs. Here we prepared and analyzed the response to several DNA vaccines based on genetic fusions of RBD to four different scaffolding domains, namely to the foldon peptide, ferritin, lumazine synthase and β-annulus peptide, presenting from 6 to 60 copies of the RBD on each particle. Scaffolding strongly augmented the immune response with production of neutralizing antibodies and T cell response including cytotoxic lymphocytes in mice upon immunization with DNA plasmids. The most potent response was observed for the 24-residue β-annulus peptide scaffold that forms large soluble assemblies, that has the advantage of low immunogenicity in comparison to larger scaffolds. Our results support the advancement of this vaccine platform towards clinical trials.
Resolvin D1 and D2 reduce SARS-Cov-2-induced inflammation in cystic fibrosis macrophages
Authors: Recchiuti Antonio , Patruno Sara , Mattoscio Domenico , Isopi Elisa , Pomilio Antonella , Lamolinara Alessia , Iezzi Manuela , Pecce Romina , Romano Mario
Published: August 2020

Resolvins (Rv) are endogenous lipid autacoids that mediate resolution of inflammation and bacterial infections. Their roles in SARS-CoV-2 and COVID-19 are of considerable interest in the context of cystic fibrosis (CF) given the paucity of data regarding the effect of this virus on immune cells from individuals with CF. Here, we provide evidence for Rv biosynthesis and regulatory actions on CF macrophage inflammatory responses.
MCART1 is required for mitochondrial NAD transport
Authors: Kory Nora , uit de Bos Jelmi , van der Rijt Sanne , Jankovic Nevena , Güra Miriam , Arp Nicholas , Pena Izabella A. , Prakash Gyan , Chan Sze Ham , Kunchok Tenzin , Lewis Caroline A. , Sabatini David M.
Published: August 2020

The nicotinamide adenine dinucleotide (NAD+/NADH) pair is a cofactor in redox reactions and is particularly critical in mitochondria as it connects substrate oxidation by the tricarboxylic acid (TCA) cycle to ATP generation by the electron transport chain (ETC) and oxidative phosphorylation. While a mitochondrial NAD+transporter has been identified in yeast, how NAD enters mitochondria in higher eukaryotes is unknown. Here, we mine gene essentiality data from human cell lines to identifyMCART1(SLC25A51) as co-essential with ETC components.MCART1-null cells have large decreases in TCA cycle flux, mitochondrial respiration, ETC complex I activity, and mitochondrial levels of NAD+and NADH. Isolated mitochondria from cells lacking or overexpressingMCART1have greatly decreased or increased NAD uptake in vitro, respectively. Moreover,MCART1andNDT1, a yeast mitochondrial NAD+transporter, can functionally complement for each other. Thus, we propose that MCART1 is the long sought mitochondrial transporter for NAD in human cells.
Breadth and function of antibody response to acute SARS-CoV-2 infection in humans
Authors: Huang Kuan-Ying A. , Tan Tiong Kit , Chen Ting-Hua , Huang Chung-Guei , Harvey Ruth , Hussain Saira , Chen Cheng-Pin , Harding Adam , Gilbert-Jaramillo Javier , Liu Xu , Knight Michael , Schimanski Lisa , Shih Shin-Ru , Lin Yi-Chun , Cheng Chien-Yu , Cheng Shu-Hsing , Huang Yhu-Chering , Lin Tzou-Yien , Jan Jia-Tsrong , Ma Che , James William , Daniels Rodney S. , McCauley John W. , Rijal Pramila , Townsend Alain R.
Published: August 2020

Serological and plasmablast responses and plasmablast-derived IgG monoclonal antibodies (MAbs) have been analysed in three COVID-19 patients with different clinical severities. Potent humoral responses were detected within 3 weeks of onset of illness in all patients and the serological titre was elicited soon after or concomitantly with peripheral plasmablast response. An average of 13.7% and 13.0% of plasmablast-derived MAbs were reactive with virus spike glycoprotein or nucleocapsid, respectively. A subset of anti-spike (10 of 32) and over half of anti-nucleocapsid (19 of 35) antibodies cross-reacted with other betacoronaviruses tested and harboured extensive somatic mutations, indicative of an expansion of memory B cells upon SARS-CoV-2 infection. Fourteen of 32 anti-spike MAbs, including five anti-RBD, three anti-non-RBD S1 and six anti-S2, neutralised wild-type SARS-CoV-2 in independent assays. Anti-RBD MAbs were further grouped into four cross-inhibiting clusters, of which six antibodies from three separate clusters blocked the binding of RBD to ACE2 and five were neutralising. All ACE2-blocking anti-RBD antibodies were isolated from two patients with prolonged fever, which is compatible with substantial ACE2-blocking response in their sera. At last, the identification of non-competing pairs of neutralising antibodies would offer potential templates for the development of prophylactic and therapeutic agents against SARS-CoV-2.
A PCR amplicon–based SARS-CoV-2 replicon for antiviral screening
Authors: Kotaki Tomohiro , Xie Xuping , Shi Pei-Yong , Kameoka Masanori
Published: August 2020

The development of specific antiviral compounds to SARS-CoV-2 is an urgent task. One of the obstacles for the antiviral development is the requirement of biocontainment because infectious SARS-CoV-2 must be handled in a biosafety level-3 laboratory. Replicon, a non-infectious self-replicative viral RNA, could be a safe and effective tool for antiviral screening; however, SARS-CoV-2 replicon has not been reported yet. Herein, we generated a PCR-based SARS-CoV-2 replicon. Eight fragments covering the entire SARS-CoV-2 genome except S, E, and M genes were amplified with HiBiT-tag sequence by PCR. The amplicons were ligated andin vitrotranscribed to RNA. The cells electroporated with the replicon RNA showed more than 3,000 times higher luminescence than MOCK control cells at 24 hours post-electroporation, indicating robust viral translation and RNA replication. The replication was drastically inhibited by remdesivir, an RNA polymerase inhibitor for SARS-CoV-2. The IC50of remdesivir in this study was 0.29 μM, generally consistent to the IC50obtained using infectious SARS-CoV-2 in a previous study (0.77 μM). Taken together, this system could be applied to the safe and effective antiviral screening without using infectious SARS-CoV-2. Because this is a transient replicon, further improvement including the establishment of stable cell line must be achieved.
A SARS-CoV-2 BioID-based virus-host membrane protein interactome and virus peptide compendium: new proteomics resources for COVID-19 research
Authors: St-Germain Jonathan R. , Astori Audrey , Samavarchi-Tehrani Payman , Abdouni Hala , Macwan Vinitha , Kim Dae-Kyum , Knapp Jennifer J. , Roth Frederick P. , Gingras Anne-Claude , Raught Brian
Published: August 2020

Key steps of viral replication take place at host cell membranes, but the detection of membrane-associated protein-protein interactions using standard affinity-based approaches (e.g. immunoprecipitation coupled with mass spectrometry, IP-MS) is challenging. To learn more about SARS-CoV-2 - host protein interactions that take place at membranes, we utilized a complementary technique, proximity-dependent biotin labeling (BioID). This approach uncovered a virus-host topology network comprising 3566 proximity interactions amongst 1010 host proteins, highlighting extensive virus protein crosstalk with: (i) host protein folding and modification machinery; (ii) membrane-bound vesicles and organelles, and; (iii) lipid trafficking pathways and ER-organelle membrane contact sites. The design and implementation of sensitive mass spectrometric approaches for the analysis of complex biological samples is also important for both clinical and basic research proteomics focused on the study of COVID-19. To this end, we conducted a mass spectrometry-based characterization of the SARS-CoV-2 virion and infected cell lysates, identifying 189 unique high-confidence virus tryptic peptides derived from 17 different virus proteins, to create a high quality resource for use in targeted proteomics approaches. Together, these datasets comprise a valuable resource for MS-based SARS-CoV-2 research, and identify novel virus-host protein interactions that could be targeted in COVID-19 therapeutics.
Prunella vulgarisextract and suramin block SARS-coronavirus2virus Spike protein D614 and G614 variants mediated receptor association and virus entry in cell culture system
Authors: Ao Zhujun , Chan Mable , Ouyang Maggie Jing , Abiola Olukitibi Titus , Mahmoudi Mona , Kobasa Darwyn , Yao Xiaojian
Published: August 2020

Until now, no approved effective vaccine and antiviral therapeutic are available for treatment or prevention of SARS-coronavirus 2 (SCoV-2) virus infection. In this study, we established a SCoV-2 Spike glycoprotein (SP), including a SP mutant D614G, pseudotyped HIV-1-based vector system and tested their ability to infect ACE2-expressing cells. This study revealed that a C-terminal 17 amino acid deletion in SCoV-2 SP significantly increases the incorporation of SP into the pseudotyped viruses and enhanced its infectivity, which may be helpful in the design of SCoV2-SP-based vaccine strategies. Moreover, based on this system, we have demonstrated that an aqueous extract from the Chinese herbPrunella vulgaris(CHPV) and a compound, suramin, displayed potent inhibitory effects on both wild type and mutant (G614) SCoV-2 SP pseudotyped virus (SCoV-2-SP-PVs)-mediated infection. The 50% inhibitory concentration (IC50) for CHPV and suramin on SCoV-2-SP-PVs are 30, and 40 μg/ml, respectively. To define the mechanisms of their actions, we demonstrated that both CHPV and suramin are able to directly interrupt SCoV-2–SP binding to its receptor ACE2 and block the viral entry step. Importantly, our results also showed that CHPV or suramin can efficiently reduce levels of cytopathic effect caused by SARS-CoV-2 virus (hCoV-19/Canada/ON-VIDO-01/2020) infection in Vero cells. Furthermore, our results demonstrated that the combination of CHPV/suramin with an anti-SARS-CoV-2 neutralizing antibody mediated more potent blocking effect against SCoV2-SP-PVs. Overall, this study provides evidence that CHPV and suramin has anti-SARS-CoV-2 activity and may be developed as a novel antiviral approach against SARS-CoV-2 infection.
SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generatedin vitroduring propagation in TMPRSS2-deficient cells
Authors: Sasaki Michihito , Uemura Kentaro , Sato Akihiko , Toba Shinsuke , Sanaki Takao , Maenaka Katsumi , Hall William W. , Orba Yasuko , Sawa Hirofumi
Published: August 2020

The spike (S) protein of Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) binds to a host cell receptor which facilitates viral entry. A polybasic motif detected at the cleavage site of the S protein has been shown to broaden the cell tropism and transmissibility of the virus. Here we examine the properties of SARS-CoV-2 variants with mutations at the S protein cleavage site that undergo inefficient proteolytic cleavage. Virus variants with S gene mutations generated smaller plaques and exhibited a more limited range of cell tropism compared to the wild-type strain. These alterations were shown to result from their inability to utilize the entry pathway involving direct fusion mediated by the host type II transmembrane serine protease, TMPRSS2. Notably, viruses with S gene mutations emerged rapidly and became the dominant SARS-CoV-2 variants in TMPRSS2-deficient cells including Vero cells. Our study demonstrated that the S protein polybasic cleavage motif is a critical factor underlying SARS-CoV-2 entry and cell tropism. As such, researchers should be alert to the possibility ofde novoS gene mutations emerging in tissue-culture propagated virus strains.
Differential adhesion regulates neurite placement via a retrograde zippering mechanism
Authors: Sengupta Titas , Koonce Noelle L. , Moyle Mark W. , Duncan Leighton H. , Vázquez-Martínez Nabor , Emerson Sarah E. , Han Xiaofei , Shao Lin , Wu Yicong , Santella Anthony , Fan Li , Bao Zhirong , Mohler William A. , Shroff Hari , Colón-Ramos Daniel A.
Published: August 2020

During development, neurites and synapses segregate into specific neighborhoods or layers within nerve bundles. The developmental programs guiding placement of neurites in specific layers, and hence their incorporation into specific circuits, are not well understood. We implement novel imaging methods and quantitative models to document the embryonic development of theC. elegansbrain neuropil, and discover that differential adhesion mechanisms control precise placement of single neurites onto specific layers. Differential adhesion is orchestrated via developmentally-regulated expression of the IgCAM SYG-1, and its partner ligand SYG-2. Changes in SYG-1 expression across neuropil layers result in changes in adhesive forces, which sort SYG-2-expressing neurons. Sorting to layers occurs, not via outgrowth from the neurite tip, but via an alternate mechanism of retrograde zippering, involving interactions between neurite shafts. Our study indicates that biophysical principles from differential adhesion govern neurite placement and synaptic specificityin vivoin developing neuropil bundles.
Exploring the distribution of statistical feature parameters for natural sound textures
Authors: Mishra Ambika P. , Harper Nicol S. , Schnupp Jan W.H.
Published: August 2020

Sounds like “running water” and “buzzing bees” are classes of sounds which are a collective result of many similar acoustic events and are known as “sound textures”. Recent psychoacoustic study using sound textures by [1] reported that natural sounding textures can be synthesized from white noise by imposing statistical features such as marginals and correlations computed from the outputs of cochlear models responding to the textures. The outputs being the envelopes of bandpass filter responses, the ‘cochlear envelope’. This suggests that the perceptual qualities of many natural sounds derive directly from such statistical features, and raises the question of how these statistical features are distributed in the acoustic environment. To address this question, we collected a corpus of 200 sound textures from public online sources and analyzed the distributions of the textures’ marginal statistics (mean, variance, skew, and kurtosis), cross-frequency correlations and modulation power statistics. A principal component analysis of these parameters revealed a great deal of redundancy in the texture parameters. For example, just two marginal principal components, which can be thought of as measuring the sparseness or burstiness of a texture, capture as much as 66% of the variance of the 128 dimensional marginal parameter space, while the first two principal components of cochlear correlations capture as much as 90% of the variance in over 1000 correlation parameters. Knowledge of the statistical distributions documented here may help guide the choice of acoustic stimuli with high ecological validity in future research.
miRNA-mediated loss of m6A increases nascent translation in glioblastoma
Authors: Zepecki John P. , Karambizi David , Fajardo J. Eduardo , Snyder Kristin M. , Guetta-Terrier Charlotte , Tang Oliver Y. , Chen Jia-Shu , Sarkar Atom , Fiser Andras , Toms Steven A. , Tapinos Nikos
Published: August 2020

Within the glioblastoma cellular niche, glioma stem cells (GSCs) can give rise to differentiated glioma cells (DGCs) and, when necessary, DGCs can reciprocally give rise to GSCs to maintain the cellular equilibrium necessary for optimal tumor growth. Here, using ribosome profiling, transcriptome and m6A RNA sequencing, we show that GSCs from patients with different subtypes of glioblastoma share a set of transcripts, which exhibit a pattern of m6A loss and increased protein translation during differentiation. The target sequences of a group of miRNAs overlap the canonical RRACH m6A motifs of these transcripts, many of which confer a survival advantage in glioblastoma. Ectopic expression of the RRACH-binding miR-145 induces loss of m6A, formation of FTO/AGO1/ILF3/miR-145 complexes on a clinically relevant tumor suppressor gene (CLIP3) and significant increase in its nascent translation. Inhibition of miR-145 maintains RRACH m6A levels of CLIP3 and inhibits its nascent translation. This study highlights a critical role of miRNAs in assembling complexes for m6A demethylation and induction of protein translation during GSC state transition.

Author Summary

Cellular plasticity and epigenetic adaptation of human glioblastoma stem cells to the tumor microenvironment is a hallmark of this devastating disease. With our present work, we discover the relationship between miRNAs and the RNA methylation machinery in human glioblastoma and show how miRNA-induced loss of m6A results in increase in protein translation of clinically important transcripts during glioblastoma stem cell differentiation. Leveraging the dynamic functions of these miRNAs can be important in the design of optimal therapeutics targeted at cancer cell plasticity.
Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase
Authors: Teixeira Raphael D. , Holzschuh Fabian , Schirmer Tilman
Published: August 2020

Diguanylate cyclases (DGCs) synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR fromLeptospira biflexais a constitutively dimeric prototype of this class of DGCs. Full-length crystal structures revealed that BeF3-pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coilviaa localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many DGCs with N-terminal coiled-coil linkers.
Myomixer is expressed during embryonic and post-larval hyperplasia, muscle regeneration and fusion of myoblats in rainbow trout (Oncorhynchus mykiss)
Authors: Perello-Amoros Miquel , Rallière Cécile , Gutiérrez Joaquim , Gabillard Jean-Charles
Published: August 2020

1.

In contrast to mice or zebrafish, trout exhibits post-larval muscle growth through hypertrophy and formation of new myofibers (hyperplasia). The muscle fibers are formed by the fusion of mononucleated cells (myoblasts) regulated by several muscle-specific proteins such as myomaker or myomixer. In this work, we identified a unique gene encoding a myomixer protein of 77 amino acids (aa) in the trout genome. Sequence analysis and phylogenetic tree, showed moderate conservation of the overall protein sequence across teleost fish (61% of aa identity between trout and zebrafish myomixer sequences). Nevertheless, the functionally essential motif, AxLyCxL is perfectly conserved in all studied sequences of vertebrates. Usingin situhybridization, we observed that myomixer was highly expressed in the embryonic myotome, particularly in the hyperplasic area. Moreover, myomixer remained readily expressed in white muscle of juvenile (1 and 20 g) although its expression decreased in mature fish. We also showed that myomixer is up-regulated during muscle regeneration andin vitromyoblasts fusion. Together, these data indicate that myomixer expression is consistently associated with the formation of new myofibers during somitogenesis, post-larval growth and muscle regeneration in trout.
SynapsEM: computer-assisted synapse morphometry
Authors: Watanabe Shigeki , Davis M Wayne , Kusick Grant F , Iwasa Janet , Jorgensen Erik M
Published: August 2020

The structural features of a synapse, in part, determine its output. Synapses are extremely small and tightly packed with vesicles and other organelles. Visualizing synaptic structure requires imaging by electron microscopy, and the features in micrographs must be quantified using morphometry. Three parameters are typically assessed from each specimen: 1) the sizes of individual vesicles and organelles, 2) the absolute number and densities of organelles, and 3) distances between organelles and key features at synapses such as active zone membranes and dense projections. For data to be valid, the analysis must be repeated from hundreds or thousands of images from several biological replicates, a daunting task. Here we report a custom computer program to analyze these features: SynapsEM. In short, we developed macros for ImageJ/Fiji to record x,y-coordinates of segmented structures; the coordinates are then exported as text files. Independent investigators can reload the images and text files to confirm or re-evaluate the segmentation using ImageJ. The Matlab program calculates and reports key synaptic parameters from the coordinates. Since the values are calculated, rather than measured from each micrograph, other parameters can be extracted in Matlab by additional scripting. Thus, this program can accelerate morphometry of synapses and promote a more comprehensive analysis of synaptic ultrastructure.
Long-read sequencing resolves structural variants inSERPINC1causing antithrombin deficiency and identifies a complex rearrangement and a retrotransposon insertion not characterized by routine diagnostic methods
Authors: de la Morena-Barrio Belén , Stephens Jonathan , de la Morena-Barrio María Eugenia , Stefanucci Luca , Padilla José , Miñano Antonia , Gleadall Nicholas , García Juan Luis , López-Fernández María Fernanda , Morange Pierre-Emmanuel , Puurunen Marja K , Undas Anetta , Vidal Francisco ,   NIHR BioResource, Raymond F Lucy , García Vicente Vicente , Ouwehand Willem H , Corral Javier , Sanchis-Juan Alba
Published: August 2020

The identification and characterization of structural variants (SVs) in clinical genetics have remained historically challenging as routine genetic diagnostic techniques have limited ability to evaluate repetitive regions and SVs. Long-read whole-genome sequencing (LR-WGS) has emerged as a powerful approach to resolve SVs. Here, we used LR-WGS to study 19 unrelated cases with type I Antithrombin Deficiency (ATD), the most severe thrombophilia, where routine molecular tests were either negative, ambiguous, or not fully characterized. We developed an analysis workflow to identify disease-associated SVs and resolved 10 cases. For the first time, we identified a germline complex rearrangement involved in ATD previously misclassified as a deletion. Additionally, we provided molecular diagnoses for two unresolved individuals that harbored a novel SINE-VNTR-Alu retroelement insertion that we fully characterized byde novoassembly and confirmed by PCR amplification in all affected relatives. Finally, the nucleotide-level resolution achieved for all the SVs allowed breakpoint analysis, which revealed a replication-based mechanism for most of the cases. Our study underscores the utility of LR-WGS as a complementary diagnostic method to identify, characterize, and unveil the molecular mechanism of formation of disease-causing SVs, and facilitates decision making about long-term thromboprophylaxis in ATD patients.
Neoplastic and immune single cell transcriptomics define subgroup-specific intra-tumoral heterogeneity of childhood medulloblastoma
Authors: Riemondy Kent A. , Venkataraman Sujatha , Willard Nicholas , Nellan Anandani , Sanford Bridget , Griesinger Andrea M. , Amani Vladimir , Mitra Siddhartha , Hankinson Todd C. , Handler Michael H. , Sill Martin , Ocasio Jennifer , Weir Seth J. , Malawsky Daniel S , Gershon Timothy R. , Garancher Alexandra , Wechsler-Reya Robert J. , Hesselberth Jay R. , Foreman Nicholas K. , Donson Andrew M. , Vibhakar Rajeev
Published: August 2020

Medulloblastoma (MB) is a heterogeneous disease in which neoplastic cells and associated immune cells contribute to disease progression. To better understand cellular heterogeneity in MB we use single-cell RNA sequencing, immunohistochemistry and deconvolution of transcriptomic data to profile neoplastic and immune populations in childhood MB samples. Neoplastic cells cluster primarily according to individual sample of origin which is in part due to the effect of chromosomal copy number gains and losses. Harmony alignment reveals novel MB subgroup/subtype-associated subpopulations that recapitulate neurodevelopmental processes and are associated with clinical outcomes, including discrete photoreceptor-like cells in MB subgroups GP3 and GP4 and nodule-associated neuronally-differentiated cells in subgroup SHH. We definitively chart the spectrum of MB immune cell infiltrates, which include subgroup/subtype-associated developmentally-related neuron-pruning and antigen presenting myeloid cells. MB cellular diversity is recapitulated in genetically engineered mouse subgroup-specific models of MB. These findings provide a clearer understanding of both the neoplastic and immune cell heterogeneity in MB.
Quantifying the dynamics of viral recombination during free virus and cell-to-cell transmission in HIV-1 infection
Authors: Kreger Jesse , Garcia Josephine , Zhang Hongtao , Komarova Natalia L. , Wodarz Dominik , Levy David N.
Published: August 2020

Recombination has been shown to contribute to HIV-1 evolutionin vivo, but the underlying dynamics are extremely complex, depending on the nature of the fitness landscapes and of epistatic interactions. A less well-studied determinant of recombinant evolution is the mode of virus transmission in the cell population. HIV-1 can spread by free virus transmission, resulting largely in singly infected cells, and also by direct cell-to-cell transmission, resulting in the simultaneous infection of cells with multiple viruses. We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models toin vitroexperimental data on the growth of fluorescent reporter viruses under static conditions (where both transmission pathways operate), and under gentle shaking conditions, where cell-to-cell transmission is largely inhibited. The parameterized mathematical models are then used to extrapolate the viral evolutionary dynamics beyond the experimental settings. Assuming a fixed basic reproductive ratio of the virus (independent of transmission pathway), we find that recombinant evolution is fastest if virus spread is driven only by cell-to-cell transmission, and slows down if both transmission pathways operate. Recombinant evolution is slowest if all virus spread occurs through free virus transmission. This is due to cell-to-cell transmission (i) increasing infection multiplicity, (ii) promoting the co-transmission of different virus strains from cell to cell, and (iii) increasing the rate at which point mutations are generated as a result of more reverse transcription events. This work further resulted in the estimation of various parameters that characterize these evolutionary processes. For example, we estimate that during cell-to-cell transmission, an average of 3 viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to free virus transmission. In general, our study points towards the importance of infection multiplicity and cell-to-cell transmission for HIV-evolution.
A role of territory formation in disruption of heterologous pairings inDrosophilamale meiosis
Authors: Hylton Christopher A. , Dean John E. Tomkiel
Published: August 2020

Pairings between heterologous chromosomes in meiosis can lead to nondisjunction and the production of aneuploid gametes. To minimize these aberrant outcomes, organisms have evolved mechanisms to disrupt such improper pairings prior to orientation and segregation. In the male fruit fly,Drosophila melanogaster, bivalents segregate to distinct nuclear domains in prophase I, and it has been proposed that the formation of these distinct territories may play a role in disrupting interactions between limited homologies on heterologous chromosomes. To test this, we used fluorescent in situ hybridization to examine pairing between the X chromosome andDp(1;3)chromosomes in which a segment of the X had been transposed to chromosome 3. We found that 120kb of homology was sufficient to insure nearly complete pairing but was not sufficient to direct merotelic segregation of the paired elements, suggesting that such pairings were being disrupted. We compared the perdurance of X /Dp(1;3)pairings to that of X /Dp(1;Y)pairings (in which homologs are paired),and found that heterologous pairings were disrupted at a higher frequency at the S2b stage of prophase I, the stage at which territory formation is initiated. Our results support the model that movement of bivalents into distinct domains in prophase I provides a mechanism to disrupt pairings between limited regions of homology, and thus may be one means of preventing improper segregation of heterologs in this organism.
Comprehensive synthetic genetic array analysis of alleles that interact with mutation of theSaccharomyces cerevisiaeRecQ helicases Hrq1 and Sgs1
Authors: Sanders Elsbeth , Nguyen Phoebe A. , Rogers Cody M. , Bochman Matthew L.
Published: August 2020

Most eukaryotic genomes encode multiple RecQ family helicases, including five such enzymes in humans. For many years, the yeastSaccharomyces cerevisiaewas considered unusual in that it only contained a single RecQ helicase, named Sgs1. However, it has recently been discovered that a second RecQ helicase, called Hrq1, resides in yeast. Both Hrq1 and Sgs1 are involved in genome integrity, functioning in processes such as DNA inter-strand crosslink repair, double-strand break repair, and telomere maintenance. However, it is unknown if these enzymes interact at a genetic, physical, or functional level as demonstrated for their human homologs. Thus, we performed synthetic genetic array (SGA) analyses ofhrq1Δandsgs1Δmutants. As inactive alleles of helicases can demonstrate dominant phenotypes, we also performed SGA analyses on thehrq1-K318Aandsgs1-K706AATPase/helicase-null mutants, as well as all combinations of deletion and inactive double mutants. We crossed these eight query strains (hrq1Δ, sgs1Δ, hrq1-K318A, sgs1-K706A, hrq1Δ sgs1Δ, hrq1Δ sgs1-K706A, hrq1-K318A sgs1Δ, andhrq1-K318A sgsl-K706A) to theS. cerevisiaesingle gene deletion and temperature-sensitive allele collections to generate double and triple mutants and scored them for synthetic positive and negative genetic effects based on colony growth. These screens identified hundreds of synthetic interactions, supporting the known roles of Hrq1 and Sgs1 in DNA repair, as well as suggesting novel connections to rRNA processing, mitochondrial DNA maintenance, transcription, and lagging strand synthesis during DNA replication.