bluuebunny/crossref_metadata_2025 huggingface dataset:
scvi-tools: a library for deep probabilistic analysis of single-cell omics data
Authors: Gayoso Adam , Lopez Romain , Xing Galen , Boyeau Pierre , Wu Katherine , Jayasuriya Michael , Melhman Edouard , Langevin Maxime , Liu Yining , Samaran Jules , Misrachi Gabriel , Nazaret Achille , Clivio Oscar , Xu Chenling , Ashuach Tal , Lotfollahi Mohammad , Svensson Valentine , Beltrame Eduardo da Veiga , Talavera-López Carlos , Pachter Lior , Theis Fabian J. , Streets Aaron , Jordan Michael I. , Regier Jeffrey , Yosef Nir
Published: April 2021

Abstract

Probabilistic models have provided the underpinnings for state-of-the-art performance in many single-cell omics data analysis tasks, including dimensionality reduction, clustering, differential expression, annotation, removal of unwanted variation, and integration across modalities. Many of the models being deployed are amenable to scalable stochastic inference techniques, and accordingly they are able to process single-cell datasets of realistic and growing sizes. However, the community-wide adoption of probabilistic approaches is hindered by a fractured software ecosystem resulting in an array of packages with distinct, and often complex interfaces. To address this issue, we developed scvi-tools (https://scvi-tools.org), a Python package that implements a variety of leading probabilistic methods. These methods, which cover many fundamental analysis tasks, are accessible through a standardized, easy-to-use interface with direct links to Scanpy, Seurat, and Bioconductor workflows. By standardizing the implementations, we were able to develop and reuse novel functionalities across different models, such as support for complex study designs through nonlinear removal of unwanted variation due to multiple covariates and reference-query integration via scArches. The extensible software building blocks that underlie scvi-tools also enable a developer environment in which new probabilistic models for single cell omics can be efficiently developed, benchmarked, and deployed. We demonstrate this through a code-efficient reimplementation of Stereoscope for deconvolution of spatial transcriptomics profiles. By catering to both the end user and developer audiences, we expect scvi-tools to become an essential software dependency and serve to formulate a community standard for probabilistic modeling of single cell omics.
Temporal single-cell transcriptomes of zebrafish spinal cord pMN progenitors reveal distinct neuronal and glial progenitor populations
Authors: Scott Kayt , O’Rourke Rebecca , Winkler Caitlin C. , Kearns Christina A. , Appel Bruce
Published: April 2021

Ventral spinal cord progenitor cells, which express the basic helix loop helix transcription factor Olig2, sequentially produce motor neurons and oligodendrocyte precursor cells (OPCs). Following specification some OPCs differentiate as myelinating oligodendrocytes while others persist as OPCs. Though a considerable amount of work has described the molecular profiles that define motor neurons, OPCs, and oligodendrocytes, less is known about the progenitors that produce them. To identify the developmental origins and transcriptional profiles of motor neurons and OPCs, we performed single-cell RNA sequencing on isolated pMN cells from embryonic zebrafish trunk tissue at stages that encompassed motor neurogenesis, OPC specification, and initiation of oligodendrocyte differentiation. Downstream analyses revealed two distinct pMN progenitor populations: one that appears to produce neurons and one that appears to produce OPCs. This latter population, called Pre-OPCs, is marked by expression ofGS Homeobox 2(gsx2), a gene that encodes a homeobox transcription factor. Using fluorescent in situ hybridizations, we identifiedgsx2-expressing Pre-OPCs in the spinal cord prior to expression of canonical OPC marker genes. Our data therefore reveal heterogeneous gene expression profiles among pMN progenitors, supporting prior fate mapping evidence.

Highlights

Single-cell RNA sequencing reveals the developmental trajectories of neurons and glia that arise from spinal cord pMN progenitor cells in zebrafish embryos

Transcriptionally distinct subpopulations of pMN progenitors are the apparent sources of neurons or oligodendrocytes, consistent with fate mapping data

gsx2expression marks pMN progenitors that produce oligodendrocyte lineage cells
Chromatin-interacting transposon RNAs linking to the core trans-inhibition circuitry for embryonic stem cell identity
Authors: Xu Wenqiu , Ren Likun , Zheng Caihong , Cai Jun
Published: April 2021

Transposable DNA sequences constitute more than half of the human and mouse genomes. A large number of non-coding RNAs, named as transposon RNAs, are derived from these transposable elements. The cis-regulatory function of transposable DNA elements, such as LINE-1 and Alu has been largely explored. But the biological roles of transposon RNAs aren’t well understood. Here, investigations of RNA-chromatin interactions provide us with comprehensive evidence that specific families of transposon RNAs play roles in trans-regulation linking to the core inhibition circuitry for embryonic stem cell identity. Alternative modes of the RNA-DNA hybrid duplex and protein-recruited RNA scaffold are required for the regulatory activities of transposon RNAs. LINE-1 RNAs co-locating with KAP1 form a negative feedback loop stabilizing the transcription of LINE-1 DNA elements via RNA-DNA hybrids. In another way LINE-1 RNAs, together with the reprogramming three factors and Polycomb repressive complexes, participate in the inhibition on dozens of differentiation-relative genes.
A snapshot of a pandemic: the interplay between social isolation and COVID-19 dynamics in Brazil
Authors: P. Ferreira Cláudia , Marcondes Diego , Melo Mariana P. , Oliva Sérgio M. , M. Peixoto Cláudia , Peixoto Pedro S.
Published: April 2021

In response to the COVID-19 pandemic, most governments around the world implemented some kind of social distancing policy in an attempt to block the spreading of the virus within a territory. In Brazil, this mitigation strategy was first implemented in March 2020 and mainly monitored by social isolation indicators built from mobile geolocation data. While it is well known that social isolation has been playing a crucial role in epidemic control, the precise connections between mobility data indicators and epidemic dynamic parameters have a complex interdependence. In this work, we investigate this dependence for several Brazilian cities, looking also at socioeconomic and demographic factors that influence it. As expected, the increase in the social isolation indicator was shown to be related to the decrease in the speed of transmission of the disease, but the relation was shown to depend on the urban hierarchy level of the city, the human development index and also the epidemic curve stage. Moreover, a high social isolation at the beginning of the epidemic relates to a strong positive impact on flattening the epidemic curve, while less efficacy of this mitigation strategy was observed when it has been implemented later. Mobility data plays an important role in epidemiological modeling and decision-making, however, we discuss in this work how a direct relationship between social isolation data and COVID-19 data is hard to be established. Understanding this interplay is a key factor to better modeling, for which we hope this study contributes.
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Authors: Pardo Brenda , Spangler Abby , Weber Lukas M. , Hicks Stephanie C. , Jaffe Andrew E. , Martinowich Keri , Maynard Kristen R. , Collado-Torres Leonardo
Published: April 2021

Motivation

Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissuespecific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary.

Results

We describespatialLIBD, an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application.

Availability

spatialLIBDis available at bioconductor.org/packages/spatialLIBD.

Supplementary information

Supplementary data are available atBioinformaticsonline.
Tractography-based targeting of ventral intermediate nucleus: A comparison between conventional stereotactic targeting and diffusion tensor imaging-based targeting
Authors: Vijayakumari Anupa A. , Parker Drew , Yang Andrew I , Ramayya Ashwin G. , Wolf Ronald L. , Aunapu Darien , Baltuch Gordon H. , Verma Ragini
Published: April 2021

Background

The ventral intermediate (VIM) nucleus of the thalamus is the main target for lesioning using magnetic resonance imaging (MRI) guided focused ultrasound (MRgFUS) or deep brain stimulation (DBS). Targeting of VIM still depends on standard stereotactic coordinates, which do not account for inter-individual variability. Several approaches have been proposed including visualization of dentato-rubro-thalamic tract (DRTT) using diffusion tensor imaging tractography.

Objective

To compare probabilistic tracking of DRTT with deterministic tracking of DRTT and stereotactic coordinates to identify the most appropriate approach to target VIM.

Methods

In this retrospective study, we assessed the VIM targeted using stereotactic coordinates, deterministic and probabilistic tracking of DRTT in 19 patients with essential tremor who underwent DBS with VIM targeted using microelectrode recordings. We subsequently determined the positions of VIM derived from these three approaches and compared with that of DBS lead position using paired samplet-tests.

Results

The probabilistic tracking of DRTT was significantly anterior to the lead (1.45 ± 1.61 mm (P< 0.0001)), but not in the medial/lateral position (−0.29±2.42 mm (P=0.50)). Deterministic tracking of DRTT was significantly lateral (2.16 ± 1.94 mm (P< 0.0001)) and anterior to the lead (1.66 ± 2.1 mm (P< 0.0001)). The stereotactic coordinates were significantly lateral (2.41 ± 1.41 mm (P< 0.0001)) and anterior (1.23 ± 0.89 mm (P< 0.0001)) to the lead.

Conclusion

Probabilistic tracking of DRTT was found to be superior in targeting VIM compared to deterministic tracking and stereotactic coordinates.
Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure
Authors: Francis Joshua M. , Leistritz-Edwards Del , Dunn Augustine , Tarr Christina , Lehman Jesse , Dempsey Conor , Hamel Andrew , Rayon Violeta , Liu Gang , Wang Yuntong , Wille Marcos , Durkin Melissa , Hadley Kane , Sheena Aswathy , Roscoe Benjamin , Ng Mark , Rockwell Graham , Manto Margaret , Gienger Elizabeth , Nickerson Joshua ,   MGH COVID-19 Collection and Processing Team, Moarefi Amir , Noble Michael , Malia Thomas , Bardwell Philip D. , Gordon William , Swain Joanna , Skoberne Mojca , Sauer Karsten , Harris Tim , Goldrath Ananda W. , Shalek Alex K. , Coyle Anthony J. , Benoist Christophe , Pregibon Daniel C.
Published: April 2021

Effective presentation of antigens by HLA class I molecules to CD8+ T cells is required for viral elimination and generation of long-term immunological memory. In this study, we applied a single-cell, multi-omic technology to generate the first unified ex vivo characterization of the CD8+ T cell response to SARS-CoV-2 across 4 major HLA class I alleles. We found that HLA genotype conditions key features of epitope specificity, TCR α/β sequence diversity, and the utilization of pre-existing SARS-CoV-2 reactive memory T cell pools. Single-cell transcriptomics revealed functionally diverse T cell phenotypes of SARS-CoV-2-reactive T cells, associated with both disease stage and epitope specificity. Our results show that HLA variations influence pre-existing immunity to SARS-CoV-2 and shape the immune repertoire upon subsequent viral exposure.

One-Sentence Summary

We perform a unified, multi-omic characterization of the CD8+ T cell response to SARS-CoV-2, revealing pre-existing immunity conditioned by HLA genotype.
New Segmentation and Feature Extraction Algorithm for Classification of White Blood Cells in Peripheral Smear Images
Authors: Tavakoli Sajad , Ghaffari Ali , Kouzehkanan Zahra Mousavi , Hosseini Reshad
Published: April 2021

This article addresses a new method for the classification of white blood cells (WBCs) using image processing techniques and machine learning methods. The proposed method consists of three steps: detecting the nucleus and cytoplasm, extracting features, and classification. At first, a new algorithm is designed to segment the nucleus. For the cytoplasm to be detected, only a part of it located inside the convex hull of the nucleus is involved in the process. This attitude helps us overcome the difficulties of segmenting the cytoplasm. In the second phase, three shapes and four novel color features are devised and extracted. Finally, by using an SVM model, the WBCs are classified. The segmentation algorithm can detect the nucleus with a dice similarity coefficient of 0.9675. The proposed method can categorize WBCs in Raabin-WBC, LISC, and BCCD datasets with accuracies of 94.65 %, 92.21 %, and 94.20 %, respectively. It is worth mentioning that the hyperparameters of the classifier are fixed only with the Raabin-WBC dataset, and these parameters are not readjusted for LISC and BCCD datasets. The obtained results demonstrate that the proposed method is robust, fast, and accurate.
Low effective mechanical advantage of giraffes’ limbs during walking reveals trade-off between limb length and locomotor performance
Authors: Basu Christopher , Hutchinson John R.
Published: April 2021

Giraffes (Giraffa camelopardalis) possess specialised locomotor morphology, namely elongate and gracile distal limbs. Whilst this contributes to their overall height (and enhanced feeding behaviour), we propose that the combination of long limb segments and modest muscle lever arms results in low effective mechanical advantage (EMA, the ratio of in-lever to out-lever moment arms), when compared with other cursorial mammals. To test this, we used a combination of experimentally measured kinematics and ground rection forces (GRFs), musculoskeletal modelling, and inverse dynamics to calculate giraffe forelimb EMA during walking. Giraffes walk with an EMA of 0.34 (±0.05 S.D.), with no evident association with speed within their walking gait. Giraffe EMA was markedly below the expectations extrapolated from other mammals ranging from 0.03 – 297 kg, and provides further evidence that EMA plateaus or even diminishes in mammals exceeding horse size. We further tested the idea that limb segment length is a factor which determines EMA, by modelling the GRF and muscle moment arms in the extinct giraffidSivatherium giganteumand the other extant giraffidOkapia johnstoni. GiraffaandOkapiashared similar EMA, despite a 4-6 fold difference in body mass (OkapiaEMA = 0.38). In contrastSivatherium, sharing a similar body mass toGiraffa, had greater EMA (0.59), which we propose reflects behavioural differences, such athletic performance. Our modelling approach suggests that limb length is a determinant of GRF moment arm magnitude, and that unless muscle moment arms scale isometrically with limb length, tall mammals are prone to low EMA.

Significance Statement

Giraffes are the tallest living animals - using their height to access food unavailable to their competitors. It is not clear how their specialized anatomy impacts their athletic ability. We made musculoskeletal models of the forelimbs from a giraffe and two close relatives, and used motion-capture and forceplate data to measure how efficient they are when walking in a straight line. A horse for example, uses just 1 unit of muscle force to oppose 1 unit of force on the ground. Giraffe limbs however are comparatively disadvantaged – their muscles must develop 3 units of force to oppose 1 unit of force at the ground. This explains why giraffes walk and run at relatively slow speeds.
ATXN10 is required for embryonic heart development and maintenance of epithelial cell phenotypes in the adult kidney and pancreas
Authors: Bentley-Ford Melissa R. , Andersen Reagan S. , Croyle Mandy J. , Haycraft Courtney J. , Clearman Kelsey R. , Foote Jeremy B. , Reiter Jeremy F. , Yoder Bradley K.
Published: April 2021

Atxn10is a gene known for its role in cytokinesis during the cell cycle and is associated with Spinocerebellar Ataxia (SCA10), a slowly progressing cerebellar syndrome caused by an intragenic pentanucleotide repeat expansion.Atxn10is also implicated in the ciliopathy syndromes Nephronophthisis (NPHP) and Joubert Syndrome (JBTS), which are caused by disruption of cilia function leading to nephron loss, impaired renal function, and cerebellar hypoplasia. HowAtxn10disruption contributes to these disorders remains unknown. Here we generatedAtxn10congenital and conditional mutant mouse models. Our data indicate that while ATXN10 protein can be detected around the base of the cilium as well as in the cytosol, its loss does not cause overt changes in cilia formation or morphology. Congenital loss ofAtxn10results in embryonic lethality around E10.5 associated with pericardial effusion and loss of trabeculation. Similarly, tissue specific loss of ATXN10 in the developing endothelium (Tie2-Cre) and myocardium (cTnT-Cre) also results in embryonic lethality with severe cardiac malformations occurring in the latter. Using an inducible Cagg-CreER to disrupt Atxn10 systemically, we show that ATXN10 is also required for survival in adult mice. Loss of ATXN10 results in severe pancreatic and renal abnormalities leading to lethality within a few weeks post ATXN10 deletion in adult mice. Evaluation of these phenotypes further identified rapid epithelial to mesenchymal transition (EMT) in these tissues. In the pancreas, the phenotype includes signs of both acinar to ductal metaplasia and EMT with aberrant cilia formation and severe defects in glucose homeostasis related to pancreatic insufficiency or defects in feeding or nutrient intake. Collectively this study identifies ATXN10 as an essential protein for survival.
Nuclei are mobile processors enabling specialization in a gigantic single-celled syncytium
Authors: Gerber Tobias , Loureiro Cristina , Schramma Nico , Chen Siyu , Jain Akanksha , Weber Anne , Weigert Anne , Santel Malgorzata , Alim Karen , Treutlein Barbara , Camp J. Gray
Published: April 2021

In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. Here we performed spatial transcriptome analysis of the slime moldPhysarum polycephalumin the plasmodium state under different environmental conditions, and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile, and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleated cells, we analyzed states in singlePhysarumamoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization, and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.
Actin-based myosin XXI (13) molecular motor is involved in early phase ofLeishmaniacytokinesis
Authors: Bajaj Rani , Gupta Chhitar M.
Published: April 2021

Leishmaniagenome encodes for two isoforms of myosin, but only Myosin XXI (Myo21), which is a novel form of myosin in that it contains two ubiquitin associated-like (UBA) domains towards the end of its tail structure, is expressed in both the promastigote and amastigote forms of this protozoan. Earlier studies have shown that inLeishmaniapromastigotes Myo21 besides localizing throughout the cell body and flagellum, it is prominently localized to the base of the flagellum. It has further been shown that this protein in the promastigotes plays an important role in regulating the cell morphology, motility, flagellum dynamics, growth and intracellular trafficking, As Myo21 depletion has been shown to result in reduced cell growth in culture, we considered it of interest to investigate whether the observed effect of Myo21 on the cell growth is mediated through its possible role inLeishmaniacell division cycle. For this, we prepared heterozygous Myo21 mutants ofLeishmaniapromastigotes (Myo21+/−cells) and then analyzed their morphology, growth and cell division cycle, using wild typeLeishmaniapromastigotes (Myo21+/+cells) as control. The cell division cycle was analyzed by employing flow cytometry and immunofluorescence microscopy. Flow cytometric analysis revealed that the G2/M to G1 phase transition in Myo21+/−cell is significantly delayed, as compared to Myo21+/+cells. Immunofluorescence confocal microscopic analysis indicated that Myo21+/−cells encountered a significant delay in initiation of cytokinesis, which was mainly due to delay in the flagellar pocket division. Further analysis revealed that actin-based Myo21 motor is essentially required in the initiation phase ofLeishmaniacytokinesis.
Blood vessels regulate primary motor neuronal pathfinding in zebrafish via exosome contained microRNA-22
Authors: Sheng Jiajing , Gong Jie , Shi Yunwei , Wang Xin , Liu Dong
Published: April 2021

A precise neuro-vascular communication is crucial to orchestrate directional migration and patterning of the complex vascular network and neural system. However, how blood vessels are involved in shaping the proper neuronal formation has not been fully understood. So far, limited studies have reported the discovery and functions of microRNAs (miRNAs) in guiding vascular and neural pathfinding. Currently, we showed that the deficiency of miRNA-22a, an endothelial-enriched miRNA, caused dramatic pathfinding defects both in intersegmental vessels (ISVs) and primary motor neurons (PMNs) in zebrafish embryos. Furthermore, we found the specific inhibition of miR-22a in ECs resulted in the patterning defects of both ISVs and PMNs. However, neuronal block of miR-22a mainly led to the axonal defects of PMN. Then we demonstrated that endothelial miR-22a regulates PMNs axonal navigation via exosome pathway. Sema4c was identified as a potential target of miR-22a through transcriptomic analysis andin silicoanalysis. Furthermore, luciferase assay and EGFP sensor assayin vivoconfirmed the binding of miR-22a with 3’-UTR ofsema4c. In addition, Down-regulation ofsema4cin the miR-22a morphants significantly neutralized the aberrant patterning of vascular and neural networks. Our study revealed that miR-22a acted as a dual guidance cue coordinating vascular and neuronal patterning and expanded the repertoire of guidance molecules, which might be of use therapeutically to guide vessels and nerves in the relevant diseases that affect both systems.
Cluster Size Distribution of Cells Disseminating from a Primary Tumor
Authors: Mukherjee Mrinmoy , Levine Herbert
Published: April 2021

The first stage of the metastatic cascade often involves motile cells emerging from a primary tumor either as single cells or as clusters. These cells enter the circulation, transit to other parts of the body and finally are responsible for growth of secondary tumors in distant organs. The mode of dissemination is believed to depend on the EMT nature (epithelial, hybrid or mesenchymal) of the cells. Here, we calculate the cluster size distribution of these migrating cells, using a mechanistic computational model, in presence of different degree of EMT-ness of the cells; EMT is treated as given rise to changes in their active motile forces (μ) and cell-medium surface tension (Γ). We find that, for (μ > μmin, Γ > 1), when the cells are hybrid in nature, the mean cluster size,, whereμminincreases with increase in Γ. For Γ ≤ 0,, the cells behave as completely mesenchymal. In presence of spectrum of hybrid states with different degree of EMT-ness (motility) in primary tumor, the cells which are relatively more mesenchymal (higherμ) in nature, form larger clusters, whereas the smaller clusters are relatively more epithelial (lowerμ). Moreover, the heterogeneity inμis comparatively higher for smaller clusters with respect to that for larger clusters. We also observe that more extended cell shapes promote the formation of smaller clusters. Overall, this study establishes a framework which connects the nature and size of migrating clusters disseminating from a primary tumor with the phenotypic composition of the tumor, and can lead to the better understanding of metastasis.

Author summary

In the process of metastasis, tumor cells disseminate from the primary tumor either as single cells or multicellular clusters. These clusters are potential contributor to the initiation of secondary tumor in distant organs. Our computational model captures the size distribution of migrating clusters depending on the adhesion and motility of the cells (which determine the degree of their EMT nature). Furthermore, we investigate the effect of heterogeneity of cell types in the primary tumor on the resultant heterogeneity of cell types in clusters of different sizes. We believe that the understanding the formation and nature of these clusters, dangerous actors in the deadly aspect of cancer progression, will be useful for improving prognostic methods and eventually better treatments.
Evolutionary history and origin of Tre1 superfamily shed light on its role in regulating blood brain barrier
Authors: Kubick Norwin , Klimovich Pavel , Bieńkowska Irmina , Sacharczuk Mariusz , Mickael Michel-Edwar
Published: April 2021

Understanding how the evolutionary relationship between immune cells and the blood-brain is important to devise therapeutic strategies that can regulate their critical function. In vertebrates, immune cells follow either a paracellular or transcellular pathway to infiltrate the BBB. In drosophila glial cells form the BBB that regulates the access of immune-like cells to the drosophila brain. However, it is still not known which route immune-like cells follow to infiltrate the drosophila brain. In vertebrates, paracellular migration is dependent on PECAM1, while transcellular migration is dependent on the expression of CAV1. Interestingly drosophila genome lacks both genes. Tre1 superfamily (Tre1, Moody, and Dmel_CG4313) play a diverse role in regulating transepithelial migration in drosophila. However, its evolutionary history and origin are not yet known. We performed phylogenetic analysis, together with HH search, positive selection, and ancestral reconstruction to investigate the Tre1 family Interestingly we found that Tre1 exists in mollusks, insects, ambulacria, and sclaidphora. Moody is shown to be a more ancient protein and it existed since cnidaria emergence and has a homolog (GPCR84) in mammals. The third family member (Dmel_CG4313) only exists in insects. The origin of the family seems to be related to the rhodopsin-like family and in particular family α. We found that opsin is the nearest receptor to have a common ancestor with the Tre1 superfamily that seems to have diverged in sponges. We investigated the positive selection of the Tre1 family using PAML. Tre1 seems to have evolved under negative selection, whereas Moody has evolved during positive selection. The sites that we found under positive selection are Likely to play a role in the speciation of function in the case of Moody. We have identified an SH3, in Tre1 and, moody and Dmel_CG4313. Sh3 is known to play a fundamental role in regulating actin movement in a Rho-dependent manner. We suggest that Tre1 could be playing an important role in paracellular diapedesis in drosophila.
Genome-wide mutational signatures of immunological diversification in normal lymphocytes
Authors: Machado Heather E , Mitchell Emily , Øbro Nina F , Kübler Kirsten , Davies Megan , Maura Francesco , Leongamornlert Daniel , Sanders Mathijs A. , Cagan Alex , McDonald Craig , Belmonte Miriam , Shepherd Mairi S. , Osborne Robert J. , Mahbubani Krishnaa , Martincorena Iñigo , Laurenti Elisa , Green Anthony R , Getz Gad , Polak Paz , Saeb-Parsy Kourosh , Hodson Daniel J , Kent David , Campbell Peter J
Published: April 2021

A lymphocyte suffers many threats to its genome, including programmed mutation during differentiation, antigen-driven proliferation and residency in diverse microenvironments. After developing protocols for single-cell lymphocyte expansions, we sequenced whole genomes from 717 normal naive and memory B and T lymphocytes and hematopoietic stem cells. Lymphocytes carried more point mutations and structural variation than stem cells, accruing at higher rates in T than B cells, attributable to both exogenous and endogenous mutational processes. Ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every one on-targetIGVmutation during the germinal center reaction. Structural variation was 16-fold higher in lymphocytes than stem cells, with ~15% of deletions being attributable to off-target RAG activity.

One Sentence Summary:

The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.
Aqnr-plasmid allows aminoglycosides to induce SOS inEscherichia coli
Authors: Babosan Anamaria , Skurnik David , Muggeo Anaëlle , Pier Gerald B. , Baharoglu Zeynep , Jové Thomas , Ploy Marie-Cécile , Griveau Sophie , Bedioui Fethi , Vergnolle Sébastien , Moussalih Sophie , de Champs Christophe , Mazel Didier , Guillard Thomas
Published: April 2021

The plasmid-mediated quinolone resistance (PMQR) genes have been shown to promote high-level bacterial resistance to fluoroquinolone antibiotics, potentially leading to clinical treatment failures.

InEscherichia coli, sub-inhibitory concentrations (sub-MIC) of the widely used fluoroquinolones are known to induce the SOS response. Interestingly, the expression of several PMQRqnrgenes is controlled by the SOS master regulator.

During the characterization of a smallqnrD-plasmid carried inE. coli,we observed that the aminoglycosides become able to induce the SOS response in this species, thus leading to the transcription ofqnrD.

We found that induction of the SOS response is due to nitric oxide (NO) accumulation in presence of sub-MIC of aminoglycosides. We demonstrated that the NO accumulation is driven by two plasmid genes, ORF3 and ORF4, whose products act at two levels. ORF3 encode aFAD-binding oxidoreductase which helps NO synthesis, while ORF4 code for anFNR-type transcription factor, related to an O2-responsive regulator ofhmpexpression, able to repress the Hmp-mediated NO detoxification pathway ofE. coli.

Thus, this discovery, that other major classes of antibiotics may induce the SOS response could have worthwhile implications for antibiotic stewardship efforts in preventing the emergence of resistance.
UnderstandingLactobacillus paracaseiandStreptococcus oralisbiofilm interactions through agent-based modeling
Authors: Archambault Linda , Koshy-Chenthittayil Sherli , Thompson Angela , Dongari-Bagtzoglou Anna , Laubenbacher Reinhard , Mendes Pedro
Published: April 2021

As common commensals residing on mucosal tissues,Lactobacillusspecies are known to encourage health, while recent findings highlight the pathogenic roles ofStreptococcusspecies in these environments. In this study we used a combination ofin vivoimaging experiments and computational modeling to explore biofilm interactions betweenStreptococcus oralis, an accessory pathogen in oral Candidiasis, andLactobacillus paracasei, an organism with known probiotic properties. A computational agent-based model was created where the two species only interact by competing for space and nutrients. Quantification of bacterial growth in live biofilms indicated thatS. oralisbiomass and cell numbers were much lower than predicted by the model. Two subsequent models were then created to examine more complex interactions between these species, one whereL. paracaseisecretes a surfactant, and another whereL. paracaseisecretes an inhibitor ofS. oralisgrowth. Further biofilm experiments support the hypothesis thatL. paracaseimay secrete an inhibitor ofS. oralisgrowth, although they do not exclude that a surfactant could also be involved. This contribution shows how agent-based modeling and experiments can be used in synergy to address multiple species biofilm interactions, with important roles in mucosal health and disease.

IMPORTANCE

We previously discovered a role of the oral commensalStreptococcus oralisas an accessory pathogen.S. oralisincreases the virulence ofCandida albicansinfections in murine oral candidiasis and epithelial cell models through mechanisms which promote the formation of tissue-damaging biofilms.Lactobacillusspecies have known inhibitory effects on biofilm formation of many microbes, includingStreptococcusspecies. Agent-based modeling has great advantages as a means of exploring multifaceted relationships between organisms in complex environments such as biofilms. Here we used an iterative collaborative process between experimentation and modeling to reveal aspects of the mostly unexplored relationship betweenS. oralisandL. paracaseiin biofilm growth. The inhibitory nature ofL. paracaseionS. oralisin biofilms may be exploited as a means of preventing or alleviating mucosal fungal infections.
Early life stress affects the miRNA cargo in epididymal extracellular vesicles in mouse
Authors: Alshanbayeva Anar , Tanwar Deepak K. , Roszkowski Martin , Manuella Francesca , Mansuy Isabelle M.
Published: April 2021

Sperm RNA can be modified by environmental factors and has been implicated in communicating signals about changes in a father’s environment to the offspring. The RNA composition of sperm is influenced during its final stage of maturation in the epididymis by extracellular vesicles released by epididymal cells. We studied the effect of exposure to stress in postnatal life on the transcriptome of epididymal extracellular vesicles using a mouse model of transgenerational transmission. We found that the small RNA signature of epididymal extracellular vesicles, particularly miRNAs, is altered in adult males exposed to postnatal stress. miRNAs changes correlate with differences in the expression of their target genes in sperm and zygotes generated from that sperm. These results suggest that stressful experiences in early life can have persistent biological effects on the male reproductive tract that may in part be responsible for the transmission of the effects of exposure to the offspring.

Summary Sentence

miRNA cargo of extracellular vesicles in cauda epididymis is changed by paternal exposure to early life stress, which correlates with differences in the expression of their target genes in sperm and zygotes generated from that sperm
A behavioral paradigm for measuring perceptual distances in mice
Authors: Nakayama Hirofumi , Rinberg Dmitry
Published: April 2021

Perceptual similarities between a specific stimulus and other stimuli of the same modality provide valuable information about the structure and geometry of sensory spaces. While typically a subject of behavioral experiments in humans, perceptual similarities, or distances, are rarely measured in other species. However, understanding the neural computations responsible for sensory representations requires the monitoring and sometime manipulating of neural activity, which is more readily achieved in other experimental models. Here we develop a behavioral paradigm that allows for the quantifying of perceptual similarity between sensory stimuli using mouse olfaction as a model system.
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes
Authors: Sun Pengchuan , Jiao Beibei , Yang Yongzhi , Shan Lanxing , Li Ting , Li Xiaonan , Xi Zhenxiang , Wang Xiyin , Liu Jianquan
Published: April 2021

Evidence of whole-genome duplications (WGDs) and subsequent karyotype changes has been detected in most major lineages of life on Earth. To clarify the complex resulting multiple-layered patterns of gene collinearity in genome analyses there is a need for convenient and accurate toolkits. To meet this need, we introduce here WGDI (Whole-GenomeDuplicationIntegrated analysis), a Python-based command-line tool that facilitates comprehensive analysis of recursive polyploidizations and cross-species genome alignments. WGDI supports three main workflows (polyploid inference, hierarchical inference of genomic homology, and ancestral chromosomal karyotyping) that can improve detection of WGD and characterization of related events. It incorporates a more sensitive and accurate collinearity detection algorithm than previous softwares, and can accelerate WGD-related karyotype research. As a freely available toolkit at GitHub (https://github.com/SunPengChuan/wgdi), WGDI outperforms similar tools in terms of efficiency, flexibility and scalability. In an illustrative example of its application, WGDI convincingly clarified karyotype evolution inAquilegia coeruleaandVitis viniferafollowing WGDs and rejected the hypothesis thatAquilegiacontributed as a parental lineage to the allopolyploid origin of core dicots.
Melbournevirus-encoded histone doublets are recruited to virus particles and form destabilized nucleosome-like structures
Authors: Liu Yang , Toner Chelsea Marie , Philippe Nadege , Jeudy Sandra , Zhou Keda , Bowerman Samuel , White Alison , Edwards Garrett , Abergel Chantal , Luger Karolin
Published: April 2021

The organization of genomic DNA into defined nucleosomes has long been viewed as a hallmark of eukaryotes. This paradigm has been challenged by the identification of ‘minimalist’ histones in archaea, and more recently by the discovery of genes that encode fused remote homologs of the four eukaryotic histones inMarseilleviridae, a subfamily of giant viruses that infect amoebae. We demonstrate that viral doublet histones localize to the cytoplasmic viral factories after virus infection, and ultimately to mature virions. CryoEM structures of viral nucleosome-like particles show strong similarities to eukaryotic nucleosomes, despite the limited sequence identify. The unique connectors that link the histone chains contribute to the observed instability of viral nucleosomes, and some histone tails assume structural roles. Our results further expand the range of ‘organisms’ that have nucleosomes and suggest a specialized function of histones in the biology of these unusual viruses.

One Sentence Summary

Some large DNA viruses encode fused histone doublets that are targeted to viral factories and assemble into open nucleosome-like structures.
EGFR-driven profibrotic signals in AKI-to-CKD transition are blocked by TNF inhibition: Opportunities for etanercept treatment
Authors: Abdelmageed Mai M , Kefaloyianni Eirini , Arthanarisami Akshayakeerthi , Khamissi Fatima Zohra , Atkinson Jeffrey J. , Herrlich Andreas
Published: April 2021

Proximal-tubule-cell EGFR activation mediates tubule cell proliferation and repair early after kidney injury, while sustained EGFR activation causes kidney fibrosis. Inflammation is a key driver of AKI-to-CKD transition and fibrosis, but mechanisms of EGFR-driven profibrotic responses are not well understood. In a mouse model of AKI-to-CKD transition and CKD progression, we show that EGFR-inhibition significantly reduced kidney expression of many immunoregulatory molecules already by day two after injury, including the potent inflammatory cytokine tumor-necrosis-factor (TNF). Single nuclei RNA-sequencing analysis showed that macrophages were among the main early cellular sources of TNF in the injured kidney.In vitro, EGFR activation in macrophages increased macrophage TNF expression, while EGFR inhibitionin vivoreduced kidney macrophage accumulation, as early as two days after injury. Thus, profibrotic EGFR signaling increases kidney TNF levels both directly and indirectly. TNF inhibition did not alter tubule EGFR activation and in contrast to EGFR inhibition did not reduce early macrophage accumulation in the kidney, suggesting that TNF does not promote early infiltration of immune cells in the kidney, but rather regulates profibrotic functions of kidney and/or immune cells. TNF inhibition with etanerceptin vivoin AKI-injured mice downregulated a number of cytokines, including TNF itself. This cytokine downregulation overlapped with EGFR inhibition, and additional non-overlapping downregulated cytokines shared the same functions, predicting that TNF inhibition would prevent AKI-to-CKD transition like EGFR inhibition. Indeed, TNF-inhibition with etanercept reduced AKI-induced fibrosis to the same degree as the EGFR-inhibition, while the combination of both treatments showed no additive effect. In conclusion, our results identify TNF as a downstream effector of profibrotic EGFR activation and motivate the examination of TNF pathway inhibition in human AKI or CKD.

Translational statement

Proximal tubule epidermal-growth-factor (EGFR) activation in mice and likely also in humans drives inflammation in the kidney after acute-kidney-injury (AKI) and causes chronic-kidney-disease (CKD) with fibrosis in a process termed AKI-to-CKD transition. Recent retrospective data shows that patients treated with TNF inhibitors show decreased incidence and progression of CKD. Our current work shows that TNF inhibition in mice is equally as effective as EGFR inhibition in preventing AKI-to-CKD transition and fibrosis. Thus, our results have translational potential and may stimulate examination of short-term TNF inhibition in AKI to prevent AKI-to-CKD transition or possibly of longer-term TNF inhibition in CKD to prevent CKD progression.
Spatiotemporal patterns of neuronal subtype genesis suggest hierarchical development of retinal diversity
Authors: West Emma R. , Lapan Sylvain W. , Lee ChangHee , Kajderowicz Kathrin M. , Li Xihao , Cepko Connie L.
Published: April 2021

How do neuronal subtypes emerge during development? Recent molecular studies have expanded our knowledge of existing neuronal diversity. However, the genesis of neuronal subtypes remains elusive and previous studies have been limited by a lack of quantitative methods for simultaneous detection of subtype diversityin situ. The bipolar interneurons of the mammalian retina represent a diverse neuronal class, characterized by distinct functions, morphologies, and recently discovered transcriptional profiles. Here, we developed a comprehensive spatiotemporal map of bipolar subtype genesis in the retina. Combining multiplexed detection of 16 RNA markers with timed delivery of EdU and BrdU, we analyzed more than 30,000 single cells in full retinal sections to classify all bipolar subtypes and their birthdates. We found that bipolar subtype birthdates are ordered and follow a centrifugal developmental axis. Spatial analysis revealed a striking oscillatory wave pattern of bipolar subtype birthdates, and lineage analyses suggest clonal restriction on homotypic subtype production. These results inspired a hierarchical model of neuronal subtype genesis in the mammalian retina, with the wave pattern of subtype birthdates arising from early asymmetric cell divisions among founding retinal progenitor cells. Our results provide an outline of the developmental logic that generates diverse neuronal subtypes, and establishes a framework for studying subtype diversification.
Design of the recombinant influenza neuraminidase antigen is crucial for protective efficacy
Authors: Gao Jin , Klenow Laura , Parsons Lisa , Malik Tahir , Phue Je-Nie , Gao Zhizeng , Withers Stephen G. , Cipollo John , Daniels Robert , Wan Hongquan
Published: April 2021

Supplementing influenza vaccines with recombinant neuraminidase (rNA) remains a promising approach for improving the suboptimal efficacy. However, correlations among rNA designs, properties, and protection have not been systematically investigated. Here, we performed a comparative analysis of several rNAs produced from different construct designs using the baculovirus/insect cell system. The rNAs were designed with different tetramerization motifs and NA domains from a recent H1N1 vaccine strain (A/Brisbane/02/2018) and were analyzed for enzymatic properties, antigenicity, thermal and size stability, and protection in mice. We found that rNAs containing the NA head-domain versus the full-ectodomain possess distinct enzymatic properties and that the molecular size stability is tetramerization domain-dependent, whereas protection is more contingent on the combination of the tetramerization and NA domains. Following single-dose immunizations, a rNA possessing the full-ectodomain, non-native enzymatic activity, and the tetramerization motif from the human vasodilator-stimulated phosphoprotein provided substantially higher protection than a rNA possessing the head-domain, native activity and the same tetramerization motif. In contrast, these two rNAs provided comparable protection when the tetramerization motif was exchanged with the one from the tetrabrachion protein. These findings demonstrate that the rNA design is crucial for the protective efficacy and should be thoroughly evaluated for vaccine development, as the unpredictable nature of the heterologous domain combination can result in rNAs with similar key attributes but vastly differ in protection.

IMPORTANCE

For several decades it has been proposed that influenza vaccines could be supplemented with recombinant neuraminidase (rNA) to improve the efficacy. However, some key questions for manufacturing stable and immunogenic rNA remain to be answered. We show here that the tetramerization motifs and NA domains included in the rNA construct design can have a profound impact on the biochemical, immunological and protective properties. We also show that the single-dose immunization regimen is more informative for assessing the rNA immune response and protective efficacy, which is surprisingly more dependent on the specific combination of NA and tetramerization domains than common attributes for evaluating NA. Our findings may help to optimize the design of rNAs that can be used to improve or develop influenza vaccines.