bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specification of axial identity by Hoxa2 distinguishes between a phenotypic and molecular ground state in mouse cranial neural crest cells
Authors: Pushel Irina , Trainor Paul A , Krumlauf Robb 
Published: February 2021

AbstractHoxgenes play a key role in head formation by specifying the axial identity of neural crest cells (NCCs) migrating into embryonic pharyngeal arches. In the absence ofHoxa2, NCC derivatives of the second pharyngeal arch (PA2) undergo a homeotic transformation and duplicate structures formed by first arch (PA1) NCCs. Current models postulate that PA1 represents a NCC ‘ground state’ and loss ofHoxa2causes a reversion of PA2 NCCs to the PA1 ‘ground state’. We use bulk and single-cell RNAseq to investigate the molecular mechanisms driving this phenotypic transformation in the mouse. InHoxa2-/-mutants, PA2 NCCs generally maintain expression of the PA2 transcriptional signature and fail to strongly upregulate a PA1 transcriptional signature. Our analyses identify putative HOXA2 targets and suggest that subsets of NCCs may respond to HOXA2 activity in distinct manners. This separation of phenotypic and molecular states has significant implications for understanding craniofacial development.
Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells
Authors: Bernadskaya Yelena Y. , Yue Haicen , Copos Calina , Christiaen Lionel , Mogilner Alex 
Published: February 2021

AbstractPhysiological and pathological morphogenetic events involve a wide array of collective movements, suggesting that these multicellular arrangements confer biochemical and biomechanical properties that contribute to tissue scale organization. The cardiopharyngeal progenitors of the tunicate Ciona provide the simplest possible model of collective cell migration. They form cohesive bilateral cell pairs, leader-trailer polarized along the migration path as they migrate between the ventral epidermis and trunk endoderm. Here, circumventing difficulties in quantifying cellular mechanics in live embryos, we use the Cellular Potts Model to computationally probe the distributions of forces consistent with the shapes and collective polarity of migrating cell pairs. Combining computational modeling, confocal microscopy, and molecular perturbations, we first determine that cardiopharyngeal progenitors display hallmarks of supracellular organization, with differential distributions of protrusive forces, cell-matrix adhesion, and myosin-based retraction forces along the leader-trailer axis. Combined 4D simulations and experimental observations suggest that cell-cell communication helps establish a hierarchy that contributes to aligning collective polarity with the direction of migration, as observed with three or more cells bothin silicoandin vivo. Our approach reveals emerging properties of the migrating collective. Specifically, cell pairs are more persistent, thus migrating over longer distances, and presumably with higher accuracy. Finally, simulations suggest that polarized cell pairs literally join forces to deform the trunk endoderm, as they migrate through the extracellular space. We thus propose that the polarized supracellular organization of cardiopharyngeal progenitors confers emergent physical properties that determine mechanical interactions with their environment during morphogenesis.
High Throughput Nanopore Sequencing of SARS-CoV-2 Viral Genomes from Patient Samples
Authors: Pater Adrian A. , Bosmeny Michael S. , Parasrampuria Mansi , Eddington Seth B. , Ovington Katy N. , White Adam A. , Barkau Christopher L. , Metz Paige E. , Sylvain Rourke J. , Chilamkurthy Ramadevi , Yinusa Abadat O. , Benzinger Scott W. , Hebert Madison M. , Gagnon Keith T. 
Published: February 2021

ABSTRACTIn late 2019, a novel coronavirus began spreading in Wuhan, China, causing a potentially lethal respiratory viral infection. By early 2020, the novel coronavirus, called SARS-CoV-2, had spread globally, causing the COVID-19 pandemic. The infection and mutation rates of SARS-CoV-2 make it amenable to tracking movement and evolution by viral genome sequencing. Efforts to develop effective public health policies, therapeutics, or vaccines to treat or prevent COVID-19 are also expected to benefit from tracking mutations of the SARS-CoV-2 virus. Here we describe a set of comprehensive working protocols, from viral RNA extraction to analysis using online visualization tools, for high throughput sequencing of SARS-CoV-2 viral genomes using a MinION instrument. This set of protocols should serve as a reliable ‘how-to’ reference for generating quality SARS-CoV-2 genome sequences with ARTIC primer sets and next-generation nanopore sequencing technology. In addition, many of the preparation, quality control, and analysis steps will be generally applicable to other sequencing platforms.
Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome
Authors: Khan Salahuddin , Hill Janet E. 
Published: February 2021

AbstractNegative frequency-dependent selection is one possible mechanism for maintenance of rare species in communities, but the selective advantage of rare species may be checked at lower overall population densities where resources are abundant. Gardnerella spp. belonging to cpn60 subgroup D, are detected at low levels in vaginal microbiomes and are nutritional generalists relative to other more abundant Gardnerella spp., making them good candidates for negative frequency-dependent selection. The vaginal microbiome is a dynamic environment and the resulting changes in density of the microbiota may explain why subgroup D never gains dominance. To test this, we co-cultured subgroup D isolates with isolates from the more common and abundant subgroup C. Deep amplicon sequencing of rpoB was used to determine proportional abundance of each isolate at 0 h and 72 h in 152 co-cultures, and to calculate change in proportion. D isolates had a positive change in proportional abundance in most co-cultures regardless of initial proportion. Initial density affected the change in proportion of subgroup D isolates either positively or negatively depending on the particular isolates combined, suggesting that growth rate, population density and other intrinsic features of the isolates influenced the outcome. Our results demonstrate that population density is an important factor influencing the outcome of competition between Gardnerella spp. isolated from the human vaginal microbiome.
ACE2-lentiviral transduction enables mouse SARS-CoV-2 infection and mapping of receptor interactions
Authors: Rawle Daniel J. , Le Thuy T. , Dumenil Troy , Yan Kexin , Tang Bing , Bishop Cameron , Suhrbier Andreas 
Published: February 2021

ABSTRACTSARS-CoV-2 uses the human ACE2 (hACE2) receptor for cell attachment and entry, with mouse ACE2 (mACE2) unable to support infection. Herein we describe an ACE2-lentivirus system and illustrate its utility forin vitroandin vivoSARS-CoV-2 infection models. Transduction of non-permissive cell lines with hACE2 imparted replication competence, and transduction with mACE2 containing N30D, N31K, F83Y and H353K substitutions, to match hACE2, rescued SARS-CoV-2 replication. Intranasal hACE2-lentivirus transduction of C57BL/6J mice permitted significant virus replication in lungs. RNA-Seq analyses illustrated that the model involves an acute inflammatory disease followed by resolution and tissue repair, with a transcriptomic profile similar to that seen in COVID-19 patients. Intranasal hACE2-lentivirus transduction of IFNAR-/-and IL-28RA-/-mice lungs was used to illustrate that loss of type I or III interferon responses have no significant effect on virus replication. However, their importance in driving inflammatory responses was illustrated by RNA-Seq analyses. We also demonstrate the utility of the hACE2-lentivirus transduction system for vaccine evaluation in C57BL/6J mice. The ACE2-lentivirus system thus has broad application in SARS-CoV-2 research, providing a tool for both mutagenesis studies and mouse model development.AUTHOR SUMMARYSARS-CoV-2 uses the human ACE2 (hACE2) receptor to infect cells, but cannot infect mice because the virus cannot bind mouse ACE2 (mACE2). We use an ACE2-lentivirus systemin vitroto identify four key amino acids in mACE2 that explain why SARS-CoV-2 cannot infect mice. hACE2-lentivirus was used to express hACE2 in mouse lungsin vivo, with the inflammatory responses after SARS-CoV-2 infection similar to those seen in human COVID-19. Genetically modified mice were used to show that type I and III interferon signaling is required for the inflammatory responses. We also show that the hACE2-lentivirus mouse model can be used to test vaccines. Overall this paper demonstrates that our hACE2-lentivirus system has multiple applications in SARS-CoV-2 and COVID-19 research.
A rigid body framework for multi-cellular modelling
Authors: Brown Phillip J. , Green J. Edward F. , Binder Benjamin J. , Osborne James M. 
Published: February 2021

ABSTRACTMulti-cellular modelling, where tissues and organs are represented by a collection of individual interacting agents, is a well established field, encapsulating several different approaches. In particular, off-lattice models, which represent cells using points that are free to move in space, have been applied to numerous biological problems in both two and three dimensions. The fact that a cell can be represented by point objects is useful in a wide range of settings, particularly when large populations are involved. However, a purely point-based representation is not naturally equipped to deal with objects that inherently have length like cell boundaries or external membranes.In this paper we introduce a novel off-lattice modelling framework that exploits rigid body mechanics to represent cells using a collection of one-dimensional edges (rather than zero-dimensional points) in a viscosity-dominated system. The rigid body framework can be used, among other things, to represent cells as free moving polygons, to allow epithelial layers to smoothly interact with themselves, and to model rod shaped cells like bacteria. We demonstrate the value of our new framework by using it in these three applications, showing that this approach can replicate established results, as well as offer solutions to problems that limit the scope of current off-lattice multi-cellular models.
Long non-coding RNA Neat1 and paraspeckle components are translational regulators in hypoxia
Authors: Godet Anne-Claire , Roussel Emilie , David Florian , Hantelys Fransky , Morfoisse Florent , Alves Joffrey , Pujol Françoise , Ader Isabelle , Bertrand Edouard , Burlet-Schiltz Odile , Froment Carine , Henras Anthony K. , Vitali Patrice , Lacazette Eric , Tatin Florence , Garmy-Susini Barbara , Prats Anne-Catherine 
Published: February 2021

SUMMARYInternal ribosome entry sites (IRESs) drive translation initiation during stress. In response to hypoxia, (lymph)angiogenic factors responsible for tissue revascularization in ischemic diseases are induced by the IRES-dependent mechanism. Here we searched for IREStrans-acting factors (ITAFs) active in early hypoxia in mouse cardiomyocytes. Using knock-down and proteomics approaches, we show a link between a stressed-induced nuclear body, the paraspeckle, and IRES-dependent translation. Furthermore, smiFISH experiments demonstrate the recruitment of IRES-containing mRNA into paraspeckle during hypoxia. Our data reveal that the long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator, active on IRESs of (lymph)angiogenic and cardioprotective factor mRNAs. In addition, paraspeckle proteins p54nrband PSPC1 as well as nucleolin and Rps2, two p54nrb-interacting proteins identified by mass spectrometry, are ITAFs for IRES subgroups. Paraspeckle thus appears as a platform to recruit IRES-containing mRNAs and possibly host IRESome assembly. Polysome PCR array shows that Neat1 isoforms regulate IRES-dependent translation and, more widely, translation of mRNAs involved in stress response.HighlightsParaspeckle formation correlates with activation of translation via internal ribosome entry sites (IRES) in mouse hypoxic cardiomyocytes as well as in tumoral cells.The long non-coding RNA Neat1, an essential paraspeckle component, is a key translational regulator of (lymph)angiogenic and cardioprotective factor expression in this process.IRES-containing mRNA is recruited into paraspeckles during hypoxia.Paraspeckle proteins p54nrband PSPC1 as well as two p54nrb-interacting proteins, nucleolin and RPS2, contribute to this process.Paraspeckle appears as a platform for IRESome formation in the nucleus.The Neat1 isoforms widely regulate the translation of mRNAs containing IRESs and of genes involved in the stress response.GRAPHICAL ABSTRACT
A screen for Twist-interacting proteins identifies Twinstar as a regulator of muscle development during embryogenesis
Authors: Balakrishnan Mridula , Howard Austin , Yu Shannon F. , Sommer Katie , Nowak Scott J. , Baylies Mary K. 
Published: February 2021

ABSTRACTMyogenesis inDrosophilarelies on the activity of the transcription factor Twist during several key events of mesoderm differentiation. To identify the mechanism(s) by which Twist establishes a unique gene expression profile in specific spatial and temporal locales, we employed a yeast-based double interaction screen to discover new Twist-interacting proteins (TIPs) at themyocyte enhancer factor 2 (mef2)andtinman (tinB)myogenic enhancers. We identified a number of proteins that interacted with Twist at one or both enhancers, and whose interactions with Twist and roles in muscle development were previously unknown. Through genetic interaction studies, we find that Twinstar (Tsr), and its regulators are required for muscle formation. Loss of function and null mutations intsrand its regulators result in missing and/or misattached muscles. Our data suggest that the yeast double interaction screen is a worthy approach to investigate spatial-temporal mechanisms of transcriptional regulation in muscle and in other tissues.
Capturing effects of blood flow on the transplanted decellularized nephron with intravital microscopy
Authors: Corridon Peter R. 
Published: February 2021

AbstractOrgan decellularization creates cell-free, collagen-based extracellular matrices that can be used as scaffolds for tissue engineering applications. This technique has recently gained much attention, yet adequate scaffold repopulation and implantation remain a challenge. Specifically, there still needs to be a greater understanding of scaffold responses post-transplantation and ways we can improve scaffold durability to withstand the in vivo environment. Recent studies have outlined vascular events that limit organ decellularization/recellularization scaffold viability for long-term transplantation. However, these insights have relied on in vitro/in vivo approaches that need enhanced spatial and temporal resolutions to investigate such issues at the microvascular level. This study uses intravital microscopy to gain instant feedback on their structure, function, and deformation dynamics. Thus, the objective of this study was to capture the effects of in vivo blood flow on the decellularized glomerulus, peritubular capillaries, and tubules after autologous and allogeneic orthotopic transplantation into rats. Large molecular weight dextran molecules label the vasculature. They revealed substantial degrees of translocation from glomerular and peritubular capillary tracks to the decellularized tubular epithelium and lumen as early as 12 hours after transplantation, providing real-time evidence of the increases in microvascular permeability. Macromolecular extravasation persisted for a week, during which the decellularized microarchitecture was significantly and comparably compromised and thrombosed in both autologous and allogeneic approaches. These results indicate that in vivo multiphoton microscopy is a powerful approach for studying scaffold viability and identifying ways to promote scaffold longevity and vasculogenesis in bioartificial organs.
CD29 enriches for cytotoxic human CD4+T cells
Authors: Nicolet Benoît P. , Guislain Aurelie , Wolkers Monika C. 
Published: February 2021

ABSTRACTCD4+T cell are key contributors in the induction of adaptive immune responses against pathogens. Even though CD4+T cells are primarily classified as non-cytotoxic helper T cells, it has become appreciated that a subset of CD4+T cells is cytotoxic. However, tools to identify these cytotoxic CD4+T cells are lacking. We recently showed that CD29 (Integrin Beta 1, ITGB1) expression on human CD8+T cells enriches for the most potent cytotoxic T cells. Here, we questioned whether CD29 expression also associates with cytotoxic CD4+T cells. We show that human peripheral blood-derived CD29hiCD4+T cells display a cytotoxic gene expression profile, which closely resembles that of CD29hicytotoxic CD8+T cells. This CD29hicytotoxic phenotype was observedex vivoand was maintained inin vitrocultures. CD29 expression enriched for CD4+T cells, which effectively produced the pro-inflammatory cytokines IFN-γ, IL-2, and TNF-α, and cytotoxic molecules. Lastly, CD29-expressing CD4+T cells transduced with a MART-1 specific TCR showed target cell killingin vitro. In conclusion, we here demonstrate that CD29 can be employed to enrich for cytotoxic human CD4+T cells.
Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes
Authors: Canals Oriol , Mendibil Iñaki , Santos María , Irigoien Xabier , Rodríguez-Ezpeleta Naiara 
Published: February 2021

AbstractThe deep-sea remains among the most unknown ecosystems on Earth despite its relevant role in carbon sequestration and increasing threat due to interest by fishing and mining industries. This, together with the recent discovery that the upper layer of this ecosystem (mesopelagic zone) harbors about 90% of the fish biomass on Earth, claims for a deeper understanding of the deep-sea so that the foundations for a sustainable use of its resources can be established. The analysis of environmental DNA (eDNA) collected from the water column emerges as an alternative to traditional methods to acquire this elusive information, but its application to the deep ocean is still incipient. Here, we have amplified and sequenced the fish eDNA contained in vertical profile samples (from surface to 2000 m depth) collected during day and night-time throughout the Bay of Biscay. We found that eDNA-derived deep-sea fish richness and abundance follow a day-night pattern that is consistent with the diel migratory behavior of many mesopelagic species, and that eDNA can reveal species-specific distribution and movement through the water column. These results highlight the potential of eDNA-based studies to improve our knowledge on the species inhabiting the dark ocean before this still pristine ecosystem is exploited.
Full-likelihood genomic analysis clarifies a complex history of species divergence and introgression: the example of theerato-saragroup ofHeliconiusbutterflies
Authors: Thawornwattana Yuttapong , Seixas Fernando A. , Yang Ziheng , Mallet James 
Published: February 2021

AbstractIntrogressive hybridization plays a key role in adaptive evolution and species diversification in many groups of species. However, frequent hybridization and gene flow between species makes estimation of the species phylogeny and key population parameters challenging. Here, we show that by accounting for phasing and using full-likelihood analysis methods, introgression histories and population parameters can be estimated reliably from whole-genome sequence data. We employ full-likelihood methods under the multispecies coalescent (MSC) model with and without gene flow to analyze the genomic data from six members of theerato-saraclade ofHeliconiusbutterflies and infer the species phylogeny and cross-species introgression events. The methods naturally accommodate random fluctuations in genealogical history across the genome due to deep coalescence. To avoid heterozygote phasing errors in haploid sequences commonly produced by genome assembly methods, we process and compile unphased diploid sequence alignments and use analytical methods to average over uncertainties in heterozygote phase resolution. There is robust evidence for introgression across the genome, both among distantly related species deep in the phylogeny and between sister species in shallow parts of the tree. We obtain chromosome-specific estimates of key population parameters such as introgression directions, times and probabilities, as well as species divergence times and population sizes for modern and ancestral species. We confirm ancestral gene flow between thesaraclade and an ancestral population ofH. telesiphe, a likely hybrid speciation origin forH. hecalesia, and gene flow between sister speciesH. eratoandH. himera. Inferred introgression among ancestral species also explains the history of two chromosomal inversions deep in the phylogeny of the group. This study illustrates how a full-likelihood approach based on the multispecies coalescent makes it possible to extract rich historical information of species divergence and gene flow from genomic data.
Key experiences for the transdisciplinary approach: fieldwork-based training in sustainability science education
Authors: Kudo Shogo , Omi Kanako , Florentin Kevin , Allasiw Doreen Ingosan 
Published: February 2021

Purpose
This paper aims to describe how a sustainability-focused program in higher education can provide training and key experiences for implementing transdisciplinary approaches. The case is a fieldwork-based training course called the Global Field Exercise (GFE) at the Graduate Program in Sustainability Science, The University of Tokyo. The GFE is a methodological training course that emphasizes generating locally relevant research questions on sustainability.

Design/methodology/approach
This research is a case study regarding how a sustainability science program can offer a fieldwork-based training course that focuses on a transdisciplinary approach. Five students from diverse academic disciplines and cultural backgrounds participated in the GFE in QwaQwa where they conducted semi-structured interviews with six local entrepreneurs to identify the challenges and opportunities of entrepreneurship. The authors investigated the learning process and outcomes of the students through participatory observation in preparatory meetings, daily reflection sessions during fieldwork and a content analysis of feedback reports.

Findings
Four learning outcomes of the students were suggested: the reexamination of assumptions, managing misunderstanding and miscommunication, mutual learning and being empathic toward the local people.

Research limitations/implications
This paper suggests three key opportunistic experiences for the transdisciplinary approach: discuss the normative dimension of sustainability; build intersubjectivity among team members and adopt methodological pluralism; and become empathetic to diverse stakeholder groups to facilitate the cogeneration of knowledge.

Originality/value
How to design training on a transdisciplinary approach in educational programs remains an area for further exploration. This study addresses this knowledge gap by establishing a link between sustainability education and sustainability in practice.