bluuebunny/crossref_metadata_2025 huggingface dataset:
Replicative fitness SARS-CoV-2 20I/501Y.V1 variant in a human reconstituted bronchial epithelium
Authors: Touret Franck , Luciani Léa , Baronti Cécile , Cochin Maxime , Driouich Jean-Sélim , Gilles Magali , Thirion Laurence , Nougairède Antoine , de Lamballerie Xavier
Published: March 2021

Since its emergence in 2019, circulating populations of the new coronavirus continuously acquired genetic diversity. At the end of 2020, a variant named 20I/501Y.V1 (lineage B.1.1.7) emerged and replaced other circulating strains in several regions. This phenomenon has been poorly associated to biological evidence that this variant and original strain exhibit different phenotypic characteristics. Here, we analyse the replication ability of this new variant in different cellular models using for comparison an ancestral D614G European strain (lineage B1). Results from comparative replication kinetics experimentsin vitroand in a human reconstituted bronchial epithelium showed no difference. However, when both viruses were put in competition in a human reconstituted bronchial epithelium, the 20I/501Y.V1 variant outcompeted the ancestral strain. Altogether, these findings demonstrate that this new variant replicates more efficiently and could contribute to better understand the progressive replacement of circulating strains by the SARS-CoV-2 20I/501Y.V1 variant.

Importance

The emergence of several SARS-CoV-2 variants raised numerous questions concerning the future course of the pandemic. We are currently observing a replacement of the circulating viruses by the variant from the United Kingdom known as 20I/501Y.V1 from B.1.1.7 lineage but there is little biological evidence that this new variant exhibit a different phenotype. In the present study, we used different cellular models to assess the replication ability of the 20I/501Y.V1 variant. Our results showed that this variant replicate more efficiently in a human reconstituted bronchial epithelium, which may explain why it spreads so rapidly in human populations.
Differential effects of the second SARS-CoV-2 mRNA vaccine dose on T cell immunity in naïve and COVID-19 recovered individuals
Authors: Camara Carmen , Lozano-Ojalvo Daniel , Lopez-Granados Eduardo , Paz-Artal Estela , Pion Marjorie , Correa-Rocha Rafael , Ortiz Alberto , Lopez-Hoyos Marcos , Iribarren Marta Erro , Portoles Jose , Portoles Pilar , Perez-Olmeda Mayte , Oteo Jesus , Berin Cecilia , Guccione Ernesto , Bertoletti Antonio , Ochando Jordi
Published: March 2021

The rapid development and deployment of mRNA-based vaccines against the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) led to the design of accelerated vaccination schedules that have been extremely effective in naïve individuals. While a two-dose immunization regimen with the BNT162b2 vaccine has been demonstrated to provide a 95% efficacy in naïve individuals, the effects of the second vaccine dose in individuals who have previously recovered from natural SARS-CoV-2 infection has been questioned. Here we characterized SARS-CoV-2 spike-specific humoral and cellular immunity in naïve and previously infected individuals during full BNT162b2 vaccination. Our results demonstrate that the second dose increases both the humoral and cellular immunity in naïve individuals. On the contrary, the second BNT162b2 vaccine dose results in a reduction of cellular immunity in COVID-19 recovered individuals, which suggests that a second dose, according to the current standard regimen of vaccination, may be not necessary in individuals previously infected with SARS-CoV-2.
A toxic friend: Genotoxic and mutagenic activity of the probiotic strainEscherichia coliNissle 1917
Authors: Nougayrède Jean-Philippe , Chagneau Camille , Motta Jean-Paul , Bossuet-Greif Nadège , Belloy Marcy , Taieb Frédéric , Gratadoux Jean-Jacques , Thomas Muriel , Langella Philippe , Oswald Eric
Published: March 2021

The probioticEscherichia colistrain Nissle 1917 (DSM 6601, Mutaflor), generally considered as beneficial and safe, has been used for a century to treat various intestinal diseases. However, Nissle 1917 hosts in its genome thepkspathogenicity island that codes for the biosynthesis of the genotoxin colibactin. Colibactin is a potent DNA alkylator, suspected to play a role in colorectal cancer development. We show in this study that Nissle 1917 is functionally capable of producing colibactin and inducing interstrand crosslinks in the genomic DNA of epithelial cells exposed to the probiotic. This toxicity was even exacerbated with lower doses of the probiotic, when the exposed cells started to divide again but exhibited aberrant anaphases and increased gene mutation frequency. DNA damage was confirmedin vivoin mouse models of intestinal colonization, demonstrating that Nissle 1917 produces the genotoxin in the gut lumen. Although it is possible that daily treatment of adult humans with their microbiota does not produce the same effects, administration of Nissle 1917 as a probiotic or as a chassis to deliver therapeutics might exert long term adverse effects and thus should be considered in a risk versus benefit evaluation.

Importance

Nissle 1917 is sold as a probiotic and considered safe even though it is known since 2006 that it encodes the genes for colibactin synthesis. Colibactin is a potent genotoxin that is now linked to causative mutations found in human colorectal cancer. Many papers concerning the use of this strain in clinical applications ignore or elude this fact, or misleadingly suggest that Nissle 1917 does not induce DNA damage. Here, we demonstrate that Nissle 1917 produces colibactinin vitroandin vivoand induces mutagenic DNA damage. This is a serious safety concern that must not be ignored, for the interests of patients, the general public, health care professionals and ethical probiotic manufacturers.
Pax6 loss alters the morphological and electrophysiological development of mouse prethalamic neurons
Authors: Tian Tian , Quintana-Urzainqui Idoia , Kozić Zrinko , Pratt Thomas , Price David J.
Published: March 2021

Pax6 is a well-known regulator of early neuroepithelial progenitor development. Its constitutive loss has a particularly strong effect on the developing prethalamus, causing it to become extremely hypoplastic. To overcome this difficulty in studying the long-term consequences of Pax6 loss for prethalamic development, we used conditional mutagenesis to delete Pax6 at the onset of neurogenesis and studied the developmental potential of the mutant prethalamic neurons in vitro. We found that Pax6 loss affected their rates of neurite elongation, the location and length of their axon initial segments and their electrophysiological properties. Our results broaden our understanding of the long-term consequences of Pax6 deletion in the developing mouse forebrain, suggesting that it can have cell autonomous effects on the structural and functional development of some neurons.

SUMMARY STATEMENT

Pax6 impacts neurite extension, axon initial segment properties and ability to fire normal action potentials in maturing neurons, revealing actions extending beyond those previously characterized in progenitors.
Decoding nonspecific interactions between human nuclear transport proteins: A computational study
Authors: Rathod Shravan B.
Published: March 2021

The nuclear protein transport between the nucleus and cytosol can be considered a core process of cell regulation. Specially designed proteins in nature such as importins, exportins, and some other transporters facilitate this transport in the cell and control the cellular processes. Transient and weak protein–protein interactions are basis of these various biomolecular processes. Prior to cargo transports, the transport proteins recognize the Nuclear localization signals (NLSs) and Nuclear export signals (NESs) of cargo proteins and, bind to the RanGTP. Also, these proteins bind with other similar protein subunits along with RanGTP to transport cargos. Cell is enormously crowded place where DNA, RNA, proteins, lipids and small molecules cooperatively facilitate numerous cellular processes. In such environment, existence of nonspecific interactions between proteins is quite obvious. Considering this hypothesis, in this study, protein-protein docking approach was applied to determine the binding affinities of 12 human nuclear transport proteins. Results showed that KPNA1, TNPO1 and TNPO3 have greater affinity to bind with other transport proteins. Also, among 78 complexes (12 homodimers and 66 heterodimers), KPNA1-KPNB1, KPNA1-TNPO1 and KPNA1-TNPO3 complexes have the highest stability.

Graphical abstract

Initially, 12 human nuclear transport proteins PDB structures were retrieved from the 1. Protein data bank (PDB). These proteins had some missing terminals and residues thus, we used 2. SWISS-MODEL and 3. MODELLER v.10.1 to model those regions in these proteins. Next, we used widely popular web server, 4. ClusPro v.2.0 for protein-protein docking analysis among 12 proteins. Then, we employed 5. PRODIGY web server to calculate the binding affinities of 78 complexes (12 homodimers & 66 heterodimers). Finally, we utilised three web tools, 6. Arpeggio, 7. PIMA and 8. PDBePISA to analyse top-three complexes (KPNA1-KPNB1, KPNA1-TNPO1 & TNPO3) for in-depth interactions and energetics.
Cancer models and statistical analysis of age distribution of cancers
Authors: Tetearing Alexandr N.
Published: March 2021

In this paper, mathematical mutational models of the age distribution of cancers are obtained. These are two models – a simple model and a complex model, which takes into account the growth of the cell population and the transmission of mutations to daughter cells. Using the resulting formulas, we approximated real age-specific cancer incidence datasets in women (colon, lung, mammary, stomach) and men (colon, lung, prostate, stomach). We estimated parameters such as the average number of mutations (per cell per unit of time) and number of mutations required for cancer to occur.

The number of mutations averaged (over four types of cancer) required for cancer to occur is 5.5 (mutations per cell for women) and 6.25 (mutations per cell for men) for the complex mutational model.

As an alternative to mutational models, we also consider the model of delayed carcinogenic event.
Isochoric supercooled preservation and revival of human cardiac microtissues
Authors: Powell-Palm Matthew J. , Charwat Verena , Charrez Berenice , Siemons Brian , Healy Kevin E. , Rubinsky Boris
Published: March 2021

Low-temperatureex vivopreservation and tissue engineering based on human induced pluripotent stem cells (hiPSC) represent two of the most promising routes towards on-demand access to organs for transplantation. While these fields are often considered divergent from one another, advances in both fields present critical new opportunities for crossover. Herein we demonstrate the first-ever sub-zero centigrade preservation and revival of autonomously beating three-dimensional hiPSC-derived cardiac microtissues1via isochoric supercooling2, without the use of chemical cryoprotectants. We show that these tissues can cease autonomous beating during preservation and resume it after warming, that the supercooling process does not affect sarcomere structural integrity, and that the tissues maintain responsiveness to drug exposure following revival. Our work suggests both that functional three dimensional (3D) engineered tissues may provide an excellent high-content, low-risk testbed to study organ preservation in a genetically human context, and that isochoric supercooling may provide a robust method for preserving and reviving engineered tissues themselves.
First come, first served: Superinfection exclusion in Deformed wing virus is dependent upon sequence identity and not the order of virus acquisition
Authors: Gusachenko Olesya N , Woodford Luke , Balbirnie-Cumming Katharin , Evans David J
Published: March 2021

Deformed wing virus (DWV) is the most important globally distributed pathogen of honey bees and, when vectored by the ectoparasiteVarroa destructor, is associated with high levels of colony losses. Divergent DWV types may differ in their pathogenicity and are reported to exhibit superinfection exclusion upon sequential infections, an inevitability in aVarroa-infested colony. We used a reverse genetic approach to investigate competition and interactions between genetically distinct or related virus strains, analysing viral load over time, tissue distribution with reporter gene-expressing viruses and recombination between virus variants. Transient competition occurred irrespective of the order of virus acquisition, indicating no directionality or dominance. Over longer periods, the ability to compete with a pre-existing infection correlated with the genetic divergence of the inoculae. Genetic recombination was observed throughout the DWV genome with recombinants accounting for ~2% of the population as determined by deep sequencing. We propose that superinfection exclusion, if it occurs at all, is a consequence of a cross-reactive RNAi response to the viruses involved, explaining the lack of dominance of one virus type over another. A better understanding of the consequences of dual- and superinfection will inform development of cross-protective honey bee vaccines and landscape-scale DWV transmission and evolution.
Characterisation of B.1.1.7 and Pangolin coronavirus spike provides insights on the evolutionary trajectory of SARS-CoV-2
Authors: Dicken Samuel J. , Murray Matthew J. , Thorne Lucy G. , Reuschl Ann-Kathrin , Forrest Calum , Ganeshalingham Maaroothen , Muir Luke , Kalemera Mphatso D. , Palor Machaela , McCoy Laura E. , Jolly Clare , Towers Greg J. , Reeves Matthew B. , Grove Joe
Published: March 2021

The recent emergence of SARS-CoV-2 variants with increased transmission, pathogenesis and immune resistance has jeopardised the global response to the COVID-19 pandemic. Determining the fundamental biology of viral variants and understanding their evolutionary trajectories will guide current mitigation measures, future genetic surveillance and vaccination strategies. Here we examine virus entry by the B.1.1.7 lineage, commonly referred to as the UK/Kent variant. Pseudovirus infection of model cell lines demonstrate that B.1.1.7 entry is enhanced relative to the Wuhan-Hu-1 reference strain, particularly under low expression of receptor ACE2. Moreover, the entry characteristics of B.1.1.7 were distinct from that of its predecessor strain containing the D614G mutation. These data suggest evolutionary tuning of spike protein function. Additionally, we found that amino acid deletions within the N-terminal domain (NTD) of spike were important for efficient entry by B.1.1.7. The NTD is a hotspot of diversity across sarbecoviruses, therefore, we further investigated this region by examining the entry of closely related CoVs. Surprisingly, Pangolin CoV spike entry was 50-100 fold enhanced relative to SARS-CoV-2; suggesting there may be evolutionary pathways by which SARS-CoV-2 may further optimise entry. Swapping the NTD between Pangolin CoV and SARS-CoV-2 demonstrates that changes in this region alone have the capacity to enhance virus entry. Thus, the NTD plays a hitherto unrecognised role in modulating spike activity, warranting further investigation and surveillance of NTD mutations.
Single-cell methylation sequencing data reveal succinct metastatic migration histories and tumor progression models
Authors: Liu Yuelin , Li Xuan Cindy , Rashidi Mehrabadi Farid , Schäffer Alejandro A. , Pratt Drew , Crawford David R. , Malikić Salem , Molloy Erin K. , Gopalan Vishaka , Mount Stephen M. , Ruppin Eytan , Aldape Kenneth , Sahinalp S. Cenk
Published: March 2021

Recent studies exploring the impact of methylation in tumor evolution suggest that while the methylation status of many of the CpG sites are preserved across distinct lineages, others are altered as the cancer progresses. Since changes in methylation status of a CpG site may be retained in mitosis, they could be used to infer the progression history of a tumor via single-cell lineage tree reconstruction. In this work, we introduce the first principled distance-based computational method,Sgootr, for inferring a tumor’s single-cell methylation lineage tree and jointly identifying lineage-informative CpG sites which harbor changes in methylation status that are retained along the lineage. We applySgootron the single-cell bisulfite-treated whole genome sequencing data of multiregionally-sampled tumor cells from 9 metastatic colorectal cancer patients made available by Bianet al., as well as multiregionally-sampled single-cell reduced-representation bisulfite sequencing data from a glioblastoma patient made available by Chaligneet al.. We demonstrate that the tumor lineages constructed reveal a simple model underlying colorectal tumor progression and metastatic seeding. A comparison ofSgootragainst alternative approaches shows thatSgootrcan construct lineage trees with fewer migration events and more in concordance with the sequential-progression model of tumor evolution, in time a fraction of that used in prior studies. Interestingly, lineage-informative CpG sites identified bySgootrare in inter-CpG island (CGI) regions, as opposed to CGI’s, which have been the main regions of interest in genomic methylation-related analyses.Sgootris implemented as aSnakemakeworkflow, available athttps://github.com/algo-cancer/Sgootr.

Abstract Figure
Influence of delayed density and ultraviolet radiation on caterpillar baculovirus infection and mortality
Authors: Pepi Adam , Pan Vincent , Rutkowski Danielle , Mase Vinay , Karban Richard
Published: March 2021

Infectious disease is an important potential driver of population cycles, but this must occur through delayed density-dependent infection and resulting fitness effects. Delayed density-dependent infection by baculoviruses can be caused by environmental persistence of viral occlusion bodies, which can be influenced by environmental factors. In particular, ultraviolet radiation is potentially important in reducing the environmental persistence of viruses by inactivating viral occlusion bodies.

Delayed density-dependent viral infection has rarely been observed empirically at the population level although theory predicts that it is necessary for these pathogens to drive population cycles. Similarly, field studies have not examined the potential effects of ultraviolet radiation on viral infection rates in natural animal populations. We tested if viral infection is delayed density-dependent with the potential to drive cyclic dynamics and if ultraviolet radiation influences viral infection levels.

We censused 18 Ranchman’s tiger moth (Arctia virginalis) populations across nearly 9° of latitude over two years and quantified the effects of direct and delayed density and ultraviolet radiation on baculovirus infection rates, infection severity, and survival to adulthood. Caterpillars were collected from each population in the field and reared in the laboratory. Baculovirus has not previously been described infectingArctia virginalis, and we used genetic methods to confirm the identity of the virus.

We found that infection rate, infection severity, and survival to adulthood exhibited delayed density-dependence. Ultraviolet radiation in the previous summer decreased infection severity, and increased survival probability of the virus. Structural equation modelling indicated that the effect of lagged density on moth survival was mediated through infection rate and infection severity, and was 2.5 fold stronger than the effect of ultraviolet radiation on survival through infection severity. We successfully amplified polh, lef-8, and lef-9 viral genes from caterpillar samples, and BLAST search results confirmed that the virus was a nucleopolyhedrovirus.

Our findings provide clear evidence that delayed density dependence can arise through viral infection rate and severity in insects, which supports the role of viral disease as a potential mechanism, among others, that may drive insect population cycles. Furthermore, our findings support predictions that ultraviolet radiation can modify viral disease dynamics in insect populations, most likely through attenuating viral persistence in the environment.
The cryo-EM structure of the bacterial type I DNA segregation ATPase filament reveals its conformational plasticity upon DNA binding
Authors: Parker AV , Mann D , Tzokov SB , Hwang LC , Bergeron JRC
Published: March 2021

The efficient segregation of replicated genetic material is an essential step for cell division. In eukaryotic cells, sister chromatids are separated via the mitotic spindles. In contrast, bacterial cells use several evolutionarily-distinct genome segregation systems. The most common of these is the Type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood.

Here, we report the cryo-EM structure of a ParA filament bound to its DNA template, using the chromosome 2 (Chr2) ofVibrio choleraeas a model system. We also report the crystal structures of this protein in various nucleotide states, which collectively offer insight into its conformational changes from dimerization through to DNA binding and filament assembly. Specifically, we show that the ParA dimer is stabilized by nucleotide binding, and forms a left-handed filament using DNA as a scaffold. Our structural analyses also reveal dramatic structural rearrangements upon DNA binding and filament assembly. Finally, we show that filament formation is controlled by nucleotide hydrolysis. Collectively, our data provide the structural basis for ParA’s cooperative binding to DNA and the formation of high ParA density regions on the nucleoid, and suggest a role for its filament formation.
Encapsulation and recovery of murine hematopoietic stem and progenitor cells in a thiol-crosslinked maleimide-functionalized gelatin hydrogel
Authors: Gilchrist Aidan E. , Serrano Julio F. , Ngo Mai T. , Hrnjak Zona , Kim Sanha , Harley Brendan A.C.
Published: March 2021

Biomaterial platforms are an integral part of stem cell biomanufacturing protocols. The collective biophysical, biochemical, and cellular cues of the stem cell niche microenvironment play an important role in regulating stem cell fate decisions. Three-dimensional (3D) culture of stem cells within biomaterials provides a route to present biophysical and biochemical stimuli such as cell-matrix interactions and cell-cell interactions via secreted biomolecules. Herein, we describe a maleimide-functionalized gelatin (GelMAL) hydrogel that can be crosslinked via thiol-Michael addition click reaction for the encapsulation of sensitive stem cell populations. The maleimide functional units along the gelatin backbone enables gelation via the addition of a dithiol crosslinker without requiring external stimuli (e.g., UV light, photoinitiator), reducing reactive oxide species generation. Additionally, the versatility of crosslinker selection enables easy insertion of thiol-containing bioactive or bioinert motifs. Hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs) were encapsulated in GelMAL, with mechanical properties tuned to mimic thein vivobone marrow niche. We report insertion of a cleavable peptide crosslinker that can be degraded by the proteolytic action of SortaseA, a mammalian-inert enzyme. Notably, SortaseA exposure preserves stem cell surface markers, an essential metric of hematopoietic activity used in immunophenotyping. This novel GelMAL system enables a route to producing artificial stem cell niches with tunable biophysical properties with intrinsic cell-interaction motifs and orthogonal addition of bioactive crosslinks.
TCF-1 in CD4 T cells regulates GVHD severity and persistence
Authors: Harris Rebecca , Mammadli Mahinbanu , May Adriana , Yang Qi , Fung Ivan Ting Hin , Sen Jyoti Misra , Karimi Mobin
Published: March 2021

Graft-versus-host disease (GVHD) is a leading cause of mortality following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Mature donor T cells in the graft mediate graft-versus-leukemia (GVL) responses against residual tumor cells, which may persist after pre-transplant conditioning regimens. Importantly, the same mature T cells also mediate GVHD. The transcription factor T Cell Factor-1 (TCF-1) is critical for T cell development in the thymus. Using a unique mouse model of allo-HSCT leading to GVHD, we investigated the role of TCF-1 in alloactivated T cell functioning and in GVHD. Here, we report that loss of TCF-1 in mature CD4 T cells reduces GVHD severity and persistence, improving survival of recipient mice. This was due to reduced proliferation, survival, and cytokine production of T cells, as well as increased exhaustion. Gene pathways involved in cytokine response, immune signaling, chemokine signaling, cell cycle, and T cell differentiation were altered by loss of TCF-1 in donor cells. Our companion paper shows that regulation of alloactivated CD4 T cells by TCF-1 differs from regulation of CD8 T cells, suggesting that TCF-1 plays a unique role in each subset. Therefore, targeting of TCF-1 or downstream signaling pathways may be an effective strategy for reducing GVHD following allo-HSCT.
TCF-7is dispensable for anti-tumor response but required for persistent function of mature CD8 T cells
Authors: Harris Rebecca , Mammadli Mahinbanu , Hiner Shannon , Suo Liye , Yang Qi , Sen Jyoti Misra , Karimi Mobin
Published: March 2021

T Cell Factor-1, encoded byTCF-7,is a transcription factor that plays an essential role during T cell development and differentiation. In this manuscript we utilized a pre-clinical model provided evidence thatTCF-7is dispensable for the anti-tumor response, and thatTCF-7suppresses key transcriptional factors Eomes and T-bet and molecules responsible for peripheral CD8 T cell cytolytic function. We discovered thatTCF-7regulates NKG2D expression on naïve and activated mouse CD8 T cells, and that peripheral CD8 T cells fromTCF-7cKO utilize NKG2D to clear tumor cells.

We also provide evidence thatTCF-7regulates key signaling molecules, including LCK, LAT, ITK, PLC-γ1, P65, ERKI/II, and JAK/STATs required for peripheral CD8 T cell persistent function. Our data transcriptomic and protein data uncovered the mechanism of howTCF-7impacting peripheral CD8 T cell inflammatory cytokine production, CD8 T cell activation, and apoptosis. Our pre-clinical model showed that CD8 T cells fromTCF-7cKO mice did not cause GVHD, but effectively cleared primary tumor cells.
VICTOR: A visual analytics web application for comparing cluster sets
Authors: Karatzas Evangelos , Gkonta Maria , Hotova Joana , Baltoumas Fotis A. , Kontou Panagiota I. , Bobotsis Christopher J. , Bagos Pantelis G. , Pavlopoulos Georgios A.
Published: March 2021

Clustering is the process of grouping together different data objects based on similar properties. Clustering has applications in various case studies from several fields such as graph theory, image analysis, pattern recognition, statistics and others. Nowadays, there are numerous algorithms and tools able to generate clustering results. However, different algorithms or parameterization may result in very different clusters. This way, the user is often forced to manually filter and compare these results in order to decide which of them produce the ideal clusters. To automate this process, in this study, we present VICTOR, the first fully interactive and dependency-free visual analytics web application which allows the comparison and visualization of various clustering algorithms. VICTOR can handle multiple clustering results simultaneously and compare them using ten different metrics. Clustering results can be filtered and compared to each other with the use of interactive heatmaps, bar plots, correlation networks, sankey and circos plots. We demonstrate VICTOR’s functionality using three examples. In the first case, we compare five different algorithms on a protein-protein interaction dataset whereas in the second example, we test four different parameters of the same clustering algorithm applied on the same dataset. Finally, as a third example, we compare four different meta-analyses with hierarchically clustered differentially expressed genes found to be involved in myocardial infarction. VICTOR is available athttp://bib.fleming.gr:3838/VICTOR.
HiCBin: Binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps
Authors: Du Yuxuan , Sun Fengzhu
Published: March 2021

Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Conventional shotgun-based binning approaches may encounter barriers when multiple samples are scarce. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. Several Hi-C-based binning pipelines have been put forward and yielded state-of-the-art results using a single sample. We conclude that normalization and clustering are two vital steps in the Hi-C-based binning analyses, and develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the HiCzin normalization method and the Leiden community detection algorithm based on the Potts spin-glass model and includes the spurious contact detection into binning pipelines for the first time. Using the metagenomic yeast sample with a perfect ground truth of contigs’ species identity, we comprehensively evaluate the impacts on the binning performance of different normalization methods and clustering algorithms from the HiCBin and other available metagenomic Hi-C analysis pipelines, demonstrate that the HiCzin and the Leiden algorithm achieve the best binning accuracy, and show that the spurious contact detection can improve the retrieval performance. We also validate our method and compare the capability to recover high-quality MAGs of HiCBin against other state-of-the-art Hi-C-based binning tools including ProxiMeta, bin3C, and MetaTOR, and one popular shotgun-based binning software MetaBAT2 on a human gut sample and a wastewater sample. HiCBin provides the best performance and applicability in resolving MAGs and is available athttps://github.com/dyxstat/HiCBin.
The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection
Authors: Sandoval Daniel R. , Clausen Thomas Mandel , Nora Chelsea , Cribbs Adam P. , Denardo Andrea , Clark Alex E. , Garretson Aaron F. , Coker Joanna K.C. , Narayanan Anoop , Majowicz Sydney A. , Philpott Martin , Johansson Catrine , Dunford James E. , Spliid Charlotte B. , Golden Gregory J. , Payne N. Connor , Tye Mark A. , Nowell Cameron J. , Griffis Eric R. , Piermatteo Ann , Grunddal Kaare V. , Alle Thibault , Magida Jason A. , Hauser Blake M. , Feldman Jared , Caradonna Timothy M. , Pu Yuan , Yin Xin , McVicar Rachael N. , Kwong Elizabeth M. , Weiss Ryan J. , Downes Michael , Tsimikas Sotirios , Smidt Aaron G. , Ballatore Carlo , Zengler Karsten , Evans Ron M. , Chanda Sumit K. , Croker Ben A. , Leibel Sandra L. , Jose Joyce , Mazitschek Ralph , Oppermann Udo , Esko Jeffrey D. , Carlin Aaron F. , Gordts Philip L.S.M.
Published: March 2021

Summary Paragraph

We identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone1, a compound in clinical trials for anti-fibrotic and anti-inflammatory applications2, as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry3. We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir4. Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginone’s translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.
Analysis of immune subtypes across the epithelial-mesenchymal plasticity spectrum
Authors: Chakraborty Priyanka , Chen Emily , McMullens Isabelle , Armstrong Andrew J. , Jolly Mohit Kumar , Somarelli Jason A.
Published: March 2021

Epithelial-mesenchymal plasticity plays a critical role in many solid tumor types as a mediator of metastatic dissemination and treatment resistance. In addition, there is also a growing appreciation that the epithelial/mesenchymal status of a tumor plays a role in immune evasion and immune suppression. A deeper understanding of the immunological features of different tumor types has been facilitated by the availability of large gene expression datasets and the development of methods to deconvolute bulk RNA-Seq data. These resources have generated powerful new ways of characterizing tumors, including classification of immune subtypes based on differential expression of immunological genes. In the present work, we combine scoring algorithms to quantify epithelial-mesenchymal plasticity with immune subtype analysis to understand the relationship between epithelial plasticity and immune subtype across cancers. We find heterogeneity of epithelial-mesenchymal transition (EMT) status both within and between cancer types, with greater heterogeneity in the expression of EMT-related factors than of MET-related factors. We also find that specific immune subtypes have associated EMT scores and differential expression of immune checkpoint markers.
Moonlighting adenylyl cyclases in plants – anArabidopsis thaliana9-cis-epoxycarotenoid dioxygenase as point in case
Authors: Al-Younis Inas , Wong Aloysius , Moosa Basem , Kwiatkowski Mateusz , Jaworski Krzysztof , Gehring Chris
Published: March 2021

Adenylyl cyclases (ACs) and their catalytic product cAMP are regulatory components of plant responses. AC domains are intrinsic components of complex molecules with multiple functions, some of which are co-regulated by cAMP. Here we used an amino acid search motif based on annotated ACs in organisms across species to identify 12 uniqueArabidopsis thalianacandidate ACs, four of which have a role in the biosynthesis of the stress hormone abscisic acid (ABA). One of these, the 9-cis-epoxycarotenoid dioxygenase (NCED3, At3g14440), was identified by sequence and structural analysis as a putative AC and then tested experimentally for activity. We show that an NCED3 AC fragment can complement an AC deficientE. colimutant and this rescue is nullified when key amino acids in the AC motif are mutated. AC activity was also confirmed by tandem liquid chromatography mass spectrometry (LC-MS/MS). Our results are consistent with a moonlighting role for mononucleotide cyclases in multi-domain proteins that have at least one other distinct molecular function such as catalysis or ion channel activation and promise to yield new insights into tuning mechanisms of ABA dependent plant responses. Finally, our search method can also be applied to discover ACs in other species includingHomo sapiens.

Highlights

An adenylyl cyclase (AC) catalytic center motif identifies novel ACs in plants

ACs can moonlight in complex proteins with other enzymatic domains

A 9-cis-epoxycarotenoid dioxygenase essential for abscisic acid synthesis contains an AC

This finding implicates cAMP in abscisic acid synthesis and signaling
Genome-wide decoupling of H2Aub and H3K27me3 in early mouse development
Authors: Zhu Yezhang , Yu Jiali , Rong Yan , Wu Yun-Wen , Fan Heng-Yu , Shen Li
Published: March 2021

Polycomb group (PcG) proteins are crucial chromatin regulators during development. H2Aub and H3K27me3 are catalyzed by Polycomb-repressive Complex 1 and 2 (PRC1/2) respectively, and largely overlap in the genome due to mutual recruitment of the two complexes. However, whether PRC1/H2Aub and PRC2/H3K27me3 can function independently remains obscure. Here we uncovered a genome-wide decoupling of H2Aub and H3K27me3 in preimplantation mouse embryos, at both canonical PcG targets and broad distal domains. H2Aub represses future bivalent genes without H3K27me3 but does not contribute to maintenance of H3K27me3-dependent non-canonical imprinting. Our study thus revealed their distinct and independent functions in early mammalian development.
A novel type of IRES having variable numbers of eIF4E-binding site and synergistic effect in RNA2 of WYMV isolates
Authors: Guowei Geng , Chengming Yu , Xiangdong Li , Kerong Shi , Xuefeng Yuan
Published: March 2021

Some viral proteins were translated in cap-independent manner via internal ribosome entry site (IRES), which ever maintained conservative characteristic among different isolates of same species of virus. However, IRES activity presented 7-fold of variance in RNA2 of wheat yellow mosaic virus (WYMV) HC and LYJN isolates. Based on RNA structure probing and mutagenesis assay, the loosened middle stem of H1 and hepta-nucleotide top loop of H2 in LYJN isolate synergistically ensured the higher IRES activity than that in HC isolate. In addition, the conserved top loop of H1 ensured basic IRES activity in HC and LYJN isolates. RNA2 5′-UTR specifically interacted with the wheat eIF4E, which was accomplished by the top loop of H1 in HC isolate or the top loop of H1 and H2 in LYJN isolate. Different IRES activity of WYMV RNA2 was regulated by different numbers of eIF4E-binding site and their synergistic effect, which was accomplished by the proximity of H1 and H2 due to the flexibility of middle stem in H1. It is represented a novel evolution pattern of IRES.
Dry Swab Method of sample collection for SARS-CoV2 testing can be used for culturing virus
Authors: Ram Sushma , Enayathullah M. Ghalib , Parekh Yash , Tallapaka Karthik Bharadwaj , Mishra Rakesh K , Bokara Kiran Kumar
Published: March 2021

Back ground

Earlier studies suggested the use of dry swab method for SARS-CoV-2 detection as it does not need VTM and subsequent RNA extraction step making the process cheaper, safer and faster. In this study we explore whether the virus in the dry swab is viable and can be cultured and propagated.

Method

Swabs were spiked with SARS-CoV-2 and stored in three different conditions: a) as dry swab (SD, eluted in 1 mL DMEM), b) in 1 mL of Viral Transport Medium (SVTM), and c) in 1 mL of Tris-EDTA buffer (STE). The sample groups were stored either at room temperature (RT, 25°C±1°C) or at 4°C for 1, 4, 8, 12, 24, 48 and 72 hours before being used as viral inoculums for the propagation studies in Vero cells.

Results

The RT-qPCR data suggests that SDincubated both at RT and 4°C harbors viral particles that are viable and culturable at par with SVTMand STE.

Conclusion

The dry swab method, in addition to its advantages in detection of the virus, also renders viable viral particles that can be cultured and propagated.
Biophysical demonstration of co-packaging of glutamate and GABA in individual synaptic vesicles in the central nervous system
Authors: Kim SeulAh , Wallace Michael L. , El-Rifai Mahmoud , Knudsen Alexa R. , Sabatini Bernardo L.
Published: March 2021

Many mammalian neurons release multiple neurotransmitters to activate diverse classes of ionotropic receptors on their postsynaptic targets. Entopeduncular nucleus somatostatin (EPSst+) neurons that project to the lateral habenula (LHb) release both glutamate and GABA, but it is unclear if these are packaged into the same or segregated pools of synaptic vesicles. Here we describe a novel method combining electrophysiology, spatially-patterned optogenetics, and computational modeling designed to analyze the mechanism of glutamate/GABA corelease. We find that the properties of PSCs elicited in LHb neurons by optogenetic activation of EPSst+terminals are only consistent with co-packaging of glutamate and GABA into individual vesicles. Furthermore, serotonin, which acts presynaptically to weaken EPSst+to LHb synapses, does so by altering the release probability of vesicles containing both transmitters. Our approach is broadly applicable to the study of multi-transmitter neurons throughout the brain and our results constrain mechanisms of neuromodulation in LHb.
PHAROH lncRNA regulates c-Myc translation in hepatocellular carcinoma via sequestering TIAR
Authors: Yu Allen T , Berasain Carmen , Bhatia Sonam , Rivera Keith , Liu Bodu , Rigo Frank , Pappin Darryl J , Spector David L
Published: March 2021

Hepatocellular carcinoma, the most common type of liver malignancy, is one of the most lethal forms of cancer. We identified a long non-coding RNA, Gm19705, that is overexpressed in hepatocellular carcinoma and mouse embryonic stem cells. We named this RNA Pluripotency and Hepatocyte Associated RNA Overexpressed in HCC, or PHAROH. Depletion of PHAROH impacts cell proliferation and migration, which can be rescued by ectopic expression of PHAROH. RNA-seq analysis of PHAROH knockouts revealed that a large number of genes with decreased expression contain a c-Myc motif in their promoter. C-MYC is decreased at the protein level, but not the mRNA level. RNAantisense pulldown identified nucleolysin TIAR, a translational repressor, to bind to a 71-nt hairpin within PHAROH, sequestration of which increases c-MYC translation. In summary, our data suggest that PHAROH regulates c-MYC translation by sequestering TIAR and as such represents a potentially exciting diagnostic or therapeutic target in hepatocellular carcinoma.
With a Little Help from “Nuestros Amigos”: Hispanics and Kidney Transplants
Authors: Hennessy Julie
Published: March 2021

Dr. Juan Caicedo was educated in general medicine and surgery at Universidad Nacional de Colombia and practiced transplant medicine in Bogota. He determined that he would need to go to the United States to advance his training, and ultimately was awarded a fellowship in transplant surgery at Northwestern Memorial Hospital.

During his three years as a fellow, Caicedo was struck by the number of Hispanic patients on the kidney transplant waiting list. Not only were Hispanics the highest growth group on the transplant waiting list, they also waited longer for transplants and died while waiting at higher rates than non-Hispanic whites or African-Americans. Caicedo also was alarmed by Hispanic patients' lower utilization of living donors for transplantation they were underrepresented not only as live donor transplant patients, but also as donors.

As he neared the end of his fellowship in 2006, Caicedo wondered if the Hispanic population encountered unique barriers to transplantation and living donor usage, and began to think about creating a program to address these barriers.
The Fall of Banco Espírito Santo: Holy Spirit or Devil in Disguise?
Authors: Shein James B. , Hawbecker Jason P.
Published: March 2021

In 2014, after nearly 150 years as one of Portugal's most wealthy and powerful families, the Espirito Santo family completely lost control of its empire, which included Banco Espirito Santo, Portugal's largest bank by market capitalization and second-largest private-sector bank in terms of assets, along with stakes in numerous financial, non-financial, privately held, and publicly traded companies. During the European financial crisis of 2010 to 2014, many of the family's companies required capital investment. To avoid family equity dilution, the family's patriarch, Ricardo Espirito Santo Silva Salgado, engaged in a creative money-go-round structure whereby Banco Espirito Santo would legally raise short-term commercial paper with high interest rates and sell them to third parties that were partially owned by the Espirito Santo family. These third parties then would sell that paper back to the bank's retail clients as safe investments similar to Portuguese deposits. The plan failed, and the house of cards that was the Espirito Santo empire collapsed. Students will consider whether Salgado and the board of Banco Espirito Santo acted appropriately or if they failed their fiduciary duties to the non-family shareholders of the bank.
Kueski: Revolutionizing Consumer Credit in Mexico
Authors: Markovich Sarit , Achwal Nilima
Published: March 2021

This case asks students to step into the role of Adalberto Flores, co-founder and CEO of Kueski, one of the first companies to develop a proprietary algorithm for online loan approval in Mexico. Mexico lacks a standardized credit scoring system, making it difficult for many Mexicans to get approved for a loan or credit card. This, together with the fact that Mexicans generally do not trust traditional banks, makes Mexico an attractive opportunity for fintech companies. Growth, however, could require fintech companies to partner with traditional banks. Students assume the role of Flores to think about the benefits and risks associated with a partnership between Kueski and traditional banks. Students are also challenged to compare the structure of U.S. financial services markets with the Mexican structure and consider the implications on the sustainability of fintech companies in the two markets. The teaching note analyzes the Mexican financial market and the benefits and threats it holds for fintech companies, and outlines a framework for evaluating the risk associated with partnerships.
Scott Family Enterprises: Building the Path to Effective Governance
Authors: Ward John L.
Published: March 2021

As founders of First Interstate BancSystem, which held $8.6 billion in assets and had recently become a public company, and Padlock Ranch, which had over 11,000 head of cattle, the Scott family had to think carefully about business and family governance. Now entering its fifth generation, the family had over 80 shareholders across the US. In early 2016, the nine-member Scott Family Council (FC) and other family and business leaders considered the effectiveness of the Family Governance Leadership Development Initiative launched two years earlier. The initiative's aim was to ensure a pipeline of capable family leaders for the business boards, two foundation boards, and FC.

Seven family members had self-nominated for governance roles in mid-2015. As part of the development initiative, each was undergoing a leadership development process that included rigorous assessment and creation of a comprehensive development plan. As the nominees made their way through the process and other family members considered nominating themselves for future development, questions remained around several interrelated areas, including how to foster family engagement with governance roles while guarding against damaging competition among members; how to manage possible conflicts of interest around dual employee and governance roles; and how to extend the development process to governance for the foundations and FC. The FC considered how best to answer these and other questions, and whether the answers indicated the need to modify the fledgling initiative.

This case illustrates the challenges multigenerational family-owned enterprises face in developing governance leaders within the family. It serves as a good example of governance for a large group of cousins within a multienterprise portfolio. Students can learn and apply insights from this valuable illustration of family values, vision, and mission statement.