Top 10 Biorxiv Papers Today in Immunology


2.006 Mikeys
#1. Non-apoptotic pioneer neutrophils initiate an endogenous swarming response in a zebrafish tissue injury model
Hannah Isles, Clare F Muir, Anastasia Kadochnikova, Catherine A Loynes, Visakan Kadirkamanathan, Philip M Elks, Stephen A Renshaw
Neutrophils are rapidly recruited to sites of infection and inflammation where they play a crucial role in host defence. Within inflamed tissue neutrophils are able to coordinate their migration to form clusters and amplify recruitment signals to distant regions, a process termed neutrophil swarming. The factors which initiate the neutrophil swarming response within inflamed interstitial tissues are not understood, hence the development of new in vivo models to study neutrophil swarming is essential. Using inflammation and infection assays in transgenic zebrafish larvae we demonstrate that neutrophil swarming is conserved in zebrafish immunity, sharing essential features with mammalian systems. Our analysis of neutrophil migration patterns identified that one pioneer neutrophil was sufficient to induce a swarming response. Upon arrival at the wound site this pioneer neutrophil adopted a striking and distinct morphology, which was followed by the coordinated migration of neutrophils to drive swarm formation. Using a real time FRET...
more | pdf
Figures
Tweets
NiethammerLab: Interesting paper on biorxiv (https://t.co/TeI2HXCixL): Neutrophil swarming to S. aureus ear infection in zebrafish as previously reported by us for P. aeruginosa ear infection in https://t.co/t7YJf4ItOV. Swarming is conserved between mammals and zebrafish!
joachimgoedhart: RT @NiethammerLab: Interesting paper on biorxiv (https://t.co/TeI2HXCixL): Neutrophil swarming to S. aureus ear infection in zebrafish as p…
Alexis_Lomakin: RT @NiethammerLab: Interesting paper on biorxiv (https://t.co/TeI2HXCixL): Neutrophil swarming to S. aureus ear infection in zebrafish as p…
AlessandraCambi: RT @NiethammerLab: Interesting paper on biorxiv (https://t.co/TeI2HXCixL): Neutrophil swarming to S. aureus ear infection in zebrafish as p…
marteyn_lab: RT @NiethammerLab: Interesting paper on biorxiv (https://t.co/TeI2HXCixL): Neutrophil swarming to S. aureus ear infection in zebrafish as p…
Stem_Alchemist: RT @NiethammerLab: Interesting paper on biorxiv (https://t.co/TeI2HXCixL): Neutrophil swarming to S. aureus ear infection in zebrafish as p…
Github
None.
Youtube
None.
Other stats
Sample Sizes : [14, 6, 2]
Authors: 7
Total Words: 11374
Unqiue Words: 3286

1.998 Mikeys
#2. Identification of regulatory genes through global gene expression analysis of a Helicobacter pylori co-culture system
Raquel Hontecillas, Nuria Tubau-Juni, Josep Bassaganya-Riera, Andrew Leber, Victoria Zoccoli-Rodriguez, Barbara Kronsteiner, Monica Viladomiu, Vida Abedi
Helicobacter pylori is a gram-negative bacterium that establishes life-long infections by inducing immunoregulatory responses. We have developed a novel ex vivo H. pylori co-culture system to identify new regulatory genes based on expression kinetics overlapping with that of genes with known regulatory functions. Using this novel experimental platform, in combination with global transcriptomic analysis, we have identified five lead candidates, validated them using mouse models of H. pylori infection and in vitro co-cultures under pro-inflammatory conditions. Plexin domain containing 2 ( Plxdc2 ) was selected as the top lead immunoregulatory target. Gene silencing and ligand-induced activation studies confirmed its predicted regulatory function. Our integrated bioinformatics analyses and experimental validation platform has enabled the discovery of new immunoregulatory genes. This pipeline can be used for the identification of genes with therapeutic applications for treating infectious, inflammatory, and autoimmune diseases.
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : [4]
Authors: 8
Total Words: 16265
Unqiue Words: 4873

1.998 Mikeys
#3. Molecular design, optimization and genomic integration of chimeric B cell receptors in murine B cells
Theresa Pesch, Lucia Bonati, William Kelton, Cristina Parola, Roy A Ehling, Lucia Csepregi, Daisuke Kitamura, Sai T Reddy
Immune cell therapies based on the integration of synthetic antigen receptors provide a powerful strategy for the treatment of diverse diseases, most notably retargeting T cells engineered to express chimeric antigen receptors (CAR) for cancer therapy. In addition to T lymphocytes, B lymphocytes may also represent valuable immune cells that can be engineered for therapeutic purposes such as protein replacement therapy or recombinant antibody production. In this article, we report a promising concept for the molecular design, optimization and genomic integration of a novel class of synthetic antigen receptors, chimeric B cell receptors (CBCR). We initially optimized CBCR expression and detection by modifying the extracellular surface tag, the transmembrane regions and intracellular signaling domains. For this purpose, we stably integrated a series of CBCR variants into immortalized B cell hybridomas using CRISPR-Cas9. Subsequently, we developed a reliable and consistent pipeline to precisely introduce cassettes of several kilobases...
more | pdf
Figures
Tweets
CyrilPedia: 'we stably integrated a series of chimeric B cell receptors variants into immortalized B cell hybridomas using CRISPR-Cas9' https://t.co/xxNW6A72fk
Github
None.
Youtube
None.
Other stats
Sample Sizes : [2, 3, 3]
Authors: 8
Total Words: 13285
Unqiue Words: 4044

0.0 Mikeys
#4. IFITM3 protects the heart during influenza virus infection
Adam Kenney, Temet M. McMichael, Alexander Imas, Nicholas M. Chesarino, Lizhi Zhang, Lisa E. Dorn, Qian Wu, Omar Alfaour, Foued Amari, Min Chen, Ashley Zani, Mahesh Chemudupati, Federica Accornero, Vincenzo Coppola, Murugesan V.S. Rajaram, Jacob S. Yount
Influenza virus primarily targets the lungs, but dissemination and damage to heart tissue is also known to occur in severe infections. Despite this knowledge, influenza virus-induced cardiac pathogenesis and its underlying mechanisms have been difficult to study due to a lack of small animal models. In humans, polymorphisms in the gene encoding interferon-induced transmembrane protein 3 (IFITM3), an antiviral restriction factor, are associated with susceptibility to severe influenza, but whether IFITM3 deficiencies contribute to other aspects of pathogenesis, including cardiac dysfunction, is unknown. We now show that IFITM3 deficiency in a newly generated knockout (KO) mouse model exacerbates illness and mortality following influenza A virus infection. Enhanced pathogenesis correlated with increased replication of virus in the lungs, spleens, and hearts of KO mice relative to wildtype (WT) mice. IFITM3 KO mice exhibited normal cardiac function at baseline, but developed severely aberrant electrical activity upon infection,...
more | pdf
Figures
Tweets
YountLabOSU: Our new preprint shows IFITM3 protects the heart from uncontrolled virus replication, fibrosis, and dysfunction during influenza virus infection. IFITM3 KOs are one of the first models for studying cardiac complications of flu. https://t.co/JEzy5qzypA
Github
None.
Youtube
None.
Other stats
Sample Sizes : [21, 4, 10]
Authors: 16
Total Words: 8451
Unqiue Words: 2616

0.0 Mikeys
#5. Integrated multi-omics analysis to study the effects of simulated weightlessness on rhesus macaques (Macaca mulatta)
Zhang Peng, Shao Libin, Zhang Jie, Li Wenjiong, Fan Guangyi, Zhou Ying, Kan Guanghan, Liu Hongju, Li Weidong, Wang Fei, Chu Xixia, Han Peng, Peng Ling, Liu Xingmin, Chen Jianwei, Liang Xinming, Ji Jingkai, Du Shiyi, Mei Zhanlong, Li Ronghui, Xu Xun, Chen Shanguang, Liu Xin, Chen Xiaoping
Safety and health of astronauts in space is one of the most important aspects of space exploration, however, the genomic research about how a weightless space can affect astronaut's health was limited. In this study, we sequenced 25 transcriptomic, 42 metabolomic and 35 metagenomic data of 15 rhesus macaques (Macaca mulatta) spanning seven simulated weightlessness experiment stages. We identified 84 genes, 1911 features and 55 genera which are significantly changed in blood and muscle, hippocampal region, dorsomedial prefrontal cortex as well as fecal, respectively. Furthermore, performing the integrated analysis of three omics data, we found several pathways which were related to regulation of immune system process, glucose uptake, reaction to threatens, neurotoxic and bone or joints damage, such as tyrosine metabolism and tryptophan metabolism. Our results provided an initial attempt of "multi-omics" approaches which combined transcriptomics, metabolomics and metagenomics to illustrate some molecular clues for simulated...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 24
Total Words: 7499
Unqiue Words: 3097

0.0 Mikeys
#6. Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection
Fabio Zanini, Makeda Robinson, Derek Croote, Malaya Kumar Sahoo, Ana Maria Sanz, Eliana Ortiz-Lasso, Ludwig Luis Albornoz, Fernando Rosso Suarez, Jose G Montoya, Benjamin A Pinsky, Stephen Quake, Shirit Einav
Dengue virus (DENV) infection can result in severe complications. Yet, the understanding of the molecular correlates of severity is limited, partly due to difficulties in defining the peripheral blood mononuclear cells (PBMCs) that are associated with DENV in vivo. Additionally, there are currently no biomarkers predictive of progression to severe dengue (SD). Bulk transcriptomics data are difficult to interpret because blood consists of multiple cell types that may react differently to infection. Here we applied virus-inclusive single cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of disease from six dengue patients and four healthy controls, and to characterize distinct DENV-associated leukocytes. Multiple genes, particularly interferon response genes, were upregulated in a cell-specific manner prior to progression to SD. Expression of MX2 in naive B cells and CD163 in CD14+ CD16+ monocytes was predictive of SD. The majority of DENV-associated cells in the...
more | pdf
Figures
Tweets
mmw_lmw: #Predicting_Infection_Severity | GeneExpression with ViralSequence at the #SingleCell level in #DengueVirus infection | Shirit Einav @Stanford @biorxivpreprint https://t.co/EwF1Uhg29E https://t.co/EW7YFuOBUM
mmw_lmw: #Predicting_Infection_Severity | GeneExpression with ViralSequence at the #SingleCell level in #DengueVirus infection | Shirit Einav @Stanford @biorxivpreprint https://t.co/EwF1Uhg29E https://t.co/lfYdiZUboN
mmw_lmw: #Predicting_Infection_Severity | GeneExpression with ViralSequence at the #SingleCell level in #DengueVirus infection | Shirit Einav @Stanford @biorxivpreprint https://t.co/EwF1Uhg29E https://t.co/Coankm1efH
biorxivpreprint: Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection https://t.co/VRXIjo2awM #bioRxiv
jmbarnet: virus-inclusive single cell RNA-seq approach (viscRNA-Seq) to profile transcriptomes of thousands of single PBMCs derived early in the course of #Dengue infection https://t.co/sv6X87LyM4
DerekCroote: New #singlecell preprint from the Quake lab: "Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection" - https://t.co/vIImeUH3jN https://t.co/Gi29D9T5Se
fabiousername: #dengue #singlecell preprint: "Virus-inclusive single cell RNA sequencing reveals molecular signature predictive of progression to severe dengue infection" - https://t.co/VfBCtvDtJd https://t.co/utJFtJKFBK
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 12
Total Words: 7257
Unqiue Words: 2543

0.0 Mikeys
#7. The length distribution and multiple specificity of naturally presented HLA-I ligands
David Gfeller, Philippe Guillaume, Justine Michaux, Hui-Song Pak, Roy T Daniel, Julien Racle, George Coukos, Michal Bassani-Sternberg
HLA-I molecules bind short peptides and present them for recognition by CD8+ T cells. The length of HLA-I ligands typically ranges from 8 to 12 amino acids, but variability is observed across different HLA-I alleles. Here we collected recent in-depth HLA peptidomics data, including 12 newly generated HLA peptidomes (31,896 unique peptides) from human meningioma samples, to analyze the peptide length distribution and multiple specificity across 84 different HLA-I alleles. We observed a clear clustering of HLA-I alleles with distinct peptide length distributions, which enabled us to study the structural basis of peptide length distributions and predict peptide length distributions from HLA-I sequences. We further identified multiple specificity in several HLA-I molecules and validated these observations with binding assays. Explicitly modeling peptide length distribution and multiple specificity improved predictions of naturally presented HLA-I ligands, as demonstrated in an independent benchmarking based on the new human meningioma samples.
more | pdf
Figures
Tweets
Github

Tool for motif deconvolution in large peptide ligand datasets

Repository: MixMHCp
User: GfellerLab
Language: HTML
Stargazers: 0
Subscribers: 2
Forks: 0
Open Issues: 0
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 8
Total Words: 12282
Unqiue Words: 3361

0.0 Mikeys
#8. PTGER2-β-Catenin Axis Links High Salt Environments to Autoimmunity by Balancing IFNγ and IL-10 in FoxP3+ Regulatory T cells
Tomokazu Sumida, Matthew R Lincoln, Chinonso M Ukeje, Donald M Rodriguez, Hiroshi Akazawa, Tetsuo Noda, Atsuhiko T Naito, Issei Komuro, Margarita Dominguez-Villar, David A Hafler
Foxp3+ regulatory T cells (Tregs) are the central component of peripheral immune tolerance. While dysregulation of the Treg cytokine signature has been observed in autoimmune diseases such as multiple sclerosis (MS) and type 1 diabetes, the regulatory mechanisms balancing pro- and anti-inflammatory cytokine production are not known. Here, we identify imbalance between IFNγ and IL-10 as a shared Treg signature, present in patients with MS and under high salt conditions. By performing RNA-seq analysis on human Treg subpopulations, we identify β-catenin as a key regulator that controls the expression of IFNγ and IL-10. The activated β-catenin signature is enriched specifically in IFNγ+Tregs in humans, and this was confirmed in vivo with Treg-specific β-catenin-stabilized mice exhibiting lethal autoimmunity with a dysfunctional, IFNγ- producing, Treg phenotype. Moreover, we identify PTGER2 as a major factor balancing IFNγ and IL-10 production in the context of a high salt environment, with skewed activation of the β-catenin/SGK1/Foxo...
more | pdf
Figures
Tweets
biorxivpreprint: PTGER2-{beta}-Catenin Axis Links High Salt Environments to Autoimmunity by Balancing IFN{gamma} and IL-10 in FoxP3+ Regulatory T cells https://t.co/TQDqRXxKYJ #bioRxiv
Github
None.
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 10
Total Words: 20963
Unqiue Words: 4702

0.0 Mikeys
#9. Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets
James Hay, Karen Laurie, Michael White, Steven Riley
The strength and breadth of an individual's antibody repertoire are important predictors of their response to influenza infection or vaccination. Although progress has been made in understanding qualitatively how repeated exposures shape the antibody mediated immune response, quantitative understanding remains limited. We developed a set of mathematical models describing short-term antibody kinetics following influenza infection or vaccination and fit them to haemagglutination inhibition (HI) titres from 5 groups of ferrets which were exposed to different combinations of trivalent inactivated influenza vaccine (TIV with or without adjuvant), priming inoculation with A/H3N2 and post-vaccination inoculation with A/H1N1. Based on the parameter estimates of the best supported model, we describe a number of key immunological features. We found quantifiable differences in the degree of homologous and cross-reactive antibody boosting elicited by different exposure types. Infection and adjuvanted vaccination generally resulted in strong,...
more | pdf
Figures
Tweets
AdamJKucharski: Characterising antibody kinetics across influenza infections and vaccination in ferrets. New preprint from @jameshay218 @SRileyIDD and co https://t.co/oU3hqi6Ink https://t.co/ZY3jOVxjgX
outbreaksci: Read it? Rate it. If you read "Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets" (https://t.co/4LAktzVCt0), provide an @outbreaksci rapid review here [prototype]: https://t.co/acDeHAyHI3
outbreaksci: New #influenza preprint: Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets https://t.co/4LAktzVCt0
Github

Repository for code relating to the ferret antibody kinetics modelling project

Repository: antibodyKinetics
User: jameshay218
Language: R
Stargazers: 0
Subscribers: 1
Forks: 1
Open Issues: 0
Youtube
None.
Other stats
Sample Sizes : None.
Authors: 4
Total Words: 9224
Unqiue Words: 2762

0.0 Mikeys
#10. Low Replication Capacity Virus Is Preferentially Transmitted In Mother-To-Child-Transmission But Not In Adult-To-Adult-Transmission Of HIV-1
Emily Adland, Louisa Iselin, Francesca Roxburgh, Jane Millar, Anna Csala, Vanessa Naidoo, Christie Noble, Jake Thomas, Alessia De'Felice, Ago Szabo, Nicholas Grayson, Amber Moodley, Krista Dong, Bruce Walker, Thumbi Ndung'u, Samantha McInally, Eric Hunter, Philip Goulder
Previous studies of the transmitted/founder virus compared to viral quasispecies in the donor have yielded conflicting results. In heterosexual adult-to-adult transmission (ATAT), the viral replicative capacity (VRC) of transmitted virus is reportedly either similar to, or somewhat higher than, that of donor virus, whilst transmitted virus in mother-to-child transmission (MTCT) has a significantly lower VRC than that of maternal virus. These discrepancies may be explained by the different methodologies used in these studies, or they may reflect true differences in the transmission bottleneck. To resolve this question, we here use the same methodology to compare transmitted versus donor virus in MTCT and ATAT. We show that, in a South African mother-child cohort, infant virus samples obtained at 1-2 days after birth had VRC significantly lower than in the mothers (p=0.0003). By contrast, in Zambian ATAT transmission pairs, VRC of transmitted virus was similar to or somewhat higher than donor virus (p=ns). The VRC of virus...
more | pdf
Figures
Tweets
Github
None.
Youtube
None.
Other stats
Sample Sizes : [28, 58, 15, 9, 5, 4, 86, 9, 8, 8, 8, 8, 10, 26, 58, 28, 15, 9]
Authors: 18
Total Words: 7749
Unqiue Words: 2432

About

Assert is a website where the best academic papers on arXiv (computer science, math, physics), bioRxiv (biology), BITSS (reproducibility), EarthArXiv (earth science), engrXiv (engineering), LawArXiv (law), PsyArXiv (psychology), SocArXiv (social science), and SportRxiv (sport research) bubble to the top each day.

Papers are scored (in real-time) based on how verifiable they are (as determined by their Github repos) and how interesting they are (based on Twitter).

To see top papers, follow us on twitter @assertpub_ (arXiv), @assert_pub (bioRxiv), and @assertpub_dev (everything else).

To see beautiful figures extracted from papers, follow us on Instagram.

Tracking 72,893 papers.

Search
Sort results based on if they are interesting or reproducible.
Interesting
Reproducible
Feedback
Online
Stats
Tracking 72,893 papers.