bluuebunny/crossref_metadata_2025 huggingface dataset:
Recent advances of natural and bioengineered extracellular vesicles and their application in vascular regeneration
Authors: Xu Jianxiong , Wang Jinxuan , Chen Yidan , Hou Yuanfang , Hu Jianjun , Wang Guixue
Published: September 2022

The progression of cardiovascular diseases such as atherosclerosis and myocardial infarction leads to serious vascular injury, highlighting the urgent need for targeted regenerative therapy. Extracellular vesicles (EVs) composed of a lipid bilayer containing nuclear and cytosolic materials are relevant to the progression of cardiovascular diseases. Moreover, EVs can deliver bioactive cargo in pathological cardiovascular and regulate the biological function of recipient cells, such as inflammation, proliferation, angiogenesis and polarization. However, because the targeting and bioactivity of natural EVs are subject to several limitations, bioengineered EVs have achieved wide advancements in biomedicine. Bioengineered EVs involve three main ways to acquire including (i) modification of the EVs after isolation; (ii) modification of producer cells before EVs’ isolation; (iii) synthesize EVs using natural or modified cell membranes, and encapsulating drugs or bioactive molecules into EVs. In this review, we first summarize the cardiovascular injury-related disease and describe the role of different cells and EVs in vascular regeneration. We also discuss the application of bioengineered EVs from different producer cells to cardiovascular diseases. Finally, we summarize the surface modification on EVs which can specifically target abnormal cells in injured vascular.
Flavobacterium soyae sp. nov., isolated from the rhizosphere of soya bean
Authors: Zhao Hui , Pan Jie , Su Yue , Gu Qihui , Zhang Jumei , Xie Xinqiang , Wu Qingping
Published: September 2022

A Gram-stain-negative, aerobic, rod-shaped bacterium without ﬂagella, designated SCIV07T, was isolated from soya bean rhizosphere soil collected from Bazhong, Sichuan Province, PR China and characterized by using polyphasic taxonomy. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCIV07T belonged to the genus

Flavobacterium

and most closely related to the type strains

Flavobacterium chungangense

LMG 26729T (97.91 %),

Flavobacterium reichenbachii

LMG 25512T (97.77 %),

Flavobacterium oncorhynchi

CCUG 59446T (97.7 %),

Flavobacterium chilense

LMG 26360T (97.7 %) and

Flavobacterium plurextorum

CCUG 60112T (97.63 %). The average nucleotide identity and in silico DNA–DNA hybridization values between strain SCIV07T and closely related

Flavobacterium

species were lower than thresholds of 95 and 70 %, respectively, for species delineation. Catalase and oxidase were positive. Strain SCIV07T produced flexirubin-type pigments. Menaquinone-6 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and two unidentified lipids. The predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3OH and summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c). Physiological and biochemical features differentiated strain SCIV07T from the closely related

Flavobacterium

species. Based on the polyphasic taxonomic data, strain SCIV07T represents a novel species of the genus

Flavobacterium

, for which the name Flavobacterium soyae sp. nov. is proposed. The type strain is SCIV07T (=GDMCC 1.2481T=JCM 34673T).
KineticMSI, an R-based framework for relative quantification of spatial isotopic incorporation in mass spectrometry imaging experiments
Authors: Farzana Farheen , Martinez-Seidel Federico , Hannan Anthony J. , Hatters Danny , Boughton Berin A
Published: September 2022

Kinetic mass spectrometry imaging (kMSI) integrates imaging-MS with stable isotope labelling to elucidate metabolic fluxes in a spatiotemporal manner. kMSI studies are hampered by high volumes of complex data and a lack of computational workflows for data analysis that additionally address replicated experiments. To meet these challenges, we developed KineticMSI, an open-source R-based tool for processing and analyzing kMSI datasets. KineticMSI includes statistical tools to quantify tracer incorporation across replicated treatment groups spatially in tissues. It allows users to make data-driven decisions by elucidating affected pathways associated with changes in metabolic turnover. We demonstrate a validation of our method by identifying metabolic changes in the hippocampus of a transgenic Huntington’s disease (HD) mouse model as compared to wild-type mice. We discovered significant changes in metabolism of neuronal cell body lipids (phosphatidylinositol and cardiolipins) in HD mice, previously masked by conventional statistical approaches that compare mean tracer incorporation across brain regions.
ATRAP - Accurate T cell Receptor Antigen Pairing through data-driven filtering of sequencing information from single-cells
Authors: Povlsen Helle Rus , Bentzen Amalie Kai , Kadivar Mohammad , Jessen Leon Eyrich , Hadrup Sine Reker , Nielsen Morten
Published: September 2022

Novel single-cell based technologies hold the promise of matching T cell receptor (TCR) sequences with their cognate peptide-MHC recognition motif in a high-throughput manner. Parallel capture of TCR transcripts and peptide-MHC is enabled through the use of reagents labeled with DNA barcodes. However, analysis and annotation of such single-cell sequencing (SCseq) data is challenged by dropout, random noise, and other technical artifacts that must be carefully handled in the downstream processing steps.

We here propose a rational, data-driven method termed ATRAP (Accurate T cell Receptor Antigen Paring) to deal with these challenges, filtering away likely artifacts, and enable the generation of large sets of TCR-pMHC sequence data with a high degree of specificity and sensitivity, thus outputting the most likely pMHC target per T cell. We have validated this approach across 10 different virus-specific T cell responses in 16 healthy donors. Across these samples we have identified up to 1494 high-confident TCR-pMHC pairs derived from 4135 single-cells.
Transcriptional and clonal characterization of cytotoxic CD8+ T cells in crescentic glomerulonephritis
Authors: Zhao Yu , Mueller Anne , Cicek Hakan , Paust Hans-Joachim , Sivayoganathan Amirrtavarshni , Linke Alexandra , Wegscheid Claudia , Wiech Thorsten , Huber Tobias B. , Meyer-Schwesinger Catherine , Bonn Stefan , Panzer Ulf , Tiegs Gisa , Krebs Christian F. , Neumann Katrin
Published: September 2022

Crescentic glomerulonephritis (cGN), most often caused by anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis, is an aggressive form of immune-mediated kidney disease and represents an important cause of end-stage renal failure. Although it is known that T cells infiltrate the kidney in cGN, their precise role in autoimmune kidney disease remains to be fully elucidated. By performing single-cell analysis, we identified activated, clonally expanded CD8+ T cells with a cytotoxic gene expression profile in the kidneys of patients with ANCA-associated cGN. Using an experimental model of cGN, we demonstrated that clonally expanded murine CD8+ T cells highly expressed the cytotoxic molecule granzyme B. Moreover, lack of CD8+ T cells or granzyme B resulted in an ameliorated course of cGN. This was associated with reduced cleaved caspase-3 induction in renal tissue cells. Our data indicate that clonally expanded cytotoxic CD8+ T cells have a previously unrecognized pathogenic function in aggravating immune-mediated kidney disease.
Age and musical training effects on auditory short-term, long-term, and working memory
Authors: Rubio G. Fernández , Olsen E. R. , Klarlund M. , Mallon O. , Carlomagno F. , Vuust P. , Kringelbach M.L. , Brattico E. , Bonetti L.
Published: September 2022

Cognitive aging is characterized by a gradual decline in cognitive functioning. One of the most worrying deficits for older adults is a decreased capacity to memorize and remember new information. In this study, we assessed auditory short-term memory (STM), long-term memory (LTM), and working memory (WM) abilities of young and older adults using musical and numerical tasks. Additionally, we measured musical training and tested whether this capacity influences memory performance. Regarding STM, young adults scored higher than older adults when making same/different judgements of rhythmic sequences, but their performance was alike for melodic sequences. Higher levels of musical training were associated with enhanced STM capacity for melodic sequences. In relation to LTM, young adults outperformed older adults in identifying new musical sequences. Moreover, younger and older individuals with high musical training outperformed those with low musical training. No group differences were found in the recognition of previously memorized musical sequences. Finally, we found no group differences in WM capacity, although there was a non-significant tendency for young adults to outperform older adults. Overall, we found that aging differently affects several types of auditory memory and that, for certain musical memory tasks, a higher level of musical training provides significant advantages.
Multivariable Graphical User Interface for Simulation of Tethered Particle Motion
Authors: Ramdin Khovesh A. , Hackl Markus , Chundawat Shishir P. S.
Published: September 2022

The analysis of particles bound to a surface by flexible tethers can facilitate understanding of various biophysical phenomena (e.g., molecular dynamics of DNA-protein or protein-ligand binding interactions, DNA extensibility and polymer biophysics). Being able to model such systems theoretically can aid in understanding experimentally observed motions and furthermore the limitations of such models can provide insight into modeling complex systems that basic theory sometimes cannot account for. The simulation of tethered particle motion (TPM) allows for efficient analysis of complex behaviors exhibited by such systems, however this type of experiment is rarely taught in undergraduate science classes. We have developed a MATLAB simulation package intended to be used in academic contexts to concisely model and graphically represent the behavior of different tether-particle systems. We show how analysis of the simulation results can be used in biophysical research employing single molecule force spectroscopy (SMFS). Here, our simulation package is capable of modeling any given particle-tether-substrate system and allows the user to generate a parameter space with static and dynamic model components. Our simulation was successfully able to recreate generally observed experimental trends using a recently developed SMFS technique called Acoustic Force Spectroscopy (AFS). Further, the simulation was validated through consideration of the conservation of energy of the tether-bead system, trend analyses, and comparison of particle positional data from actual TPM in silico experiments conducted to simulate data with a parameter space similar to the AFS experimental setup. Overall, our TPM simulator and graphical user interface is suitable for use in an academic context and serves as a template for researchers to set up TPM simulations to mimic their specific SMFS experimental setup.
Rapid Identity and Quantity CQA Test for Multivalent mRNA Drug Product Formulations
Authors: Gao Rachel Y. , Riley Christine M. , Toth Evan , Blair Rebecca H. , Gerold Megan N. , McCormick Caitlin , Taylor Amber W. , Hu Tianjing , Rowlen Kathy L. , Dawson Erica D.
Published: September 2022

The COVID-19 pandemic highlighted mRNA as a promising platform for vaccines and therapeutics. Many of the analytical tools used to characterize the critical quality attributes of mRNA are inherently singleplex and are not necessarily optimal from a labor and cost perspective. Here we demonstrate feasibility of a multiplexed platform (VaxArray) for efficient identity verification and concentration determination for both monovalent and multivalent mRNA formulations. A model system comprised of mRNA constructs for influenza hemagglutinin and neuraminidase was used to characterize the analytical performance metrics for a VaxArray mRNA assay. The assay presented herein had a time to result of less than 2 hours, required no PCR-based amplification nor extraction of mRNA from lipid nanoparticles, and exhibited high construct specificity that enabled application to the bivalent mixture. The sensitivity for influenza hemagglutinin and neuraminidase mRNA was sub-µg/mL, which is vaccine-relevant, and the average accuracy (%recovery) and precision were 104%±2%and 9%±2%, respectively.
Re-expression of CA1 and entorhinal activity patterns preserves temporal context memory at long timescales
Authors: Zou Futing , Guo Wanjia , Allen Emily J. , Wu Yihan , Charest Ian , Naselaris Thomas , Kay Kendrick , Kuhl Brice A. , Hutchinson J. Benjamin , DuBrow Sarah
Published: September 2022

Converging, cross-species evidence indicates that memory for time is supported by hippocampal area CA1 and entorhinal cortex. However, limited evidence characterizes how these regions preserve temporal memories over long timescales (e.g., months). At long timescales, memoranda may be encountered in multiple temporal contexts, potentially creating interference. Here, using 7T fMRI, we measured CA1 and entorhinal activity patterns as human participants viewed thousands of natural scene images distributed, and repeated, across many months. We show that memory for an image’s original temporal context was predicted by the degree to which CA1/entorhinal activity patterns from the first encounter with an image were re-expressed during re-encounters occurring minutes to months later. Critically, temporal memory signals were dissociable from predictors of recognition confidence, which were carried by distinct medial temporal lobe expressions. These findings suggest that CA1 and entorhinal cortex preserve temporal memories across long timescales by coding for and reinstating temporal context information.
Associations between thinner retinal neuronal layers and suboptimal brain structural integrity: Are the eyes a window to the brain?
Authors: Barrett-Young Ashleigh , Abraham Wickliffe C. , Cheung Carol Y. , Gale Jesse , Hogan Sean , Ireland David , Keenan Ross , Knodt Annchen R. , Melzer Tracy R. , Moffitt Terrie E. , Ramrakha Sandhya , Tham Yih Chung , Wilson Graham A. , Wong Tien Yin , Hariri Ahmad. R. , Poulton Richie
Published: September 2022

We investigated the extent to which measures of retinal neuronal thickness capture variability in the structural integrity of the brain in a large population-based cohort followed from birth to midlife. Using data from the Dunedin Multidisciplinary Health and Development Study (n=1037; analyticn=828, aged 45 years), we specifically tested for associations between optical coherence tomography-measured retinal neuronal layers and MRI-measured structural brain integrity. We found that Study members who had thinner retinal neuronal layers had thinner average cortex, smaller total cortical surface area, smaller subcortical grey matter volumes, larger volume of white matter hyperintensities as well as older looking brains. This suggests that retinal neuronal thickness reflects differences in midlife structural brain integrity consistent with accelerated cognitive decline and increased risk for later dementia, further supporting the proposition that the retina may be a biomarker of brain aging as early as midlife.
Fluorescent peptomer substrates for differential degradation by metalloproteases
Authors: Austin Mariah J. , Schunk Hattie C. , Watkins Carolyn M. , Ling Natalie R. , Chauvin Jeremy M. , Morton Logan D. , Rosales Adrianne M.
Published: September 2022

Proteases, especially MMPs, are attractive biomarkers given their central role in both physiological and pathological processes. Distinguishing MMP activity with degradable substrates, however, is a difficult task due to overlapping substrate specificity profiles. Here, we developed a system of peptomers (peptide-peptoid hybrids) to probe the impact of non-natural residues on MMP specificity for a MMP peptide consensus sequence. Peptoids are non-natural, N-substituted glycines with a large side chain diversity. Given the presence of a hallmark proline residue in the P3 position of MMP consensus sequences, we hypothesized that peptoids may offer N-substituted alternatives to generate differential interactions with MMPs. To investigate this hypothesis, peptomer substrates were exposed to five different MMPs, as well as bacterial collagenase, and monitored by fluorescence resonance energy transfer and liquid chromatography-mass spectrometry to determine the rate of cleavage and the composition of degraded fragments, respectively. We found that peptoid residues are well-tolerated in the P3 and P3’ substrate sites and that the identity of the peptoid in these sites displays moderate influence on the rate of cleavage. However, peptoid residues were even better tolerated in the P1 substrate site where activity was more strongly correlated with sidechain identity than sidechain position. All MMPs explored demonstrated similar trends in specificity for the peptomers but exhibited different degrees of variability in proteolytic rate. These kinetic profiles served as “fingerprints” for the proteases and yielded separation by multivariate data analysis. To further demonstrate practical application of this tunability in degradation kinetics, peptomer substrates were tethered into hydrogels and released over distinct timescales. Overall, this work represents a significant step toward the design of probes that maximize differential MMP behavior and presents design rules to tune degradation kinetics with peptoid substitutions, which has promising implications for diagnostic and prognostic applications using array-based sensors.
The anti-caspase 1 inhibitor VX-765 reduces immune activation, CD4+T cell depletion, viral load and total HIV-1 DNA in HIV-1 infected humanized mice
Authors: Amand Mathieu , Adams Philipp , Schober Rafaela , Iserentant Gilles , Servais Jean-Yves , Moutschen Michel , Seguin-Devaux Carole
Published: September 2022

Background

HIV-1 infection results in the activation of inflammasome involving NLRP3, IFI16, caspase-1 and release of IL-1 β and IL-18. Early inflammasome activation may facilitate viral spread and establishment of the viral reservoir. We evaluated the effect of the caspase-1 inhibitor VX-765 on virological and immunological parameters after HIV-1 infection in humanized mice.

Methods

NSG mice were engrafted with human CD34+hematopoietic stem cells and were infected with HIV-1 JRCSF. 15 mice were first sacrificed serially to investigate kinetics of the HIV-1 related inflammasome activation. Infected mice (n=24) were then treated with VX-765 or vehicle from day 1 post infection for 21 days. Blood and organs were collected at different time points, and analysed for inflammasome genes expression, cytokines levels, viral load, CD4 cell count, and total HIV-1 DNA.

Results

Expression of caspase-1, NLRP3 and IL1-β was increased in lymph nodes and bone marrow on day 1 and 3 post infection (mean fold change (FC) of 2.08, 3.23, and 6.05, p< 0.001 respectively between day 1 and 3). IFI16 expression peaked at D24 in lymph node and bone marrow (FC 1.49 and 1.64, p<0.05) and coincides with increased IL-18 levels in plasma (6.89 vs. 83.19 pg/ml, p=0.004). AIM2 and IFI16 expression correlated with increased viral load in tissues (p<0.005 for the spleen) and loss of CD4+T cells percentage in blood (p<0.0001 for the spleen). Treatment with VX-765 significantly reduced TNF-α at day 11 (0.47 vs. 2.2 pg/ml, p=0.045), IL-18 at day 22 (7.8 vs 23.2 pg/ml, p=0.04), CD4+T cells (44.3% vs 36,7%, p=0.01) and the CD4/CD8 ratio (0.92 vs 0.67, p=0.005) in plasma. Importantly, viral load (4.26 vs. 4.89 log 10 copies/ml, p=0.027) and total HIV-1 DNA (1 054 vs. 2 889 copies /106cells, p=0.029) were decreased in VX-765-treated mice as compared to vehicle-treated mice.

Discussion

we report here an early inflammasome activation before detectable viral dissemination in humanized mice. We demonstrated that targeting inflammasome activation early after HIV-1 infection may represent a potential therapeutic strategy to prevent CD4+T cell depletion as well as to reduce immune activation, viral load and the HIV-1 reservoir formation.
Differential scanning fluorimetry as a measure of functionality of refolded anti-malarial antibody fragments
Authors: Valiyaparambil Ashwathi , Jagannath Deepak K , Viswanath Vysakh K , Kumar Naveen , Shukla Jay Prakash , Pradhan Sabyasachi , Lakshminarasimhan Anirudha
Published: September 2022

Transmission blocking monoclonal antibodies, 4B7 and 1245, targeting Pfs25, have been demonstrated to block the developmental stages of the malarial parasite inside the mosquitoes. In this work, anti-Plasmodium antibody fragments of 4B7 and 1245, designated as diabodies, were expressed in bacteria and refolded using a standardized method, with a yield of 0.1 and 0.4 mg per litre of culture, respectively. Dimeric species was detected for 4B7-Db, but not for 1245-Db, using glutaraldehyde cross-linking experiment. The quality of the purified refolded fraction was assessed with differential scanning fluorimetry (DSF). Refolded 4B7-Db, with a melting temperature of 59°C, recognized Pfs25 expressed on the surface of ookinete and zygote stages of Plasmodium in an immunofluorescence-based assay, whereas, 1245-Db, exhibiting a skewed melt profile, showed weak recognition. Further, refolded 4B7-Db recognized the linear epitope, on purified Pfs25 protein, both in the denatured and native state. Differential scanning fluorimetry can be potentially employed as a qualitative measure of functionality, to evaluate refolded proteins, with applicability for antibody engineering in passive immunization.
Population structure and evolution of Salmonella enterica serotype Typhi in Zimbabwe before a typhoid conjugate vaccine immunization campaign
Authors: Thilliez Gaetan , Mashe Tapfumanei , Chaibva Blessmore V. , Robertson Valerie , Bawn Matt , Tarupiwa Andrew , Takawira Faustinos Tatenda , Kock Marleen M. , Midzi Stanley , Mwamakamba Lusubilo W. , Matheu Jorge , Kingsley Robert A. , Ehlers Marthie M.
Published: September 2022

Background

The continued emergence of Salmonella enterica serovar Typhi (S. Typhi) with ever increasing antimicrobial resistance (AMR), necessitates the use of vaccines in endemic countries. A typhoid fever outbreak in Harare, Zimbabwe in 2018 from a multidrug resistant S. Typhi with additional resistance to ciprofloxacin was the catalyst for the introduction of a typhoid conjugate vaccine program. To investigate the historic emergence and evolution of AMR of endemic S. Typhi in Zimbabwe and determined the population structure, gene flux and sequence polymorphisms of strains isolated prior to mass typhoid vaccination to provide a baseline for future evaluation of the effect of the vaccination program.

Methods

We determined the population structure, gene flux and sequence polymorphisms and reconstructed the evolution of AMR. The S. Typhi population structure was investigated in the context the genome sequence of 1904 strains isolated from 65 countries to reconstruct spread of endemic strains into Zimbabwe.

Findings

The population structure of S. Typhi in Zimbabwe is dominated by multidrug resistant genotype 4.3.1.1 (H58) that spread to Zimbabwe from neighboring countries around 2009. Evolution of AMR within Zimbabwe included acquisition of an IncN plasmid carrying a qnrS gene and a mutation in the quinolone resistance determining region of gyrA gene, both implicated in resistance to quinolone antibiotics. A minority population of antimicrobial susceptible S. Typhi genotype 3.3.1 strains was detected in typhoid cases.

Interpretation

The currently dominant S. Typhi population is genotype 4.3.1.1 that spread to Zimbabwe and acquired additional AMR though acquisition of a plasmid and mutation of the gyrA gene. This study provides a baseline for future evaluation of the impact of the Typhoid Conjugate Vaccine program in Harare.

Funding

RAK and GT were supported by Bill and Melinda Gates Foundation project OPP1217121 and the BBSRC Institute Strategic Programme BB/R012504/1 and its constituent project BBS/E/F/000PR10348.
MHC-II expressing neutrophils circulate in blood and milk during mastitis and show high microbicidal activity
Authors: Rambault Marion , Gilbert Florence B. , Roussel Philippe , Tessier Alexia , David Valérie , Germon Pierre , Winter Nathalie , Remot Aude
Published: September 2022

Bovine mastitis are mainly caused by bacterial infection. They are responsible for economic losses and have an impact on the health and welfare of animals. The increase in the somatic cell count in milk during mastitis is mainly due to the influx of neutrophils which have a crucial role in the elimination of pathogens. For a long time, these first line defenders has been view as microbes’ killers with limited role in the orchestration of the immune response. However, their role is more complex and we recently characterized a MHC-II expressing neutrophil subset with regulatory capacities in cattle. In this study, we questioned the implication of different neutrophils subsets in the mammary gland immunity during clinical and subclinical mastitis. Here, we described for the first time that, in blood as in milk, neutrophils are a heterogeneous population and encompass at least two subsets distinguishable with their expression of MHC-II. We observed higher bactericidal capacities of milk MHC-IIpos neutrophils as compared to their classical counterparts, due to a higher production of ROS and phagocytosis ability. MHC-IIpos neutrophils are enriched in milk during a subclinical mastitis as compared to blood. Moreover, we observed a positive and highly significant correlation between MHC-IIpos neutrophils and T lymphocytes present in milk during subclinical mastitis. To conclude, our study could open the way to the discovery of new biomarkers of mastitis inflammation.
Risk factors and spatiotemporal analysis of classical swine fever in Ecuador
Authors: Acosta Alfredo , Dietze Klaas , Baquero Oswaldo , Vizzotto Osowski Germana , Imbacuan Christian , Burbano Lidia Alexandra , Ferreira Fernando , Depner Klaus
Published: September 2022

1.

Classical swine fever (CSF) is one of the most important re-emergent swine diseases worldwide. Despite concerted control efforts in the Andean countries, the disease remains endemic in several areas, limiting production and trade opportunities. In this study, we aim to determine herd-level risk factors and spatiotemporal implications associated with CSF. We analysed passive surveillance datasets and vaccination programmes from 2014 to 2020; Then, structured a herd-level case-control study using a multivariable logistic model containing 339 cases, and a spatiotemporal Bayesian model, considering 115 thousand premises, 2.3 million annual vaccine doses and a population of 1.6 million pigs distributed in 1,006 parishes. Our results showed that the risk factors that increased the odds of CSF occurrence were swill feeding (OR 9.28), time of notification (OR 2.18), animal entry in the last 30 days (OR 2.08), lack of CSF vaccination (OR 1.88), age of animals between 3-6 months (OR 1.58) and being in the coastal region (OR 1.87). Spatiotemporal models showed that the vaccination campaign reduced the risk by 33% while temperature increased the risk by 17%. The calculated priority index aims to facilitate the intervention process that should be focused on a couple of provinces, mainly in Morona Santiago and Los Rios as well as in specific parishes around the country. Our findings provide insight and understanding of the risk factors associated with CSF in Ecuador, which stands for the Andean region; even though the results are specific for the implementation of risk-based surveillance for CSF, data and methods could be valuable for the prevention and control of diseases such as African swine fever, or porcine reproductive and respiratory syndrome. In conclusion, the results highlight the complexity of the CSF control programme, the need to inform decision-makers, involve stakeholders and implement better strategies to update continental health policies to eradicate swine diseases.
Enhanced Effector Activity of Mediator Kinase Module Deficient CAR-T Cells
Authors: Freitas Katherine A. , Belk Julia A. , Sotillo Elena , Daniel Bence , Sandor Katalin , Klysz Dorota , Duong Vandon T. , Burdsall Kylie , Xu Peng , Malipatlolla Meena , Donovan Micah G. , Weber Evan W. , Majzner Robbie G. , Chang Howard Y. , Espinosa Joaquin M. , Satpathy Ansuman T. , Mackall Crystal L.
Published: September 2022

Adoptive T cell immune therapies mediate impressive clinical benefit in a fraction of patients, but anti-tumor effects are often limited by inadequate T cell potency. To identify genes limiting T cell effector function, we conducted genome-wide CRISPR knock-out screens in human primary CAR-T cells. The top hits were MED12 and CCNC, components of the cyclin-dependent kinase (CDK) module of the Mediator complex, an evolutionarily conserved regulator of gene transcription. MED12 or CCNC deficient CAR-T cells manifest increased expansion, cytokine production, metabolic fitness, effector function, anti-tumor activity and reduced terminal effector differentiation. Chemical inhibition of CDK8/19 kinase activity recapitulated some features of genetic loss of MED12, including increased T cell expansion. MED12 deficient CAR-T cells showed widespread but selective increases in chromatin accessibility, MED1 chromatin occupancy, and H3K27 acetylation at enhancers used by transcription factors playing a critical role in T cell fate, including several STAT and AP1 family members. The most pronounced enhancement was observed for STAT5 which manifested as increased sensitivity to IL-2 in MED12 deficient T cells. These results link Mediator induced transcriptional coactivation with T cell effector programming and identify the CDK module as a target for enhancing the potency of anti-tumor T cell responses.

One Sentence Summary

The Mediator kinase module is a primary regulator of T cell differentiation, and genetic or small molecule-based inhibition of this module enhances effector T cell potency.
Parity modulates impact of BMI and Gestational Weight Gain on gut microbiota in human pregnancy
Authors: Kennedy Katherine M. , Plagemann Andreas , Sommer Julia , Hofmann Marie , Henrich Wolfgang , Barrett Jon F.R. , Surette Michael G. , Atkinson Stephanie , Braun Thorsten , Sloboda Deborah M.
Published: September 2022

Pregnancy requires maternal adaptations to support fetal growth: whether these adaptations include temporal shifts in the gut microbiome is still unclear. We investigated the maternal gut microbiome longitudinally over the course of pregnancy and the impact of pre-pregnancy BMI (pBMI) and GWG. We also determined whether parity modulated observed associations. We show that the gut microbiota of participants with higher pBMI changed less over the course of pregnancy in primiparous, but not multiparous participants. This suggests that previous pregnancies may have persistent impacts on maternal adaptations to pregnancy. This ecological memory appears to be passed to the next generation, as parity modulated the impact of maternal GWG on the infant gut microbiome. This work supports a role for the gut microbiome in maternal adaptations to pregnancy and highlights the need for longitudinal sampling and accounting for parity as key considerations for studies of the microbiome in pregnancy and infants.
Modular Streaming Pipeline of Eye/Head Tracking Data Using Tobii Pro Glasses 3
Authors: Nasrabadi Hamed Rahimi , Alonso Jose-Manuel
Published: September 2022

Abstract

Head-mounted tools for eye/head tracking are increasingly used for assessment of visual behavior in navigation, sports, sociology, and neuroeconomics. Here we introduce an open-source python software (TP3Py) for collection and analysis of portable eye/head tracking signals using Tobii Pro Glasses 3. TP3Py’s modular pipeline provides a platform for incorporating user-oriented functionalities and comprehensive data acquisition to accelerate the development in behavioral and tracking research. Tobii Pro Glasses 3 is equipped with embedded cameras viewing the visual scene and the eyes, inertial measurement unit (IMU) sensors, and video-based eye tracker implemented in the accompanying unit. The program establishes a wireless connection to the glasses and, within separate threads, continuously leverages the received data in numerical or string formats accessible for saving, processing, and graphical purposes. Built-in modules for presenting eye, scene, and IMU data to the experimenter have been adapted as well as communicating modules for sending the raw signals to stimulus/task controllers in live fashion. Closed-loop experimental designs are limited due to the 140ms time delay of the system, but this limitation is compensated by the portability of the eye/head tracking. An offline data viewer has been also incorporated to allow more time-consuming computations. Lastly, we demonstrate example recordings involving vestibulo-ocular reflexes, saccadic eye movements, optokinetic responses, or vergence eye movements to highlight the program’s measurement capabilities to address various experimental goals. TP3Py has been tested on Windows with Intel processors, and Ubuntu operating systems with Intel or ARM (Raspberry Pie) architectures.
Hippocampal-cortical functional connectivity during memory encoding and retrieval
Authors: Raud Liisa , Sneve Markus H. , Vidal-Piñeiro Didac , Sørensen Øystein , Folvik Line , Ness Hedda T. , Mowinckel Athanasia M. , Grydeland Håkon , Walhovd Kristine B. , Fjell Anders M.
Published: September 2022

Memory encoding and retrieval are critical sub-processes of episodic memory. While the hippocampus is involved in both, its connectivity with the neocortex during memory processing in humans has been elusive. This is partially due to variations in demands in common memory tasks, which inevitably recruit cognitive processes other than episodic memory. Conjunctive analysis of data from different tasks with the same core elements of encoding and retrieval can reduce the intrusion of patterns related to subsidiary perceptual and cognitive processing. Leveraging data from two large-scale functional resonance imaging studies with different episodic memory tasks (514 and 237 participants), we identified core hippocampal-cortical networks active during memory processing. Anterior and posterior hippocampus had distinct connectivity profiles, which were stable across resting state and memory tasks. Whereas no encoding-specific connectome emerged across tasks, during retrieval hippocampal connectivity was increased with areas known to be active during recollection, including medial prefrontal, inferior parietal, and parahippocampal cortices. This indicates that the stable functional connectivity of the hippocampus along its longitudinal axis is superposed by increased functional connectivity with the recollection network during retrieval, while encoding connectivity likely reflects contextual factors.
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
Authors: Neron Bertrand , Denise Remi , Coluzzi Charles , Touchon Marie , Rocha Eduardo P. C. , Abby Sophie S.
Published: September 2022

Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models' constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.
Elongation of Very Long Chain Fatty Acids Like- 3 (Elovl3) is activated by ZHX2 and is a regulator of cell cycle progression
Authors: Creasy Kate Townsend , Ren Hui , Jiang Jieyun , Peterson Martha L. , Spear Brett T.
Published: September 2022

Zinc fingers and homeoboxes 2 (ZHX2) functions as a tumor suppressor in several models of hepatocellular carcinoma (HCC), presumably through its control of target genes. Previous microarray data suggested that Elongation of Very Long Chain Fatty Acids 3 (Elovl3), a member of the Elovl family which synthesize very long chain fatty acids (VLCFAs), is a putative ZHX2 target gene. VLCFAs are core component of ceramides and other bioactive sphingolipids, which are often dysregulated in diseases, including HCC. Since several previously identified ZHX2 targets become dysregulated in HCC, we investigated the relationship between ZHX2 and Elovl3 in liver damage and HCC. Here, using mouse and cell models, we demonstrate that Zhx2 positively regulates Elovl3 expression in the liver and that male-biased hepatic Elovl3 expression is established between 4-8 weeks of age in mice. Elovl3 is dramatically repressed in mouse models of liver regeneration and HCC and the reduced Elovl3 levels in the regenerating liver are associated with changes in hepatic very long chain fatty acids. Human hepatoma cell lines with forced Elovl3 expression have lower rates of cell growth; analysis of synchronized cells indicate that this reduced proliferation correlates with cells stalling in S-phase. Taken together, these data indicate that Elovl3 expression helps regulate cellular proliferation, possibly through control of VLCFAs, and its repression may be a contributing factor to HCC and explain, in part, the function of ZHX2 as a suppressor of HCC progression.
Metabolic integration of spectral and chemical cues mediating plant responses to competitors and herbivores
Authors: Chautá Alexander , Kessler André
Published: September 2022

Light quality and chemicals in a plant’s environment can provide crucial information about the presence and nature of antagonists, such as competitors and herbivores. Here we evaluate the roles of three sources of information - shifts in the red:far red (FR) ratio of light reflected off of potentially competing neighbors, induced metabolic changes to damage by insect herbivores, and induced changes to volatile organic compounds emitted from herbivore–damaged neighboring plants - to affect metabolic responses in the tall goldenrod, Solidago altissima. We address the hypothesis, that plants integrate the information available about competitors and herbivory to optimize metabolic responses to interacting stressors by exposing plants to the different types of environmental information in isolation and combination. We found strong interactions between the exposure to decreased Red:FR light ratios and damage on the induction of secondary metabolites (volatile and non-volatile) in the receiver plants. Similarly, the perception of VOCs emitted from neighboring plants was altered by the simultaneous exposure to spectral cues from neighbors. These results suggest that plants integrate spectral and chemical environmental cues to change the production and perception of volatile and non-volatile compounds and highlight the role of plant context-dependent metabolic responses in mediating population and community dynamics.

Highlight

Plants integrate spectral and chemical environmental cues to differentially induce production of volatile and non-volatile compounds
Tyramine and itsAmtyr1receptor modulate attention in honey bees (Apis mellifera)
Authors: Latshaw Joseph S , Mazade Reece E , Petersen Mary , Mustard Julie A , Sinakevitch Irina , Wissler Lothar , Guo Xiaojiao , Cook Chelsea N. , Lei Hong , Gadau Jürgen , Smith Brian H
Published: September 2022

Animals must learn to ignore stimuli that are irrelevant to survival and attend to ones that enhance survival. When a stimulus regularly fails to be associated with an important consequence, subsequent excitatory learning about that stimulus can be delayed, which is a form of non-associative conditioning called ‘latent inhibition’. Honey bees show latent inhibition toward an odor they have experienced without association with food reinforcement. Moreover, individual honey bees from the same colony differ in the degree to which they show latent inhibition, and these individual differences have a genetic basis. To investigate the mechanisms that underly individual differences in latent inhibition, we selected two honey bee lines for high and low latent inhibition, respectively. We crossed those lines and mapped a Quantitative Trait Locus (QTL) for latent inhibition to a region of the genome that contains the tyramine receptor geneAmtyr11. We then show that disruption ofAmtyr1signaling either pharmacologically or through RNAi qualitatively changes the expression of latent inhibition but has little effect on appetitive conditioning, and these results suggest that AmTYR1 modulates inhibitory processing in the CNS. Electrophysiological recordings from the brain during pharmacological blockade are consistent with a model that AmTYR1 indirectly regulates Hebbian plasticity at inhibitory synapses in the CNS. Finally, sequencingAmtyr1and its up and downstream genomic region for high and low line workers suggested that individual differences might arise from variation in transcriptional control rather than structural changes in the coding region. Our results therefore identify a distinct modulatory pathway for this type of non-associative learning, and we propose a model for how it modulates Hebbian plasticity at defined synapses in the CNS. We have shown elsewhere how this modulation also underlies potentially adaptive intracolonial learning differences among individuals that benefit colony survival.
Zinc Fingers and Homeoboxes 2 is Required for Diethylnitrosamine-induced Liver Tumor Formation in C57BL/6 Mice
Authors: Jiang Jieyun , Turpin Courtney , Qiu Guofang (Shirley) , Xu Mei , Lee Eun , Hinds Terry D. , Peterson Martha L. , Spear Brett T.
Published: September 2022

Liver cancer, comprised mainly of hepatocellular carcinoma (HCC), is the third leading cause of cancer deaths worldwide and increasing in Western countries. We previously identified the transcription factor Zinc Fingers and Homeoboxes 2 (Zhx2) as a regulator of hepatic gene expression, and many Zhx2 target genes are dysregulated in HCC. Here, we investigate HCC in Zhx2-deficient mice using the Diethylnitrosamine (DEN)-induced liver tumor model. Our study using whole-body Zhx2 knock-out (Zhx2KO) mice revealed the complete absence of liver tumors 9 and 10 months after DEN exposure.Analysis soon after DEN treatment showed no differences in expression of the DEN bioactivating enzyme CYP2E1 and DNA polymerase delta 2, or in the numbers of γH2AX foci between Zhx2KO and wild-type (Zhx2wt) mice. The absence of Zhx2, therefore, did not alter DEN bioactivation or DNA damage. Zhx2KO livers showed fewer positive foci for Ki67 staining and reduced IL-6 and AKT2 expression compared to Zhx2wt livers, suggesting that Zhx2 loss reduces liver cell proliferation and may account for reduced tumor formation. Tumors were reduced but not absent in DEN-treated liver-specific Zhx2 knock-out mice, suggesting that Zhx2 acts in both hepatocytes and non-parenchymal cells to inhibit tumor formation. Analysis of data from The Cancer Genome Atlas and Clinical Proteomic Tumor Consortium indicated that ZHX2 mRNA and protein levels were significantly higher in HCC patients and associated with clinical pathological parameters.

Conclusions

In contrast to previous studies in human hepatoma cell lines and other HCC mouse models showing that Zhx2 acts as a tumor suppressor, our data indicate that Zhx2 acts as an oncogene in the DEN-induced HCC model and is consistent with the higher ZHX2 expression in HCC patients.
Hsp90 provides a platform for kinase dephosphorylation by PP5
Authors: Jaime-Garza Maru , Nowotny Carlos , Coutandin Daniel , Wang Feng , Tabios Mariano , Agard David A.
Published: September 2022

The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone to maintain kinase proteostasis through the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is activated by phosphorylation at specific regulatory sites. The cochaperone phosphatase PP5 dephosphorylates CRaf but also Cdc37 in an Hsp90-dependent manner. Although dephosphorylating Cdc37 has been proposed as a mechanism for releasing Hsp90-bound kinases, here we show that Hsp90 bound kinases sterically inhibit Cdc37 dephosphorylation indicating kinase release must occur before Cdc37 dephosphorylation. The cryo-EM structure of PP5 in complex with Hsp90:Cdc37:CRaf reveals how Hsp90 both activates PP5 and scaffolds its association with the bound CRaf to dephosphorylate a site at the C-terminus of the kinase domain. Thus, we directly show how Hsp90’s role in maintaining protein homeostasis goes beyond folding and activation to include post translationally modifying its client kinases.
A Beefy-R culture medium: replacing albumin with rapeseed protein isolates
Authors: Stout Andrew J. , Rittenberg Miriam L. , Shub Michelle , Saad Michael K. , Mirliani Addison B. , Kaplan David L.
Published: September 2022

The development of cost-effective serum-free media is essential for the economic viability of cultured meat. A key challenge facing this goal is high-cost recombinant albumin that is necessary in some available serum-free media formulations. As such, there is substantial interest in finding albumin alternatives which are low-cost, effective, scalable, sustainable, and suitable for food applications. Recently, a serum-free medium termed Beefy-9 was developed for bovine satellite cells (BSCs), which relied on recombinant albumin as a key component to replace fetal bovine serum. Here we alter Beefy-9 by replacing albumin with rapeseed protein isolate, a bulk-protein solution obtained from agricultural waste-streams through simple isoelectric protein precipitation. This new medium, termed Beefy-R, improves BSC growth compared with Beefy-9 while maintaining cell phenotype and myogenicity. These results offer an effective, low-cost, and sustainable alternative to albumin for serum-free culture of muscle stem cells, thereby addressing a key hurdle facing cultured meat production.