bluuebunny/crossref_metadata_2025 huggingface dataset:
Cortical and thalamic influences on striatal involvement in instructed, serial reversal learning; implications for the organisation of flexible behaviour
Authors: Williams Brendan , Christakou Anastasia
Published: December 2021

Cognitive flexibility is essential for enabling an individual to respond adaptively to changes in their environment. Evidence from human and animal research suggests that the control of cognitive flexibility is dependent on an array of neural architecture. Cortico-basal ganglia circuits have long been implicated in cognitive flexibility. In particular, the role of the striatum is pivotal, acting as an integrative hub for inputs from the prefrontal cortex and thalamus, and modulation by dopamine and acetylcholine. Striatal cholinergic modulation has been implicated in the flexible control of behaviour, driven by input from the centromedian-parafascicular nuclei of the thalamus. However, the role of this system in humans is not clearly defined as much of the current literature is based on animal work. Here, we aim to investigate the roles corticostriatal and thalamostriatal connectivity in serial reversal learning. Functional connectivity between the left centromedian-parafascicular nuclei and the associative dorsal striatum was significantly increased for negative feedback compared to positive feedback. Similar differences in functional connectivity were observed for the right lateral orbitofrontal cortex, but these were localised to when participants switched to using an alternate response strategy following reversal. These findings suggest that connectivity between the centromedian-parafascicular nuclei and the striatum may be used to generally identify potential changes in context based on negative outcomes, and the effect of this signal on striatal output may be influenced by connectivity between the lateral orbitofrontal cortex and the striatum.
MIAAIM: Multi-omics image integration and tissue state mapping using topological data analysis and cobordism learning
Authors: Hess Joshua M. , Ilieş Iulian , Schapiro Denis , Iskra John J. , Abdelmoula Walid M. , Regan Michael S. , Theocharidis Georgios , Wu Chin Lee , Veves Aristidis , Agar Nathalie Y.R. , Sluder Ann E. , Poznansky Mark C. , Reeves Patrick M. , Sîrbulescu Ruxandra F.
Published: December 2021

High-parameter tissue imaging enables detailed molecular analysis of single cells in their spatial environment. However, the comprehensive characterization and mapping of tissue states through multimodal imaging across different physiological and pathological conditions requires data integration across multiple imaging systems. Here, we introduce MIAAIM (Multi-omics Image Alignment and Analysis by Information Manifolds) a modular, reproducible computational framework for aligning data across bioimaging technologies, modeling continuities in tissue states, and translating multimodal measures across tissue types. We demonstrate MIAAIM’s workflows across diverse imaging platforms, including histological stains, imaging mass cytometry, and mass spectrometry imaging, to link cellular phenotypic states with molecular microenvironments in clinical biopsies from multiple tissue types with high cellular complexity. MIAAIM provides a robust foundation for the development of computational methods to integrate multimodal, high-parameter tissue imaging data and enable downstream computational and statistical interrogation of tissue states.
Inductive inference of novel protein-molecule interactions using Heterogeneous Graph Transformer (HGT) AutoEncoder
Authors: Arrigoni Alberto
Published: December 2021

1

Protein-molecule interactions are promoted by the physicochemical characteristics of the actors involved, but structural information alone does not capture expression patterns, localization and pharmacokinetics. In this work we propose an integrative strategy for protein-molecule interaction discovery that combines different layers of information through the use of convolutional operators on graph, and frame the problem as missing link prediction task on an heterogeneous graph constituted by three node types: 1) molecules 2) proteins 3) diseases. Physicochemical information of the actors are encoded using shallow embedding techniques (SeqVec, Mol2Vec, Doc2Vec respectively) and are supplied as feature vectors to a Graph AutoEncoer (GAE) that uses a Heterogeneous Graph Transformer (HGT) in the encoder module. We show in this work that HGT Autoencoder can be used to accurately recapitulate the proteinmolecule interactions set and propose novel relationships in inductive settings that are grounded in biological and functional information extracted from the graph.
Transcriptomes and metabolism define mouse and human MAIT cell heterogeneity
Authors: Chandra Shilpi , Ascui Gabriel , Riffelmacher Thomas , Chawla Ashu , Ramirez-Suastegui Ciro , Castelan Viankail Cedillo , Seumois Gregory , Simon Hayley , Murray Mallory Paynich , Seo Goo-Young , Premlal Ashmitaa Logandha Ramamoorthy , Verstichel Greet , Li Yingcong , Lin Chia-Hao , Greenbaum Jason , Lamberti John , Murthy Raghav , Nigro John , Cheroutre Hilde , Ottensmeier Christian H. , Hedrick Stephen M. , Lu Li-Fan , Vijayanand Pandurangan , Kronenberg Mitchell
Published: December 2021

Mucosal-associated invariant T (MAIT) cells are a subpopulation of T lymphocytes that respond to microbial metabolites. We performed single-cell RNA sequencing and metabolic analyses of MAIT cell subsets in thymus and peripheral tissues from mice and humans to define the heterogeneity and developmental pathway of these innate-like lymphocytes. We show that the predominant mouse subset, which produces IL-17 (MAIT17), and the subset that produces IFNγ (MAIT1), have greatly different transcriptomes and metabolic states in the thymus and periphery. A splenic MAIT subset has a transcriptome similar to circulating lymphocytes, and in mice these also are found in recent thymic emigrants, suggesting partially mature cells emigrate from the thymus. Human MAIT cells are predominantly MAIT1 cells, but have a different metabolism from their mouse counterparts with increased fatty acid uptake and storage. Although mouse and human subsets are similar in thymus, in the periphery they diverge, likely reflecting environmental influences.
The origins and functional effects of postzygotic mutations throughout the human lifespan
Authors: Rockweiler Nicole B. , Ramu Avinash , Nagirnaja Liina , Wong Wing H. , Noordam Michiel J. , Drubin Casey W. , Huang Ni , Miller Brian , Todres Ellen Z. , Vigh-Conrad Katinka A. , Zito Antonino , Small Kerrin S. , Ardlie Kristin G. , Cohen Barak A. , Conrad Donald F.
Published: December 2021

Postzygotic mutations (PZMs) begin to accrue in the human genome immediately after fertilization, but how and when PZMs affect development and lifetime health remains unclear. To study the origins and functional consequences of PZMs, we generated a multi-tissue atlas of PZMs from 948 donors using the final major release of the Genotype-Tissue Expression (GTEx) project. Nearly half the variation in mutation burden among tissue samples can be explained by measured technical and biological effects, while 9% can be attributed to donor-specific effects. Through phylogenetic reconstruction of PZMs, we find that their type and predicted functional impact varies during prenatal development, across tissues, and the germ cell lifecycle. Remarkably, a class of prenatal mutations was predicted to be more deleterious than any other category of genetic variation investigated and under positive selection as strong as somatic mutations in cancers. In total, the data indicate that PZMs can contribute to phenotypic variation throughout the human lifespan, and, to better understand the relationship between genotype and phenotype, we must broaden the long-held assumption of one genome per individual to multiple, dynamic genomes per individual.

One-Sentence Summary

The predicted rates, functional effects and selection pressure of postzygotic mutations vary through the human lifecycle.
Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data
Authors: Schmid Clemens , Schiffels Stephan
Published: December 2021

The recent increase in openly available ancient human DNA samples allows for new, large-scale meta analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to, since changes in ancestry – unlike cultural changes seen in the archaeological record – necessarily reflect movements of people. Here we present a new algorithm to quantify past human mobility from large ancient genomic datasets. The key idea of the method is for each individual to compare a hypothetical genetic “origin” point with its actual burial point in space. This is achieved by first creating an interpolated ancestry field through space and time based on Multidimensional scaling and Gaussian process regression, and then using this field to map the ancient individuals into space according to their genetic profile. We apply this new algorithm to a dataset of 3191 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 years and derive a diachronic measure of mobility for subregions in Western, Central, Southern and Eastern Europe. For regions and periods with sufficient data coverage, our mobility estimates show general concordance with previous results, but also reveal new signals of movements beyond the well-known key events.

Significance Statement

Ancient human DNA (aDNA) extracted from archaeological contexts (e.g. burials) allows to reconstruct past population movements. Relevant methods work by calculating proportions of shared ancestry among individuals or groups in order to answer specific, regional research questions. Here, we propose a largescale algorithm to quantify human mobility through time and space using bulk aDNA data. The algorithm has two core components: i) Interpolation of the spatio-temporal distribution of genetic ancestry to obtain a continuous ancestry information field and ii) estimation of the spatial origin of each input sample by projecting its ancestry into this field. We apply this to thousands of published genomic samples in the last 10,000 years to trace diachronic mobility patterns across Western Eurasia.
Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues
Authors: Wang Shengbo , García-Seisdedos David , Prakash Ananth , Kundu Deepti Jaiswal , Collins Andrew , George Nancy , Fexova Silvie , Moreno Pablo , Papatheodorou Irene , Jones Andrew R. , Vizcaíno Juan Antonio
Published: December 2021

The increasingly large amount of proteomics data in the public domain enables, among other applications, the combined analyses of datasets to create comparative protein expression maps covering different organisms and different biological conditions. Here we have reanalysed public proteomics datasets from mouse and rat tissues (14 and 9 datasets, respectively), to assess baseline protein abundance. Overall, the aggregated dataset contained 23 individual datasets, including a total of 211 samples coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively.

In all cases, we studied the distribution of canonical proteins between the different organs. The number of canonical proteins per dataset ranged from 273 (tendon) and 9,715 (liver) in mouse, and from 101 (tendon) and 6,130 (kidney) in rat. Then, we studied how protein abundances compared across different datasets and organs for both species. As a key point we carried out a comparative analysis of protein expression between mouse, rat and human tissues. We observed a high level of correlation of protein expression among orthologs between all three species in brain, kidney, heart and liver samples, whereas the correlation of protein expression was generally slightly lower between organs within the same species. Protein expression results have been integrated into the resource Expression Atlas for widespread dissemination.

Author summary

We have reanalysed 23 baseline mass spectrometry-based public proteomics datasets stored in the PRIDE database. Overall, the aggregated dataset contained 211 samples, coming from 34 different tissues across 14 organs, comprising 9 mouse and 3 rat strains, respectively. We analysed the distribution of protein expression across organs in both species. We also studied how protein abundances compared across different datasets and organs for both species. Then we performed gene ontology and pathway enrichment analyses to identify enriched biological processes and pathways across organs. We also carried out a comparative analysis of baseline protein expression across mouse, rat and human tissues, observing a high level of expression correlation among orthologs in all three species, in brain, kidney, heart and liver samples. To disseminate these findings, we have integrated the protein expression results into the resource Expression Atlas.
Therapeutic potential of methylxanthine drug on alpha synuclein protein in Parkinson’s disease
Authors: Rana Nishant Kumar , Srivastava Neha , Kumar Bhupendra , Pathak Abhishek , Mishra Vijay Nath
Published: December 2021

Parkinson’s disease (PD) is the second most common neurodegenerative disorder after Alzheimer. It exists in sporadic (90 to 95%) and familial (5 to 10%) form. Its pathogenesis is due to oxidative stress, glutamate excitotoxicity, protein aggregation, neuroinflammation and neurodegeneration. There is currently no cure for this disease. The protein-protein interaction and gene ontology/functional enrichment analysis have been performed to find out the prominent interactor protein and shared common biological pathways, especially PD pathway. Further in silico docking analysis was performed on target protein to investigate the prominent drug molecule for PD. Through computational molecular virtual screening of small molecules from selected twelve natural compounds, and among these compounds methylxanthine was shown to be prominent inhibitor to SNCA protein that ultimately prevent PD. The interaction of methylxanthine compound with the target protein SNCA suggested that, it interacted with prominent binding site with good docking score and might be involved in blocking the binding of neuroinducing substances like: 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) to SNCA protein. Thus methylxanthine compounds can be explored as promising drugs for the prevention of Parkinson’s disease.
BESFA: Bioinformatics based Evolutionary, Structural & Functional Analysis of Prostrate, Placenta, Ovary, Testis, and Embryo (POTE) Paralogs
Authors: Qazi Sahar , Jit Bimal Prasad , Das Abhishek , Karthikeyan Muthukumarasamy , Saxena Amit , Ray M.D , Singh Angel Rajan , Raza Khalid , Jayaram B. , Sharma Ashok
Published: December 2021

The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins’ structure, function, and Adaptive Divergence. Our result discerns that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study’s outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.
fastMSA: Accelerating Multiple Sequence Alignment with Dense Retrieval on Protein Language
Authors: Hong Liang , Sun Siqi , Zheng Liangzhen , Tan Qingxiong , Li Yu
Published: December 2021

Evolutionarily related sequences provide information for the protein structure and function. Multiple sequence alignment, which includes homolog searching from large databases and sequence alignment, is efficient to dig out the information and assist protein structure and function prediction, whose efficiency has been proved by AlphaFold. Despite the existing tools for multiple sequence alignment, searching homologs from the entire UniProt is still time-consuming. Considering the success of AlphaFold, foreseeably, large- scale multiple sequence alignments against massive databases will be a trend in the field. It is very desirable to accelerate this step. Here, we propose a novel method, fastMSA, to improve the speed significantly. Our idea is orthogonal to all the previous accelerating methods. Taking advantage of the protein language model based on BERT, we propose a novel dual encoder architecture that can embed the protein sequences into a low-dimension space and filter the unrelated sequences efficiently before running BLAST. Extensive experimental results suggest that we can recall most of the homologs with a 34-fold speed-up. Moreover, our method is compatible with the downstream tasks, such as structure prediction using AlphaFold. Using multiple sequence alignments generated from our method, we have little performance compromise on the protein structure prediction with much less running time. fastMSA will effectively assist protein sequence, structure, and function analysis based on homologs and multiple sequence alignment.
Revisiting the number of self-incompatibility alleles in finite populations: from old models to new results
Authors: Czuppon Peter , Billiard Sylvain
Published: December 2021

Under gametophytic self-incompatibility (GSI), plants are heterozygous at the self-incompatibility locus (S-locus) and can only be fertilized by pollen with a different allele at that locus. The last century has seen a heated debate about the correct way of modeling the allele diversity in a GSI population that was never formally resolved. Starting from an individual-based model, we derive the deterministic dynamics as proposed by Fisher (1958), and compute the stationary S-allele frequency distribution. We find that the stationary distribution proposed by Wright (1964) is close to our theoretical prediction, in line with earlier numerical confirmation. Additionally, we approximate the invasion probability of a new S-allele, which scales inversely with the number of resident S-alleles. Lastly, we use the stationary allele frequency distribution to estimate the population size of a plant population from an empirically obtained allele frequency spectrum, which complements the existing estimator of the number of S-alleles. Our expression of the stationary distribution resolves the long-standing debate about the correct approximation of the number of S-alleles and paves the way to new statistical developments for the estimation of the plant population size based on S-allele frequencies.
Cellular development and evolution of the mammalian cerebellum
Authors: Sepp Mari , Leiss Kevin , Sarropoulos Ioannis , Murat Florent , Okonechnikov Konstantin , Joshi Piyush , Leushkin Evgeny , Mbengue Noe , Schneider Céline , Schmidt Julia , Trost Nils , Spänig Lisa , Giere Peter , Khaitovich Philipp , Lisgo Steven , Palkovits Miklós , Kutscher Lena M. , Anders Simon , Cardoso-Moreira Margarida , Pfister Stefan M. , Kaessmann Henrik
Published: December 2021

The expansion of the neocortex, one of the hallmarks of mammalian evolution1,2, was accompanied by an increase in the number of cerebellar neurons3. However, little is known about the evolution of the cellular programs underlying cerebellum development in mammals. In this study, we generated single-nucleus RNA-sequencing data for ∼400,000 cells to trace the development of the cerebellum from early neurogenesis to adulthood in human, mouse, and the marsupial opossum. Our cross-species analyses revealed that the cellular composition and differentiation dynamics throughout cerebellum development are largely conserved, except for human Purkinje cells. Global transcriptome profiles, conserved cell state markers, and gene expression trajectories across neuronal differentiation show that the cerebellar cell type-defining programs have been overall preserved for at least 160 million years. However, we also discovered differences. We identified 3,586 genes that either gained or lost expression in cerebellar cells in one of the species, and 541 genes that evolved new expression trajectories during neuronal differentiation. The potential functional relevance of these cross-species differences is highlighted by the diverged expression patterns of several human disease-associated genes. Altogether, our study reveals shared and lineage-specific programs governing the cellular development of the mammalian cerebellum, and expands our understanding of the evolution of mammalian organ development.
Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain.
Authors: Etherington Graham John , Ciezarek Adam , Shaw Rebecca , Michaux Johan , Croose Elizabeth , Haerty Wilfried , Di Palma Federica
Published: December 2021

The European polecat (Mustela putorius) is a mammalian predator which occurs across much of Europe east to the Ural Mountains. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as pure polecats. We quantify this introgression and find introgressed genes under selection that may assist in cognitive function and sight.
TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses
Authors: Barrat-Charlaix Pierre , Vaughan Timothy G. , Neher Richard A.
Published: December 2021

When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortments events from viral sequence data, little is known about its role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments.
Δ9-tetrahydrocannabinol (THC) vapor exposure produces conditioned place preference in male and female rats
Authors: Moore Catherine F. , Davis Catherine M. , Sempio Cristina , Klawitter Jost , Christians Uwe , Weerts Elise M.
Published: December 2021

Background

The use of place conditioning procedures and drug vapor exposure models can increase our understanding of the rewarding and aversive effects of vaped cannabis products. Currently there are limited data on the conditioned rewarding effects of vaporized Δ9-tetrahydrocannabinol (THC), the primary psychoactive constituent of cannabis in rats, and no studies to date examining sex differences.

Methods

Male and female Sprague-Dawley rats (N=96; 12 per sex/group) underwent place conditioning sessions immediately after exposure to THC or vehicle (propylene glycol, PG) vapor. Locomotor activity was measured by beam breaks during conditioning sessions. THC vapor-conditioned rats received one of three THC vapor exposure amounts (low: 5 puffs of 100 mg/ml THC, medium: 5 puffs of 200 mg/ml THC, or high: 10 puffs of 200 mg/ml THC) and matched vehicle vapor (PG) exposure on alternate days for 16 daily sessions. A ‘no THC’ control group of vehicle-conditioned rats received only PG vapor exposure each day. After the 8th and 16th conditioning sessions, untreated rats were tested for conditioned place preference (CPP) or avoidance (CPA). Next, extinction tests and a THC vapor-primed reinstatement test were conducted.

Results

THC vapor produced CPP and locomotor effects in an exposure dependent manner, and some sex differences were observed. Low THC vapor exposure did not produce CPP in males or females. Medium THC vapor exposure produced CPP in males, but not females. High THC vapor exposure produced CPP in both males and females. Medium and high THC vapor exposure amounts produced hyperactivity in female rats, but not male rats. CPP was more resistant to extinction in females than males. THC vapor re-exposure (i.e., drug-prime) after extinction did not result in reinstatement of CPP for either sex.

Conclusion

This study demonstrates conditioned rewarding effects of THC vapor in both male and female rats and provides evidence for sex differences in amounts of THC vapor that produce CPP and in time to extinction. CPA was not observed at any of the THC vapor exposure amounts tested. These data provide a foundation for future exploration of the conditioned effects of cannabis constituents and extracts using vapor exposure models.
Effectiveness and relationship between biased and unbiased measures of dopamine release and clearance
Authors: Everett Anna C. , Graul Ben E. , Robinson J. Kayden , Watts Daniel B. , España Rodrigo A. , Siciliano Cody A. , Yorgason Jordan T.
Published: December 2021

Fast-scan cyclic voltammetry (FSCV) is an effective tool for measuring dopamine (DA) release and clearance throughout the brain, including the ventral and dorsal striatum. Striatal DA terminals are abundant with signals heavily regulated by release machinery and the dopamine transporter (DAT). Peak height is a common method for measuring release but can be affected by changes in clearance. The Michaelis-Menten model has been a standard in measuring DA clearance, but requires experimenter fitted modeling subject to experimenter bias. The current study presents the use of the first derivative (velocity) of evoked DA signals as an alternative approach for measuring dopamine release and clearance and can be used to distinguish the two measures. Maximal upwards velocity predicts reductions in DA peak height due to D2 and GABAB receptor stimulation and by alterations in calcium concentrations. The Michaelis-Menten maximal velocity (Vmax) measure, an approximation for DAT numbers, predicted maximal downward velocity in slices and in vivo. Dopamine peak height and upward velocity were similar between wildtype C57 (WT) and DAT knock out (DATKO) mice. In contrast, downward velocity was considerably reduced and exponential decay (tau) was increased in DATKO mice, supporting use of both measures for changes in DAT activity. In slices, the competitive DAT inhibitors cocaine, PTT and WF23 increased peak height and upward velocity differentially across increasing concentrations, with PTT and cocaine reducing these measures at high concentrations. Downward velocity and tau values decreased and increased respectively across concentrations, with greater potency and efficacy observed with WF23 and PTT. In vivo recordings demonstrated similar effects of WF23 and PTT on measures of release and clearance. Tau was a more sensitive measure at low concentrations, supporting its use as a surrogate for the Michaelis-Menten measure of apparent affinity (Km). Together, these results inform on the use of these measures for DA release and clearance.
Delivery of CAR-T Cells in a Transient Injectable Stimulatory Hydrogel Niche Improves Treatment of Solid Tumors
Authors: Grosskopf Abigail K. , Labanieh Louai , Klysz Dorota D. , Roth Gillie A. , Xu Peng , Adebowale Omokolade , Gale Emily C. , Jons Carolyn K. , Klich John H. , Yan Jerry , Maikawa Caitlin L. , Correa Santiago , Ou Ben S. , d’Aquino Andrea I. , Cochran Jennifer R. , Chaudhuri Ovijit , Mackall Crystal L. , Appel Eric A.
Published: December 2021

Adoptive cell therapy (ACT) has proven to be highly effective in treating blood cancers such as B cell malignancies, but traditional approaches to ACT are poorly effective in treating the multifarious solid tumors observed clinically. Locoregional cell delivery methods have shown promising results in treating solid tumors compared to standard intravenous delivery methods, but the approaches that have been described to date have several critical drawbacks ranging from complex manufacturing and poor modularity to challenging adminstration. In this work, we develop a simple-to-implement self-assembled and injectable hydrogel material for the controlled co-delivery of CAR-T cells and stimulatory cytokines that improves treatment of solid tumors. We evaluate a range of hydrogel formulations to optimize the creation of a transient inflammatory niche that affords sustained exposure of CAR-T cells and cytokines. This facile approach yields increased CAR-T cell expansion, induces a more tumor-reactive CAR-T phenotype, and improves efficacy in treating solid tumors in mice.
ORA47 is a transcriptional regulator of a general stress response hub
Authors: Zeng Liping , Chen Hao , Wang Yaqi , Hicks Derrick , Ke Haiyan , Pruneda-Paz Jose , Dehesh Katayoon
Published: December 2021

Transcriptional regulators of general stress response (GSR) reprogram expression of selected genes to transduce informational signals into cellular events, ultimately manifested in plant’s ability to cope with environmental challenges. Identification of the core GSR regulatory proteins will uncover the principal modules and their mode of action in the establishment of adaptive responses. To define the GSR regulatory components, we employed a yeast-one-hybrid assay to identify the protein(s) that binds to the previously established functional GSR motif, coined Rapid Stress Response Element (RSRE). This led to the isolation of ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47), a Methyl jasmonate (MeJA) inducible protein. Subsequently, the ORA47 transcriptional activity was confirmed using RSRE-driven Luciferase (LUC) activity assay performed in the ORA47 loss- and gain-of-function lines introgressed into the 4xRSRE::Luc background. In addition, the prime contribution of CALMODULIN-BINDING TRANSCRIPTIONAL ACTIVATOR3 (CAMTA3) protein in induction of RSRE was reaffirmed by genetic studies. Moreover, exogenous application of MeJA led to enhanced levels of ORA47 and CAMTA3 transcripts, and the induction of RSRE::LUC activity. Metabolic analyses illustrated the reciprocal functional inputs of ORA47 and CAMTA3 in increasing JA levels. Lastly, transient assays identified JASMONATE ZIM-domain1 (JAZ1) as a repressor of RSRE::LUC activity.

Collectively, the report provides a fresh insight into the initial mechanistic features of transducing the informational signals into adaptive responses in part via the complex functional interplay between JA biosynthesis/signaling cascade and the transcriptional reprogramming necessary for potentiation of GSR, while offering a window into the role of intraorganellar communication in the establishment of adaptive responses.

Significance

The work unmasks the initial mechanistic features of adaptive responses that include tight cooperativity between JA biosynthesis and signaling cascade and the nuclear transcriptional machinery comprised of two activators (CAMTA3 and ORA47) and a suppressor JAZ1). The work further identifies CAMTA3 as a functional link between JA signaling and activation of a general stress transcriptional hub.
Structural flexibility of the SARS-CoV-2 genome relevant to variation, replication, pathogenicity, and immune evasion
Authors: Patarca Roberto , Haseltine William A.
Published: December 2021

The SARS-CoV-2 pandemic continues to be driven by viral variants. Most research has focused on structural proteins and on site-specific mutations. Here, we describe recombination events involving genomic terminal sequences in SARS-CoV-2 and related viruses leading to structural rearrangements in terminal and coding regions and discuss their potential contributions to viral variation, replication, pathogenicity, and immune evasion.
Identification of novel genetic regions associated with resistance to European canker in apple
Authors: Karlström Amanda , Gómez-Cortecero Antonio , Nellist Charlotte F , Ordidge Matthew , Dunwell Jim M. , Harrison Richard J
Published: December 2021

Resistance to Neonectria ditissima, the fungus causing European canker in apple, was studied in a multiparental population of apple scions using several phenotyping methods. The studied population consists of individuals from multiple families connected through a common pedigree. The degree of disease of each individual in the population was assessed in three experiments: artificial inoculations of detached dormant shoots, potted trees in a glasshouse and in a replicated field experiment. The genetic basis of the differences in disease was studied using a pedigree-based analysis (PBA). Three quantitative trait loci (QTL), on linkage groups (LG) 6, 8 and 10 were identified in more than one of the phenotyping strategies. An additional four QTL, on LG 2, 5, 15 and 16 were only identified in the field experiment. The QTL on LG2 and 16 were further validated in a biparental population. QTL effect sizes were small to moderate with 4.3 to 19 % of variance explained by a single QTL. A subsequent analysis of QTL haplotypes revealed a dynamic response to this disease, in which the estimated effect of a haplotype varied over the field time-points. Two groups of QTL-haplotypes could be distinguished, one that displayed increased effect and one with a constant effect across time-points. These results suggest that there are different modes of control of N. ditissima in the early stages of infection compared to later time-points of disease development. It also shows that multiple QTL will need to be considered to improve resistance to European canker in apple breeding germplasm.
Endogenous DAF-16 Spatiotemporal Activity Quantitatively Predicts Lifespan Extension Induced by Dietary Restriction
Authors: Huayta Javier , San-Miguel Adriana
Published: December 2021

In many organisms, dietary restriction (DR) leads to lifespan extension through the activation of cell protection and pro-longevity gene expression programs. In the nematode C. elegans, the DAF-16 transcription factor is a key aging regulator that governs the Insulin/IGF-1 signaling pathway and undergoes translocation from the cytoplasm to the nucleus of cells when animals are exposed to food limitation. In this work, we assess the endogenous activity of DAF-16 under various DR regimes by coupling CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image analysis and machine learning. Our results indicate that lifelong DAF-16 endogenous activity is a robust predictor of mean lifespan in C. elegans, and it accounts for 78% of the lifespan variability induced by DR. We found that this lifespan-extending mechanism occurs mainly in the intestine and neurons, and that DR drives DAF-16 activity in unexpected locations such as the germline and intestinal nucleoli.
Transcriptional signature in microglia isolated from an Alzheimer’s disease mouse model treated with scanning ultrasound
Authors: Leinenga Gerhard , Bodea Liviu-Gabriel , Schröder Jan , Sun Giuzhi , Chen Yi , Grubman Alexandra , Polo Jose M. , Götz Jürgen
Published: December 2021

Rationale

Intracranial scanning ultrasound combined with intravenously injected microbubbles (SUS+MB) has been shown to transiently open the blood-brain barrier and reduce amyloid-β (Aβ) pathology in the APP23 mouse model of Alzheimer’s disease (AD). This has been accomplished, at least in part, through the activation of microglial cells; however, their response to the SUS treatment is only incompletely understood.

Methods

Wild-type (WT) and APP23 mice were subjected to SUS+MB, using non-SUS+MB-treated mice as sham controls. After 48 hours, the APP23 mice were injected with methoxy-XO4 to label Aβ aggregates, followed by microglial isolation into XO4+and XO4-populations using flow cytometry. Both XO4+and XO4-cells were subjected to RNA sequencing and their transcriptome was analyzed through a bioinformatics pipeline.

Results

The transcriptomic analysis of the microglial cells revealed a clear segregation depending on genotype (AD model versus WT mice), as well as treatment (SUS+MBversus sham) and Aβ internalization (XO4+versus XO4-microglia). Differential gene expression analysis detected 278 genes that were significantly changed by SUS+MBin the XO4+cells (248 up/30 down) and 242 in XO-cells (225 up/17 down). Not surprisingly given previous findings of increased phagocytosis of plaques following SUS+MB, the pathway analysis highlighted that the treatment induced an enrichment in genes related to the phagosome pathway in XO4+microglia; however, when comparing SUS+MBto sham, the analysis revealed an enrichment in genes involved in the cell cycle in both the XO4+and XO4-microglial population.

Conclusion

Our data provide a comprehensive analysis of microglia in an AD mouse model subjected to ultrasound treatment as a function of Aβ internalization, one of the defining hallmarks of AD. Several differentially expressed genes are highlighted, pointing to an ultrasound-induced activation of cell cycle mechanisms in microglial cells isolated from APP23 mice treated with SUS+MB.

Graphical abstract
Intestinal Enteroid Monolayers Model the Human Intestinal Environment for Escherichia coli Infection
Authors: Small Jason , Weiss Alison
Published: December 2021

Enterohemorrhagic Escherichia coli O157:H7 is an enteric pathogen responsible for bloody diarrhea, hemolytic uremic syndrome, and in severe cases even death. The study of O157:H7 is difficult due to the high specificity of the bacteria for the human intestine, along with our lack of sufficiently complex human cell culture models. The recent development of human intestinal enteroids derived from intestinal crypt multipotent stem cells has allowed us to construct 2-dimensional differentiated epithelial monolayers grown in transwells that mimic the human intestine. Unlike previous studies, saline was added to the apical surface, while maintaining culture media in the basolateral well. The monolayers continued to grow and differentiate with apical saline. Apical infection with O157:H7 or commensal E. coli resulted in robust bacterial growth from 105 to over 108 over 24 hours. Despite this robust bacterial growth, commensal E. coli neither adhered to nor damaged the epithelial barrier over 30 hours. However, O157:H7 was almost fully adhered (>90%) by 18 hours with epithelial damage observed by 30 hours. O157:H7 contains the locus of enterocyte effacement (LEE) pathogenicity island responsible for attachment and damage to the intestinal epithelium. Previous studies report the ability of nutrients such as biotin, D-serine, and L-fucose to downregulate LEE gene expression. O157:H7 treated with biotin or L-fucose, but not D-serine displayed both decreased attachment and reduced epithelial damage over 36 hours. These data illustrate enteroid monolayers can serve as a suitable model for the study of O157:H7 pathogenesis, and identification of potential therapeutics.

Importance

O157:H7 is difficult to study due to its high specificity for the human intestine and the lack of sufficiently complex human cell culture models. The recent development of human intestinal enteroids derived from intestinal crypt multipotent stem cells has allowed us to construct 2-dimensional differentiated epithelial monolayers grown in transwells that mimic the human intestine. Our data illustrates enteroid monolayers can serve as a suitable model for the study of O157:H7 pathogenesis, and allow for identification of potential therapeutics.
5-aminolevulinic acid-photodynamic therapy ameliorates cutaneous granuloma by killing drug-resistant Mycobacterium marinum
Authors: Yang Zhiya , Feng Yahui , Pang Zhiping , Li Dongmei , Wang Sisi , Chen Huiqi , Jiang Mingze , Yan Hongxia , Li Tianhang , Fu Hongjun , Xiong Hubao , Shi Dongmei
Published: December 2021

Background

Although 5-aminolevulinic acid photodynamic therapy (ALA-PDT) has been extensively used to treat to various skin disease, the application of ALA-PDT on cutaneous infection caused by Mycobacterium marinum (M. marinum), especially by drug-resistant M. marinum is still not clear.

Objectives

We evaluated the therapeutic efficacy of ALA-PDT on M. marinum in a mouse infection model and tested its killing effect on M. marinum in vitro. Finally, we investigated the clinical effect of ALA-PDT in treating cutaneous granuloma caused by drug-resistant M. marinum.

Materials and methods

We isolated total 9 strains of M. marinum from patients and confirmed by morphological and molecular approaches. The strains were identified by anti-mycobacterial susceptibility. Then we evaluated the killing effect of ALA-PDT on M. marinum in vitro and in a mouse model to observe the antimycobacterial effect of ALA-PDT. Therapeutic efficacy was further assessed in patients with cutaneous granuloma caused by drug-resistant M. marinum.

Results

We demonstrated that the ALA-PDT directly killed M. marinum in vitro. The paws cutaneous lesions of mice caused by M. marinum were fully recovered 2 weeks after ALA-PDT treatment. However, there was no significant difference for immune cells in peripheral blood before and after ALA-PDT therapy. Finally, ALA-PDT proved to be effective in treat two patients with cutaneous infection caused by drug-resistant M. marinum.

Conclusions

The results suggest that ALA-PDT is effective in treating M. marinum cutaneous infections by killing M. marinum directly, independent of systemic immune responses. The data highlight the ALA-PDT as a promising therapeutic choice for M. marinum infection, especially for drug-resistant strains.
Breakthrough Infections with SARS-CoV-2 in Vaccinated Students After a Festive Event – Identification of Risk Factors
Authors: Bertram Ralph , Bartsch Vanessa , Sodmann Johanna , Hennig Luca , Müjde Engin , Stock Jonathan , Ruedig Vivienne , Sodmann Philipp , Todt Daniel , Steinmann Eike , Hitzl Wolfgang , Steinmann Joerg
Published: December 2021

We report an outbreak with SARS-CoV-2 breakthrough infections related to a festive event in Northern Bavaria, Germany in October 2021, with 24 of 95 participants infected. Correlation analyses among 15 interrogated variables revealed that duration at the event and conversation with the supposed index person were significant risk factors.

Article Summary Line

The risk of infection with SARS-CoV-2 in a vaccinated cohort associated with a private festive event was significantly increased upon conversation with the putative index person and positively correlated to the duration of stay at the event.
Hydroxychloroquine in the Pregnancies of Women with Lupus: A Meta-Analysis of Individual Participant Data
Authors: Clowse Megan E. B. , Eudy Amanda M. , Balevic Stephen , Sanders-Schmidler Gillian , Kosinski Andrzej , Fischer-Betz Rebecca , Gladman Dafna , Molad Yair , Nalli Cecilia , Mokbel Abir , Tincani Angela , Urowitz Murray , Bay Caroline , van Noord Megan , Petri Michelle
Published: December 2021

Objective

Multiple guidelines recommend continuing hydroxychloroquine (HCQ) for systemic lupus erythematosus (lupus) during pregnancy based on observational data. The goal of this individual patient data meta-analysis was to combine multiple datasets to compare pregnancy outcomes in women with lupus on and off HCQ.

Methods

Eligible studies included prospectively-collected pregnancies in women with lupus. After a manuscript search, 7 datasets were obtained. Pregnancy outcomes and lupus activity were compared for pregnancies with a visit in the first trimester in women who did or did not take HCQ throughout pregnancy. Birth defects were not systematically collected. This analysis was conducted in each dataset and results were aggregated to provide a pooled odds ratio.

Results

Seven cohorts provided 938 pregnancies in 804 women. After selecting one pregnancy per patient with a 1st trimester visit, 668 pregnancies were included; 63% took HCQ throughout pregnancy. Compared to pregnancies without HCQ, those with HCQ had lower rates of highly active lupus, but did not have different rates of fetal loss, preterm birth, or preeclampsia. Among women with low lupus activity, HCQ reduced the risk for preterm delivery.

Conclusion

This large study of prospectively-collected lupus pregnancies demonstrates a decrease in SLE activity among woman who continue HCQ through pregnancy and no harm to pregnancy outcomes. Like all studies of HCQ in lupus pregnancy, this study is confounded by indication and non-adherence. As this study confirms the safety of HCQ and diminished SLE activity with use, it is consistent with current recommendations to continue HCQ throughout pregnancy.
Maternal transfer of IgA and IgG SARS-CoV-2 specific antibodies transplacentally and via breastfeeding
Authors: Sajadi Mohammad M. , Shokatpour Narjes , Bathula Allison , Tehrani Zahra Rikhtegaran , Lankford Allison , Purcell Madeleine , Campbell James D. , Hammershaimb Elizabeth Adrianne , Deatrick Kristopher B. , Bor Casey , Parsell Dawn M. , Dugan Colleen , Levine Andrea R. , Ramelli Sabrina C. , Chertow Daniel S. , Herr Daniel L , Lewis George K. , Grazioli Alison
Published: December 2021

Although there have been many studies on antibody responses to SARS-CoV-2 in breastmilk, very few have looked at the fate of these in the baby. We carried out a study in 22 mother/baby pairs (mothers who breastfed and who were SARS-CoV-2 vaccinated before or after delivery) looking at mother blood, mother milk, baby blood, baby nose, and baby stool. Breastfed infants only acquired systemic anti-SARS-CoV-2 IgG antibodies if their mothers were vaccinated antepartum. None of the infants had SARS-CoV-2-specific IgA in the blood, but surprisingly, half of the infants in the Antepartum group had high titer SARS-CoV-2-specific IgA in the nose that exceeded titers found in breastmilk. Vaccination antepartum followed by breastfeeding appears to be the best way to provide systemic and local anti-SARS-CoV-2 antibodies for infants.