bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic variation impacts ancestry-associated differences in the transcriptional response to influenza infection
Authors: Aracena Katherine A , Lin Yen-Lung , Luo Kaixuan , Pacis Alain , Gona Saideep , Mu Zepeng , Yotova Vania , Sindeaux Renata , Pramatarova Albena , Simon Marie-Michelle , Chen Xun , Groza Cristian , Lougheed David , Gregoire Romain , Brownlee David , Li Yang , He Xin , Bujold David , Pastinen Tomi , Bourque Guillaume , Barreiro Luis B
Published: May 2022

Humans display remarkable inter-individual variation in immune response when exposed to identical immune challenges. Yet, our understanding of the genetic and epigenetic factors contributing to such variation remains limited. Here we carried out in-depth genetic, epigenetic, and transcriptional profiling on primary macrophages derived from a panel of European and African-ancestry individuals before and after infection with influenza A virus (IAV). We show that baseline epigenetic profiles are strongly predictive of the transcriptional response to IAV across individuals, and that ancestry-associated differences in gene expression are tightly coupled with variation in enhancer activity. Quantitative trait locus (QTL) mapping revealed highly coordinated genetic effects on gene regulation with many cis-acting genetic variants impacting concomitantly gene expression and multiple epigenetic marks. These data reveal that ancestry-associated differences in the epigenetic landscape are genetically controlled, even more so than variation in gene expression. Lastly, we show that among QTL variants that colocalized with immune-disease loci, only 7% were gene expression QTL, the remaining corresponding to genetic variants that impact one or more epigenetic marks, which stresses the importance of considering molecular phenotypes beyond gene expression in disease-focused studies.
Single molecule microscopy to profile the effect of zinc status of transcription factor dynamics
Authors: Damon Leah J. , Aaron Jesse , Palmer Amy E.
Published: May 2022

Transcription factors (TFs) are DNA binding proteins that control the expression of genes. The regulation of transcription is a complex process that involves binding of TFs to specific sequences, recruitment of cofactors and chromatin remodelers, assembly of the pre-initiation complex and ultimately the recruitment of RNA polymerase II. Increasing evidence suggests that TFs are highly dynamic and interact only transiently with DNA. Single molecule microscopy techniques are powerful approaches for visualizing and tracking individual TF molecules as they diffuse in the nucleus and interact with DNA. In this work, we employ multifocus microscopy and highly inclined and laminated optical sheet microscopy to track TF dynamics in response to perturbations in labile zinc inside cells. We sought to define whether zinc-dependent TFs sense changes in the labile zinc pool by determining whether their dynamics and DNA binding can be modulated by zinc. While it is widely appreciated that TFs need zinc to bind DNA, whether zinc occupancy and hence TF function are sensitive to changes in cellular zinc remain open questions. We utilized fluorescently tagged versions of the glucocorticoid receptor (GR), with two C4 zinc finger domains, and CCCTC-binding factor (CTCF), with eleven C2H2 zinc finger domains. We found that the biophysical dynamics of both TFs are susceptible to changes in zinc, but in subtly different ways. These results indicate that at least some transcription factors are sensitive to zinc dynamics, revealing a potential new layer of transcriptional regulation.
A versatile, chemically-controlled DNA binding switch enables temporal modulation of Cas9-based effectors
Authors: Wei Cindy T. , Peleg Omri , Borenstein Elhanan , Maly Dustin J. , Fowler Douglas M.
Published: May 2022

CRISPR-Cas9’s RNA-guided genome targeting ability has been leveraged to develop a plethora of effectors including targeted transcriptional activators, DNA base editors, and DNA prime editors. Although systems for inducibly modulating Cas9 activity have been developed, current approaches for conferring temporal control require extensive screening of functional protein components. A simpler and general strategy for conferring temporal control over diverse Cas9-based effector activities is needed. Here we describe a versatile chemically-controlled and rapidly-activated DNA binding Cas9 module (ciCas9) that is able to confer temporal control over a variety of Cas9-based effectors. Using the ciCas9 module, we engineer temporally-controlled cytidine and adenine DNA base editors. We employ the ciCas9 base editors to reveal that in vivo bystander editing kinetics occurs via a dependent process where editing at a preferred nucleotide position increases the frequency of edits at a second nucleotide within a target site. Finally, we demonstrate the versatility of the ciCas9 module by creating a temporally-controlled transcriptional activator, a dual cytidine and adenine base editor, and a prime editor.
Classification of Extracellular Vesicles based on Surface Glycan Structures by Spongy-like Separation Media
Authors: Kanao Eisuke , Wada Shuntaro , Nishida Hiroshi , Kubo Takuya , Tanigawa Tetsuya , Imami Koshi , Shimoda Asako , Umezaki Kaori , Sasaki Yoshihiro , Akiyoshi Kazunari , Adachi Jun , Otsuka Koji , Ishihama Yasushi
Published: May 2022

Extracellular vesicles (EVs) are lipid bilayer vesicles that enclose various biomolecules. EVs hold promise as sensitive biomarkers to detect and monitor various diseases. However, they have heterogenous molecular compositions. The compositions of EVs from identical donor cells obtained using the same purification methods may differ, which is a significant obstacle for elucidating objective biological functions. Herein the potential of a novel lectin-based affinity chromatography (LAC) method to classify EVs based on their glycan structures is demonstrated. The proposed method utilizes a spongy-like monolithic polymer (spongy monolith, SPM), which consists of poly(ethylene-co-glycidyl methacrylate) with continuous micropores and allows an efficient in-situ protein reaction with epoxy groups. Two distinct lectins with different specificities, Sambucus sieboldiana agglutinin and concanavalin A, are effectively immobilized on SPM without impacting the binding activity. Moreover, high recovery rates of liposomal nanoparticles as a model of EVs are achieved due to the large flow-through pores (>10 μm) of SPM. Finally, lectin-immobilized SPMs are employed to classify EVs based on the surface glycan structures and demonstrate different subpopulations by proteome profiling.
Macroscale Thalamic Functional Organization Disturbances and Underlying Core Cytoarchitecture in Early-Onset Schizophrenia
Authors: Fan Yun-Shuang , Xu Yong , Bayrak Şeyma , Shine James M. , Wan Bin , Li Haoru , Li Liang , Yang Siqi , Meng Yao , Valk Sofie Louise , Chen Huafu
Published: May 2022

Schizophrenia is a polygenetic mental disorder with heterogeneous positive and negative symptom constellations, and is associated with abnormal cortical connectivity. The thalamus has a coordinative role in cortical function and is key to the development of the cerebral cortex. Conversely, altered functional organization of the thalamus might relate to overarching cortical disruptions in schizophrenia, anchored in development. Here, we contrasted resting-state fMRI in 99 antipsychotic-naive first-episode early-onset schizophrenia (EOS) patients and 100 typically developing controls to study whether macroscale thalamic organization is altered in EOS. Employing dimensional reduction techniques on thalamocortical functional connectome, we derived lateral-medial and anterior-posterior thalamic functional axes. We observed increased segregation of macroscale thalamic functional organization in EOS patients, which was related to altered thalamocortical interactions both in unimodal and transmodal networks. Using anex vivoapproximation of core-matrix cell distribution, we found that core cells particularly underlie the macroscale abnormalities in EOS patients. Moreover, the disruptions were associated with schizophrenia-related gene expression maps. Behavioral and disorder decoding analyses indicated that the macroscale hierarchy disturbances might perturb both perceptual and abstract cognitive functions and contribute to negative syndromes in schizophrenia, suggesting a unitary pathophysiological framework of schizophrenia.
A honey authenticity test by interphase emulsion reveals biosurfactant activity and biotechnology in the stingless bee nest ofScaptotrigonasp. ‘Catiana’ from Ecuador
Authors: Vit Patricia
Published: May 2022

Bees are valuable pollinators of fruit trees and grasses. Honey is a medicinal food of plant and animal origin, with social impact for the wellbeing of bee keepers. The Neotropical apifauna has about 500 species of stingless bees (Meliponini). Commercial beekeeping withApis melliferaunderestimates the cultural legacy of meliponiculture, and both are affected by the presence of fake honeys in the market. Three alternative techniques (interphase emulsion, sensory analysis, and pollen residue) to nuclear magnetic resonance (NMR) were investigated to detect false honeys. One technique was based on an interphase emulsion test, which can be performed by beekeepers, farmers, housekeepers, professionals and consumers of honey in general. Another technique was sensory analysis by a tasting panel, and the third consisted on a palynological preparation with a simplified observation. Five genuine honeys produced byApis mellifera, Geotrigona leucogastra, Melipona mimetica, Scaptotrigonasp.,Tetragonisca angustulaand a fake honey from Ecuador were analyzed. The honey authenticity test by interphase emulsion was fast and effective to detect fake honey (two phases), and genuine honeys (one and three phases). A further screening of was done in 51 Asian, Australia, European and Latinamerican honeys. Additionally the HATIE generated a new application as a test to detect unique biosurfactants in honey (HBT) ofScaptotrigonasp. ‘Catiana’ (one phase) with potential microbial origin, and its entomological origin in this set of honeys. ‘Catiana’ nests smell like Roquefort cheese, indicating a fungus association with this rural stingless bee highlighted by its distribution, productivity and the peculiarities described in this research, 80 years after its description as a new genusScaptotrigonaMoure, 1942. Paradoxically, this communication without microbiological analysis, infers the fungal presence in the nest ofScaptotrigonasp. by sensory observations different from the classic sensory evaluation of honey.
Clones on the run - the genomics of a recently expanded facultative asexual species
Authors: Pereyra Ricardo T. , Rafajlović Marina , De Wit Pierre , Pinder Matthew , Kinnby Alexandra , Töpel Mats , Johannesson Kerstin
Published: May 2022

Why, in facultative asexual species, marginal populations are often richer in clones than are core populations, remains unclear. Cloning freezes genotypes but hampers recombination and local adaptation. During expansion, clones are favoured over non-selfing sexuals by uniparental reproduction. To better understand the dynamics of clones and sexual lineage, we used genome-wide sequencing to analyse a recently expanded seaweed. We found large clones and sexual populations mixed close to range margins. Clones had evolved repeatedly from sexual populations but were unexpectedly low in genetic variation. Modelling suggested clones form from sexual populations after repeated bottlenecks at the expansion front. A clonal wave of depauperate genotypes thereafter spread ahead of the sexual population. As we observed, these early formed clones may survive side-by-side sexual individuals, which suggests they lost their sexual capacity. Our study illustrates how range expansion can result in complex and dynamic patterns of genetic variation in facultative asexual species.

Teaser

We use genome data and modelling to find out why large clones are only found at range margins in a recently expanded seaweed
A spatial map of antennal-expressed olfactory ionotropic receptors in the malaria mosquito
Authors: Raji Joshua I. , Potter Christopher J.
Published: May 2022

The malaria mosquito Anopheles coluzzii uses odors to guide various behaviors such as host-seeking. The detection of behaviorally relevant odors is mediated by a diverse family of receptors including the olfactory Ionotropic Receptors (IRs). Olfactory receptors are expressed on olfactory neurons, with the mosquito antennae representing the main olfactory appendage for detecting volatile chemical cues from the environment. It is currently unknown how many neurons across the antenna express a certain IR, or how these IR-expressing neurons are spatially arranged. Here, we performed whole mount fluorescent in situ hybridization of all IRs expressed in the antennae. The organization of IR-positive cells within an antennal segment (flagellomere) appeared stereotyped across multiple antennae. The spatial map of IR-expressing neurons revealed that the antenna might be organized into proximal and distal functional domains. Highly expressed tuning (odor-binding) IRs exhibit distinct co-localization patterns with cognate IR co-receptor(s) in a combinatorial fashion that might predict their functional properties. These findings reveal organizing principles of Anopheles IR-expressing neurons in the mosquito which might underlie their functional contribution to the detection of behaviorally relevant odors.
Proteogenomic characterization of age and sex interactions in cardiac gene expression
Authors: Han Yu , Wennersten Sara A. , Wright Julianna , Ludwig R. W. , Lau Edward , Lam Maggie P. Y.
Published: May 2022

The risks of heart diseases are significantly modulated by biological age and sex, but how these factors influence baseline cardiac gene expression remains incompletely understood. Here we characterized young adult and early aging mouse hearts using proteogenomics to identify age and sex dependent gene expression signatures in the mouse heart. RNA sequencing from 4 months old and 20 months old female and male C57BL/6J hearts identified thousands of genes with differential transcript abundances both between sexes (male vs. female) and across age groups (20 mo. vs. 4 mo.). Sex-associated cardiac genes are broadly distributed, functioning in the TCA cycle, mitochondrial translation, autophagy, and other processes. In addition, we found over 800 genes with differential aging response between male and female, which are enriched in calmodulin signaling and cell cycle regulations. Comparison with mass spectrometry data shows a cluster of metabolism genes with up-regulated transcripts but down-regulated protein levels in aging hearts, consistent with an uncoupling of transcriptional regulations in the genetic program with protein compositions. An analysis of sex-adjusted aging cardiac transcriptomes further revealed widespread remodeling of exon usage patterns that is largely independent from differential gene expression, concomitant with upstream changes in RNA-binding protein and splice factor transcripts. To evaluate the potential impact of the splicing events on proteoform composition in the heart, we applied an RNA-guided-proteomics computational pipeline to analyze the mass spectrometry data, and putatively identified hundreds of splice events with the potential to rewire the cardiac proteome through producing detectable splice isoform specific peptides. Taken together, this study contributes to emerging evidences for considerable sexual dimorphism in the cardiac aging process involving sex-biased aging genes and regulatory networks. Aging hearts are associated with a rewiring of RNA splicing programs, including sex- and age-dependent changes in exon usages and splice patterns that have the potential to influence cardiac protein structure and function. These changes represent an under-investigated aspect of cardiac aging that should be considered in the search for disease mechanisms.
Rapidly changing speciation and extinction rates can be inferred in spite of non-identifiability
Authors: Kopperud Bjørn T. , Magee Andrew F. , Höhna Sebastian
Published: May 2022

The birth-death model is commonly used to infer speciation and extinction rates by fitting the model to extant phylogenetic trees. Recently, it was demonstrated that speciation and extinction rates are not identifiable if the rates are allowed to vary freely over time. The group of birth-death models that are not identifiable from each other is called a congruence class. Every model in a congruence class is equally likely, and there is no statistical evidence that can be used to favor one over the other. This issue has led researchers to question if and what patterns can reliably be inferred, and whether time-variable birth-death models should be fitted at all. We explore the congruence class in the context of several empirical phylogenies as well as hypothetical scenarios and summarize shared patterns in the congruence class. We show that strong directional trends in speciation and extinction rates are ubiquitous among most models within the congruence class, and conclude that inference of strong directional trends is therefore robust. Conversely, estimates of constant rates or gentle slopes are not robust and must be treated with caution. Additionally, most conflict in trends within the congruence class is observed near the present, implying that very recent rate changes should be treated carefully. Interestingly, the space of valid speciation rates is limited in contrast to extinction rates, which are less constrained. These results provide further evidence and insights that speciation rates can be estimated more reliably than extinction rates.
RAS and PP2A activities converge on epigenetic gene regulation
Authors: Aakula Anna , Sharma Mukund , Tabaro Francesco , Honkanen Henrik , Schapira Matthieu , Arrowsmith Cheryl , Nykter Matti , Westermarck Jukka
Published: May 2022

RAS-mediated human cell transformation requires inhibition of the tumor suppressor Protein Phosphatase 2A (PP2A). Both RAS and PP2A mediate their effects by phosphoregulation, but phosphoprotein targets and cellular processes in which RAS and PP2A activities converge in human cancers have not been systematically analyzed. Here, based on mass spectrometry phosphoproteome data we discover that phosphosites co-regulated by RAS and PP2A are enriched on proteins involved in epigenetic gene regulation. As examples, RAS and PP2A co-regulate the same phosphorylation sites on HDAC1/2, KDM1A, MTA1/2, RNF168 and TP53BP1. Mechanistically, we validate co-regulation of NuRD chromatin repressor complex by RAS and PP2A. Consistent with their known synergistic effects in cancer, RAS activation and PP2A inhibition resulted in epigenetic reporter de-repression and activation of oncogenic transcription. Notably, transcriptional de-repression by PP2A inhibition was associated with increased euchromatin and decrease in global DNA methylation. Further, targeting of RAS- and PP2A-regulated epigenetic proteins decreased viability of KRAS-mutant human lung cancer cells. Collectively the results indicate that epigenetic protein complexes involved in oncogenic gene expression constitute a significant point of convergence for RAS hyperactivity and PP2A inhibition in cancer. Further, the results provide a rich source for future understanding of phosphorylation as a previously unappreciated layer of regulation of epigenetic gene regulation in cancer, and in other RAS/PP2A-regulated cellular processes.
Antimicrobial resistance genes predict plasmid generalism and network structure in wastewater
Authors: Risely Alice , Stalder Thibault , Simmons Benno I. , Top Eva M. , Buckling Angus , Sanders Dirk
Published: May 2022

Plasmids are mobile genetic elements that can act as mutualists or parasites to their bacterial hosts depending on their accessory genes and environment. Ecological network theory predicts that mutualists, such as plasmids with antimicrobial resistance (AMR) genes in the presence of antimicrobials, should act as generalists, while plasmids without beneficial genes are expected to be more specialised. Therefore, whether the relationship between plasmid and host is mutualistic or antagonistic is likely to have a strong impact on the formation of interaction network structures and the spread of AMR genes across microbial networks. Here we re-analyse Hi-C metagenome data from wastewater samples and identify plasmid signatures with machine learning to generate a natural host-plasmid network. We found that AMR-carrying plasmids indeed interacted with more hosts than non-AMR plasmids (on average 14 versus 3, respectively). The AMR plasmid-host subnetwork showed a much higher connectedness and nestedness than the subnetwork associated with non-AMR plasmids. The overall network was clustered around Proteobacteria and AMR-carrying plasmids giving them a crucial role in network connectivity. Therefore, by forming mutualistic networks with their hosts, beneficial AMR plasmids lead to more connected network structures that ultimately share a larger gene pool of AMR genes across the network.
Context-dependent transcriptional regulation by Drosophila Polycomb Response Elements
Authors: Coleman Rory T. , Struhl Gary
Published: May 2022

Polycomb Response Elements (PREs) are cis-acting DNA sequences that confer heritable states of Drosophila HOX gene expression by anchoring Polycomb and Trithorax Group (PcG and TrxG) chromatin modifiers. PREs are also associated with hundreds of other Drosophila genes, most of which are regulated dynamically in response to developmental and physiological context, rather than heritably like HOX genes. Here, we assess the role(s) PREs play at these other loci by analyzing how genomic inserts of a transgenic form of the HOX gene Ultrabithorax (Ubx) can both control and respond to neighboring genes depending on the presence of a single, excisable PRE. Our results support the view that PREs and their associated PcG and TrxG modifiers act primarily to confer quantitative, rather than qualitative, influences on gene expression with the response of any given gene depending on how it integrates this information with other regulatory elements in the local genomic milieu. They also show that PREs can act on neighboring genes selectively and at remarkably long range, but that any given gene can be susceptible or impervious to PRE/PcG/TrxG input depending on context. Finally, we find that transcription and PRE/PcG-dependent silencing are not mutually exclusive: a Ubx transgene inside the intron of a continuously transcribed “host” gene is nevertheless silenced by its resident PRE. We posit that the widely accepted roles of PcG and TrxG complexes in maintaining heritable states of gene expression apply only to a limited coterie of target genes such as HOX genes that are evolutionarily selected to exclude regulatory elements that can over-ride this control.
eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways
Authors: Ahmed Ibrahim , Yang Shen-Hsi , Ogden Samuel , Zhang Wei , Li Yaoyong ,   the OCCAMS consortium, Sharrocks Andrew D.
Published: May 2022

Cancer is driven by both genetic and epigenetic changes that impact on gene expression profiles and the resulting tumourigenic phenotype. Enhancers are transcriptional regulatory elements that are key to our understanding of how this rewiring of gene expression is achieved in cancer cells. Here we have harnessed the power of RNA-seq data from hundreds of patients with oesophageal adenocarcinoma (OAC) or its precursor state Barrett’s oesophagus (BO) coupled with open chromatin maps to identify potential enhancer RNAs (eRNAs) and their associated enhancer regions in this cancer. We identify ∼1000 OAC-specific enhancers and use this data to uncover new cellular pathways that are operational in OAC. Among these are enhancers for JUP, MYBL2 and CCNE1, and we show that their activity is required for cancer cell viability. We also demonstrate the clinical utility of our dataset for identifying disease stage and patient prognosis. Our data therefore identify an important set of regulatory elements that enhance our molecular understanding of OAC and point to potential new therapeutic directions.
What the book of Lambda doesn’t tell us about temperate phages and lysogeny in the real world
Authors: Berryhill Brandon A. , Garcia Rodrigo , McCall Ingrid C. , Chaudhry Waqas , Petit Marie-Agnès , Levin Bruce R.
Published: May 2022

The most significant difference between bacteriophages functionally and ecologically is whether they are purely lytic (virulent) or temperate. Virulent phages can only be transmitted horizontally by infection, most commonly with the death of their hosts. Temperate phages can also be transmitted horizontally, but upon infection of susceptible bacteria, their genomes can be incorporated into that of their host’s as a prophage and be transmitted vertically in the course of cell division by their lysogenic hosts. From what we know from studies with the temperate phage Lambda and other temperate phages, in laboratory culture, lysogenic bacteria are protected from killing by the phage coded for by their prophage by immunity; where upon infecting lysogens, the free temperate phage coded by their prophage are lost. Why are lysogens not also resistant as well as immune to the phage coded by their prophage since immunity does not confer protection against virulent phages? To address this question, we used a mathematical model and performed experiments with temperate and virulent mutants of the phage Lambda in laboratory culture. Our models predict and experiments confirm that selection would favor the evolution of resistant as well as immune lysogens, particularly if the environment includes virulent phage that share the same receptors as the temperate. To explore the validity and generality of this prediction, we examined ten lysogenic Escherichia coli from natural populations. All ten were capable of forming immune lysogens but their original hosts were resistant to the phage coded by their prophage.

Significance Statement

This jointly theoretical and experimental study predicted that lysogenic bacteria, will be resistant as well as immune to the phage coded for by their prophage. All ten naturally occurring lysogenic Escherichia coli tested were resistant to the temperate phage coded for by their prophage.
DINAVID: A Distributed and Networked Image Analysis System for Volumetric Image Data
Authors: Han Shuo , Chen Alain , Lee Soonam , Fu Chichen , Yang Changye , Wu Liming , Winfree Seth , El-Achkar Tarek M. , Dunn Kenneth W. , Salama Paul , Delp Edward J.
Published: May 2022

Background

The advancement of high content optical microscopy has enabled the acquisition of very large 3D image datasets. Image analysis tools and three dimensional visualization are critical for analyzing and interpreting 3D image volumes. The analysis of these volumes require more computational resources than a biologist may have access to in typical desktop or laptop computers. This is especially true if machine learning tools are being used for image analysis. With the increased amount of data analysis and computational complexity, there is a need for a more accessible, easy-to-use, and efficient network-based/cloud-based 3D image processing system.

Results

The Distributed and Networked Analysis of Volumetric Image Data (DINAVID) system was developed to enable remote analysis of 3D microscopy images for biologists. DINAVID is a server/cloud-based system with a simple web interface that allows biologists to upload 3D volumes for analysis and visualization. DINAVID is designed using open source tools and has two main sub-systems, a computational system for 3D microscopy image processing and analysis as well as a 3D visualization system.

Conclusions

In this paper, we will present an overview of the DINAVID system and compare it to other tools currently available for microscopy image analysis.
Inhibition of DNMT1 methyltransferase activity via glucose-regulatedO-GlcNAcylation alters the epigenome
Authors: Shin Heon , Leung Amy , Costello Kevin R. , Senapati Parijat , Kato Hiroyuki , Lee Michael , Lin Dimitri , Tang Xiaofang , Chen Zhen Bouman , Schones Dustin E.
Published: May 2022

The DNA methyltransferase activity of DNMT1 is vital for genomic maintenance of DNA methylation. We report here that DNMT1 function is regulated byO-GlcNAcylation, a protein modification that is sensitive to glucose levels, and that elevatedO-GlcNAcylation of DNMT1 from high glucose environment leads to alterations to the epigenome. Using mass spectrometry and complementary alanine mutation experiments, we identified S878 as the major residue that isO-GlcNAcylated on DNMT1. Functional studies further revealed thatO-GlcNAcylation of DNMT1-S878 results in an inhibition of methyltransferase activity, resulting in a general loss of DNA methylation that is preferentially at partially methylated domains (PMDs). This loss of methylation corresponds with an increase in DNA damage and apoptosis. These results establishO-GlcNAcylation of DNMT1 as a mechanism through which the epigenome is regulated by glucose metabolism and implicates a role for glycosylation of DNMT1 in metabolic diseases characterized by hyperglycemia.
AtlasXbrowser enables spatial multi-omics data analysis through the precise determination of the region of interest
Authors: Barnett Joshua , Silverman Jonah , Wetzel Molly , Rao Poorvi , Sotudeh Noori , Wang Liya
Published: May 2022

Recent developments in novel spatial sequencing technologies allow for the incorporation of spatial information into high-throughput sequencing assays. One such method, Deterministic Barcoding in Tissue for spatial omics sequencing (DBiT-seq, abbreviated herein as DBiT), utilizes perpendicular microfluidic channels to deliver DNA barcodes across the tissue in a spatially-encoded manner, allowing for sequenced reads to be mapped back onto the 2-D coordinates of the tissue to provide spatial coordinates to cells. DBiT has been the first spatial sequencing technology developed for epigenomic assays beyond transcriptome and proteome. However, despite existing of many open-source software packages for downstream bioinformatics analysis, there is no software available for processing DBiT image data with evenly spaced channels. To facilitate the integration of DBiT spatial and sequenced data, here we proposed a new method to precisely capture the spatial information and further developed AtlasXbrowser based on the new method to extract spatial data from the image data.

AtlasXbrowser is a python-based tool with GUI that requires no technical expertise to operate and enables researchers to incorporate brightfield and epifluorescence images of processed tissue samples into downstream bioinformatics analysis tools.

Availability and implementation

Freely available at https://github.com/atlasxomics/AtlasXbrowser.
High throughput peptidomics elucidates immunoregulatory functions of plant thimet oligopeptidase-directed proteostasis
Authors: Iannetta Anthony A. , Berg Philip , Nejat Najmeh , Smythers Amanda L. , Setu Rezwana R. , Wesser Uyen , Purvis Ashleigh L. , Brown Zoe A. , Wommack Andrew J. , Popescu Sorina C. , Hicks Leslie M. , Popescu George V.
Published: May 2022

Targeted proteolysis activities activated during the plant immune response catalyze the synthesis of stable endogenous peptides. Little is known about their biogenesis and biological roles. Herein, we characterize an Arabidopsis thaliana mutant top1top2 in which targeted proteolysis of immune-active peptides is drastically impaired during effector-triggered immunity (ETI). For effective ETI, the redox-sensitive thimet oligopeptidases TOP1 and TOP2 are required. Quantitative mass spectrometry-based peptidomics allowed differential peptidome profiling of wild type (WT) and top1top2 mutant at the early ETI stages. Biological processes of energy-producing and redox homeostasis were enriched, and TOPs were necessary to maintain the dynamics of ATP and NADP(H) accumulation in the plant during ETI. Subsequently, a set of novel TOPs substrates validated in vitro enabled the definition of the TOP-specific cleavage motif and informed an in-silico model of TOP proteolysis to generate bioactive peptide candidates. Several candidates, including those derived from proteins associated with redox metabolism, were confirmed in planta. The top1top2 background rescued WT’s ETI deficiency caused by treatment with peptides derived from targeted proteolysis of the negative immune regulator FBR12, the reductive enzyme APX1, the isoprenoid pathway enzyme DXR, and ATP-subunit β. These results demonstrate TOPs role in orchestrating the production and degradation of phytocytokines.
Mapping odorant sensitivities reveals a sparse but structured representation of olfactory chemical space by sensory input to the mouse olfactory bulb
Authors: Burton Shawn D. , Brown Audrey , Eiting Thomas P. , Youngstrom Isaac A. , Rust Thomas C. , Schmuker Michael , Wachowiak Matt
Published: May 2022

In olfactory systems, convergence of sensory neurons onto glomeruli generates a map of odorant receptor identity. How glomerular maps relate to sensory space remains unclear. We sought to better characterize this relationship in the mouse olfactory system by defining glomeruli in terms of the odorants to which they are most sensitive. Using high-throughput odorant delivery and ultrasensitive imaging of sensory inputs, we imaged responses to 185 odorants presented at concentrations determined to activate only one or a few glomeruli across the dorsal olfactory bulb. The resulting datasets defined the tuning properties of glomeruli - and, by inference, their cognate odorant receptors - in a low-concentration regime, and yielded consensus maps of glomerular sensitivity across a wide range of chemical space. Glomeruli were extremely narrowly tuned, with ~25% responding to only one odorant, and extremely sensitive, responding to their effective odorants at sub-picomolar to nanomolar concentrations. Such narrow tuning in this concentration regime allowed for reliable functional identification of many glomeruli based on a single diagnostic odorant. At the same time, the response spectra of glomeruli responding to multiple odorants was best predicted by straightforward odorant structural features, and glomeruli sensitive to distinct odorants with common structural features were spatially clustered. These results define an underlying structure to the primary representation of sensory space by the mouse olfactory system.
HumanMine: advanced data searching, analysis and cross-species comparison
Authors: Lyne Rachel , Bazaga Adrián , Butano Daniela , Contrino Sergio , Heimbach Joshua , Hu Fengyuan , Kalderimis Alexis , Lyne Mike , Reierskog Kevin , Stepan Radek , Sullivan Julie , Wise Archie , Yehudi Yo , Micklem Gos
Published: May 2022

HumanMine (www.humanmine.org) is an integrated database of human genomics and proteomics data that provides a powerful interface to support sophisticated exploration and analysis of data compiled from experimental, computational and curated data sources. Built using the InterMine data integration platform, HumanMine includes genes, proteins, pathways, expression levels, SNPs, diseases and more, integrated into a single searchable database. HumanMine promotes integrative analysis, a powerful approach in modern biology that allows many sources of evidence to be analysed together. The data can be accessed through a user-friendly web interface as well as a powerful, scriptable web service API to allow programmatic access to data. The web interface includes a useful identifier resolution system, sophisticated query options and interactive results tables that enable powerful exploration of data, including data summaries, filtering, browsing and export. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other biological entities. HumanMine can be used for integrative multi-staged analysis that can lead to new insights and uncover previously unknown relationships.

Database URL: https://www.humanmine.org
A novel triple-action inhibitor targeting B-cell receptor signaling and BRD4 demonstrates preclinical activity in chronic lymphocytic leukemia
Authors: Smith Audrey L. , Eiken Alexandria P. , Moore Dalia Y. , Umeta Lelisse T. , Smith Lynette M. , Lyden Elizabeth R. , D’Angelo Christopher R. , Kallam Avyakta , Vose Julie M. , Kutateladze Tatiana G. , El-Gamal Dalia
Published: May 2022

B-cell chronic lymphocytic leukemia (CLL) results from intrinsic genetic defects and complex microenvironment stimuli that fuel CLL cell growth through an array of survival-signaling pathways. Novel small-molecule agents targeting the B-cell receptor pathway and anti-apoptotic proteins alone or in combination have revolutionized the management of CLL, yet combination therapy carries significant toxicity and CLL still remains an incurable disease due to residual disease and relapse. Single-molecule inhibitors that can target multiple disease-driving factors are thus an attractive approach to combat both drug resistance and combination therapy-related toxicities. Using SRX3305, a novel small-molecule BTK/PI3K/BRD4 inhibitor that targets three distinctive facets of CLL biology, we demonstrate that SRX3305 attenuates CLL cell proliferation and promotes apoptosis in a dose-dependent fashion. SRX3305 also inhibits activation-induced proliferation of primary CLL cells in vitro, and effectively blocks microenvironment-mediated survival signals including stromal cell contact. Furthermore, SRX3305 blocks CLL cell migration toward CXCL-12 and CXCL-13, major chemokines involved in CLL cell homing and retention in microenvironment niches. Importantly, SRX3305 maintains its anti-tumor effects in ibrutinib-resistant CLL cells. Collectively, this study establishes the preclinical efficacy of SRX3305 in CLL providing significant rationale for its development as a therapeutic agent for CLL and related disorders.
IL-13-programmed airway tuft cells produce PGE2, which promotes CFTR-dependent mucociliary function
Authors: Kotas Maya E. , Moore Camille M. , Gurrola Jose G. , Pletcher Steven D. , Goldberg Andrew N. , Alvarez Raquel , Yamato Sheyla , Bratcher Preston E. , Shaughnessy Ciaran A. , Zeitlin Pamela L. , Zhang Irene , Li Yingchun , Montgomery Michael T. , Lee Keehoon , Cope Emily K. , Locksley Richard M. , Seibold Max A. , Gordon Erin D.
Published: May 2022

Chronic type 2 (T2) inflammatory diseases of the respiratory tract are characterized by mucus overproduction and disordered mucociliary function, which are largely attributed to the effects of IL-13 on common epithelial cell types (mucus secretory and ciliated cells). The role of rare cells in airway T2 inflammation is less clear, though tuft cells have been shown to be critical in the initiation of T2 immunity in the intestine. Using bulk and single cell RNA sequencing of airway epithelium and mouse modeling, we find that IL-13 expands and programs airway tuft cells towards eicosanoid metabolism, and that tuft cell deficiency leads to a reduction in airway prostaglandin E2 (PGE2) concentration. Allergic airway epithelia bear a signature of prostaglandin E2 activation, and PGE2 activation leads to CFTR-dependent ion and fluid secretion and accelerated mucociliary transport. Together these data reveal a role for tuft cells in regulating epithelial mucociliary function in the allergic airway.
Pytri: A multi-weight detection system for biological entities
Authors: Mehdi Ali , Vu Kieu-Nhi , Lambert Felix
Published: May 2022

The enumeration of biological entities is a critical part of experimental assays and usually requires large lengths of time. The standard method is to count the entities by hand or with OpenCV-based software, which can lead to inaccurate results. Here, we propose an online platform for biologists consisting of a system with multiple trained machine learning weights to detect various biological entities such as yeast colonies, bacterial colonies, and melanoma clusters. The Pytri model achieved a median relative error rate of 7.56% for bacterial and yeast colonies on Petri dishes, 6.58% for colonies on 96-well plates and 10.28% for melanoma cluster microscopy images. We showcase the application of state-of-the-art deep learning tools in bacterial entity detection, achieving significantly higher accuracy than traditional methods when compared to our base standard manual count.
Parasites, infections and inoculation in synthetic minimal cells
Authors: Cash Brock , Gaut Nathaniel J. , Deich Christopher , Johnson Laura L. , Engelhart Aaron E. , Adamala Katarzyna P.
Published: May 2022

Synthetic minimal cells provide a controllable and engineerable model for an increasing amount of biological processes. While much simpler than any live natural cell, synthetic cells offer a chassis for investigating the foundations of key biological processes. Here we show a synthetic cell system describing host cells interacting with parasites and infections of varying severity. We demonstrate how the host can be engineered to resist infection, we investigate the metabolic cost of carrying resistance, and we show a simple inoculation system that immunizes the host against pathogens. Our work expands the synthetic cell engineering toolbox by demonstrating host pathogen interactions and mechanisms for acquiring immunity. This brings synthetic cell systems one step closer to providing a comprehensive model of complex, natural life.
Improving peptide-level mass spectrometry analysis via double competition
Authors: Lin Andy , Short Temana , Noble William Stafford , Keich Uri
Published: May 2022

The analysis of shotgun proteomics data often involves generating lists of inferred peptide-spectrum matches (PSMs) and/or of peptides. The canonical approach for generating these discovery lists is by controlling the false discovery rate (FDR), most commonly through target-decoy competition (TDC). At the PSM level, TDC is implemented by competing each spectrum’s best-scoring target (real) peptide match with its best match against a decoy database. This PSM-level procedure can be adapted to the peptide level by selecting the top-scoring PSM per peptide prior to FDR estimation. Here we first highlight and empirically augment a little-known previous work by He et al., which showed that TDC-based PSM-level FDR estimates can be liberally biased. We thus propose that researchers instead focus on peptide-level analysis. We then investigate three ways to carry out peptide-level TDC and show that the most common method (“PSM-only”) offers the lowest statistical power in practice. An alternative approach that carries out a double competition, first at the PSM and then at the peptide level (“PSM-and-peptide”), is the most powerful method, yielding an average increase of 17% more discovered peptides at a 1% FDR threshold relative to the PSM-only method.
Optogenetic rejuvenation of mitochondrial membrane potential extendsC. eleganslifespan
Authors: Berry Brandon J. , Vodičková Anežka , Müller-Eigner Annika , Meng Chen , Ludwig Christina , Kaeberlein Matt , Peleg Shahaf , Wojtovich Andrew P.
Published: May 2022

Despite longstanding scientific interest in the centrality of mitochondria to biological aging, directly controlling mitochondrial function to test causality has eluded researchers. We show that specifically boosting mitochondrial membrane potential through a light-activated proton pump reversed age-associated phenotypes and extendedC. eleganslifespan. We show that harnessing the energy of light to experimentally increase mitochondrial membrane potential during adulthood alone is sufficient to slow the rate of aging.
Hippocampus Modulates Natural Sound Processing at Early Auditory Centers
Authors: Wong Eddie C. , Wang Xunda , Wu Ed X. , Leong Alex T. L.
Published: May 2022

Despite its prominence in learning and memory, hippocampal influence in early auditory processing centers remains unknown. Here, we examined how hippocampal activity modulates sound-evoked responses in the auditory midbrain and thalamus using optogenetics and functional MRI (fMRI) in rodents. Ventral hippocampus (vHP) excitatory neuron stimulation at 5 Hz evoked robust hippocampal activity that propagates to the primary auditory cortex. We then tested 5Hz vHP stimulation paired with either natural vocalizations or artificial/noise acoustic stimuli. vHP stimulation enhanced auditory responses to vocalizations (with a negative or positive valence) in the inferior colliculus, medial geniculate body, and auditory cortex, but not to their temporally reversed counterparts (artificial sounds) or broadband noise. Meanwhile, pharmacological vHP inactivation diminished response selectivity to vocalizations. These results directly reveal the large-scale hippocampal participation in natural sound processing at early centers of the ascending auditory pathway. They expand our present understanding of hippocampus in global auditory networks.
Genome-wide analysis of dendritic cell differentiation
Authors: Tiniakou Ioanna , Hsu Pei-Feng , Lopez-Zepeda Lorena S. , Lau Colleen M. , Soni Chetna , Esteva Eduardo , Adams Nicholas M. , Liu Fan , Khodadadi-Jamayran Alireza , Rodrick Tori C. , Jones Drew , Tsirigos Aristotelis , Ohler Uwe , Bedford Mark T. , Nimer Stephen D. , Reizis Boris
Published: May 2022

Dendritic cells (DCs) are immune sentinel cells that comprise antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs). Cytokine Flt3 ligand (Flt3L) supports the proliferation of hematopoietic progenitors, and is also necessary and sufficient for DC differentiation. Here we characterized the spontaneous differentiation of a Flt3L-dependent murine progenitor cell line into pDCs and “myeloid” cDCs (cDC2s), and interrogated it using a genome-wide CRISPR/Cas9 dropout screen. The screen revealed multiple regulators of DC differentiation including the glycosylphosphatidylinositol transamidase complex, the Nieman-Pick type C cholesterol transporter and arginine methyltransferase Carm1; the role of Carm1 in pDC and cDC2 differentiation was confirmed by conditional targeting in vivo. We also found that negative regulators of mTOR signaling, including the subunits of TSC and GATOR1 complexes, restricted progenitor growth but enabled DC differentiation. The results provide a comprehensive forward genetic analysis of DC differentiation, and help explain how the opposing processes of proliferation and differentiation could be driven by the same cytokine.