bluuebunny/crossref_metadata_2025 huggingface dataset:
The Enterococcus secretome inhibits the growth of Mycobacterium tuberculosis complex mycobacteria.
Authors: ACHACHE Wafaa , MEGE Jean Louis , FELLAG Mustapha , DRANCOURT Michel
Published: August 2022

Enterococcus mundtii ( E. mundtii ), a commensal intestinal bacterium, was demonstrated to inhibit the growth of some Mycobacterium tuberculosis ( M. tuberculosis ) complex (MTC) species that cause tuberculosis in humans and mammals. To further expand this preliminary observation, we cross-investigated five E. mundtii strains and seven MTC strains representative of four MTC species using a standardized quantitative agar well diffusion assay. All five E. mundtii strains, calibrated at 3.10 9 colony forming units/mL, inhibited the growth of all M. tuberculosis strains with various susceptibility profiles, but no inhibition was observed with lower inoculums. Further, 9 Enterococcus species freeze-dried cell-free culture supernatants (CFCS) including Enterococcus avium, Enterococcus devriesei , Enterococcus durans , Enterococcus dispar , Enterococcus hirae , Enterococcus casseliflavus , Enterococcus faecalis , Enterococcus faecium , and E. mundtii, inhibited the growth of M. tuberculosis , Mycobacterium africanum ( M. africanum ), Mycobacterium bovis ( M. bovis ) and Mycobacterium canettii ( M. canettii ), the most susceptible MTC species (inhibition diameter 25 ±1 mm), proportionally to CFCS protein concentrations. Data reported here indicated that the Enterococcus secretome inhibits growth of main MTC species of medical interest, which broadens previously reported data. In the gut, the Enterococcus secretome may modulate the expression of tuberculosis, exhibiting an anti-tuberculosis effect, with some protective roles in human and animal health.
Integrated transcriptome analysis of Huntington’s disease iPSC-derived and mouse astrocytes implicates dysregulated synaptogenesis, actin, and astrocyte maturation
Authors: Reyes-Ortiz Andrea M. , Abud Edsel M. , Burns Mara S. , Wu Jie , Hernandez Sarah J. , Geller Nicolette , Wang Keona Q. , Schulz Corey , Miramontes Ricardo , Lau Alice , Michael Neethu , Miyoshi Emily , Blurton-Jones Mathew , Van Vactor David , Reidling John C. , Swarup Vivek , Poon Wayne W. , Lim Ryan G. , Thompson Leslie M.
Published: August 2022

Huntington’s disease (HD) is a neurodegenerative disease caused by an expanded CAG repeat within the Huntingtin (HTT) gene having dysregulated cellular homeostasis in the central nervous system, particularly in the striatum and cortex. Astrocytes establish and maintain neuronal functions through the secretion of soluble factors and physical interactions with other neurovascular unit cell types. Under pathological conditions, astrocytes can become reactive, causing cell state transitions that affect brain function. To investigate transitions between cellular states in unaffected and HD astrocytes at high resolution, single-nuclei RNA-sequencing (snRNA-seq) was performed on human HD patient induced pluripotent stem cell (iPSC)-derived astrocytes and on striatal and cortical tissue from a rapidly progressing HD mouse model (R6/2). Analysis of HD human and mouse astrocytes revealed both models have alterations in morphology, glutamate uptake, and dysregulation of astrocyte identity and maturation, whereas dysregulated actin-mediated signaling was unique to human iPSC-derived astrocytes. Representative proteins showed altered levels by Western. In both species, HD transcriptional changes reveal potential astrocyte maturation deficits that were potentially driven by astrogliogenesis transcription factors, including ATF3 and NFIA. When perturbed in a drosophila model of HD, knockdown of NFIA in glia rescued the climbing deficit. These data further support the hypothesis that mutant HTT induces dysregulated astrocyte cell states resulting in dysfunctional astrocytic properties, suggests that some of these states are cell autonomous and maybe unique to human HD, and implicate ATF3 and maturation deficits in HD pathogenesis.
Sensbio: An online server for biosensor design
Authors: Tellechea-Luzardo Jonathan , Moreno López Raul , Carbonell Pablo
Published: August 2022

Allosteric transcription factor (aTF) based biosensors can be used to engineer genetic circuits for a wide range of applications. The literature and online databases contain hundreds of experimentally validated molecule-TF pairs, however the knowledge is scattered and often incomplete. Additionally, compared to the number of compounds that can potentially be produced using living systems, the number of those discovered with TF-based interactions is low. For these reasons, new tools that help researchers find new possible TF-ligand pairs are called for. In this work we present Sensbio (https://bit.ly/3OF4msH), an online web server that through similarity comparison against a TF-ligand reference database, is able to identify putative transcription factors that may be activated by a given input molecule. As a complement to the application, a predictive model has been developed to find new possible matches based on machine learning.
TraceTrack, an Open-Source Software for Batch Processing, Alignment and Visualization of Sanger Sequencing Chromatograms
Authors: Brazdilova Kveta , Prihoda David , Ton Quynh , Klock Heath , Bitton Danny A.
Published: August 2022

Background

Despite the advent of Next Generation Sequencing technology and its widespread applications, Sanger sequencing remains instrumental for molecular biology subcloning work in biological and medical research and indispensable for drug discovery campaigns. Although Sanger sequencing technology has been long established, existing software for processing and visualization of trace file chromatograms are limited in terms of functionality, scalability, and availability for commercial use.

Results

To fill this gap, we developed TraceTrack, an open-source web application tool for batch alignment, analysis and visualization of Sanger trace files. TraceTrack offers high throughput matching of trace files to reference sequences, rapid identification of mutations and an intuitive chromatogram analysis. Comparative analysis between TraceTrack and existing software tools highlights the advantages of TraceTrack with regards to batch processing, visualization and export functionalities. TraceTrack is available at https://github.com/Merck/TraceTrack and also at https://tracetrack.dichlab.org as a web application.

Conclusion

TraceTrack is a web application for batch processing and visualization of Sanger trace file chromatograms that meets the increasing demand of industrial sequence validation workflows in pharmaceutical settings.
Distance estimation in the Goldfish (Carassius auratus)
Authors: Sibeaux Adelaide , Karlsson Cecilia , Newport Cait , de Perera Theresa Burt
Published: August 2022

Neurophysiological advances have given us exciting insights into the systems responsible for spatial mapping in mammals. However, we are still lacking information on the evolution of these systems and whether the underlying mechanisms identified are universal across phyla, or specific to the species studied. Here we address these questions by exploring whether a species that is evolutionarily distant from mammals can perform a task central to mammalian spatial mapping – distance estimation. We developed a behavioural paradigm allowing us to test whether goldfish (Carassius auratus) can estimate distance and explored the behavioural mechanisms that underpin this ability. Fish were trained to swim a set distance within a narrow tank covered with striped pattern. After changing the background pattern, we found that goldfish use the spatial frequency of their visual environment to estimate distance; doubling the spatial frequency of optic flow pattern resulted in a large overestimation of the swimming distance. These results provide robust evidence that goldfish can accurately estimate distance, and show that they use optic flow to do so. These results provide a compelling basis to utilise goldfish as a model system to interrogate the evolution of the mechanisms that underpin spatial cognition, from brain to behaviour.
Molecular and anatomical roadmap of stroke pathology in immunodeficient mice
Authors: Weber Rebecca Z , Mulders Geertje , Perron Patrick , Tackenberg Christian , Rust Ruslan
Published: August 2022

Background

Stroke remains a leading cause of disability and death worldwide. It has become apparent that inflammation and immune mediators have a pre-dominant role in initial tissue damage and long-term recovery following the injury. Still, different immunosuppressed mouse models are necessary in stroke research e.g., to evaluate therapies using human cell grafts. Despite mounting evidence delineating the importance of inflammation in the stroke pathology, it is poorly described to what extent partial immune deficiency influences the overall stroke outcome.

Methods

Here, we assessed the stroke pathology of popular genetic immunodeficient mouse models, i.e., NOD scid gamma (NSG) and recombination activating gene 2 (Rag2-/-) mice as well as pharmacologically immunosuppressed mice and compared them to immune competent, wildtype (WT) C57BL/6J mice up to three weeks after injury. We performed histology, gene expression profiling, serum analysis and functional behavioural tests to identify the impact of immunosuppression on the stroke progression.

Results

We detected distinct changes in microglia infiltration, scar-forming and vascular repair in immune-suppressed mice three weeks after injury. Gene expression analysis of stroked tissue revealed the strongest deviation from immune competent mice was observed in NSG mice, for instance, affecting immunological and angiogenic pathways. Pharmacological immunosuppression resulted in the least variation in gene expression compared with the WT. Major differences have been further identified in the systemic inflammatory response following stroke acutely and three weeks following injury. These anatomical, genetic, and systemic changes did not affect functional deficits and recovery in a time course of three weeks. To determine whether the timing of immunosuppression after stroke is critical, we compared mice with acute and delayed pharmacological immunosuppression after stroke. Mice with a delayed immunosuppression (7d) after stroke showed increased inflammatory and scarring responses compared to animals acutely treated with tacrolimus, thus more closely resembling WT pathology. Transplantation of human cells in the brains of immunosuppressed mouse models led to prolonged cell survival in all immunosuppressed mouse models, which was most consistent in NSG and Rag2-/-mice.

Conclusions

In sum, we detected distinct anatomical and molecular changes in the stroke pathology between the individual immunosuppressed mouse models that should be carefully considered when selecting an appropriate mouse model for stroke research.
Graph-Based Reconstruction and Analysis of Disease Transmission Networks using Viral Genomic Data
Authors: Ke Ziqi , Vikalo Haris
Published: August 2022

Understanding the patterns of viral disease transmissions helps establish public health policies and aids in controlling and ending a disease outbreak. Classical methods for studying disease transmission dynamics that rely on epidemiological data, such as times of sample collection and duration of exposure intervals, struggle to provide desired insight due to limited informativeness of such data. A more precise characterization of disease transmissions may be acquired from sequencing data that reveals genetic distance between viral populations in patient samples. Indeed, genetic distance between viral strains present in hosts contains valuable information about transmission history, thus motivating the design of methods that rely on genomic data to reconstruct a directed disease transmission network, detect transmission clusters, and identify significant network nodes (e.g., super-spreaders). In this paper, we present a novel end-to-end framework for the analysis of viral transmissions utilizing viral genomic (sequencing) data. The proposed framework groups infected hosts into transmission clusters based on reconstructed viral quasispecies; the genetic distance between a pair of hosts is calculated using Earth Mover’s Distance, and further used to infer transmission direction between the hosts. To quantify the significance of a host in the transmission network, the importance score is calculated by a graph convolutional auto-encoder. The viral transmission network is represented by a directed minimum spanning tree utilizing the Edmond’s algorithm modified to incorporate constraints on the importance scores of the hosts. Results on realistic synthetic as well as experimental data demonstrate that the proposed framework outperforms state-of-the-art techniques for the analysis of viral transmission dynamics.

CCS CONCEPTS

Applied computing → Bioinformatics.

ACM Reference Format

Ziqi Ke and Haris Vikalo. 2022. Graph-Based Reconstruction and Analysis of Disease Transmission Networks using Viral Genomic Data. In Proceedings of The Seventh International Workshop on Computational Network Biology (CNB-MAC 2022). ACM, New York, NY, USA, 10 pages. https://doi.org/XXXXXXX.XXXXXXX
Ubigen: Interactive Ranking and Enrichment Test for Ubiquitously Expressed Genes
Authors: Projahn Elias , Möller Steffen
Published: August 2022

We provide an interactive web service to score and rank human genes by their abundance and invariance of expression across all samples in the GTEx database. Users may provide a list of genes to have these scored and ranked accordingly. A one-sided Wilcoxon rank sum test determines a p-value to indicate if the genes from the list score higher than expected by chance. It is possible to interactively control the parameters and instantly observe the effects on the ranking for each of the submitted genes of interest. A genome-wide sliding-window analysis finds that the genes with both the highest and the lowest ranks feature more GO term annotations, indicating that the scoring carries biological relevance.

Availability and Implementation

https://ubigen.uni-rostock.de

Contact

elias.projahn@uni-rostock.de
Collective invasion of the basement membrane in breast cancer driven by forces from cell volume expansion and local contractility
Authors: Chang Julie , Saraswathibhatla Aashrith , Song Zhaoqiang , Varma Sushama , Sanchez Colline , Srivastava Sucheta , Liu Katherine , Bassik Michael C. , Marinkovich M. Peter , Hodgson Louis , Shenoy Vivek , West Robert B. , Chaudhuri Ovijit
Published: August 2022

Breast cancer becomes invasive when carcinoma cells collectively invade through the basement membrane (BM), a nanoporous layer of matrix that physically separates the primary tumor from the stroma, in a first step towards metastasis. Single cells can invade through nanoporous three-dimensional (3D) matrices via protease-mediated degradation or, when the matrix exhibits sufficient mechanical plasticity, force-mediated widening of pores. However, how cells invade collectively through physiological BM layers in cancer remains unclear. Here, we developed a 3D in vitro model of collective invasion of the BM during breast cancer. We show that cells utilize both proteases and forces to breach the BM. Forces are generated from a combination of global cell volume expansion that stretch the BM with local contractile forces that act in the plane of the BM to breach it, allowing invasion. These results uncover a mechanism by which cells collectively interact to overcome a critical barrier to metastasis.
Drug-gene interaction screens coupled to tumour data analyses identify the most clinically-relevant cancer vulnerabilities driving sensitivity to PARP inhibition
Authors: Jamal Kunzah , Galbiati Alessandro , Armenia Joshua , Illuzzi Giuditta , Hall James , Bentouati Sabrina , Barrell Daniel , Ahdesmäki Miika ,   Functional Genomics Centre, O’Connor Mark J. , Leo Elisabetta , Forment Josep V.
Published: August 2022

Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) are currently indicated for the treatment of ovarian, breast, pancreatic and prostate cancers harbouring mutations in the tumour suppressor genes BRCA1 or BRCA2. In the case of ovarian and prostate cancers, their classification as homologous recombination repair (HRR) deficient (HRD) or mutated (HRRm) also makes PARPi an available treatment option beyond BRCA1 or BRCA2 mutational status. However, identification of the most relevant genetic alterations driving the HRD phenotype has proven difficult and recent data have shown that other genetic alterations not affecting HRR are also capable of driving PARPi responses. To gain insight into the genetics driving PARPi sensitivity, we performed CRISPR-Cas9 loss-of-function screens in 6 PARPi-insensitive cell lines and combined the output with published PARPi datasets from 8 additional cell lines. Ensuing exploration of the data identified 110 genes whose inactivation is strongly linked to sensitivity to PARPi. Parallel cell line generation of isogenic gene knockouts in ovarian and prostate cancer cell lines identified that inactivation of core HRR factors is required for driving in vitro PARPi responses comparable to the ones observed for BRCA1 or BRCA2 mutations. Moreover, pan-cancer genetic, transcriptomic and epigenetic data analyses of these 110 genes highlight the ones most frequently inactivated in tumours, making this study a valuable resource for prospective identification of potential PARPi-responsive patient populations. Importantly, our investigations uncover XRCC3 gene silencing as a potential new prognostic biomarker of PARPi sensitivity in prostate cancer.

Statement of significance

This study identifies tumour genetic backgrounds where to expand the use of PARP inhibitors beyond mutations in BRCA1 or BRCA2. This is achieved by combining the output of unbiased genome-wide loss-of-function CRISPR-Cas9 genetic screens with bioinformatics analysis of biallelic losses of the identified genes in public tumour datasets, unveiling loss of the DNA repair gene XRCC3 as a potential biomarker of PARP inhibitor sensitivity in prostate cancer.
Tracking multiple conformations occurring on angstrom-and-millisecond scales in single amino-acid-transporter molecules
Authors: Zhou Yufeng , Lewis John H. , Lu Zhe
Published: August 2022

The AdiC transporter facilitates the movement of arginine and its metabolite across the membrane of pathogenic enterobacteria, enabling them to evade a host’s highly acidic gastric defense barrier to reach the intestines. Like other transporters, AdiC undergoes a series of necessary conformational changes. Detection of these changes, which occur on angstrom-and- millisecond scales, remains extremely challenging. Here, using a high-resolution polarization-microscopic method, we have successfully resolved AdiC’s four conformations by monitoring the emission-polarization changes of a fluorophore attached to an α-helix that adopts conformation-specific orientations and, furthermore, quantified their probabilities in a series of arginine concentrations. The KD values determined for arginine in four individual conformations are statistically comparable to the previously reported overall KD determined using isothermal titration calorimetry. This demonstrated strong resolving power of the present polarization-microscopy method will enable an acquisition of the quantitative information required for understanding the expected complex conformational mechanism underlying the transporter’s function, as well as those of other membrane proteins.
Duplication and losses of opsin genes in lophotrochozoan evolution
Authors: De Vivo Giacinto , Crocetta Fabio , Ferretti Miriam , Feuda Roberto , D’Aniello Salvatore
Published: August 2022

Opsins are G-coupled receptors playing a key role in metazoan visual processes. While many studies enriched our understanding of opsin diversity in several animal clades, the opsin evolution in Lophotrochozoa, one of the major metazoan groups, remains poorly understood. We investigated the opsin evolution in 74 translated lophotrochozoan genomes and capitalized on recently developed phylogenetic approaches. We found that the common ancestor of Lophotrochozoa possessed at least seven opsin paralog groups that underwent divergent evolutionary history in the different phyla. Furthermore, we showed for the first time placopsin-related molecules in Bilateria, that we named pseudopsins, which may prove critical in uncovering opsin evolution.
Inference of evolutionary transitions to self-fertilization using whole-genome sequences
Authors: Struett Stefan , Sellinger Thibaut , Glémin Sylvain , Tellier Aurélien , Laurent Stefan
Published: August 2022

The evolution from outcrossing to selfing is a transition that occurred recurrently throughout the eukaryote tree of life, in plants, animals, fungi and algae. Despite some short-term advantages, selfing is supposed to be an evolutionary dead-end reproductive strategy on the long-term and its tippy distribution on phylogenies suggests that most selfing species are of recent origin. However, dating such transitions is challenging while it is central for this hypothesis. We develop two methods making use of full genome polymorphism data to 1) test if a transition from outcrossing to selfing occurred, and 2) infer its age. The sequentially Markov coalescent based (teSMC) and the Approximate Bayesian Computation (tsABC) methods use a common framework based on a transition matrix summarizing the distribution of times to the most recent common ancestor along the genome, allowing to estimate changes in the ratio of population recombination and mutation rates in time. We first demonstrate that our methods can disentangle between past change in selfing rate from past changes in demographic history. Second, we assess the accuracy of our methods and show that transitions to selfing as old as approximatively 2.5Ne generations can be identified from polymorphism data. Third, our estimates are robust to the presence of linked negative selection on coding sequences. Finally, as a proof of principle, we apply both methods to three populations from Arabidopsis thaliana, recovering a transition to selfing which occurred approximately 600,000 years ago. Our methods pave the way to study recent transitions to predominant self-fertilization in selfing organisms.

Significance statement

Self-fertilization evolved recurrently from outcrossing in many groups of organisms. When, why, and at what pace such transitions occurred are central to understand the evolution of reproductive systems but dating them remains highly challenging. While experimental work can be conducted in ecological set-ups, it is difficult to reconstruct and empirically test the past ecological conditions which could have driven transitions from outcrossing to self-fertilizing reproduction. We suggest here to use full genome data of several individuals per population to estimate if and when a transition in reproductive strategy occurred. We develop two methods which can be applied to estimate the age of such transitions jointly with the species demographic history.
Overexpression profiling reveals cellular requirements in context of genetic backgrounds and environments
Authors: Saeki Nozomu , Yamamoto Chie , Eguchi Yuichi , Sekito Takayuki , Shigenobu Shuji , Yoshimura Mami , Yashiroda Yoko , Boone Charles , Moriya Hisao
Published: August 2022

Overexpression due to copy number variation, promoter mutation, or aneuploidy is often observed, but its adaptive role is not clearly understood. Using a novel “overexpression profiling” method designated ADOPT, we systematically obtained genes whose overexpression was functionally adaptive (GOFAs) under stress conditions in budding yeast to elucidate the nature of adaptive overexpression. GOFAs obtained under heat, salt, and oxidative stress were unique genes that differed from known stress response genes. GOFAs under salt (NaCl) stress were genes involved in calcium homeostasis, reflecting the calcium deficiency of the medium. GOFAs from different genetic backgrounds and co-overexpressing strains revealed that calcium and potassium requirements in salt stress tolerance differ among strains, which is reflected. Profiling of the knockout collection suggested that the effect of calcium was to prevent mitochondrial outbursts. Mitochondria-enhancing GOFAs were adaptive only when calcium was sufficient and conversely non-adaptive in calcium deficiency, supporting the above hypothesis. Adaptive overexpression, thus, reflects the cellular requirements for maximizing the organism’s adaptive capacity within a given environmental and genetic context.
Probabilistic Edge Inference of Gene Networks with Bayesian Markov Random Field Modelling
Authors: Huang Yu-Jyun , Mukherjee Rajarshi , Hsiao Chuhsing Kate
Published: August 2022

Gaussian graphical models (GGMs), also known as Gaussian Markov random field (MRF) models, are commonly used for gene regulatory network construction. Most current approaches to estimating network structure via GGMs can be categorized into a binary decision that determines if an edge exists through penalized optimization and a probabilistic approach that incorporates graph uncertainty. Analyses in the first category usually adopt the perspective of variable (edge) selection without consideration of probabilistic interpretation. Methods in the second group, particularly the Bayesian approach, often quantify the uncertainty in the network structure with a stochastic measure on the precision matrix. Nevertheless, these methods overlook the existence probability of an edge and its strength related to the dependence between nodes. This study simultaneously investigates the existence and intensity of edges for network structure learning. We propose a method that combines the Bayesian MRF model and conditional autoregressive model for the relationship between gene nodes. This analysis can evaluate the relative strength of the edges and further prioritize the edges of interest. Simulations and a glioblastoma cancer study were carried out to assess the proposed model’s performance and compare it with existing methods. The proposed approach shows stable performance and may identify novel structures with biological insights.
Quantitative comparison of manuka and clover honey proteomes with royal jelly
Authors: Paget B.W. , Kleffmann T. , Whiteman K.E. , Thomas M.F. , McMahon C.D.
Published: August 2022

Royal jelly and honey are two substances produced successively by the worker bee caste. Sequential window acquisition of all theoretical fragment-ion spectra mass spectrometry (SWATH-MS) was used to compare protein quantities of bee origin in manuka and clover honey to royal jelly. Two analysis techniques identified 75 proteins in total. Peptide intensity was directly compared for a subset of 32 proteins that were identified with high confidence, and the relative changes in protein abundance were compared between each honey and royal jelly. A total of 16 proteins were found only in honey, 9 of which were common to manuka and clover honeys, and 7 found only in manuka honey. None of the identified proteins were unique to clover honey, while four proteins were unique to royal jelly. Major Royal Jelly Proteins (MRJPs) had similar profiles in both honeys, except MRJP6, which was significantly more abundant in clover honey.

Quantitative data suggests changes of the protein composition as bees develop through the worker caste, with subtle changes in MRJP amounts, and extensive changes in proteins with enzymatic function. Metabolism enzymes were more abundant in honey than in royal jelly, where the trend revealed a potential catalytic role for two uncharacterised proteins (MRJP6 and LOC408608). Differences in the proteomes of the two types of honey probably reflects differences in the type of nectar foraged.
Arabidopsis LSH10 transcription factor interacts with the co-repressor histone deubiquitinase OTLD1 to recruit it to the target promoters
Authors: Vo Phan Mi Sa , Keren Ido , Tran Phu Tri , Lapidot Moshe , Citovsky Vitaly
Published: August 2022

Histone ubiquitylation/deubiquitylation plays a major role in the epigenetic regulation of gene expression. In plants, OTLD1, a member of the ovarian tumor (OTU) deubiquitinase family, deubiquitylates monoubiquitylated histone 2B and represses the expression of genes involved in growth, cell expansion, and hormone signaling. Like many other histone-modifying enzymes, OTLD1 lacks the intrinsic ability to bind DNA. How OTLD1, as well as most other known plant histone deubiquitinases, is recruited specifically to the promoters of its target genes remains unknown. Here, we show that Arabidopsis transcription factor LSH10, a member of the ALOG protein family, interacts with OTLD1 in living plant cells. Loss-of-function LSH10 mutations relieve the OTLD1-promoted transcriptional repression of the target genes, resulting in their elevated expression, whereas recovery of the LSH10 function results in down-regulated transcription of the same genes. We then show that LSH10 associates directly with the target gene chromatin as well as with the specific DNA sequence motifs in the promoter regions of the target genes. Furthermore, in the absence of LSH10, the degree of H2B monoubiquitylation in the target promoter chromatin increases. Hence, our data suggest that OTLD1-LSH10 acts as a co-repressor complex, in which LSH1 recruits OTLD1 to the target gene promoters, potentially representing a general mechanism for recruitment of plant histone deubiquitinases to the target chromatin.
Reduced γ-glutamyl hydrolase activity likely contributes to high folate levels in Periyakulam-1 tomato
Authors: Tyagi Kamal , Sunkum Anusha , Gupta Prateek , Kilambi Himabindu Vasuki , Sreelakshmi Yellamaraju , Sharma Rameshwar
Published: August 2022

Tomato cultivars show wide variation in nutraceutical folate in ripe fruits, yet the loci regulating folate levels in fruits remain unexplored. To decipher regulatory points, we compared two contrasting tomato cultivars: Periyakulam-1 (PKM-1) with high folate and Arka Vikas (AV) with low folate. The progression of ripening in PKM-1 was nearly similar to AV but had substantially lower ethylene emission. In parallel, the levels of phytohormones salicylic acid, ABA, and jasmonic acid were substantially lower than AV. The fruits of PKM-1 were also metabolically distinct from AV, with upregulation of several amino acids. Consistent with higher °Brix levels, the red ripe fruits also showed upregulation of sugars and sugar-derived metabolites. In parallel with higher folate, PKM-1 fruits also had higher carotenoid levels, especially lycopene and β-carotene. Transcript levels of genes encoding folate biosynthesis did not show a perceptible difference in relative expression. The proteome analysis showed upregulation of carotenoid sequestration and folate metabolism-related proteins in PKM-1. The deglutamylation pathway mediated by γ-glutamyl hydrolase (GGH) was substantially reduced in PKM-1 at the red-ripe stage. The red-ripe fruits had reduced transcript levels of GGHs and lower GGH activity than AV. Conversely, the percent polyglutamylation of folate was much higher in PKM-1. Our analysis indicates the regulation of GGH activity as a potential target to elevate folate levels in tomato fruits.
InterClone: Store, Search and Cluster Adaptive Immune Receptor Repertoires
Authors: Wilamowski Jan , Xu Zichang , Ismanto Hendra S , Li Songling , Teraguchi Shunsuke , Llamas- Covarrubias Mara Anais , Lu Xiuyuan , Yamasaki Sho , Standley Daron M
Published: August 2022

B and T cell receptor repertoire data has the potential to fundamentally change the way we diagnose and treat a wide range of diseases. However, there are few resources for storing or analyzing repertoire data. InterClone provides tools for storing, searching, and clustering repertoire datasets. Efficiency is achieved by encoding the complementarity-determining regions of sequences as mmseqs2 databases. Single chain search or cluster results can be merged into paired (alpha-beta or heavy-light) results for analysis of single-cell sequencing data. We illustrate the use of InterClone with two recently reported examples: 1) searching for SARS-CoV-2 infection-enhancing antibodies in bulk COVID-19 and healthy donor repertoires; 2) identification of SARS-CoV-2 specific TCRs by clustering paired and bulk sequences from COVID-19, BNT162b2 vaccinated and healthy unvaccinated donors. The core functions of InterClone have been implemented as a web server and integrated database (https://sysimm.org/interclone). All source code is available upon request.
Expansion Sequencing of RNA Barcoded Neurons in the Mammalian Brain: Progress and Implications for Molecularly Annotated Connectomics
Authors: Goodwin Daniel R. , Vaughan Alex , Leible Daniel , Alon Shahar , Henry Gilbert L. , Cheng Anne , Chen Xiaoyin , Zhang Ruihan , Xue Andrew G. , Wassie Asmamaw T. , Sinha Anubhav , Bando Yosuke , Kajita Atsushi , Marblestone Adam H. , Zador Anthony M. , Boyden Edward S. , Church George M. , Kohman Richie E.
Published: August 2022

Mapping and molecularly annotating mammalian neural circuits is challenging due to the inability to uniquely label cells while also resolving subcellular features such as synaptic proteins or fine cellular processes. We argue that an ideal technology for connectomics would have the following characteristics: the capacity for robustdistance-independent labeling, synaptic resolution, molecular interrogation, and scalable computational methods. The recent development of high-diversity cellular barcoding with RNA has provided a way to overcome the labeling limitations associated with spectral dyes, however performing all-optical circuit mapping has not been demonstrated because no method exists to image barcodes throughout cells at synaptic-resolution. Here we show ExBarSeq, an integrated method combining in situ sequencing of RNA barcodes, immunostaining, and Expansion Microscopy coupled with an end-to-end software pipeline that automatically extracts barcode identities from large imaging datasets without data processing bottlenecks. As a proof of concept, we applied ExBarSeq to thick tissue sections from mice virally infected with MAPseq viral vectors and demonstrated the extraction of 50 barcoded cells in the visual cortex as well as cell morphologies uncovered via immunostaining. The current work demonstrates high resolution multiplexing of exogenous barcodes and endogenous synaptic proteins and outlines a roadmap for molecularly annotated connectomics at a brain-wide scale.
Causal identification of single-cell experimental perturbation effects with CINEMA-OT
Authors: Dong Mingze , Wang Bao , Wei Jessica , de O. Fonseca Antonio H. , Perry Curt , Frey Alexander , Ouerghi Feriel , Foxman Ellen F. , Ishizuka Jeffrey J. , Dhodapkar Rahul M. , van Dijk David
Published: August 2022

Recent advancements in single-cell technologies allow characterization of experimental perturbations at single-cell resolution. While methods have been developed to analyze such experiments, the application of a strict causal framework has not yet been explored for the inference of treatment effects at the single-cell level. In this work, we present a causal inference based approach to single-cell perturbation analysis, termed CINEMA-OT (Causal INdependent Effect Module Attribution + Optimal Transport). CINEMA-OT separates confounding sources of variation from perturbation effects to obtain an optimal transport matching that reflects counterfactual cell pairs. These cell pairs represent causal perturbation responses permitting a number of novel analyses, such as individual treatment effect analysis, response clustering, attribution analysis, and synergy analysis. We benchmark CINEMA-OT on an array of treatment effect estimation tasks for several simulated and real datasets and show that it outperforms other single-cell perturbation analysis methods. Finally, we perform CINEMA-OT analysis of two newly-generated datasets: (1) rhinovirus and cigarette smoke-exposed airway organoids, and (2) combinatorial cytokine stimulation of immune cells. In these experiments, CINEMA-OT reveals potential mechanisms by which cigarette smoke exposure dulls the airway antiviral response, as well as the logic that governs chemokine secretion and peripheral immune cell recruitment.
CRISPR comparison toolkit (CCTK): Rapid identification, visualization, and analysis of CRISPR array diversity
Authors: Collins Alan J. , Whitaker Rachel J.
Published: August 2022

CRISPR-Cas systems provide immunity against mobile genetic elements (MGEs) through sequence-specific targeting by spacer sequences encoded in CRISPR arrays. Spacers are highly variable between microbial strains and can be acquired rapidly, making them well suited for use in strain typing of closely related organisms. However, the historical record of spacer acquisitions and deletions represented by arrays has not previously been used to reconstruct strain histories. We therefore developed the CRISPR Comparison Toolkit (CCTK) to enable analyses of array relationships. CCTK includes tools to identify arrays, analyze relationships between arrays using CRISPRdiff and CRISPRtree, and predict targets of spacers. CRISPRdiff visualizes arrays and highlights the similarities between them. CRISPRtree infers a phylogenetic tree from array relationships and presents a hypothesis of the evolutionary history of the arrays. CCTK unifies several CRISPR analysis tools into a single command line application, including the first tool to infer phylogenies from array relationships.
Comprehensive isotopomer analysis of glutamate and aspartate in small tissue samples
Authors: Cai Feng , Bezwada Divya , Cai Ling , Mahar Rohit , Wu Zheng , Pachnis Panayotis , Yang Chendong , Kelekar Sherwin , Gu Wen , Vu Hieu S. , Mathews Thomas P. , Zacharias Lauren G. , Martin-Sandoval Misty , Do Duyen , Oaxaca K. Celeste , Jin Eunsook S. , Margulis Vitaly , Malloy Craig R. , Merritt Matthew E. , DeBerardinis Ralph J.
Published: August 2022

Stable isotopes are powerful tools to assess metabolism.13C labeling is detected using nuclear magnetic resonance spectroscopy (NMRS) or mass spectrometry (MS). MS has excellent sensitivity but generally cannot discriminate among different13C positions (isotopomers), whereas NMRS is less sensitive but reports some isotopomers. Here, we develop an MS method that reports all 16 aspartate and 32 glutamate isotopomers while requiring 1% of the sample used for NMRS. This method discriminates between pathways that result in the same number of13C labels in aspartate and glutamate, providing enhanced specificity over conventional MS. We demonstrate regional metabolic heterogeneity within human tumors, document the impact of fumarate hydratase deficiency in human renal cancers, and investigate the contributions of TCA cycle turnover and CO2recycling to isotope labeling in vivo. This method can accompany NMRS or standard MS to provide outstanding sensitivity in isotope labeling experiments, particularly in vivo.
Type 17 Follicular Helper T (Tfh17) Cells are Superior for Memory Maintenance
Authors: Gao Xin , Luo Kaiming , Wang Diya , Wei Yunbo , Yao Yin , Deng Jun , Yang Yang , Zeng Qunxiong , Dong Xiaoru , Xiong Le , Gong Dongcheng , Lin Lin , Pohl Kai , Liu Shaoling , Liu Yu , Liu Lu , Nguyen Thi H. O. , Allen Lilith F. , Kedzierska Katherine , Jin Yanliang , Du Meirong , Chen Wanping , Lu Liangjing , Shen Nan , Liu Zheng , Cockburn Ian A. , Luo Wenjing , Yu Di
Published: August 2022

A defining feature of successful vaccination is the ability to induce long-lived antigen- specific memory cells. Follicular helper T (Tfh) cells specialize in providing help to B cells in mounting protective humoral immunity in infection and after vaccination. Memory Tfh cells that retain the CXCR5 expression can confer protection through enhancing humoral response upon antigen re-exposure but how they are maintained is poorly understood. CXCR5+memory Tfh cells in human blood are divided into Tfh1, Tfh2 and Tfh17 cells by the expression of chemokine receptors CXCR3 and CCR6 associated with Th1 and Th17 respectively. Here, we developed a new method to induce Tfh1, Tfh2 and Tfh17-like (iTfh1, iTfh2 and iTfh17) cellsin vitro. Although all three iTfh subsets efficiently support antibody responses in recipient mice with immediate immunization, iTfh17 cells are superior to iTfh1 and iTfh2 cells in supporting antibody response to a later immunization after extended restingin vivoto mimic memory maintenance. Notably, the counterpart human Tfh17 cells are selectively enriched in CCR7+central memory Tfh (TfhCM) with survival and proliferative advantages. Furthermore, the analysis of multiple human cohorts that received different vaccines for HBV, influenza virus, tetanus toxin or measles revealed that vaccine-specific Tfh17 cells outcompete Tfh1 or Tfh2 cells for the persistence in memory phase. Therefore, the complementary mouse and human results showing the advantage of Tfh17 cells in maintenance and memory function supports the notion that Tfh17-induced immunization might be preferable in vaccine development to confer long-term protection.
Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants
Authors: Kates Heather R. , O’Meara Brian C. , LaFrance Raphael , Stull Gregory W. , James Euan K. , Conde Daniel , Liu Shuiyin , Tian Qin , Yi Tingshuang , Kirst Matias , Ané Jean-Michel , Soltis Douglas E. , Guralnick Robert P. , Soltis Pamela S. , Folk Ryan A.
Published: August 2022

Root nodule symbiosis (RNS) allows plants to access atmospheric nitrogen converted into usable forms through a mutualistic relationship with soil bacteria. RNS is a complex trait requiring coordination from both the plant host and the bacterial symbiont, and pinpointing the evolutionary origins of root nodules is critical for understanding the genetic basis of RNS. This endeavor is complicated by data limitations and the intermittent presence of RNS in a single clade of ca. 30,000 species of flowering plants, i.e., the nitrogen-fixing clade (NFC). We developed the most extensivede novophylogeny for all major lineages of the NFC and an enhanced root nodule trait database to reconstruct the evolution of RNS. Through identification of the evolutionary pathway to RNS gain, we show that shifts among heterogeneous evolutionary rates can explain how a complex trait such as RNS can arise many times across a large phylogeny. Our analysis identifies a two-step process in which an ancestral precursor state gave rise to a more labile state from which RNS was quickly gained at specific points in the NFC. Our rigorous reconstruction of ancestral states illustrates how a two-step pathway could have led to multiple independent gains and losses of RNS, contrary to recent hypotheses invoking just a single gain and numerous losses. RNS may be an example of multi-level convergent evolution, thus requiring a broader phylogenetic and genetic scope for genome-phenome mapping to elucidate mechanisms enabling fully functional RNS.
Body mass index in parents and their adult offspring: a systematic review and meta-analysis
Authors: Zhang Jie , Clayton Gemma , Overvad Kim , Olsen Anja , Lawlor Deborah A , Dahm Christina C
Published: August 2022

Obesity may track across generations, due to genetics and family environmental factors, or possibly intrauterine programming. However, many studies only assess associations between maternal body mass index (BMI) on offspring obesity in childhood. To determine whether maternal and paternal associations with offspring BMI differ, and whether associations persist into adulthood, a systematic review and meta-analysis was done. MEDLINE, EMBASE and PubMed (to December 2019) were searched. Observational studies reporting associations between maternal or paternal BMI and adult offspring BMI were included. Offspring BMIs were reported as continuous or categorical measures. 46 studies were included in the systematic review. Meta-analyses were conducted using random effects models. Parental BMI was positively associated with offspring BMI in adulthood. The pooled mother-offspring standardized mean difference (SMD) was 0.23 (95% confidence interval (CI): 0.20, 0.26), and father-offspring SMD was similar: 0.22 (95%CI: 0.19, 0.25) in adjusted models. Maternal and paternal overweight and obesity were associated with higher offspring BMI with similar magnitudes. If these associations are causal, they support interventions targeting all family members, rather than focusing solely on mothers, to maintain a healthy weight.
HSDatabase – a database of highly similar duplicate genes from plants, animals, and algae
Authors: Zhang Xi , Hu Yining , Smith David Roy
Published: August 2022

Gene duplication is an important evolutionary mechanism capable of providing new genetic material, which can help organisms adapt to various environmental conditions. Recent studies, for example, have indicated that highly similar duplicated genes (HSDs) are involved in adaptation to extreme conditions via gene dosage. However, HSDs in most genomes remain uncharacterized. Here, we collected and curated HSDs in nuclear genomes from a diversity of species and indexed them in an online, open-access sequence repository called HSDatabase. Currently, this database contains 117,864 curated HSDs from 40 eukaryotic genomes, and it includes information on the total HSD number, gene copy number/length, and alignments of gene copies. HSDatabase also allows users to download sequences of gene copies, access genome browsers, and link out to other databases, such as Pfam and KEGG. What’s more, a built-in Basic Local Alignment Search Tool (BLAST) option is available to conveniently explore potential homologous sequences of interest within and across species. HSDatabase is presented with a user-friendly interface and provides easy access to the source data. It can be used on its own for comparative analyses of gene duplicates or in conjunction with HSDFinder, a newly developed bioinformatics tool for identifying, annotating, categorizing, and visualizing HSDs.

Database URL

http://hsdfinder.com/database/
Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries
Authors: Mehringer Svenja , Seiler Enrico , Droop Felix , Darvish Mitra , Rahn René , Vingron Martin , Reinert Knut
Published: August 2022

Searching sequences in large, distributed databases is the most widely used bioinformatics analysis done. This basic task is in dire need for solutions that deal with the exponential growth of sequence repositories and perform approximate queries very fast.

In this paper, we present a novel data structure: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it has the potential to serve as the underlying engine for many applications.

We show that the HIBF is superior in build time, index size and search time while achieving a comparable or better accuracy compared to other state-of-the art tools (Mantis and Bifrost). The HIBF builds an index up to 211 times faster, using up to 14 times less space and can answer approximate membership queries faster by a factor of up to 129. This can be considered a quantum leap that opens the door to indexing complete sequence archives like the European Nucleotide Archive or even larger metagenomics data sets.