bluuebunny/crossref_metadata_2025 huggingface dataset:
GSK-3484862 targets DNMT1 for degradation in cells
Authors: Chen Qin , Zeng Yang , Hwang Jee Won , Liu Bigang , Dai Nan , Corrêa Ivan R. , Estecio Marcos R. , Zhang Xing , Santos Margarida A. , Chen Taiping , Cheng Xiaodong
Published: November 2022

Maintenance of genomic methylation patterns at DNA replication forks by DNMT1 is the key to faithful mitotic inheritance. DNMT1 is often overexpressed in cancer cells and the DNA hypomethylating agents azacytidine and decitabine are currently used in the treatment of hematologic malignancies. However, the toxicity of these cytidine analogs and their ineffectiveness in treating solid tumors have limited wider clinical use. GSK-3484862 is a newly-developed, dicyanopyridine containing, non-nucleoside DNMT1-selective inhibitor with low cellular toxicity. Here, we show that GSK-3484862 targets DNMT1 for protein degradation in both cancer cell lines and murine embryonic stem cells (mESCs). DNMT1 depletion was rapid, taking effect within hours following GSK-3484862 treatment, leading to global hypomethylation. Inhibitor-induced DNMT1 degradation was proteasome-dependent, with no discernible loss ofDNMT1mRNA. In mESCs, GSK-3484862-induced Dnmt1 degradation requires Uhrf1, an accessory factor of Dnmt1 with E3 ubiquitin ligase activity. We also show that Dnmt1 depletion and DNA hypomethylation induced by the compound are reversible after its removal. Together, these results indicate that this DNMT1-selective degrader/inhibitor will be a valuable tool for dissecting both coordinated events linking DNA methylation to gene expression and identifying downstream effectors that ultimately regulate cellular response to altered DNA methylation patterns in a tissue/cell-specific manner.

Highlights

GSK-3484862 targets DNMT1 for protein degradation in a wide-range of cancer cell lines, without a decrease inDNMT1mRNA levels

DNMT1 depletion leads to a >50% loss of global DNA methylation in cells within 2-days of treatment with GSK-3484862

GSK-3484862-induced DNMT1 degradation is proteasome-dependent

In mESCs, Uhrf1 is required for GSK-3484862 to induce Dnmt1 degradation
Investigating the Zoonotic Origin of the Marburg Virus Outbreak in Guinea in 2021
Authors: Makenov Marat , Boumbaly Sanaba , Tolno Faya Raphael , Sacko Nouminy , N’Fatoma Leno Tamba , Mansare Oumar , Kolie Bonaventure , Stukolova Olga , Morozkin Evgeny , Kholodilov Ivan , Zhurenkova Olga , Fyodorova Marina , Akimkin Vasily , Popova Anna , Conde Namoudou , Boiro Mamadou Yero , Karan Lyudmila
Published: November 2022

In 2021, a patient died from Marburg virus (MARV) disease in Guinea, which was the first confirmed case in West Africa. The source of the outbreak has not been identified. It was revealed only that the patient had not traveled anywhere before the illness. Prior to this outbreak, MARV had been found in bats in the neighboring Sierra Leone. In Guinea, this virus has never been found before. Therefore, the question of the source of infection arose: was it an autochthonous case with spillover from a local population of bats or an imported case with spillover from fruit bats foraging/migrating from Sierra Leone?

In this paper, we aimed to conduct a study ofRousettus aegyptiacusin Guinea and determine the source of the most likely infection of a patient who died from Marburg virus disease in 2021 in Guinea.

We caught bats at 32 sites in Guéckédou prefecture, including seven caves and 25 locations on the flight path. A total of 501 fruit bats (Pteropodidae) were captured, including 66R. aegyptiacus. The subsequent screening showed three PCR-positive MARV bats. We have found and described two caves in Guéckédou prefecture where MARV-positiveR. aegyptiacusroost. Sequencing has shown that at least two different MARV genetic variants circulate inR. aegyptiacusin Guinea: an Angola-like strain and MARV strains of major marburgvirus lineages.
Liver type 1 innate lymphoid cells lacking IL-7 receptor are a native killer cell subset fostered by parenchymal niches
Authors: Asahi Takuma , Abe Shinya , Cui Guangwei , Shimba Akihiro , Nabekura Tsukasa , Miyachi Hitoshi , Kitano Satsuki , Ohira Keizo , Dijkstra Johannes M. , Miyazaki Masaki , Shibuya Akira , Ohno Hiroshi , Ikuta Koichi
Published: November 2022

Group 1 innate lymphoid cells (G1-ILCs), including circulating natural killer (NK) cells and tissue-resident type 1 ILCs (ILC1s), are innate immune sentinels critical for responses against infection and cancer. In contrast to relatively uniform NK cells through the body, diverse ILC1 subsets have been characterized across and within tissues in mice, but their developmental and functional heterogeneity remain unsolved. Here, using multimodalin vivoapproaches including fate-mapping and targeting of the interleukin 15 (IL-15)-producing microenvironment, we demonstrate that liver parenchymal niches support the development of a cytotoxic ILC1 subset lacking IL-7 receptor (7R−ILC1s). During ontogeny, fetal liver (FL) G1-ILCs arise perivascularly and then differentiate into 7R−ILC1s within sinusoids. Hepatocyte-derived IL-15 supports parenchymal development of FL G1-ILCs to maintain adult pool of 7R−ILC1s. IL-7R+(7R+) ILC1s in the liver, candidate precursors for 7R−ILC1s, are not essential for 7R−ILC1 development in physiological conditions. Functionally, 7R−ILC1s exhibit killing activity at steady state through granzyme B expression, which is underpinned by constitutive mTOR activity, unlike NK cells with exogenous stimulation-dependent cytotoxicity. Our study reveals the unique ontogeny and functions of liver-specific ILC1s, providing a detailed interpretation of ILC1 heterogeneity.
Assessment of infant outgrowth of cow’s milk allergy in relation to the faecal microbiome and metaproteome
Authors: Hendrickx Diana M. , An Ran , Boeren Sjef , Mutte Sumanth K ,   PRESTO study team, Lambert Jolanda M , Belzer Clara
Published: November 2022

Previous studies provide evidence for an association between modifications of the gut microbiota in early life and the development of food allergies. We studied the faecal microbiota composition (16S rRNA gene amplicon sequencing) and faecal microbiome functionality (metaproteomics) in a cohort of 40 infants diagnosed with cow’s milk allergy (CMA) when entering the study. Some of the infants showed outgrowth of CMA after 12 months, while others did not. Faecal microbiota composition of infants was analysed directly after CMA diagnosis (baseline) as well as 6 and 12 months after entering the study. The aim was to gain insight on gut microbiome parameters in relation to outgrowth of CMA.

The results of this study show that microbiome differences related to outgrowth of CMA can be mainly identified at the taxonomic level of the 16S rRNA gene, and to a lesser extent at the protein-based microbial taxonomy and functional protein level. At the 16S rRNA gene level outgrowth of CMA is characterized by lower relative abundance ofLachnospiraceaeat baseline and lowerBacteroidaceaeat visit 12 months.
Automated liquid-handling operations for robust, resilient, and efficient bio-based laboratory practices
Authors: Torres-Acosta Mario A. , Lye Gary J. , Dikicioglu Duygu
Published: November 2022

Increase in the adoption of liquid handling devices (LHD) can facilitate experimental activities. Initially adopted by businesses and industry-based laboratories, the practice has also moved to academic environments, where a wide range of non-standard/non-typical experiments can be performed. Current protocols or laboratory analyses require researchers to transfer liquids for the purpose of dilution, mixing, or inoculation, among other operations. LHD can render laboratories more efficient by performing more experiments per unit of time, by making operations robust and resilient against external factors and unforeseen events such as the COVID-19 pandemic, and by remote operation. The present work reviews literature that reported the adoption and utilisation of LHD available in the market and presents examples of their practical use. Applications demonstrate the critical role of automation in research development and its ability to reduce human intervention in the experimental workflow. Ultimately, this work will provide guidance to academic researchers to determine which LHD can fulfil their needs and how to exploit their use in both conventional and non-conventional applications. Furthermore, the breadth of applications and the scarcity of academic institutions involved in research and development that utilise these devices highlights an important area of opportunity for shift in technology to maximize research outcomes.
Ensemble Clustering Combined with Clustering Optimization – A Novel Workflow for Analyzing Metabolomics Data
Authors: Hislop Brady D. , Heveran Chelsea M. , June Ronald K.
Published: November 2022

Metabolomic studies have improved the understanding of a broad range of biological tissues, fluids, and systems. Typically, metabolomic analyses employ a workflow that starts with detecting peaks from mass spectrometry data and is followed by a series of statistical analysis aimed at identifying dysregulated metabolites, group differences, and group similarities in dysregulated metabolites and pathways. Generating these group similarities relies on clustering analyses. However, current clustering methods are highly subjective and can be prone to errors, indicating the need for an updated workflow that improves upon these issues. Here we present a novel metabolomics workflow that can produce unbiased, reproducible clustering results: ensemble clustering combined with cluster optimization (ECCO). The first step, clustering optimization, is used to identify an optimal number of clusters without bias. The second step, ensemble clustering, is then performed by finding the consensus clustering solution across thirteen distance algorithms. This step improves the repeatability of analyses and eliminates bias through eliminating the need to choose one distance algorithm in clustering solutions. We employ ECCO to analyze synovial fluid metabolites from patients with early and late osteoarthritis (OA). This method improves upon the detection of distinct metabolomic endotypes compared with conventional analyses. Furthermore, novel pathways were identified corresponding with different stages of OA. These results demonstrate the utility of ECCO in metabolomics workflows that involve clustering data. ECCO, which we provide as an open-source tool, can improve the repeatability, reliability, and ease-of-use of metabolomics analyses, and is therefore expected to increase the confidence of biological interpretation from these data.
Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters
Authors: Louis Marie , Korlević Petra , Nykänen Milaja , Archer Frederick , Berrow Simon , Brownlow Andrew , Lorenzen Eline D. , O’Brien Joanne , Post Klaas , Racimo Fernando , Rogan Emer , Rosel Patricia E. , Sinding Mikkel H. S. , van der Es Henry , Wales Nathan , Fontaine Michael C. , Gaggiotti Oscar , Foote Andrew D.
Published: November 2022

Parallel evolution provides among the strongest evidence of the role of natural selection in shaping adaptation to the local environment. Yet, the chronology, mode and tempo of the process of parallel evolution remains broadly debated and discussed in the field of evolutionary biology. In this study, we harness the temporal resolution of paleogenomics to understand the tempo and independence of parallel coastal ecotype adaptation in common bottlenose dolphins (Tursiops truncatus). For this, we generated whole genome resequencing data from subfossil dolphins (8,610-5,626 years BP) originating from around the formation time of new coastal habitat and compared them with data from contemporary populations. Genomic data revealed a shift in genetic affinity, with the oldest ancient sample being closer to the pelagic populations, while the younger samples had intermediate ancestry that showed greater affinity with the local contemporary coastal populations. We found coastal-associated genotypes in the genome of our highest coverage ancient sample, SP1060, providing rare evidence of rapid adaptation from standing genetic variation. Lastly, using admixture graph analyses, we found a reticulate evolutionary history between pelagic and coastal populations. Ancestral gene flow from coastal populations was the probable source of standing genetic variation present in the pelagic populations that enabled rapid adaptation to newly emerged coastal habitat. The genetic response to past climatic warming provides an understanding of how bottlenose dolphins will respond to ongoing directional climate change and shifting coastlines.
Description ofGloeomargarita ahousahtiaesp. nov., a thermophilic member of the order Gloeomargaritales with intracellular carbonate inclusions
Authors: Bacchetta Thomas , López-García Purificación , Gutiérrez-Preciado Ana , Mehta Neha , Skouri-Panet Feriel , Benzerara Karim , Ciobanu Maria , Yubuki Naoji , Tavera Rosaluz , Moreira David
Published: November 2022

A unicellular cyanobacterium, strain VI4D9, was isolated from thermophilic microbial mats thriving in a hot spring of the Ahousaht territory of Vancouver Island, Canada. The cells were elongated rods (5.1 μm in length and 1.2 μm in width on average). Their UV-visible absorption spectra revealed that they contain chlorophylla, phycocyanin, and carotenoids. Transmission electron microscopy showed the presence of thylakoids concentrated on one side of the cells. The strain grew within a temperature range of 37–50°C, with an optimum at 45°C. Its genome had a size of 3,049,282 bp and a DNA G+C content of 51.8 mol%. The cells contained numerous intracellular spherical granules easily visible under scanning electron microscopy. Energy-dispersive x-ray spectroscopy revealed that these granules were made of Ca-, Ba- and Sr-containing carbonates. A phylogenetic 16S rRNA gene tree robustly placed this strain as sister to several environmental sequences and the described speciesGloeomargarita lithophora, also characterized by the possession of intracellular carbonate inclusions. We consider strain VI4D9 to represent a newGloeomargaritaspecies based on its marked phenotypic differences withG. lithophora, notably, its thermophilic nature and different thylakoid organization. We propose the nameGloeomargarita ahousahtiaesp. nov. for this newly isolated thermophilic cyanobacterium. The type strain is VI4D9 (Culture Collection of Algae and Protozoa strain 1472/1; Laboratorio de Algas Continentales Mexico strain LAC 140).G. ahousahtiaeis the second species described within the recently discovered order Gloeomargaritales.
Chromosome-scale scaffolding of the fungus gnat genome (Diptera:Bradysia coprophila)
Authors: Urban John M. , Gerbi Susan A. , Spradling Allan C.
Published: November 2022

Background

The fungus gnat,Bradysia(Sciara)coprophila, has compelling chromosome biology. Paternal chromosomes are eliminated during spermatogenesis whereas both maternal X sister chromatids are retained. Embryos start with three copies of the X chromosome, but 1-2 copies are eliminated from somatic cells as part of sex determination, and one is eliminated in the germline to restore diploidy. These developmentally normal events present opportunities to study chromosome movements that are unusual in other systems. To support such studies, we previously generated a highly contiguous optical-map-scaffolded long-read assembly (Bcop_v1) of the male somatic genome. However, the scaffolds were not chromosome-scale, the majority of the assembly lacked chromosome assignments, and the order and orientation of the contigs along chromosomes remained unknown.

Findings

Male pupae Hi-C data was used to correct, order, and orient the contigs from Bcop_v1 into chromosome-scale scaffolds, producing the updated assembly, Bcop_v2. Several orthogonal analyses allowed us to (i) identify the corresponding chromosome for each scaffold, (ii) orient them with respect to polytene maps, and (iii) determine that they were highly concordant with the chromosomes they represent. Gene annotations produced for Bcop_v1 were lifted over to Bcop_v2. Chromosomal repeat distributions highlight a potential telomeric sequence. Finally, the Hi-C data shed new light on three “fold-back regions” seen to physically interact in images of polytene X chromosomes.

Conclusions

Studies of the unusual chromosome movements inBradysia coprophilawill benefit from the updated assembly (Bcop_v2) where each somatic chromosome is represented by a single scaffold.
Adapting protein language models for rapid DTI prediction
Authors: Sledzieski Samuel , Singh Rohit , Cowen Lenore , Berger Bonnie
Published: November 2022

We consider the problem of sequence-based drug-target interaction (DTI) prediction, showing that a straightforward deep learning architecture that leverages pre-trained protein language models (PLMs) for protein embedding outperforms state of the art approaches, achieving higher accuracy, expanded generalizability, and an order of magnitude faster training. PLM embeddings are found to contain general information that is especially useful in few-shot (small training data set) and zero-shot instances (unseen proteins or drugs). Additionally, the PLM embeddings can be augmented with features tuned by task-specific pre-training, and we find that these task-specific features are more informative than baseline PLM features. We anticipate such transfer learning approaches will facilitate rapid prototyping of DTI models, especially in low-N scenarios.
Contrasting drugs from decoys
Authors: Sledzieski Samuel , Singh Rohit , Cowen Lenore , Berger Bonnie
Published: November 2022

Protein language models (PLMs) have recently been proposed to advance drugtarget interaction (DTI) prediction, and have shown state-of-the-art performance on several standard benchmarks. However, a remaining challenge for all DTI prediction models (including PLM-based ones) is distinguishing true drugs from highly-similar decoys. Leveraging techniques from self-supervised contrastive learning, we introduce a second-generation PLM-based DTI model trained on triplets of proteins, drugs, and decoys (small drug-like molecules that do not bind to the protein). We show that our approach,CON-Plex, improves specificity while maintaining high prediction accuracy and generalizability to new drug classes. CON-Plex maps proteins and drugs to a shared latent space which can be interpreted to identify mutually-compatible classes of proteins and drugs. Data and code are available athttps://zenodo.org/record/7127229.
Extraintestinal survival and host immune response toVibrio cholerae
Authors: Agyei Foster K. , Adade Nana E. , Anabire Nsoh G. , Appiah Vincent , Bediako Yaw , Duodu Samuel
Published: November 2022

Vibrio choleraeis best known to cause the deadly disease cholera. However, in recent years this bacterial pathogen has been found to invade intestinal layers and translocate into the bloodstream of humans. The aim of this study was to investigate the molecular basis ofV. choleraebacteremia. Nine (9) strains ofV. cholerae; six (6) environmental strains of non-O1/non-O139 serogroup and three (3) clinical strains of O1 serogroup and El-Tor serotype were screened for survival in serum obtained from immunocompromised patients. Serum from immunocompetent individuals with no known underlying conditions were used as healthy controls. Five (5) environmental strains and one (1) clinical strain ofV. choleraewere identified to survive the bactericidal action of serum. Whole genome sequence analysis revealed the cholix toxin (ChxA) and genes encoding for siderophores(FepEandEntD) as possible virulence factors used by the environmental strains to cause invasive bloodstream infection. Peripheral blood mononuclear cells (PBMCs) stimulated withV. choleraerevealed increased expression of some cytokines; IL-1ß and IL-13 and the chemokine; RANTES especially among diabetics. The present study illustrates the potential survival ofV. choleraein blood, which could be aided by scavenging for iron from their host leading to severe infections.
Machine Learning Workflow for Single-Cell Antimicrobial Susceptibility Testing ofKlebsiella pneumoniaeto Meropenem in Sub-Doubling Time
Authors: Tjandra Kristel C. , Ram-Mohan Nikhil , Roshardt Manuel , Zudock Elizabeth , Qu Zhaonan , Mach Kathleen E. , Eminaga Okyaz , Liao Joseph C. , Yang Samuel , Wong Pak Kin
Published: November 2022

Multidrug-resistantEnterobacteriaceaeare among the most urgent global public health threats associated with various life-threatening infections. In the absence of a rapid method to identify antimicrobial susceptibility, empirical use of broad-spectrum antimicrobials such as carbapenem monotherapy has led to the spread of resistant organisms. Rapid determination of antimicrobial resistance is urgently needed to overcome this issue. By capturing dynamic single-cell morphological features of over thirty-nine thousand cells from nineteen strains ofKlebsiella pneumoniae, we evaluated strategies based on time and concentration differentials for classifying its susceptibility to a commonly used carbapenem, meropenem, and predicting their minimum inhibitory concentrations (MIC). We report morphometric antimicrobial susceptibility testing (MorphoAST), an image-based machine learning workflow, for rapid determination of antimicrobial susceptibility by single-cell morphological analysis within sub-doubling time. We demonstrated that our algorithm has the ability to predict MIC/antimicrobial susceptibility in a fraction of the bacterial doubling time (<50 min.). The classifiers achieved as high as 97% accuracy in 20 minutes (two-fifths of the doubling time) and reached over 99% accuracy within 50 minutes (one doubling time) in predicting the antimicrobial response. A regression model based on the concentration differential of individual cells from nineteen strains predicted the MIC with 100% categorical agreement and essential agreement for seven unseen strains, including two clinical samples from patients with urinary tract infections with different responsiveness to meropenem. The expansion of this innovation to other drug-bug combinations could have significant implications for future development of rapid antimicrobial susceptibility testing.
Reward prediction error neurons implement an efficient code for reward
Authors: Schütt Heiko H. , Kim Dongjae , Ma Wei Ji
Published: November 2022

We use efficient coding principles borrowed from sensory neuroscience to derive the optimal population of neurons to encode rewards from a probability distribution. We find that the response properties of dopaminergic reward prediction error neurons in a rodent and a primate data set are similar to those of the efficient code in many ways: the neurons have a broad distribution of midpoints covering the reward distribution; neurons with higher thresholds have higher gains, more convex tuning functions, and lower slopes; moreover, their slope is higher when the reward distribution is narrower. Furthermore, we derive learning rules that converge to this efficient code; the learning rule for the position of the neuron on the reward axis closely resembles the learning rule of distributional reinforcement learning. Thus, reward prediction error neuron responses may be optimized to broadcast an efficient reward signal, forming a connection between efficient coding and reinforcement learning, two of the most successful theories in computational neuroscience.
Evolutionary rescue in a fluctuating environment
Authors: Marrec Loïc , Bank Claudia
Published: November 2022

No environment is constant over time, and environmental fluctuations impact the outcome of evolutionary dynamics. Survival of a population not adapted to some environmental conditions is threatened unless a mutation rescues it, an eco-evolutionary process termed evolutionary rescue. We here investigate evolutionary rescue in an environment that fluctuates between a favorable state, in which the population grows, and a harsh state, in which the population declines. We develop a stochastic model that includes both population dynamics and genetics. We derive analytical predictions for the mean extinction time of a non-adapted population given that it is not rescued, the probability of rescue by a generalist mutation, and the mean appearance time of a rescue mutant, which we validate using numerical simulations. We find that evolutionary rescue is less (respectively more) likely if the environmental fluctuations are stochastic rather than deterministic and if the mean time between each environmental change is less (respectively more) than the mean survival time of the population in the harsh environment. We demonstrate that high equilibrium population sizes andper capitagrowth rates maximize the chances of evolutionary rescue. We show that an imperfectly harsh environment, which does not fully prevent births but makes the death rate to birth rate ratio much greater than unity, has almost the same rescue probability as a perfectly harsh environment, which fully prevents births. Finally, we put our results in the context of antimicrobial resistance and conservation biology.
Infection-experienced HSPCs protect against infections by generating neutrophils with enhanced bactericidal activity
Authors: Darroch Hannah , Keerthisinghe Pramuk , Sung Yih Jian , Prankerd-Gough Anneke , Crosier Philip S. , Astin Jonathan W. , Hall Christopher J.
Published: November 2022

Hematopoietic stem and progenitor cells (HSPCs) respond to infection by proliferating and generating in-demand neutrophils through a process called emergency granulopoiesis (EG). Recently, infection-induced changes in HPSCs have also been shown to underpin the longevity of trained immunity, where they generate innate immune cells with enhanced responses to subsequent microbial threats. Using larval zebrafish to live image neutrophils and HSPCs we show that infection-experienced HSPCs generate neutrophils with enhanced bactericidal functions. Transcriptomic analysis of EG neutrophils uncovered a previously unknown function for mitochondrial reactive oxygen species in elevating neutrophil bactericidal activity. We also reveal that driving expression of zebrafish C/EBPβ within infection-naïve HSPCs is sufficient to generate neutrophils with similarly enhanced bactericidal capacity. Our work suggests that this demand-adapted source of neutrophils contributes to trained immunity by providing enhanced protection towards subsequent infections. Manipulating demand-driven granulopoiesis may provide a therapeutic strategy to boost neutrophil function and treat infectious disease.
Dynamics of electrical resistance of kombucha zoogleal mats
Authors: Adamatzky Andrew
Published: November 2022

We demonstrated that zoogleal mats of kombucha exhibit spikes of electrical resistance. A kombucha is a sugared tea fermented by a symbiotic community of over twenty species of bacteria and yeasts which produce cellulosic gelatinous zoogleal mats. We recorded electrical resistance of the zoogleal mats via platinum electrodes placed at a distance one centimetre of each other. We found that the mats show temporal variations in electrical resistance in a range 0.13 MOhm to 0.19 MOhm. We discovered spikes of the mats resistance morphologically similar to action potential spikes. Average duration of a resistance spike is 1.8 min, average amplitude is 2.2 kOhm. Average interval between resistance spikes is c. 20 min. The discovered resistive spiking of kombucha mats might indicate on their memfractive properties, and thus open pathways towards prototyping neuromorphic devices with living zoogleal mats.
Integrated analysis of single-cell transcriptome of liver cancer and cirrhosis reveals cell lineage similarity and prognostic-associated subpopulations
Authors: Tong Mengsha , Luo Shijie , Gu Lin , Zhang Zheyang , Liang Chenyu , Tian Jingyi , Huang Huaqiang , Lin Yuxiang , Huang Jialiang
Published: November 2022

Background & Aims

Liver cancer is one of the most leading causes of cancer deaths. Cirrhosis is an important risk factor for liver cancer, which is the result of over-fibrosis caused by diffuse and long-term liver damage. Despite extensive research, a systematic study for characterizing similarity between liver cancer and cirrhosis at single cell resolution is still lacking.

Methods

We established a data analysis framework to elucidate cell lineage similarity between liver cancer and cirrhosis to discover prognostic-associated subpopulations. We integrated single-cell transcriptome data from liver samples at normal, cirrhotic and cancer conditions, which totally contained 78,000 cells. Gene regulation analysis, cellular interactions and trajectory analysis were performed to characterize cirrhosis-like cell subpopulations. Bulk transcriptomes were used to discover prognostic-associated subpopulations.

Results

By aligning cellular subpopulations across different samples, we found remarkable similarity betweenKNG1+hepatocytes in cirrhosis andPGA5+hepatocytes in HCC. Furthermore, gene regulation analysis and cellular interactions implicated E2F1, FOXA2, EGF, CDH and ANGPTL signaling in maintaining cirrhosis-like ecosystem. Strikingly, subpopulations with higher expression of cirrhosis-like signatures were associated with patients’ worse survival.

Conclusions

We revealed a previously unexplored cirrhosis-like ecosystem of liver cancer, which could provide novel biomarkers for therapeutic interventions in HCC. Core analysis modules in this study were integrated into a user-friendly toolkit, SIMscRNA(https://github.com/xmuhuanglab/SIM-scRNA), which could facilitate the exploration of similarity and heterogeneity between precancerous diseases and solid tumors.
Quorum sensing-dependent invasion ofRalstonia solanacearumintoFusarium oxysporumchlamydospores
Authors: Tsumori Chiaki , Matsuo Shoma , Murai Yuta , Kai Kenji
Published: November 2022

Strains ofRalstonia solanacearumspecies complex (RSSC), though known as the causative agent of bacterial wilt disease in plants, induce the chlamydospores of many fungi species and invade them through the spores. The lipopeptide ralstonins are the chlamydospore inducers produced by RSSC and are essential for this invasion. However, no mechanistic investigation of this interaction has been conducted. In this study, we report that quorum sensing (QS), which is bacterial cell–cell communication, is important for RSSC to invade the fungusFusarium oxysporum(Fo). ΔphcB, a deletion mutant of QS signal synthase, lost the ability to both produce ralstonins and invadeFochlamydospores. The QS signal methyl 3-hydroxymyristate rescued these disabilities. In contrast, exogenous ralstonin A, while inducingFochlamydospores, failed to rescue the invasive ability. Gene-deletion and -complementation experiments revealed that the QS-dependent production of extracellular polysaccharide (EPS I) is essential for this invasion. The RSSC cells adhered toFohyphae and formed biofilms there before inducing chlamydospores. This biofilm formation was not observed in the EPS I- or the ralstonin-deficient mutant. Microscopic analysis showed that RSSC infection resulted in the death ofFochlamydospores. Altogether, we reported that the RSSC QS system is important for this lethal endoparasitism. Among the factors regulated by the QS system, ralstonins, EPS I, and biofilm are important parasitic factors.

Significance

RSSC strains are Gram-negative bacteria that infect both plants and fungi. ThephcQS system of RSSC is important for parasitism in plants because it allows them to invade and increase within the host by causing appropriate system activation at each infection step. In this study, we confirmed not only the importance of ralstonins asFochlamydospore inducers, but also that of biofilm formation on the hyphae. In addition to ralstonins, EPS I turned out to be important for biofilm formation. The QS system comprehensively controls the production of these factors in the interaction withFo. Due to RSSC infection, the cell membranes and organelles ofFochlamydospores were destroyed, showing that RSSC cells are not endosymbionts but lethal invaders. This result advocates a new QS-dependent mechanism for the process by which a bacterium invades a fungus.
Detection and Whole Genome of Japanese Encephalitis Virus Genotype III strains isolated from Indian Pig and Mosquito vector
Authors: Pegu Seema R. , Das Pranab J. , Sonowal Joyshikh , Sengar Gyanendra S. , Deb Rajib , Rajkhowa Swaraj , Choudhury Manjisa , Gulati B. R. , Gupta V. K.
Published: November 2022

Japanese encephalitis virus(JEV) are globally prevalent as deadly pathogens in human and animals including pig, horse and cattle. Japanese encephalitis (JE) still remains as an important cause of epidemic encephalitis worldwide and exists in a zoonotic transmission cycle. Assam is one of the highly endemic state for JE in India. In the present study, to understand the epidemiological status of JE circulating in pigs and mosquito particularly in Assam, India, molecular detection of JEV and the complete genome sequencing of the JEV isolates from pig and mosquito were done. The complete genome analysis of two JEV isolates from pig and mosquito were revealed7 and 21 numbers of unique points polymorphism of nucleotide during alignment of the sequences with other available sequences, respectively. Phylogenetic analysis revealed that the isolates of present investigation were belongs to genotype III and closely related with the strains of neighbouring country China. This study represents the transboundary nature of the JEV genotype III circulation and maintained the same genotype through mosquito-swine transmission cycles.
Dieback of stringybark eucalypt forests in the Mount Lofty Ranges
Authors: Guerin Gregory R , Keppel Gunnar , Peters Stefan , Hurren Amelia
Published: November 2022

Canopy dieback and concerning rates of tree mortality have been noted in iconic forests of the Mount Lofty Ranges (MLR), South Australia, dominated by the stringybark eucalypt speciesEucalyptus baxteri(Brown Stringybark) andE. obliqua(Messmate Stringybark). The extent and causes of stringybark forest decline are not yet fully understood, prohibiting evidence-based management strategies. Here, we explore the distribution of MLR populations of the two species and their position in climate space relative to eastern populations. We also conducted field assessments to investigate stand health and dieback aetiology, and analysed existing tree monitoring data. Stringybarks in the MLR are disjunct from eastern populations and occupy a more summer-arid niche. The species are also susceptible to summer water stress andPhytophthora. Periods of drought during 2006–2009 and 2018–2019 may have contributed to observed dieback. However, field assessments suggest a complex landscape syndrome that includes borer infestations and fire impacts among other factors, rather than solely hydraulic failure. Messmate Stringybark has suffered widespread but patchy stand collapse. There is no obvious common pattern of collapsed sites with respect to topography or local water availability (e.g., swamps and ridges equally affected), although northern range-edge sites are heavily affected. Brown Stringybark is less affected but has notable collapse sites. We hope these studies establish a springboard for future investigations and more widespread sampling of MLR stringybark forests. Further investigations should include regional surveys of stringybark sites to record spatial and temporal patterns of tree mortality combined with multi- or hyperspectral analysis of remotely sensed imagery and visual inspection of dieback from very high resolution aerial images and ground-truthing. Our findings confirm the susceptibility of stringybark forests in the MLR to ecosystem collapse and highlight the urgent need to understand the causes and aetiology of the observed dieback.
Rational Chemical Design of Molecular Glue Degraders
Authors: Toriki Ethan S. , Papatzimas James W. , Nishikawa Kaila , Dovala Dustin , McGregor Lynn M. , Hesse Matthew J. , McKenna Jeffrey M. , Tallarico John A. , Schirle Markus , Nomura Daniel K.
Published: November 2022

Targeted protein degradation with molecular glue degraders has arisen as a powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasome-mediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify a transposable chemical handle that would convert protein-targeting ligands into molecular degraders of their corresponding targets. Using the CDK4/6 inhibitor Ribociclib as a prototype, we identified a covalent handle that, when appended to the exit vector of Ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Covalent chemoproteomic profiling of this CDK4 degrader revealed covalent interactions with cysteine 32 of the RING family E3 ubiquitin ligase RNF126. Structural modification of our initial covalent scaffold led to an improved CDK4 degrader with the development of a but-2-ene, 1,4-dione (“fumarate”) handle that showed improved interactions with RNF126. Thereafter, we worked to identify the minimum covalent motif required for interaction with RNF126, which we then transplanted onto chemically related and un-related protein-targeting ligands. This strategy successfully produced molecules which induced the degradation of several proteins across diverse protein classes, including BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, and SMARCA2. Our study undercovers a design strategy for converting protein-targeting ligands into covalent molecular glue degraders.
ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins
Authors: Abanades Brennan , Wong Wing Ki , Boyles Fergus , Georges Guy , Bujotzek Alexander , Deane Charlotte M.
Published: November 2022

Immune receptor proteins play a key role in the immune system and have shown great promise as biotherapeutics. The structure of these proteins is critical for understanding their antigen binding properties. Here, we present ImmuneBuilder, a set of deep learning models trained to accurately predict the structure of antibodies (ABodyBuilder2), nanobodies (NanoBodyBuilder2) and T-Cell receptors (TCRBuilder2). We show that ImmuneBuilder generates structures with state of the art accuracy while being far faster than AlphaFold2. For example, on a benchmark of 34 recently solved antibodies, ABodyBuilder2 predicts CDR-H3 loops with an RMSD of 2.81Å, a 0.09Å improvement over AlphaFold-Multimer, while being over a hundred times faster. Similar results are also achieved for nanobodies, (NanoBodyBuilder2 predicts CDR-H3 loops with an average RMSD of 2.89Å, a 0.55Å improvement over AlphaFold2) and TCRs. By predicting an ensemble of structures, ImmuneBuilder also gives an error estimate for every residue in its final prediction. ImmuneBuilder is made freely available, both to download (https://github.com/oxpig/ImmuneBuilder) and to use via our webserver (http://opig.stats.ox.ac.uk/webapps/newsabdab/sabpred). We also make available structural models for ~150 thousand non-redundant paired antibody sequences (https://zenodo.org/record/7258553).
Phosphoproteomic profiling highlights CDC42 and CDK2 as key players in the regulation of the TGF-β pathway inALMS1andBBS1knockout models
Authors: Bea-Mascato Brais , Giudice Girolamo , Pinheiro-de-Sousa Iguaracy , Solarat Carlos , Petsalaki Evangelia , Valverde Diana
Published: November 2022

BACKGROUND

The primary cilium is a sensory organelle that extends from the plasma membrane. It plays a vital role in physiological and developmental processes by controlling different signalling pathways such as WNT, Sonic hedgehog (SHh), and transforming growth factor β (TGF-β). Ciliary dysfunction has been related to different pathologies such as Alström (ALMS) or Bardet-Biedl (BBS) syndrome. The leading cause of death in adults with these syndromes is chronic kidney disease (CKD), which is characterised by fibrotic and inflammatory processes often involving the TGF-β pathway.

METHODS

Using genomic editing with CRISPR-CAS9 and phosphoproteomics we have studied the TGF-β signalling pathway in knockout (KO) models forALMS1andBBS1genes. We have developed a network diffusion-based analysis pipeline to expand the data initially obtained and to be able to determine which processes were deregulated in TGF-β pathway. Finally, we have analysed protein-protein and kinase-substrate interactions to prioritise candidate genes in the regulation of the TGF-β pathway in ALMS and BBS.

RESULTS

Analysis of differentially phosphorylated proteins identified 10 candidate proteins in theALMS1KO model and 41 in theBBS1KO model. After network expansion using a random walk with a restart algorithm, we were able to identify the TGF-β signalling pathway together with other related processes such as endocytosis in the case ofALMS1or the regulation of the extracellular matrix inBBS1. Protein interaction analyses demonstrated the involvement of CDC42 as a central protein in the interactome inALMS1and CDK2 in the case ofBBS1.

CONCLUSION

In conclusion, the depletion ofALMS1andBBS1affects the TGF-β signalling pathway, conditioning the phosphorylation and activation of several proteins, including CDC42 in the case ofALMS1and CDK2 in the case ofBBS1.
A Web/Cloud based Digital Pathology Platform Framework for AI Development and Deployment
Authors: Akkus Zeynettin , Dangott Bryan , Nassar Aziza
Published: November 2022

Digitization of glass slides has brought several opportunities with it for computational pathology and artificial intelligence (AI). The application of AI in digital pathology slides shows potential for QA/QC, triaging cases, and assisting pathologists in clinical decision making. We present an extensible and modular web/cloud based digital pathology framework for AI development and deployment. The proposed platform supports collaborative multi-user and multi-device annotation, remote slide access, and remote telepathology or teleconsultation tasks.
Microplastics are present in women’s and cows’ follicular fluid and polystyrene microplastics compromise bovine oocyte functionin vitro
Authors: Grechi Nicole , Franko Roksan , Rajaraman Roshini , Stöckl Jan B. , Trapphoff Tom , Dieterle Stefan , Fröhlich Thomas , Noonan Michael J. , de A. M. M. Ferraz Marcia
Published: November 2022

The past several decades have seen alarming declines in the reproductive health of humans, animals and plants. While humans have introduced numerous pollutants that can impair reproductive systems (such as well-documented endocrine disruptors), the potential for microplastics (MPs) to be contributing to the widespread declines in fertility is particularly noteworthy. Over the same timespan that declines in fertility began to be documented, there has been a correlated shift towards a “throw-away society” that is characterised by the excessive consumption of single-use plastic products and a concomitant accumulation of MPs pollution. Studies are showing that MPs can impair fertility, but data have been limited to rodents that were force-fed hundreds of thousands of times more plastics than they would be exposed in the environment. As a first step to linkin vitrohealth effects within vivoenvironmental exposure, we quantified microplastics in the follicular fluid of women and domestic cows. We found that the concentrations of polystyrene microplastics that naturally occurred in follicular fluid were sufficient to compromise the maturation of bovine oocytesin vitro. Collectively, these findings demonstrate that microplastics may also be contributing to the widespread declines in fertility that have been occurring over recent Anthropocene decades.
Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics
Authors: Siljanen Henri M.P. , Manoharan Lokesh , Hilts Angus S. , Bagnoud Alexandre , Alves Ricardo J.E. , Jones Christopher M , Kerou Melina , Sousa Filipa , Hallin Sara , Biasi Christina , Schleper Christa
Published: November 2022

Microbes are the key players in the global cycling of nitrogen (N) and carbon (C), controlling the availability and fluxes of C and N in ecosystems, as well as being responsible for losses through the emissions of the powerful greenhouse gasses nitrous oxide (N2O) and methane (CH4). Thus, characterization of microbial functional guilds involved in these processes is high on the scientific agenda. Yet, standard sequence-based characterization methods often reveal only a minor fraction of their diversity in nature due to their frequent low relative abundance, insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage and efficiency of PCR-based assays. Here, we developed and tested a targeted metagenomic approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic N and CH4 cycling. We designed comprehensive probe libraries for each of 14 target marker genes, comprising 264,000 unique probes in total. These probes were used to selectively enrich the target genes in shotgun metagenomic libraries. In validation experiments with mock communities of cultured microorganisms, the target gene profiles were similar to those of the original community when sequenced with targeted metagenomics. Furthermore, relative abundances of the marker genes obtained by targeted and shotgun metagenomics from agricultural and wetland soils correlated positively, indicating that the targeted approach did not introduce a significant quantitative bias. However, targeted metagenomics generated substantially higher diversity in terms of taxonomic coverage, and a larger number of sequence reads per sample, which allowed 41 or 1.2 times higher diversity estimates than when using shotgun metagenomics or targeted PCR amplification, respectively. Thus, targeted metagenomics complements current approaches by enabling a targeted, more detailed characterization of the diversity of key functional genes involved in N and CH4 cycling within and between ecosystems.
Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing
Authors: Yan Wenkai , Zhu Yu , Liu Wencheng , Zou Chengwu , Jia Bei , Chen Zhong-Qi , Han Yanhong , Wu Jianguo , Yang Dong-lei , Chen Baoshan , Li Rongbai , Ding Shou-Wei , Wu Qingfa , Guo Zhongxin
Published: November 2022

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host new endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector to transmit RTIV and found RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.