bluuebunny/crossref_metadata_2025 huggingface dataset:
JUN mediates senescence and immune cell recruitment to prevent prostate cancer progression
Authors: Redmer Torben , Raigel Martin , Sternberg Christina , Ziegler Roman , Probst Clara , Lindner Desiree , Aufinger Astrid , Limberger Tanja , Trachtova Karolina , Kodajova Petra , Högler Sandra , Schlederer Michaela , Stoiber Stefan , Oberhuber Monika , Bolis Marco , Neubauer Heidi A. , Miranda Sara , Tomberger Martina , Harbusch Nora S. , Garces de los Fayos Alonso Ines , Sternberg Felix , Moriggl Richard , Theurillat Jean-Philippe , Tichy Boris , Bystry Vojtech , Persson Jenny L. , Mathas Stephan , Aberger Fritz , Strobl Birgit , Pospisilova Sarka , Merkel Olaf , Egger Gerda , Lagger Sabine , Kenner Lukas
Published: December 2023

Background

Prostate cancer develops through malignant transformation of the prostate epithelium in a stepwise, mutation-driven process. Although activator protein-1 transcription factors such as JUN have been implicated as potential oncogenic drivers, the molecular programs contributing to prostate cancer progression are not fully understood.

Methods

We analyzed JUN expression in clinical prostate cancer samples across different stages and investigated its functional role in aPten-deficient mouse model. We performed histopathological examinations, transcriptomic analyses and explored the senescence-associated secretory phenotype in the tumor microenvironment.

Results

Elevated JUN levels characterized early-stage prostate cancer and predicted improved survival in human and murine samples. Immune-phenotyping ofPten-deficient prostates revealed high accumulation of tumor-infiltrating leukocytes, particularly innate immune cells, neutrophils and macrophages as well as high levels of STAT3 activation and IL-1β production.Jundepletion in aPten-deficient background prevented immune cell attraction which was accompanied by significant reduction of active STAT3 and IL-1β and accelerated prostate tumor growth. Comparative transcriptome profiling of prostate epithelial cells revealed a senescence-associated gene signature, upregulation of pro-inflammatory processes involved in immune cell attraction and of chemokines such as IL-1β, CCL3 and CCL8 inPten-deficient prostates. Strikingly, JUN depletion reversed both, senescence and senescence-associated immune cell infiltration and consequently accelerated tumor growth.

Conclusions

Our results suggest that JUN acts as tumor-suppressor and decelerates the progression of prostate cancer by transcriptional regulation of senescence- and inflammation-associated genes. This study opens avenues for novel treatment strategies that could impede disease progression and improve patient outcomes.
qDATA - an R application implementing a practical framework for analyzing quantitative Real-Time PCR data
Authors: Ionascu Adrian , Ecovoiu Alexandru Al. , Chifiriuc Mariana Carmen , Ratiu Attila Cristian
Published: December 2023

Gene expression assays that are based on quantitative real-time PCR (qRT-PCR) method are still very popular, therefore, we developed qDATA, a modern open-source R based bioinformatics application that offers a quick and intuitive analysis of raw cycle threshold (Ct) values. The application relies on a straightforward specific data input consisting in Ct values and a few other mandatory fields specifying the experimental and control groups, as well as the target and house-keeping genes. Afterwards, it automatically performs descriptive statistics, normality and statistical testing on 2-ΔCt(or ΔCt) and 2-ΔΔCtterms calculated with Livak’s method. Each computation is indicated in dedicated tabs that display their output consisting in dynamic data tables and publishing quality graphs. We also detail a qRT-PCR data analysis framework that depends on performing exhaustive ΔCt calculations within discrete biological replicates (BRs). The Livak formula is used for the complete sets of available data. These prerequisites arguably lead to an improved data analysis and statistical relevance. In order to maximize the relevance of the results we recommend using at least three BRs and three technical replicates. The efficiency of our computing approach was tested with qDATA using input Ct values corresponding to immune related gene expression evaluated in experimental infection ofDrosophila melanogasterand summer versus winterApis melliferaworkers, respectively. Our results reveal that our working strategy is very reliable and highlight the efficacy and performance of qDATA application.
OCA-B promotes pathogenic maturation of stem-like CD4+T cells and autoimmune demyelination
Authors: Hughes Erik P. , Syage Amber R. , Mehrabad Elnaz Mirzaei , Lane Thomas E. , Spike Benjamin T. , Tantin Dean
Published: December 2023

Stem-like T cells selectively contribute to autoimmunity, but the activities that promote their pathogenicity are incompletely understood. Here, we identify the transcription coregulator OCA-B as a driver of the pathogenic maturation of stem-like CD4+T cell to promote autoimmune demyelination. Using a human multiple sclerosis (MS) patient dataset, we show thatPOU2AF1, the gene encoding OCA-B, is elevated in CD4+T cells from secondary-progressive MS patient lesions. We show that T cell-intrinsic OCA-B loss protects mice from experimental autoimmune encephalomyelitis (EAE) while preserving responses to viral CNS infection. In EAE models driven by antigen reencounter, OCA-B deletion nearly eliminates CNS infiltration, proinflammatory cytokine production and clinical disease. CNS OCA-B-expressing CD4+T of mice with EAE express an encephalitogenic gene program and preferentially confer disease. In a relapsing-remitting EAE model, OCA-B loss protects mice specifically at relapse. During remission, OCA-B promotes the expression ofTcf7,Slamf6, andSellin proliferating CNS T cell populations. At relapse timepoints, OCA-B loss results in both the accumulation of an immunomodulatory CD4+T cell population expressingCcr9andBach2, and loss of pro-inflammatory gene expression from Th17 cells. These results identify OCA-B as a driver of pathogenic CD4+T cells.
Gene expression shifts in Emperor penguin adaptation to the extreme Antarctic environment
Authors: Paris Josephine R. , Fernandes Flávia A. Nitta , Pirri Federica , Greco Samuele , Gerdol Marco , Pallavicini Alberto , Benoiste Marine , Cornec Clément , Zane Lorenzo , Haas Brian , Le Bohec Céline , Trucchi Emiliano
Published: December 2023

Gene expression can accelerate ecological divergence by rapidly tweaking the response of an organism to novel environments, with more divergent environments exerting stronger selection and supposedly, requiring faster adaptive responses. Organisms adapted to extreme environments provide ideal systems to test this hypothesis, particularly when compared to related species with milder ecological niches. The Emperor penguin (Aptenodytes forsteri) is the only warm-blooded vertebrate breeding in the harsh Antarctic winter, in stark contrast with the less cold-adapted sister species, the King penguin (A. patagonicus). Assembling the firstde novotranscriptomes and analysing multi-tissue (brain, kidney, liver, muscle, skin) RNAseq data from natural populations of both species, we quantified the shifts in tissue-enhanced genes, co-expression gene networks, and differentially expressed genes characterising Emperor penguin adaptation to extreme Antarctic ecology. Our analyses revealed the crucial role played by muscle and liver in temperature homeostasis, fasting and whole-body energy metabolism (glucose/insulin regulation, lipid metabolism, fatty acid beta-oxidation, and blood coagulation). Repatterning at the regulatory level appears as more important in the brain of the Emperor penguin, showing the lowest signature of differential gene expression but the largest co-expression gene network shift. Nevertheless, over-expressed genes related to mTOR signalling in the brain and the liver support their central role in cold and fasting responses. Besides contributing to understanding the genetics underlying complex traits, like body energy reservoir management, our results provide a first insight into the role of gene expression in adaptation to one of the most extreme environmental conditions endured by an endotherm.
MAIT cells drive chronic inflammation in a genetically diverse murine model of spontaneous colitis
Authors: Loh Liyen , Orlicky David , Spengler Andrea , Levens Cassandra , Celli Sofia , Domenico Joanne , Klarquist Jared , Onyiah Joseph , Matsuda Jennifer , Kuhn Kristine , Gapin Laurent
Published: December 2023

Background & aims

Lymphocytes that produce IL-17 can confer protective immunity during infections by pathogens, yet their involvement in inflammatory diseases is a subject of debate. Although these cells may perpetuate inflammation, resulting in tissue damage, they are also capable of contributing directly or indirectly to tissue repair, thus necessitating more detailed investigation. Mucosal-Associated-Invariant-T (MAIT) cells are innate-like T cells, acquiring a type III phenotype in the thymus. Here, we dissected the role of MAIT cellsin vivousing a spontaneous colitis model in a genetically diverse mouse strain.

Methods

Multiparameter spectral flow cytometry and scRNAseq were used to characterize MAIT and immune cell dynamics and transcriptomic signatures respectively, in the collaborative-cross strain, CC011/Unc and CC011/Unc-Traj33-/-.

Results

In contrast to many conventional mouse laboratory strains, the CC011 strain harbors a high baseline population of MAIT cells. We observed an age-related increase in colonic MAIT cells, Th17 cells, regulatory T cells, and neutrophils, which paralleled the development of spontaneous colitis. This progression manifested histological traits reminiscent of human IBD. The transcriptomic analysis of colonic MAIT cells from CC011 revealed an activation profile consistent with an inflammatory milieu, marked by an enhanced type-III response. Notably, IL-17A was abundantly secreted by MAIT cells in the colons of afflicted mice. Conversely, in the MAIT cell-deficient CC011-Traj33−/− mice, there was a notable absence of significant colonic histopathology. Furthermore, myeloperoxidase staining indicated a substantial decrease in colonic neutrophils.

Conclusions

Our findings suggest that MAIT cells play a pivotal role in modulating the severity of intestinal pathology, potentially orchestrating the inflammatory process by driving the accumulation of neutrophils within the colonic environment.
On the role of mechanical feedback in synchronous to asynchronous transition during embryogenesis
Authors: Malmi-Kakkada Abdul N. , Sinha Sumit , Thirumalai D.
Published: December 2023

Experiments have shown that during the initial stage of Zebrafish morphogenesis a synchronous to asynchronous transition (SAT) occurs, as the cells divide extremely rapidly. In the synchronous phase, the cells divide in unison unlike in the asynchronous phase. Despite the wide spread observation of SAT in experiments, a theory to calculate the critical number of cell cycles,n*, at which asynchronous growth emerges does not exist. Here, using a model for the cell cycle, with the assumption that cell division times are Gaussian distributed with broadening, we predictn*and the time at which the SAT occurs. The theoretical results are in excellent agreement with experiments. The theory, supplemented by agent based simulations, establish that the SAT emerges as a consequence of biomechanical feedback on cell division. The emergence of asynchronous phase is due to linearly increasing fluctuations in the cell cycle times with each round of cell division. We also make several testable predictions, which would further shed light on the role of biomechanical feedback on the growth of multicellular systems.
A low-cost, AI-powered Measurement Verification and Reporting System for growing trees with smallholder farmers
Authors: Amoah Edward Idun , McCloskey Peter , Ouedrago Rimnoma Serge , Chelal John , Akuleut Chelsea , Mwambumba Binti Ibrahan , Meli Brian Kipchirchir , Oyudi Christabel Akinyi , Kibwamga Edna Santa , Cleophas Eunice Kwamboka , Ochola Fredrick Odhiambo , Wangiru Catherine Njeri , Morang’a Kelvin , Mushira Lyon Wilson , Maboke Maureen Kalegi , Titus Nancy Syonthi , Oltimbao Serah Lanoi , Odawa Sheilah Awour , Hughes David Peter
Published: December 2023

Limited access to low-cost tools to measure, report, and verify (MRV) tree growth with smallholder farmers limits the scaling of tree planting efforts in developing countries. Artificial Intelligence (AI) offers the potential for low-cost, reliable, and accessible measurement and verification tools to be developed for an MRV platform to scale tree planting efforts in developing countries. Here, we present an AI-powered non-contact tree diameter measurement and verification tool. We have developed an AI-powered algorithm that accurately estimates the diameter of a tree from an image of the tree with a reference object. This non-contact measurement method utilizes semantic segmentation and image processing techniques to analyze an image of the tree with the reference object. The performance of the proposed method was evaluated on 142 trees with tape-measured diameters at breast height ranging from 5 to 60 cm. A regression analysis between predicted and measured diameter values had an R2and an RMSE of 0.97 and 2.23 cm, respectively. Thus, using a smartphone application, the non-contact method developed here can empower anyone to accurately measure and report tree growth by just taking pictures of the trees with the reference object. The images submitted with on-farm measurements serve as data for future verification operations using the AI-powered algorithm. With the reference object serving as a unique tree identifier, a tree’s survival and diameter measurements can be tracked over time. The MRV system described here, with the developed AI-powered non-contact tree diameter measurement and verification tool, can empower organizations to plant, grow, and monitor trees with anyone, including smallholder farmers.
Multivariate Pattern Analysis of EEG Reveals Neural Mechanism of Naturalistic Target Processing in Attentional Blink
Authors: Jahanian Mansoure , Joanisse Marc , Wang Boyu , Mohsenzadeh Yalda
Published: December 2023

The human brain has inherent limitations in consciously processing visual information. When individuals monitor a rapid sequence of images for detecting two targets, they often miss the second target (T2) if it appears within a short time frame of 200-500ms after the first target (T1), a phenomenon known as the attentional blink (AB). The neural mechanism behind AB remains unclear, largely due to the use of simplistic visual items such as letters and digits in conventional AB experiments, which differ significantly from naturalistic vision. This study employed advanced multivariate pattern analysis (MVPA) of human EEG data to explore the neural representations associated with target processing within a naturalistic paradigm under conditions where AB does or does not occur. Our MVPA analysis successfully decoded the identity of target images from EEG data. Moreover, in the AB condition, characterized by a limited time between targets, T1 processing coincided with T2 processing, resulting in the suppression of late representational markers of both T1 and T2. Conversely, in the condition with longer inter-target interval, neural representations endured for a longer duration. These findings suggest that the attentional blink can be attributed to the suppression of neural representations in the later stages of target processing.

Significance Statement

Within a naturalistic paradigm, we investigated the phenomenon known as attentional blink, where individuals struggle to identify a second target in a rapid sequence when the first target precedes it too closely. Attentional blink is purported to reflect an apparent bottleneck in the attention system’s ability to rapidly redirect attentional resources; however, the mechanism underlying this phenomenon remains hotly debated. Our findings reveal that during a rapid presentation of natural images, a short temporal gap between targets results in reduced neural representations of targets and the occurrence of attentional blink. Conversely, when a greater temporal gap exists between targets, neural representations are preserved. This study provides valuable insights into how the human brain perceives the ever-changing visual world around us.
Digital telomere measurement by long-read sequencing distinguishes healthy aging from disease
Authors: Sanchez Santiago E. , Gu Jessica , Golla Anudeep , Martin Annika , Shomali William , Hockemeyer Dirk , Savage Sharon A. , Artandi Steven E.
Published: December 2023

Telomere length is an important biomarker of organismal aging and cellular replicative potential, but existing measurement methods are limited in resolution and accuracy. Here, we deploy digital telomere measurement by nanopore sequencing to understand how distributions of human telomere length change with age and disease. We measure telomere attrition andde novoelongation with unprecedented resolution in genetically defined populations of human cells, in blood cells from healthy donors and in blood cells from patients with genetic defects in telomere maintenance. We find that human aging is accompanied by a progressive loss of long telomeres and an accumulation of shorter telomeres. In patients with defects in telomere maintenance, the accumulation of short telomeres is more pronounced and correlates with phenotypic severity. We apply machine learning to train a binary classification model that distinguishes healthy individuals from those with telomere biology disorders. This sequencing and bioinformatic pipeline will advance our understanding of telomere maintenance mechanisms and the use of telomere length as a clinical biomarker of aging and disease.
Acetylation of WCC is dispensable for the core circadian clock but differentially regulates acute light responses inNeurospora
Authors: Wang Bin , Edamo Mark E. , Zhou Xiaoying , Wang Ziyan , Gerber Scott A. , Kettenbach Arminja N. , Dunlap Jay C.
Published: December 2023

In theNeurosporacircadian system, the White Collar Complex (WCC) formed by WC-1 and WC-2 drives expression of thefrequency(frq) gene whose product FRQ feedbacks to inhibit transcriptional activity of WCC. Phosphorylation of WCC has been extensively studied, but the extent and significance of other post-translational modifications (PTM) has been poorly studied. To this end, we used mass-spectrometry to study alkylation sites on WCC, resulting in discovery of nine acetylation sites. Mutagenesis analysis showed most of the acetylation events individually do not play important roles in period determination. Moreover, mutating all the lysines falling in either half of WC-1 or all the lysine residues in WC-2 to arginines did not abolish circadian rhythms. In addition, we also found nine mono-methylation sites on WC-1, but like acetylation, individual ablation of most of the mono-methylation events did not result in a significant period change. Taken together, the data here suggest that acetylation or mono-methylation on WCC is not a determinant of the pace of the circadian feedback loop. The finding is consistent with a model in which repression of WCC’s circadian activity is controlled mainly by phosphorylation. Interestingly, light-induced expression of some light-responsive genes has been modulated in certainwc-1acetylation mutants, suggesting that WC-1 acetylation events differentially regulate light responses.
Editing cis-regulatory elements towards generating rice stomatal morphological variation for adaptation to broad and dynamic environments
Authors: Karavolias Nicholas G. , Patel-Tupper Dhruv , Cruz Ana Gallegos , Litvak Lilian , Lieberman Samantha E. , Tjahjadi Michelle , Niyogi Krishna K. , Cho Myeong-Je , Staskawicz Brian J.
Published: December 2023

Cis-regulatory element editing can generate quantitative trait variation while mitigating against extreme phenotypes and harmful pleiotropy associated with coding sequence mutations. Here, we applied a multiplexed guide RNA design approach, informed by bioinformatic datasets, to generate genotypic variation in the promoter ofOsSTOMAGEN,a positive regulator of stomatal density in rice. Engineered genotypic variation corresponded to broad and continuous variation in stomatal density, ranging from 70% to 120% of wild-type stomatal density. This near-isogenic panel of stomatal variants was leveraged in physiological assays to establish discrete relationships between stomatal morphological variation and stomatal conductance, carbon assimilation, and intrinsic water use efficiency in steady-state and fluctuating light conditions. Additionally, promoter alleles were subjected to vegetative drought regimes to assay the effects of the edited alleles on developmental response to drought. Notably, the capacity for drought-responsive stomatal density reprogramming instomagenand two cis-regulatory edited alleles was reduced. Collectively our data demonstrate that cis-regulatory element editing can generate near-isogenic trait variation that can be leveraged for establishing relationships between anatomy, physiology, and crop improvement along diverse environmental clines.
Frustraevo: A Web Server To Localize And Quantify The Conservation Of Local Energetic Frustration In Protein Families
Authors: Parra R. Gonzalo , Freiberger Maria I. , Poley-Gil Miriam , Fernandez-Martin Miguel , Radusky Leandro G. , Wolynes Peter G. , Ferreiro Diego U. , Valencia Alfonso
Published: December 2023

According to the Principle of Minimal Frustration, folded proteins can have only a minimal number of strong energetic conflicts in their native states. However, not all interactions are energetically optimized for folding but some remain in energetic conflict, i.e. they are highly frustrated. This remaining local energetic frustration has been shown to be statistically correlated with distinct functional aspects such as protein-protein interaction sites, allosterism and catalysis. Fuelled by the recent breakthroughs in efficient protein structure prediction that have made available good quality models for most proteins, we have developed a strategy to calculate local energetic frustration within large protein families and quantify its conservation over evolutionary time. Based on this evolutionary information we can identify how stability and functional constraints have appeared at the common ancestor of the family and have been maintained over the course of evolution. Here, we present FrustraEvo, a web server tool to calculate and quantify the conservation of local energetic frustration in protein families.

The webserver is freely available at URL:https://frustraevo.qb.fcen.uba.ar
Increased multiplexity in optical tissue clearing-based 3D immunofluorescence microscopy of the tumor microenvironment by LED photobleaching
Authors: Zheng Jingtian , Wu Yi-Chien , Phillips Evan H. , Wang Xu , Lee Steve Seung-Young
Published: December 2023

Optical tissue clearing and three-dimensional (3D) immunofluorescence (IF) microscopy have been transforming imaging of the complex tumor microenvironment (TME). However, current 3D IF microscopy has restricted multiplexity; only three or four cellular and non-cellular TME components can be localized in a cleared tumor tissue. Here we report a LED photobleaching method and its application for 3D multiplexed optical mapping of the TME. We built a high-power LED light irradiation device and temperature-controlled chamber for completely bleaching fluorescent signals throughout optically cleared tumor tissues without compromise of tissue and protein antigen integrity. With newly developed tissue mounting and selected region-tracking methods, we established a cyclic workflow involving IF staining, tissue clearing, 3D confocal microscopy, and LED photobleaching. By registering microscope channel images generated through three work cycles, we produced 8-plex image data from individual 400 μm-thick tumor macrosections that visualize various vascular, immune, and cancer cells in the same TME at tissue-wide and cellular levels in 3D. Our method was also validated for quantitative 3D spatial analysis of cellular remodeling in the TME after immunotherapy. These results demonstrate that our LED photobleaching system and its workflow offer a novel approach to increase the multiplexing power of 3D IF microscopy for studying tumor heterogeneity and response to therapy.
Barcode 100K Specimens: In a Single Nanopore Run
Authors: Hebert Paul DN , Floyd Robin , Jafarpour Saeideh , Prosser Sean WJ
Published: December 2023

It is a global priority to better manage the biosphere, but action needs to be informed by monitoring shifts in the abundance and distribution of species across the domains of life. The acquisition of such information is currently constrained by the limited knowledge of biodiversity. Among the 20 million or more species of eukaryotes, just a tenth have scientific names. DNA barcoding can speed the registration of unknown animal species, the most diverse kingdom of eukaryotes, as the BIN system automates their recognition. However, inexpensive analytical protocols are critical as the census of all animal species will require processing a billion or more specimens. Barcoding involves DNA extraction followed by PCR and sequencing with the last step dominating costs until 2017. By recovering barcodes from highly multiplexed samples, the Sequel platforms from Pacific BioSciences slashed costs by 90%, but these instruments are only deployed in core facilities because of their expense. Sequencers from Oxford Nanopore Technologies provide an escape from high capital and service costs, but their low sequence fidelity has, until now, kept analytical cost above Sequel. However, the improved performance of its latest flow cells (R10.4.1) might erase this differential. This study demonstrates that a regular MinION flow cell can characterize an amplicon pool derived from 100,000 specimens while a Flongle flow cell can process one derived from several thousand. At $0.01 per specimen, DNA sequencing is now the least expensive step in the barcode workflow. By coupling simplified protocols for DNA extraction with ultra-low volume PCRs, it will be possible to move from specimen to DNA barcode for $0.10, a price point that will enable the census of all species within two decades.
Heterogeneity in lung macrophage control ofMycobacterium tuberculosisis determined by T cells
Authors: Lai Rocky , Williams Travis , Rakib Tasfia , Lee Jinhee , Behar Samuel M.
Published: December 2023

FollowingMycobacterium tuberculosisinfection, alveolar macrophages are initially infected but ineffectively restrict bacterial replication. The distribution ofM. tuberculosisamong different cell types in the lung changes with the onset of T cell immunity when the dominant infected cellular niche shifts from alveolar to monocyte-derived macrophages (MDM). We hypothesize that changes in bacterial distribution among different cell types is driven by differences in T cell recognition of infected cells and their subsequent activation of antimicrobial effector mechanisms. We show that CD4 and CD8 T cells efficiently eliminateM. tuberculosisinfection in alveolar macrophages, but they have less impact on suppressing infection in MDM, which may be a bacterial niche. Importantly, CD4 T cell responses enhance MDM recruitment to the lung. Thus, the outcome of infection depends on the interaction between the T cell subset and the infected cell; both contribute to the resolution and persistence of the infection.
Convergent evolution of desiccation tolerance in grasses
Authors: Marks Rose A. , Van Der Pas Llewelyn , Schuster Jenny , Gilman Ian S , VanBuren Robert
Published: December 2023

Desiccation tolerance has evolved repeatedly in plants as an adaptation to survive extreme environments. Plants use similar biophysical and cellular mechanisms to survive life without water, but convergence at the molecular, gene, and regulatory levels remains to be tested. Here, we explore the evolutionary mechanisms underlying the recurrent evolution of desiccation tolerance across grasses. We observed substantial convergence in gene duplication and expression patterns associated with desiccation. Syntenic genes of shared origin are activated across species, indicative of parallel evolution. In other cases, similar metabolic pathways are induced, but using different gene sets, pointing towards phenotypic convergence. Species-specific mechanisms supplement these shared core mechanisms, underlining the complexity and diversity of evolutionary adaptations to drought. Our findings provide insight into the evolutionary processes driving desiccation tolerance and highlight the roles of parallel and convergent evolution in response to environmental challenges.
Multimodal Pretraining for Unsupervised Protein Representation Learning
Authors: Nguyen Viet Thanh Duy , Hy Truong Son
Published: December 2023

In this paper, we introduce a framework of symmetry-preserving multimodal pretraining to learn a unified representation of proteins in an unsupervised manner, encompassing both primary and tertiary structures. Our approach involves proposing specific pretraining methods for sequences, graphs, and 3D point clouds associated with each protein structure, leveraging the power of large language models and generative models. We present a novel way to combining representations from multiple sources of information into a single global representation for proteins. We carefully analyze the performance of our framework in the pretraining tasks. For the fine-tuning tasks, our experiments have shown that our new multimodal representation can achieve competitive results in protein-ligand binding affinity prediction, protein fold classification, enzyme identification and mutation stability prediction. We expect that this work will accelerate future research in proteins. Our source code in PyTorch deep learning framework is publicly available athttps://github.com/HySonLab/Protein_Pretrain.
DISRUPTION OF THE ENDOGENOUS INDOLE GLUCOSINOLATE PATHWAY IMPACTS THEARABIDOPSIS THALIANAROOT EXUDATION PROFILE AND RHIZOBACTERIAL COMMUNITY
Authors: Acuña Daniel , Bletz Molly C , Sasse Joelle , Micallef Shirley A , Kosina Suzanne , Bowen Benjamin P , Northen Trent R , Colón-Carmona Adán
Published: December 2023

Root exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. We usedArabidopsis thalianamutant lines with disruptions in the indole glucosinolate pathway, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how disrupting this pathway affects the root exudate profile ofArabidopsis thaliana, and in turn, impacts the rhizosphere microbial community. Chemical analysis of the root exudates from the wild-type Columbia (Col-0), a mutant plant line overexpressing the MYB transcription factorATR1(atr1D)which increases glucosinolate production, and the loss-of-functioncyp79B2cyp79B3double mutant line with low levels of glucosinolates confirmed that alterations to the indole glucosinolate biosynthetic pathway shifts the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. This work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria (PGPR). Our results suggest that genetic alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.
Trojan horse virus delivering CRISPR-AsCas12f1 controls plant bacterial wilt caused byRalstonia solanacearum
Authors: Peng Shiwen , Xu Yanan , Qu Hao , Nong Fushang , Shu Fangling , Yuan Gaoqing , Ruan Lifang , Zheng Dehong
Published: December 2023

Plant bacterial wilt caused by theRalstonia solanacearumspecies complex results in huge food and economic losses. Accordingly, the development of an effective control method for this disease is urgently required. Traditional lytic phage biocontrol methods have inherent limitations. However, filamentous phages, which do not lyse host bacteria and exert minimal burden, offer a potential solution. A filamentous phage RSCq that infectsR. solanacearumwas isolated in this study through genome mining. We constructed engineered filamentous phages based on RSCq by employing our proposed approach with a wide applicability to non-model phages, enabling the infection ofR. solanacearumin medium and soil and delivering exogenous genes into bacterial cells. Similar to the Greek soldiers hidden within the Trojan horse, CRISPR-AsCas12f1 gene editing system that targets the key virulence regulator genehrpBwas implanted into the engineered phage, generating the engineered phage RSCqCRISPR-Cas. Our findings demonstrated that RSCqCRISPR-Cas could disarm the key “weapon”,hrpB, ofR. solanacearum, in medium and in plants. Remarkably, pretreatment with RSCqCRISPR-Cas significantly controlled tobacco bacterial wilt, highlighting the potential of engineered filamentous phages as promising biocontrol agents against plant bacterial wilt and other bacterial diseases.
Extreme miniaturization in plasmid design: generation of the 903 bp cloning vector pICOt2
Authors: Staal Jens , Beyaert Rudi
Published: December 2023

Inspired by the size optimizations in the recently published pUdO series of plasmids, we set out to break our previous world record (pICOz, 1185 bp) in designing the smallest possible self-replicating high copy cloning vector. By replacing the zeocin resistance marker with trimethoprim resistance, deleting the parts upstream of -35 in the ampicilin resistance promoter and replacing the extended multiple cloning site with a single SpeI site, we managed to reduce the plasmid size to 903 bp, almost a 24% reduction in size compared to our previous accomplishments.
metaExpertPro: a computational workflow for metaproteomics spectral library construction and data-independent acquisition mass spectrometry data analysis
Authors: Sun Yingying , Xing Ziyuan , Liang Shuang , Miao Zelei , Zhuo Lai-bao , Jiang Wenhao , Zhao Hui , Gao Huanhuan , Xie Yuting , Zhou Yan , Yue Liang , Cai Xue , Chen Yu-ming , Zheng Ju-Sheng , Guo Tiannan
Published: December 2023

Background

Analysis of mass spectrometry-based metaproteomic data, in particular large-scale data-independent acquisition MS (DIA-MS) data, remains a computational challenge. Here, we aim to develop a software tool for efficiently constructing spectral libraries and analyzing extensive datasets of DIA-based metaproteomics.

Results

We present a computational pipeline called metaExpertPro for metaproteomics data analysis. This pipeline encompasses spectral library generation using data-dependent acquisition MS (DDA-MS), protein identification and quantification using DIA-MS, functional and taxonomic annotation, as well as quantitative matrix generation for both microbiota and hosts. To enhance accessibility and ease of use, all modules and dependencies are encapsulated within a Docker container.

By integrating FragPipe and DIA-NN, metaExpertPro offers compatibility with both Orbitrap-based and PASEF-based DDA and DIA data. To evaluate the depth and accuracy of identification and quantification, we conducted extensive assessments using human fecal samples and benchmark tests. Performance tests conducted on human fecal samples demonstrated that metaExpertPro quantified an average of 45,000 peptides in a 60-minute diaPASEF injection. Notably, metaExpertPro outperformed three existing software tools by characterizing a higher number of peptides and proteins. Importantly, metaExpertPro maintained a low factual False Discovery Rate (FDR) of less than 5% for protein groups across four benchmark tests. Applying a filter of five peptides per genus, metaExpertPro achieved relatively high accuracy (F-score = 0.67–0.90) in genus diversity and demonstrated a high correlation (rSpearman= 0.73–0.82) between the measured and true genus relative abundance in benchmark tests.

Additionally, the quantitative results at the protein, taxonomy, and function levels exhibited high reproducibility and consistency across the commonly adopted public human gut microbial protein databases IGC and UHGP. In a metaproteomic analysis of dyslipidemia patients, metaExpertPro revealed characteristic alterations in microbial functions and potential interactions between the microbiota and the host.

Conclusions

metaExpertPro presents a robust one-stop computational solution for constructing metaproteomics spectral libraries, analyzing DIA-MS data, and annotating taxonomic as well as functional data.
Autoantibodies to truncated GAD(96-585) antigen stratify risk of early insulin requirement in adult-onset diabetes
Authors: Grace Sian L. , Gillespie Kathleen M. , Williams Claire L. , Lampasona Vito , Achenbach Peter , Pearson Ewan R. , Williams Alistair J.K. , Long Anna E. , McDonald Timothy J. , Jones Angus G.
Published: December 2023

Objective

We investigated whether further characterisation of full-length (f-) GADA responses could identify early insulin requirement in adult-onset diabetes.

Research Design and Methods

In 179 f-GADA positive participants diagnosed with type 2 diabetes, we assessed the association of truncated (t-)GADA positivity, f-GADA IgG subclasses, and f-GADA affinity with early insulin requirement (<5 years), type 1 diabetes genetic risk score (T1D GRS), and C-peptide. These characteristics were compared to f-GADA positive type 1 diabetes (n=141) and f-GADA negative type 2 diabetes (n=6420) cohorts.

Results

t-GADA positivity was lower in f-GADA positive without early insulin in comparison to f-GADA positive type 2 diabetes requiring insulin within 5 years, and type 1 diabetes (75% vs. 91% and 95% respectively, p<0.0001). t-GADA positivity (in those f-GADA positive) identified a group with a higher type 1 diabetes genetic susceptibility (mean T1D GRS 0.248 vs. 0.225, p=0.003), lower C-peptide (1156 pmol/L vs. 4289 pmol/L, p=1×10-7), and increased IA-2A positivity (23% vs. 6%, p=0.03). In survival analysis, t-GADA positivity was associated with early insulin requirement compared with those only positive for f-GADA, independently from age of diagnosis, f-GADA titre and duration of diabetes [adjusted HR 5.7 (95% CI 1.4, 23.5), p=0.017]. Early insulin requirement was not associated with an IgG1-restricted f-GADA response (p=0.81) or a high affinity f-GADA response (p=0.89).

Conclusions

The testing of t-GADA in f-GADA positive individuals with type 2 diabetes identifies those who have genetic and clinical characteristics comparable to type 1 diabetes and stratifies those at higher risk of early insulin requirement.

Article Highlights

Progression to insulin therapy is highly variable in adult-onset GADA positive diabetes.

We further characterised GADA characteristics in adult-onset diabetes and assessed whether these are associated with early insulin requirement.

Truncated GADA positivity was associated with a type 1 diabetes like phenotype and stratified risk of early insulin requirement. Those GADA positive who were negative for truncated GADA had the characteristics and progression of classical type 2 diabetes. Assessing full-length GADA IgG subclass and affinity did not further stratify risk of progression.

t-GADA assessment remains underutilised in clinical practice, but could assist correct therapy allocation in adult-onset diabetes.
Approaches to improve mental health care for autistic children and young people: a systematic review and meta-analysis
Authors: Pemovska Tamara , Loizou Sofia , Appleton Rebecca , Spain Debbie , Stefanidou Theodora , Kular Ariana , Cooper Ruth , Greenburgh Anna , Griffiths Jessica , Barnett Phoebe , Foye Una , Baldwin Helen , Minchin Matilda , Brady Gráinne , Saunders Katherine R. K. , Ahmed Nafiso , Jackson Robin , Olive Rachel Rowan , Parker Jennie , Timmerman Amanda , Sapiets Suzi , Driskell Eva , Chipp Beverley , Parsons Bethany , Totsika Vaso , Mandy Will , Pender Richard , Clery Philippa , Lloyd-Evans Brynmor , Simpson Alan , Johnson Sonia
Published: December 2023

Autistic children and young people (CYP) experience mental health difficulties but face many barriers to accessing and benefiting from mental health care. There is a need to explore strategies in mental health care for autistic CYP to guide clinical practice and future research and support their mental health needs. Our aim was to identify strategies used to improve mental health care for autistic CYP and examine evidence on their acceptability, feasibility, and effectiveness. A systematic review and meta-analysis were carried out. All study designs reporting acceptability/feasibility outcomes and empirical quantitative studies reporting effectiveness outcomes for strategies tested within mental health care were eligible. We conducted a narrative synthesis and separate meta-analyses by informant (self, parent, clinician). Fifty-seven papers were included, with most investigating cognitive behavioural therapy (CBT)-based interventions for anxiety and several exploring service-level strategies, such as autism screening tools, clinician training, adaptations regarding organisation of services. Most papers described caregiver involvement in therapy and reported adaptations to communication and intervention content; a few reported environmental adjustments. In the meta-analyses, parent- and clinician-reported outcomes, but not self-reported outcomes, showed with moderate certainty that CBT for anxiety was an effective treatment compared to any comparison condition in reducing anxiety symptoms in autistic individuals. The certainty of evidence for effectiveness, synthesised narratively, ranged from low to moderate. Evidence for feasibility and acceptability tended to be positive. Many identified strategies are simple, reasonable adjustments that can be implemented in services to enhance mental health care for autistic individuals. Notable research gaps persist, however.
“Nitrogen demand, supply, and acquisition strategy control plant responses to elevated CO2at different scales”
Authors: Perkowski Evan A. , Ezekannagha Ezinwanne , Smith Nicholas G.
Published: December 2023

Plants respond to elevated atmospheric CO2concentrations by reducing leaf nitrogen content and photosynthetic capacity – patterns that correspond with increased net photosynthesis rates, total leaf area, and total biomass. Nitrogen supply has been hypothesized to be the primary factor controlling these responses, as nitrogen availability limits net primary productivity globally. Recent work using evo-evolutionary optimality theory suggests that leaf photosynthetic responses to elevated CO2are independent of nitrogen supply and are instead driven by leaf nitrogen demand to build and maintain photosynthetic enzymes, which optimizes resource allocation to photosynthetic capacity and maximizes allocation to growth. Here,Glycine maxL. (Merr) seedlings were grown under two CO2concentrations, with and without inoculation withBradyrhizobium japonicum, and across nine soil nitrogen fertilization treatments in a full-factorial growth chamber experiment to reconcile the role of nitrogen supply and demand on leaf and whole-plant responses to elevated CO2. After seven weeks, elevated CO2increased net photosynthesis rates despite reduced leaf nitrogen content and maximum rates of Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) carboxylation and electron transport for RuBP regeneration. Effects of elevated CO2on net photosynthesis and indices of photosynthetic capacity were independent of nitrogen fertilization and inoculation. However, increasing nitrogen fertilization enhanced positive effects of elevated CO2on total leaf area and total biomass due to increased nitrogen uptake and reduced carbon costs to acquire nitrogen. Whole-plant responses to elevated CO2were not modified by inoculation across the nitrogen fertilization gradient, as plant investment toward symbiotic nitrogen fixation was similar between CO2treatments. These results indicate that leaf nitrogen demand to build and maintain photosynthetic enzymes drives leaf photosynthetic responses to elevated CO2, while nitrogen supply regulates whole-plant responses. Our findings build on previous work suggesting that terrestrial biosphere models may improve simulations of photosynthetic processes under future novel environments by adopting optimality principles.
Natural and age-related variation in circulating human hematopoietic stem cells
Authors: Furer N. , Rappoport N. , Milman O. , Lifshitz A. , Bercovich A. , Ben-Kiki O. , Danin A. , Kedmi M. , Shipony Z. , Lipson D. , Meiri E. , Yanai G , Shapira S. , Arber N. , Berdichevsky S. , Tavor S. , Tyner J. , Joshi S. , Landau D. , Ganesan S. , Dusaj N. , Chamely P. , Kaushansky N. , Chapal-Ilani N. , Shamir R. , Tanay A. , Shlush LI
Published: December 2023

Hematopoietic stem and progenitor cells (HSPCs) deliver life-long multi-lineage output. However, with aging, we exhibit certain characteristic blood count changes and accumulation of clonal disorders. Better understanding of inter-individual variation in HSPC behavior is needed to understand these age-related phenomena and the transition from health to chronic and acute hematological malignancies. Here we study 627K single circulating CD34+ HSPCs (cHSPCs) from 148 healthy individuals, along with their clinical information and clonal hematopoiesis (CH) profiles, to characterize population-wide and age-related hematopoietic variability. Individuals with CH were linked with reduced frequencies of lymphocyte progenitors and higher RDW. An age-related decrease in lymphoid progenitors was observed, predominantly in males. Inter-individual transcriptional variation in expression of a Lamin-A signature and stemness gene programs were linked with aging and presence of macrocytic anemia. Based on our model for healthy cHSPC variation we construct the normal reference for cHSPC subtype frequencies. We show how compositional and expression deviations from this normal reference can robustly identify myeloid malignancies and pre-malignant states. Together, our data and methodologies present a novel resource, shedding light on various age-related hematopoietic processes, and a comprehensive normal cHSPC reference, which can serve as a tool for diagnosing and characterizing hematological disorders.