bluuebunny/crossref_metadata_2025 huggingface dataset:
KnockTF 2.0: a comprehensive gene expression profile database with knockdown/knockout of transcription (co-)factors in multiple species
Authors: Feng Chenchen , Song Chao , Song Shuang , Zhang Guorui , Yin Mingxue , Zhang Yuexin , Qian Fengcui , Wang Qiuyu , Guo Maozu , Li Chunquan
Published: November 2023

Transcription factors (TFs), transcription co-factors (TcoFs) and their target genes perform essential functions in diseases and biological processes. KnockTF 2.0 (http://www.licpathway.net/KnockTF/index.html) aims to provide comprehensive gene expression profile datasets before/after T(co)F knockdown/knockout across multiple tissue/cell types of different species. Compared with KnockTF 1.0, KnockTF 2.0 has the following improvements: (i) Newly added T(co)F knockdown/knockout datasets in mice, Arabidopsis thaliana and Zea mays and also an expanded scale of datasets in humans. Currently, KnockTF 2.0 stores 1468 manually curated RNA-seq and microarray datasets associated with 612 TFs and 172 TcoFs disrupted by different knockdown/knockout techniques, which are 2.5 times larger than those of KnockTF 1.0. (ii) Newly added (epi)genetic annotations for T(co)F target genes in humans and mice, such as super-enhancers, common SNPs, methylation sites and chromatin interactions. (iii) Newly embedded and updated search and analysis tools, including T(co)F Enrichment (GSEA), Pathway Downstream Analysis and Search by Target Gene (BLAST). KnockTF 2.0 is a comprehensive update of KnockTF 1.0, which provides more T(co)F knockdown/knockout datasets and (epi)genetic annotations across multiple species than KnockTF 1.0. KnockTF 2.0 facilitates not only the identification of functional T(co)Fs and target genes but also the investigation of their roles in the physiological and pathological processes.
SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution
Authors: Wang Fang , Liu Chunpu , Li Jiawei , Yang Fan , Song Jiangning , Zang Tianyi , Yao Jianhua , Wang Guohua
Published: November 2023

The single-cell proteomics enables the direct quantification of protein abundance at the single-cell resolution, providing valuable insights into cellular phenotypes beyond what can be inferred from transcriptome analysis alone. However, insufficient large-scale integrated databases hinder researchers from accessing and exploring single-cell proteomics, impeding the advancement of this field. To fill this deficiency, we present a comprehensive database, namely Single-cell Proteomic DataBase (SPDB, https://scproteomicsdb.com/), for general single-cell proteomic data, including antibody-based or mass spectrometry-based single-cell proteomics. Equipped with standardized data process and a user-friendly web interface, SPDB provides unified data formats for convenient interaction with downstream analysis, and offers not only dataset-level but also protein-level data search and exploration capabilities. To enable detailed exhibition of single-cell proteomic data, SPDB also provides a module for visualizing data from the perspectives of cell metadata or protein features. The current version of SPDB encompasses 133 antibody-based single-cell proteomic datasets involving more than 300 million cells and over 800 marker/surface proteins, and 10 mass spectrometry-based single-cell proteomic datasets involving more than 4000 cells and over 7000 proteins. Overall, SPDB is envisioned to be explored as a useful resource that will facilitate the wider research communities by providing detailed insights into proteomics from the single-cell perspective.
standR: spatial transcriptomic analysis for GeoMx DSP data
Authors: Liu Ning , Bhuva Dharmesh D , Mohamed Ahmed , Bokelund Micah , Kulasinghe Arutha , Tan Chin Wee , Davis Melissa J
Published: November 2023

To gain a better understanding of the complexity of gene expression in normal and diseased tissues it is important to account for the spatial context and identity of cells in situ. State-of-the-art spatial profiling technologies, such as the Nanostring GeoMx Digital Spatial Profiler (DSP), now allow quantitative spatially resolved measurement of the transcriptome in tissues. However, the bioinformatics pipelines currently used to analyse GeoMx data often fail to successfully account for the technical variability within the data and the complexity of experimental designs, thus limiting the accuracy and reliability of the subsequent analysis. Carefully designed quality control workflows, that include in-depth experiment-specific investigations into technical variation and appropriate adjustment for such variation can address this issue. Here, we present standR, an R/Bioconductor package that enables an end-to-end analysis of GeoMx DSP data. With four case studies from previously published experiments, we demonstrate how the standR workflow can enhance the statistical power of GeoMx DSP data analysis and how the application of standR enables scientists to develop in-depth insights into the biology of interest.
PGS-Depot: a comprehensive resource for polygenic scores constructed by summary statistics based methods
Authors: Cao Chen , Zhang Shuting , Wang Jianhua , Tian Min , Ji Xiaolong , Huang Dandan , Yang Sheng , Gu Ning
Published: November 2023

Polygenic score (PGS) is an important tool for the genetic prediction of complex traits. However, there are currently no resources providing comprehensive PGSs computed from published summary statistics, and it is difficult to implement and run different PGS methods due to the complexity of their pipelines and parameter settings. To address these issues, we introduce a new resource called PGS-Depot containing the most comprehensive set of publicly available disease-related GWAS summary statistics. PGS-Depot includes 5585 high quality summary statistics (1933 quantitative and 3652 binary trait statistics) curated from 1564 traits in European and East Asian populations. A standardized best-practice pipeline is used to implement 11 summary statistics-based PGS methods, each with different model assumptions and estimation procedures. The prediction performance of each method can be compared for both in- and cross-ancestry populations, and users can also submit their own summary statistics to obtain custom PGS with the available methods. Other features include searching for PGSs by trait name, publication, cohort information, population, or the MeSH ontology tree and searching for trait descriptions with the experimental factor ontology (EFO). All scores, SNP effect sizes and summary statistics can be downloaded via FTP. PGS-Depot is freely available at http://www.pgsdepot.net.
Detecting and dissecting signaling crosstalk via the multilayer network integration of signaling and regulatory interactions
Authors: Martini Leonardo , Baek Seung Han , Lo Ian , Raby Benjamin A , Silverman Edwin K , Weiss Scott T , Glass Kimberly , Halu Arda
Published: November 2023

The versatility of cellular response arises from the communication, or crosstalk, of signaling pathways in a complex network of signaling and transcriptional regulatory interactions. Understanding the various mechanisms underlying crosstalk on a global scale requires untargeted computational approaches. We present a network-based statistical approach, MuXTalk, that uses high-dimensional edges called multilinks to model the unique ways in which signaling and regulatory interactions can interface. We demonstrate that the signaling-regulatory interface is located primarily in the intermediary region between signaling pathways where crosstalk occurs, and that multilinks can differentiate between distinct signaling-transcriptional mechanisms. Using statistically over-represented multilinks as proxies of crosstalk, we infer crosstalk among 60 signaling pathways, expanding currently available crosstalk databases by more than five-fold. MuXTalk surpasses existing methods in terms of model performance metrics, identifies additions to manual curation efforts, and pinpoints potential mediators of crosstalk. Moreover, it accommodates the inherent context-dependence of crosstalk, allowing future applications to cell type- and disease-specific crosstalk.
Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts
Authors: Crisalli Alicia M , Chen Yi-Tzai , Cai Ang , Li Deyu , Cho Bongsup P
Published: November 2023

Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5′-CTTCTC#G*NCCTCATTC-3′], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3′ flanking pyrimidine were better bypassed when the 5′ base was 5mC, whereas sequences with a 3′ purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.
MAJIQlopedia: an encyclopedia of RNA splicing variations in human tissues and cancer
Authors: Quesnel-Vallières Mathieu , Jewell San , Lynch Kristen W , Thomas-Tikhonenko Andrei , Barash Yoseph
Published: November 2023

Quantification of RNA splicing variations based on RNA-Sequencing can reveal tissue- and disease-specific splicing patterns. To study such splicing variations, we introduce MAJIQlopedia, an encyclopedia of splicing variations that encompasses 86 human tissues and 41 cancer datasets. MAJIQlopedia reports annotated and unannotated splicing events for a total of 486 175 alternative splice junctions in normal tissues and 338 317 alternative splice junctions in cancer. This database, available at https://majiq.biociphers.org/majiqlopedia/, includes a user-friendly interface that provides graphical representations of junction usage quantification for each junction across all tissue or cancer types. To demonstrate case usage of MAJIQlopedia, we review splicing variations in genes WT1, MAPT and BIN1, which all have known tissue or cancer-specific splicing variations. We also use MAJIQlopedia to highlight novel splicing variations in FDX1 and MEGF9 in normal tissues, and we uncover a novel exon inclusion event in RPS6KA6 that only occurs in two cancer types. Users can download the database, request the addition of data to the webtool, or install a MAJIQlopedia server to integrate proprietary data. MAJIQlopedia can serve as a reference database for researchers seeking to understand what splicing variations exist in genes of interest, and those looking to understand tissue- or cancer-specific splice isoform usage.
OpenProt 2.0 builds a path to the functional characterization of alternative proteins
Authors: Leblanc Sébastien , Yala Feriel , Provencher Nicolas , Lucier Jean-François , Levesque Maxime , Lapointe Xavier , Jacques Jean-Francois , Fournier Isabelle , Salzet Michel , Ouangraoua Aïda , Scott Michelle S , Boisvert François-Michel , Brunet Marie A , Roucou Xavier
Published: November 2023

The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases. Enhancements in this update are largely the result of user feedback and include the prediction of structure, subcellular localization, and intrinsic disorder, using cutting-edge algorithms based on machine learning techniques. The mass spectrometry pipeline now integrates a machine learning-based peptide rescoring method to improve peptide identification. We continue to help users explore this cryptic proteome by providing OpenCustomDB, a tool that enables users to build their own customized protein databases, and OpenVar, a genomic annotator including genetic variants within AltORFs and protein sequences. A new interface improves the visualization of all functional annotations, including a spectral viewer and the prediction of multicoding genes. All data on OpenProt are freely available and downloadable. Overall, OpenProt continues to establish itself as an important resource for the exploration and study of new proteins.
The DO-KB Knowledgebase: a 20-year journey developing the disease open science ecosystem
Authors: Baron J Allen , Johnson Claudia Sanchez-Beato , Schor Michael A , Olley Dustin , Nickel Lance , Felix Victor , Munro James B , Bello Susan M , Bearer Cynthia , Lichenstein Richard , Bisordi Katharine , Koka Rima , Greene Carol , Schriml Lynn M
Published: November 2023

In 2003, the Human Disease Ontology (DO, https://disease-ontology.org/) was established at Northwestern University. In the intervening 20 years, the DO has expanded to become a highly-utilized disease knowledge resource. Serving as the nomenclature and classification standard for human diseases, the DO provides a stable, etiology-based structure integrating mechanistic drivers of human disease. Over the past two decades the DO has grown from a collection of clinical vocabularies, into an expertly curated semantic resource of over 11300 common and rare diseases linking disease concepts through more than 37000 vocabulary cross mappings (v2023-08-08). Here, we introduce the recently launched DO Knowledgebase (DO-KB), which expands the DO’s representation of the diseaseome and enhances the findability, accessibility, interoperability and reusability (FAIR) of disease data through a new SPARQL service and new Faceted Search Interface. The DO-KB is an integrated data system, built upon the DO’s semantic disease knowledge backbone, with resources that expose and connect the DO’s semantic knowledge with disease-related data across Open Linked Data resources. This update includes descriptions of efforts to assess the DO’s global impact and improvements to data quality and content, with emphasis on changes in the last two years.
EVLncRNAs 3.0: an updated comprehensive database for manually curated functional long non-coding RNAs validated by low-throughput experiments
Authors: Zhou Bailing , Ji Baohua , Shen Congcong , Zhang Xia , Yu Xue , Huang Pingping , Yu Ru , Zhang Hongmei , Dou Xianghua , Chen Qingshuai , Zeng Qiangcheng , Wang Xiaoxin , Cao Zanxia , Hu Guodong , Xu Shicai , Zhao Huiying , Yang Yuedong , Zhou Yaoqi , Wang Jihua
Published: November 2023

Long noncoding RNAs (lncRNAs) have emerged as crucial regulators across diverse biological processes and diseases. While high-throughput sequencing has enabled lncRNA discovery, functional characterization remains limited. The EVLncRNAs database is the first and exclusive repository for all experimentally validated functional lncRNAs from various species. After previous releases in 2018 and 2021, this update marks a major expansion through exhaustive manual curation of nearly 25 000 publications from 15 May 2020, to 15 May 2023. It incorporates substantial growth across all categories: a 154% increase in functional lncRNAs, 160% in associated diseases, 186% in lncRNA-disease associations, 235% in interactions, 138% in structures, 234% in circular RNAs, 235% in resistant lncRNAs and 4724% in exosomal lncRNAs. More importantly, it incorporated additional information include functional classifications, detailed interaction pathways, homologous lncRNAs, lncRNA locations, COVID-19, phase-separation and organoid-related lncRNAs. The web interface was substantially improved for browsing, visualization, and searching. ChatGPT was tested for information extraction and functional overview with its limitation noted. EVLncRNAs 3.0 represents the most extensive curated resource of experimentally validated functional lncRNAs and will serve as an indispensable platform for unravelling emerging lncRNA functions. The updated database is freely available at https://www.sdklab-biophysics-dzu.net/EVLncRNAs3/.
The European Nucleotide Archive in 2023
Authors: Yuan David , Ahamed Alisha , Burgin Josephine , Cummins Carla , Devraj Rajkumar , Gueye Khadim , Gupta Dipayan , Gupta Vikas , Haseeb Muhammad , Ihsan Maira , Ivanov Eugene , Jayathilaka Suran , Kadhirvelu Vishnukumar Balavenkataraman , Kumar Manish , Lathi Ankur , Leinonen Rasko , McKinnon Jasmine , Meszaros Lili , O’Cathail Colman , Ouma Dennis , Paupério Joana , Pesant Stephane , Rahman Nadim , Rinck Gabriele , Selvakumar Sandeep , Suman Swati , Sunthornyotin Yanisa , Ventouratou Marianna , Vijayaraja Senthilnathan , Waheed Zahra , Woollard Peter , Zyoud Ahmad , Burdett Tony , Cochrane Guy
Published: November 2023

The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI). The ENA is one of the three members of the International Nucleotide Sequence Database Collaboration (INSDC). It serves the bioinformatics community worldwide via the submission, processing, archiving and dissemination of sequence data. The ENA supports data types ranging from raw reads, through alignments and assemblies to functional annotation. The data is enriched with contextual information relating to samples and experimental configurations. In this article, we describe recent progress and improvements to ENA services. In particular, we focus upon three areas of work in 2023: FAIRness of ENA data, pandemic preparedness and foundational technology. For FAIRness, we have introduced minimal requirements for spatiotemporal annotation, created a metadata-based classification system, incorporated third party metadata curations with archived records, and developed a new rapid visualisation platform, the ENA Notebooks. For foundational enhancements, we have improved the INSDC data exchange and synchronisation pipelines, and invested in site reliability engineering for ENA infrastructure. In order to support genomic surveillance efforts, we have continued to provide ENA services in support of SARS-CoV-2 data mobilisation and have adapted these for broader pathogen surveillance efforts.
STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization
Authors: Xu Zhicheng , Wang Weiwen , Yang Tao , Li Ling , Ma Xizheng , Chen Jing , Wang Jieyu , Huang Yan , Gould Joshua , Lu Huifang , Du Wensi , Sahu Sunil Kumar , Yang Fan , Li Zhiyong , Hu Qingjiang , Hua Cong , Hu Shoujie , Liu Yiqun , Cai Jia , You Lijin , Zhang Yong , Li YuXiang , Zeng Wenjun , Chen Ao , Wang Bo , Liu Longqi , Chen Fengzhen , Ma Kailong , Xu Xun , Wei Xiaofeng
Published: November 2023

Recent technological developments in spatial transcriptomics allow researchers to measure gene expression of cells and their spatial locations at the single-cell level, generating detailed biological insight into biological processes. A comprehensive database could facilitate the sharing of spatial transcriptomic data and streamline the data acquisition process for researchers. Here, we present the Spatial TranscriptOmics DataBase (STOmicsDB), a database that serves as a one-stop hub for spatial transcriptomics. STOmicsDB integrates 218 manually curated datasets representing 17 species. We annotated cell types, identified spatial regions and genes, and performed cell-cell interaction analysis for these datasets. STOmicsDB features a user-friendly interface for the rapid visualization of millions of cells. To further facilitate the reusability and interoperability of spatial transcriptomic data, we developed standards for spatial transcriptomic data archiving and constructed a spatial transcriptomic data archiving system. Additionally, we offer a distinctive capability of customizing dedicated sub-databases in STOmicsDB for researchers, assisting them in visualizing their spatial transcriptomic analyses. We believe that STOmicsDB could contribute to research insights in the spatial transcriptomics field, including data archiving, sharing, visualization and analysis. STOmicsDB is freely accessible at https://db.cngb.org/stomics/.
The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids
Authors: Lawson Catherine L , Berman Helen M , Chen Li , Vallat Brinda , Zirbel Craig L
Published: November 2023

The Nucleic Acid Knowledgebase (nakb.org) is a new data resource, updated weekly, for experimentally determined 3D structures containing DNA and/or RNA nucleic acid polymers and their biological assemblies. NAKB indexes nucleic acid-containing structures derived from all major structure determination methods (X-ray, NMR and EM), including all held by the Protein Data Bank (PDB). As the planned successor to the Nucleic Acid Database (NDB), NAKB’s design preserves all functionality of the NDB and provides novel nucleic acid-centric content, including structural and functional annotations, as well as annotations from and links to external resources. A variety of custom interactive tools have been developed to enable rapid exploration and drill-down of NAKB’s content.
DrugBank 6.0: the DrugBank Knowledgebase for 2024
Authors: Knox Craig , Wilson Mike , Klinger Christen M , Franklin Mark , Oler Eponine , Wilson Alex , Pon Allison , Cox Jordan , Chin Na Eun (Lucy) , Strawbridge Seth A , Garcia-Patino Marysol , Kruger Ray , Sivakumaran Aadhavya , Sanford Selena , Doshi Rahil , Khetarpal Nitya , Fatokun Omolola , Doucet Daphnee , Zubkowski Ashley , Rayat Dorsa Yahya , Jackson Hayley , Harford Karxena , Anjum Afia , Zakir Mahi , Wang Fei , Tian Siyang , Lee Brian , Liigand Jaanus , Peters Harrison , Wang Ruo Qi (Rachel) , Nguyen Tue , So Denise , Sharp Matthew , da Silva Rodolfo , Gabriel Cyrella , Scantlebury Joshua , Jasinski Marissa , Ackerman David , Jewison Timothy , Sajed Tanvir , Gautam Vasuk , Wishart David S
Published: November 2023

First released in 2006, DrugBank (https://go.drugbank.com) has grown to become the ‘gold standard’ knowledge resource for drug, drug–target and related pharmaceutical information. DrugBank is widely used across many diverse biomedical research and clinical applications, and averages more than 30 million views/year. Since its last update in 2018, we have been actively enhancing the quantity and quality of the drug data in this knowledgebase. In this latest release (DrugBank 6.0), the number of FDA approved drugs has grown from 2646 to 4563 (a 72% increase), the number of investigational drugs has grown from 3394 to 6231 (a 38% increase), the number of drug–drug interactions increased from 365 984 to 1 413 413 (a 300% increase), and the number of drug–food interactions expanded from 1195 to 2475 (a 200% increase). In addition to this notable expansion in database size, we have added thousands of new, colorful, richly annotated pathways depicting drug mechanisms and drug metabolism. Likewise, existing datasets have been significantly improved and expanded, by adding more information on drug indications, drug–drug interactions, drug–food interactions and many other relevant data types for 11 891 drugs. We have also added experimental and predicted MS/MS spectra, 1D/2D-NMR spectra, CCS (collision cross section), RT (retention time) and RI (retention index) data for 9464 of DrugBank's 11 710 small molecule drugs. These and other improvements should make DrugBank 6.0 even more useful to a much wider research audience ranging from medicinal chemists to metabolomics specialists to pharmacologists.
Folic Acid Ameliorates Anxiety- and Depressive-Like Behavior Induced by Nicotine Withdrawal Through Restoration of Behavioral and Biochemical Alterations in Adolescent Male Rats
Authors: Rezaei Moghadam Mikael , Khoshrou Alireza , Kakhki Samaneh , Hosseini Seyed Hossein , Shirinzadeh Feizabadi Atefeh , Beheshti Farimah
Published: November 2023

Background

The present study aimed to assess the efficacy of folic acid (FA) on withdrawal following nicotine (Nic) administration in adolescent male rats.

Aims and Methods

Adolescent male rats were divided into two groups: (1) vehicle and (2) Nic (Nic-2 mg/kg), and were under treatment from 21 to 42 days of age. After that, they continued the experiment without treatment and returned to a regular diet, except for one of those who received Nic. The rats were divided into four groups where they were treated with different doses of FA (5, 10, and 15 mg/kg) and bupropion (Bup) by oral gavage, and the final group included normal rats that received only FA (15 mg/kg) from 42 days of age for three weeks during which withdrawal occurred.

Results

Results showed that adolescent Nic exposure exacerbated the behavioral indices of anxiety- and depression-like behaviors, while FA attenuated the effects of Nic withdrawal on anxiety and depression as well as Bup. In support, the biochemical results demonstrated a balance between oxidant and antioxidant mediators in addition to the increase and decrease of serotonin and monoamine oxidase (MAO) activity in cortical tissue. TNF-α as an inflammatory agent was decreased, whereas IL-10 as an anti-inflammatory parameter was increased.

Conclusions

The present findings suggest anxiety and depression caused by Nic withdrawal were attenuated by FA more likely through the reduction activity of MAO, the important enzyme responsible for serotonin metabolism along with balance between oxidant/antioxidant and pro-inflammatory/anti-inflammatory mediators. However, various mechanisms might be involved, which requires further investigation.

Implications

Nic withdrawal-induced depression and anxiety like behavior in rats followed by neuro-oxidative damage and neuro-inflammation. FA supplementation as well as Bup improved cognitive disorders induced by Nic withdrawal by increasing neuro-inflammation and neuro-oxidative damage.
Evaluation of Dolutegravir- and Bictegravir-Based Antiretroviral Regimen Utilization in Patients who Cannot Take Medications by Mouth
Authors: LoFaso Megan , Marchionda Olivia , Bass Stephanie , Torbic Heather , Blackewicz Caitlin , Pallotta Andrea
Published: November 2023

A retrospective review of patients unable to take medications by mouth showed short interruptions of therapy for most patients. In a secondary analysis, our data showed maintenance and/or achievement of viral suppression for most patients. A retrospective review of intensive care patients unable to take antiretrovirals by mouth showed 56.6% of patients experiencing a transient interruption in therapy. Additionally, our case series further supports previous literature on crushing dolutegravir and bictegravir regimens to maintain and achieve viral suppression.
DEFECTIVE KERNEL 56 functions in mitochondrial RNA editing and maize seed development
Authors: Zang Jie , Zhang Tengfei , Zhang Zhaogui , Liu Juan , Chen Huabang
Published: November 2023

Proper seed development is essential for achieving grain production, successful seed germination, and seedling establishment in maize (Zea mays). In the past few decades, pentatricopeptide repeat (PPR) proteins have been proven to play an essential role in regulating the development of maize kernels through posttranscriptional RNA modification of mitochondrial genes. However, the underlying mechanisms remain largely unknown. Here, we characterized a mutant of DEFECTIVE KERNEL 56 (DEK56) with defective kernels that exhibited arrested development of both the embryo and endosperm. Accordingly, we isolated DEK56 through a map-based cloning strategy and found that it encoded an E subgroup PPR protein located in the mitochondria. Dysfunction of DEK56 resulted in altered cytidine (C)-to-uridine (U) editing efficiency at 48 editing sites across 21 mitochondrial transcripts. Notably, the editing efficiency of the maturase-related (matR)-1124 site was substantially reduced or abolished in the dek56 mutant. Furthermore, we found that the splicing efficiency of NADH dehydrogenase subunit 4 (nad4) Introns 1 and 3 was substantially reduced in dek56 kernels, which might be a consequence of the defective MatR function. Through a protein–protein interaction test, we hypothesized that DEK56 carries out its function by recruiting the PPR-DYW protein PPR motif, coiled-coil, and DYW domain-containing protein 1 (PCW1). This interaction is facilitated by Multiple Organellar RNA Editing Factors (ZmMORFs) and Glutamine-Rich Protein 23 (ZmGRP23). Based on these findings, we developed a working model of PPR-mediated mitochondrial processing that plays an essential role in the development of maize kernels. The present study will further broaden our understanding of PPR-mediated seed development and provide a theoretical basis for maize improvement.
Mesophyll conductance limits photosynthesis in fluctuating light under combined drought and heat stresses
Authors: Zeng Zhi-Lan , Wang Xiao-Qian , Zhang Shi-Bao , Huang Wei
Published: November 2023

Drought and heat stresses usually occur concomitantly in nature, with increasing frequency and intensity of both stresses expected due to climate change. The synergistic agricultural impacts of these compound climate extremes are much greater than those of the individual stresses. However, the mechanisms by which drought and heat stresses separately and concomitantly affect dynamic photosynthesis have not been thoroughly assessed. To elucidate this, we used tomato (Solanum lycopersicum) seedlings to measure dynamic photosynthesis under individual and compound stresses of drought and heat. Individual drought and heat stresses limited dynamic photosynthesis at the stages of diffusional conductance to CO2 and biochemistry, respectively. However, the primary limiting factor for photosynthesis shifted to mesophyll conductance under the compound stresses. Compared with the control, photosynthetic carbon gain in fluctuating light decreased by 38%, 73%, and 114% under the individual drought, heat, and compound stresses, respectively. Therefore, compound stresses caused a greater reduction in photosynthetic carbon gain in fluctuating light conditions than individual stress. These findings highlight the importance of mitigating the effects of compound climate extremes on crop productivity by targeting mesophyll conductance and improving dynamic photosynthesis.
Functional divergence of Arabidopsis REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 and 2 in repression of flowering
Authors: Chen Song , Podolec Roman , Arongaus Adriana B , Fuchs Christelle , Loubéry Sylvain , Demarsy Emilie , Ulm Roman
Published: November 2023

Photoperiodic plants coordinate the timing of flowering with seasonal light cues, thereby optimizing their sexual reproductive success. The WD40-repeat protein REPRESSOR OF UV-B PHOTOMORPHOGENESIS 2 (RUP2) functions as a potent repressor of UV RESISTANCE LOCUS 8 (UVR8) photoreceptor-mediated UV-B induction of flowering under noninductive, short-day conditions in Arabidopsis (Arabidopsis thaliana); however, in contrast, the closely related RUP1 seems to play no major role. Here, analysis of chimeric ProRUP1:RUP2 and ProRUP2:RUP1 expression lines suggested that the distinct functions of RUP1 and RUP2 in repressing flowering are due to differences in both their coding and regulatory DNA sequences. Artificial altered expression using tissue-specific promoters indicated that RUP2 functions in repressing flowering when expressed in mesophyll and phloem companion cells, whereas RUP1 functions only when expressed in phloem companion cells. Endogenous RUP1 expression in vascular tissue was quantified as lower than that of RUP2, likely underlying the functional difference between RUP1 and RUP2 in repressing flowering. Taken together, our findings highlight the importance of phloem vasculature expression of RUP2 in repressing flowering under short days and identify a basis for the functional divergence of Arabidopsis RUP1 and RUP2 in regulating flowering time.
Childhood Trauma in Clozapine-Resistant Schizophrenia: Prevalence, and Relationship With Symptoms
Authors: Dudley Robert , Turkington Douglas , Coulthard Naomi , Pyle Melissa , Gumley Andrew , Schwannauer Matthias , Kingdon David , Morrison Anthony P
Published: November 2023

Background and Hypothesis

The role of early adversity and trauma is increasingly recognized in psychosis but treatments for trauma and its consequences are lacking. Psychological treatments need to understand the prevalence of these experiences, the relationship with specific symptoms and identify potentially tractable processes that may be targeted in therapy. It was hypothesized that greater adversity, and specifically abuse rather than neglect, would be associated with positive symptoms and specifically hallucinations. In addition, negative beliefs would mediate the relationship with positive symptoms.

Study Design

292 Patients with treatment resistant psychosis completed measures of early adversity as well as current symptoms of psychosis.

Study Results

Early adversity in the form of abuse and neglect were common in one-third of the sample. Adversity was associated with higher levels of psychotic symptoms generally, and more so with positive rather than negative symptoms. Abuse rather than neglect was associated with positive but not with negative symptoms. Abuse rather than neglect was associated with hallucinations but not delusions. Abuse and neglect were related to negative beliefs about the self and negative beliefs about others. Mediation demonstrated a general relationship with adversity, negative-self, and other views and overall psychotic symptoms but not in relation to the specific experience of abuse and hallucinations. Females were more likely to be abused, but not neglected, than males.

Conclusions

Whilst most relationships were modest, they supported previous work indicating that adversity contributes to people with psychosis experiencing distressing symptoms especially hallucinations. Treatments need to address and target adversity.
“Life will never be the same”: a qualitative analysis of the impact of COVID-19 on adults with a history of insomnia
Authors: Redding Ashley , Santarossa Sara , Sagong Chaewon , Kalmbach David A , Drake Christopher L , Casement Melynda D , Cheng Philip
Published: November 2023

Study Objectives

To utilize qualitative data analysis to enrich our understanding of the impact of coronavirus (COVID-19) on those with a pre-pandemic history of insomnia.

Methods

The sample included 208 participants who completed the Coronavirus Impact Scale in April and May 2020. A content analysis was used to analyze responses to a free-response item “Please tell us about any other ways the coronavirus has impacted your life” (n = 175), using a combination of inductive and deductive coding.

Results

Both negative and positive themes emerged, including altered access to health care, negative financial impacts, and various emotions surrounding COVID-19. Some shared “silver linings” such as having more time for physical activity and deepening familial connections.

Conclusions

This analysis provides novel insight into the shared concerns and lived experiences of those with a history of insomnia. Understanding these unique stressors can enable healthcare professionals to better anticipate the needs of this population, as well as learn to navigate future stressful events.
Fungal Cell Wall-Associated Effectors: Sensing, Integration, Suppression, and Protection
Authors: John Evan , Chau Minh-Quang , Hoang Cuong V. , Chandrasekharan Neelima , Bhaskar Chibbhi , Ma Lay-Sun
Published: November 2023

The cell wall (CW) of plant-interacting fungi, as the direct interface with host plants, plays a crucial role in fungal development. A number of secreted proteins are directly associated with the fungal CW, either through covalent or non-covalent interactions, and serve a range of important functions. In the context of plant–fungal interactions many are important for fungal development in the host environment and may therefore be considered fungal CW-associated effectors (CWAEs). Key CWAE functions include integrating chemical/physical signals to direct hyphal growth, interfering with plant immunity, and providing protection against plant defenses. In recent years, a diverse range of mechanisms have been reported that underpin their roles, with some CWAEs harboring conserved motifs or functional domains, while others are reported to have novel features. As such, the current understanding regarding fungal CWAEs is systematically presented here from the perspective of their biological functions in plant–fungal interactions. An overview of the fungal CW architecture and the mechanisms by which proteins are secreted, modified, and incorporated into the CW is first presented to provide context for their biological roles. Some CWAE functions are reported across a broad range of pathosystems or symbiotic/mutualistic associations. Prominent are the chitin interacting-effectors that facilitate fungal CW modification, protection, or suppression of host immune responses. However, several alternative functions are now reported and are presented and discussed. CWAEs can play diverse roles, some possibly unique to fungal lineages and others conserved across a broad range of plant-interacting fungi.

[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Development of a Multiplex PCR Assay for the Detection of Tomato Wilt Caused by Coinfection of Fusarium brachygibbosum, Fusarium oxysporum, and Ralstonia solanacearum Based on Comparative Genomics
Authors: Liu Jun , Deng Siyi , Chang Wei , Yu Dazhao , Wang Hua
Published: November 2023

Tomato is consumed worldwide as fresh or processed food products. However, soilborne diseases of tomato plants caused by coinfection of various pathogens result in great economic losses to the tomato industry. It is difficult to accurately identify and diagnose soilborne diseases of tomato plants caused by pathogen complexes. In this study, we investigated field diseases of tomato plants by pathogen isolation and molecular identification and found that tomato wilt was caused by coinfection of Fusarium brachygibbosum, F. oxysporum, and Ralstonia solanacearum. Therefore, developing a method for simultaneous detection of DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum is of great importance to efficiently and accurately monitor disease development at different growth stages of tomato plants. In this study, we performed a comparative genomic analysis of F. brachygibbosum, F. oxysporum, and R. solanacearum and determined the primer sets for simultaneous detection of DNA from these target pathogens. Then, we tested the reagent and condition parameters of multiplex PCR, including primers, dNTP and Mg2+ concentrations, and annealing temperatures, to determine the optimal parameters of a multiplex PCR system. We evaluated the specificity, sensitivity, and stability of the multiplex PCR system based on the optimized reaction conditions. The multiplex PCR system can specifically identify 13 target pathogens from 57 different fungal and bacterial pathogens, at the lower detection limit of the three target pathogens at concentrations of 100 pg/μl. In addition, we can accurately identify the three pathogens in tomato plants using the optimized multiplex PCR method. These results demonstrated that the multiplex PCR method developed in this study can simultaneously detect DNA from F. brachygibbosum, F. oxysporum, and R. solanacearum in a single PCR system to accurately identify and diagnose the pathogen causing tomato wilt.
Identification and Distribution of the ‘Candidatus Liberibacter asiaticus’-Asian Citrus Psyllid Pathosystem in Saudi Arabia
Authors: Ibrahim Yasser E. , Al-Saleh Mohammed A. , Widyawan Arya , El Komy Mahmoud H. , Al Dhafer Hathal M. , Brown Judith K.
Published: November 2023

Citrus greening disease was first reported in Saudi Arabia during the 1970s when characteristic foliar and fruit symptoms were observed in commercial citrus groves. However, ‘Candidatus Liberibacter asiaticus’ (CLas) was not detected in symptomatic trees until 1981 to 1984 when CLas-like cells were observed by transmission electron microscopy in leaves collected from symptomatic citrus groves in southwestern Saudi Arabia. Despite the anticipated establishment of the CLas-Asian citrus psyllid (ACP) (Diaphorina citri Kuwayama) pathosystem, CLas presence has not been verified in suspect trees nor have ACP infestations been documented. Given the recent expansion of citrus production in Saudi Arabia, a systematic country-wide survey was carried out to determine the potential CLas distribution in the 13 citrus-growing regions of the country. Citrus trees were surveyed for the presence of CLas-psyllid vector(s) and characteristic disease symptoms in commercial and urban citrus trees. Adult psyllids collected from infested citrus trees were identified as ACP based on morphological characteristics. Real-time quantitative PCR amplification (qPCR) of the CLas β-subunit of the ribonucleotide reductase (RNR) gene from citrus leaf and fruit samples and/or ACP adults revealed that trees were positive for CLas detection in 10 of the 13 survey regions; however, CLas was undetectable in ACP adults. Phylogenetic and single nucleotide polymorphism (SNP) analyses of a PCR-amplified, cloned fragment of the CLas 16S rRNA gene (∼1.1 kbp) indicated Saudi Arabian isolates were most closely related to Florida, U.S.A., isolates. Analysis of climate variables indicated that the distribution of the ACP-CLas pathosystem observed in Saudi Arabia was consistent with published predictions of terrains most likely to support establishment.
Molecular Identification of ‘Candidatus Phytoplasma malaysianum’-Related Strains Associated with Areca catechu Palm Yellow Leaf Disease and Phylogenetic Diversity of the Phytoplasmas Within the 16SrXXXII Group
Authors: Yu Shao-Shuai , Zhu An-Na , Che Hai-Yan , Song Wei-Wei
Published: November 2023

Areca catechu palm is an important cash plant in Hainan Island of China and also in the tropical regions of the world. A. catechu palm yellow leaf (AcYL) disease caused by phytoplasmas is a devastating disease for plant production. In the study, the phytoplasmas associated with the AcYL disease were identified and characterized based on their conserved genes, and genetic variation and phylogenetic relationship of the phytoplasma strains in the 16SrXXXII group were demonstrated. The results indicated that A. catechu palm plants showing yellow leaf symptoms were infected by ‘Candidatus Phytoplasma malaysianum’-related strains belonging to the 16SrXXXII-D subgroup. BLAST and multiple sequence alignment analysis based on 16S rRNA and secA genes showed that the AcYL phytoplasmas shared 100% sequence identity and 100% homology with the ‘Ca. P. malaysianum’-related strains. Phylogenetic analysis indicated that the AcYL phytoplasmas and ‘Ca. P. malaysianum’-related strains belonging to the 16SrXXXII group clustered into one clade with a 100% bootstrap value. Based on computer-simulated digestions, six kinds of restriction fragment length polymorphism patterns within the 16SrXXXII group were obtained, and a novel subgroup in the 16Sr group was recommended to propose and describe the relevant strains in this 16Sr subgroup. To our knowledge, this is the first study to report that A. catechu palm showing yellow leaf symptoms was infected by ‘Ca. P. malaysianum’-related strains belonging to the 16SrXXXII group. A novel 16Sr subgroup, 16SrXXXII-F, was proposed based on the systematical analysis of genetic variation of all phytoplasmas within the 16SrXXXII group. The findings of this study will support references for monitoring the epidemiology and developing effective prevention strategies for AcYL disease.
Cochlear–Implant Simulated Signal Degradation Exacerbates Listening Effort in Older Listeners
Authors: Abramowitz Jordan C. , Goupell Matthew J. , DeRoy Milvae Kristina
Published: November 2023

Objectives:

Individuals with cochlear implants (CIs) often report that listening requires high levels of effort. Listening effort can increase with decreasing spectral resolution, which occurs when listening with a CI, and can also increase with age. What is not clear is whether these factors interact; older CI listeners potentially experience even higher listening effort with greater signal degradation than younger CI listeners. This study used pupillometry as a physiological index of listening effort to examine whether age, spectral resolution, and their interaction affect listening effort in a simulation of CI listening.

Design:

Fifteen younger normal-hearing listeners (ages 18 to 31 years) and 15 older normal-hearing listeners (ages 65 to 75 years) participated in this experiment; they had normal hearing thresholds from 0.25 to 4 kHz. Participants repeated sentences presented in quiet that were either unprocessed or vocoded, simulating CI listening. Stimuli frequency spectra were limited to below 4 kHz (to control for effects of age-related high-frequency hearing loss), and spectral resolution was decreased by decreasing the number of vocoder channels, with 32-, 16-, and 8-channel conditions. Behavioral speech recognition scores and pupil dilation were recorded during this task. In addition, cognitive measures of working memory and processing speed were obtained to examine if individual differences in these measures predicted changes in pupil dilation.

Results:

For trials where the sentence was recalled correctly, there was a significant interaction between age and spectral resolution, with significantly greater pupil dilation in the older normal-hearing listeners for the 8- and 32-channel vocoded conditions. Cognitive measures did not predict pupil dilation.

Conclusions:

There was a significant interaction between age and spectral resolution, such that older listeners appear to exert relatively higher listening effort than younger listeners when the signal is highly degraded, with the largest effects observed in the eight-channel condition. The clinical implication is that older listeners may be at higher risk for increased listening effort with a CI.