CRISPR screens identify genes essential for in vivo virulence among proteins of hyperLOPIT-unassigned subcellular localization in Toxoplasma DOI Creative Commons
Yuta Tachibana, Miwa Sasai, Masahiro Yamamoto

и другие.

mBio, Год журнала: 2024, Номер 15(9)

Опубликована: Июль 31, 2024

ABSTRACT The research field to identify and characterize genes essential for in vivo virulence Toxoplasma gondii has been dramatically advanced by a series of clustered regularly interspaced short palindromic repeats (CRISPR) screens. Although subcellular localizations thousands proteins were predicted the spatial proteomic method called hyperLOPIT, those more than 1,000 remained unassigned, their essentiality was also unknown. In this study, we generated two small-scale gRNA libraries targeting approximately 600 hyperLOPIT-unassigned performed CRISPR As result, identified several that previously unreported. We further characterized candidates, TgGTPase TgRimM, which are localized cytoplasm apicoplast, respectively. Both parasite widely conserved phylum Apicomplexa. Collectively, our current study provides resource estimating with unknown localizations. IMPORTANCE is protozoan causes severe infection immunocompromised patients or newborns. possesses 8,000 genes; however, not fully identified. apicomplexan parasites, including , developed unique organelles do exist other model organisms; thus, determining location important understanding functions. Here, used genetic screens enabled us investigate hundreds during mouse infection. screened many novel confer mice. Among top hits, virulence, Our findings will contribute how apicomplexans adapt host environment cause disease.

Язык: Английский

Ensembl 2025 DOI Creative Commons
Sarah Dyer, Olanrewaju Austine-Orimoloye, Andrey G Azov

и другие.

Nucleic Acids Research, Год журнала: 2024, Номер 53(D1), С. D948 - D957

Опубликована: Дек. 4, 2024

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity. This year has seen continued expansion in number represented, >4800 >31 300 prokaryotic genomes available. The new site, currently beta, develop, holding >2700 genome assemblies. site provides genome, gene, transcript, homology variation views, will replace current Rapid Release site; this represents key step towards provision single integrated site. Additional activities have included developing improved regulatory annotation for human, mouse agricultural species, expanding Variant Effect Predictor tool. To learn more about Ensembl, help documentation are along extensive training program that can be accessed via our pages.

Язык: Английский

Процитировано

23
Transcriptional control of the Cryptosporidium life cycle DOI
Katelyn A. Walzer, Jayesh Tandel, Jessica H. Byerly

и другие.

Nature, Год журнала: 2024, Номер 630(8015), С. 174 - 180

Опубликована: Май 29, 2024

Язык: Английский

Процитировано

17
NCBI RefSeq: reference sequence standards through 25 years of curation and annotation DOI Creative Commons

Tamara Goldfarb,

Vamsi K. Kodali, Shashikant Pujar

и другие.

Nucleic Acids Research, Год журнала: 2024, Номер 53(D1), С. D243 - D257

Опубликована: Ноя. 11, 2024

Reference sequences and annotations serve as the foundation for many lines of research today, from organism sequence identification to providing a core description genes, transcripts proteins found in an organism's genome. Interpretation data including transcriptomics, proteomics, variation comparative analyses based on reference gene informs our understanding function possible disease mechanisms, leading new biomedical discoveries. The Sequence (RefSeq) resource created at National Center Biotechnology Information (NCBI) leverages both automatic processes expert curation create robust set genomic, transcript protein spanning tree life. RefSeq continues refine its annotation quality control utilize better genomes resulting advances sequencing technologies well RNA-Seq produce high-quality annotated genomes, ortholog predictions across more organisms other products that are easily accessible through multiple NCBI resources. This report summarizes current status eukaryotic, prokaryotic viral resources, with focus eukaryotic annotation, increase taxonomic representation effect it will have genomics. is publicly https://www.ncbi.nlm.nih.gov/refseq.

Язык: Английский

Процитировано

15
What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species DOI Creative Commons
Evelina Y. Basenko, Achchuthan Shanmugasundram, Ulrike Böhme

и другие.

Genetics, Год журнала: 2024, Номер 227(1)

Опубликована: Март 26, 2024

Abstract FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for wide range of fungal oomycete species. As an integral part the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), continually both published unpublished addressing various aspects biology. Established in early 2011, database has evolved to support 674 datasets. The datasets include over 300 genomes spanning taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, well Albuginales, Peronosporales, Pythiales, Saprolegniales). In addition assemblies annotation, extra encompassing diverse information, such expression variation data, are also available. provides intuitive web-based interface, facilitating comprehensive approaches mining visualization. Users can test their hypotheses navigate through omics-scale using built-in search strategy system. Moreover, offers capabilities private analysis via integrated Galaxy platform. permits genome improvements by capturing expert knowledge User Comments system Apollo annotation editor structural functional gene curation. facilitates exploration contributes advancing research efforts

Язык: Английский

Процитировано

10
Protective antibodies target cryptic epitope unmasked by cleavage of malaria sporozoite protein DOI
Cherrelle Dacon,

Re’em Moskovitz,

Kristian E. Swearingen

и другие.

Science, Год журнала: 2025, Номер 387(6729)

Опубликована: Янв. 2, 2025

The most advanced monoclonal antibodies (mAbs) and vaccines against malaria target the central repeat region or closely related sequences within Plasmodium falciparum circumsporozoite protein (PfCSP). Here, using an antigen-agnostic strategy to investigate human antibody responses whole sporozoites, we identified a class of mAbs that cryptic PfCSP epitope is only exposed after cleavage subsequent pyroglutamylation (pGlu) newly formed N terminus. This pGlu-CSP not targeted by current anti-PfCSP included in licensed vaccines. MAD21-101, potent mAb this class, confers sterile protection Pf infection liver–chimeric mouse model. These findings reveal site vulnerability on sporozoite surface can be next-generation antimalarial interventions.

Язык: Английский

Процитировано

2
Widespread release of translational repression across Plasmodium’s host-to-vector transmission event DOI Creative Commons
Kelly T. Rios, James P. McGee, Aswathy Sebastian

и другие.

PLoS Pathogens, Год журнала: 2025, Номер 21(1), С. e1012823 - e1012823

Опубликована: Янв. 8, 2025

Malaria parasites must respond quickly to environmental changes, including during their transmission between mammalian and mosquito hosts. Therefore, female gametocytes proactively produce translationally repress mRNAs that encode essential proteins the zygote requires establish a new infection. While release of translational repression individual has been documented, details global have not. Moreover, changes in spatial arrangement composition DOZI/CITH/ALBA complex contribute control are also not known. we conducted first quantitative, comparative transcriptomics DIA-MS proteomics Plasmodium across host-to-vector event document repression. Using zygotes P . yoelii , found ~200 transcripts released for translation soon after fertilization, those encoding functions. identified many remain repressed beyond this point. TurboID-based proximity regulatory revealed substantial and/or compositional event, which consistent with recent, paradigm-shifting models control. Together, these data provide model mechanisms promote Plasmodium’s efficient from host vector.

Язык: Английский

Процитировано

2
A generalist vector-transmitted parasite exhibits population genetic structure among host genera DOI Creative Commons
Vincenzo A. Ellis, Mélanie Duc, Arif Çiloğlu

и другие.

Parasitology, Год журнала: 2025, Номер unknown, С. 1 - 33

Опубликована: Янв. 21, 2025

An abstract is not available for this content so a preview has been provided. As you have access to content, full PDF via the 'Save PDF' action button.

Язык: Английский

Процитировано

1
Analysis of metagenomic data DOI
Shaopeng Liu, Judith Rodríguez, Viorel Munteanu

и другие.

Nature Reviews Methods Primers, Год журнала: 2025, Номер 5(1)

Опубликована: Янв. 23, 2025

Язык: Английский

Процитировано

1
The essential genome of Plasmodium knowlesi reveals determinants of antimalarial susceptibility DOI Open Access
Brendan Elsworth, Sida Ye, Sheena Dass

и другие.

Science, Год журнала: 2025, Номер 387(6734)

Опубликована: Фев. 6, 2025

Measures to combat the parasites that cause malaria have become compromised because of reliance on a small arsenal drugs and emerging drug resistance. We conducted transposon mutagenesis screen in primate parasite Plasmodium knowlesi , producing most complete classification gene essentiality any spp. date, with resolution define truncatable genes. found conservation druggable genome between divergences mitochondrial metabolism. Perturbation analyses frontline antimalarial artemisinin revealed modulators both increase decrease susceptibility. Our findings aid prioritization vaccine targets for vivax clade reveal mechanisms resistance can inform therapeutic development.

Язык: Английский

Процитировано

1
paraCell: a novel software tool for the interactive analysis and visualization of standard and dual host–parasite single-cell RNA-seq data DOI Creative Commons

Edward Agboraw,

William Haese-Hill, Franziska Hentzschel

и другие.

Nucleic Acids Research, Год журнала: 2025, Номер 53(4)

Опубликована: Фев. 3, 2025

Advances in sequencing technology have led to a dramatic increase the number of single-cell transcriptomic datasets. In field parasitology, these datasets typically describe gene expression patterns given parasite species at level under experimental conditions, specific hosts or tissues, different life cycle stages. However, while this wealth available data represents significant resource, analysing often requires expert computational skills, preventing considerable proportion parasitology community from meaningfully integrating existing into their work. Here, we present paraCell, novel software tool that allows user visualize and analyse pre-loaded without requiring any programming ability. The source code is free allow remote installation. On our web server, demonstrated how re-analyse published Plasmodium Trypanosoma We also generated Toxoplasma-mouse Theileria-cow scRNA-seq highlight functionality paraCell for pathogen-host interaction. analysis highlights impact host interferon-γ response profiles associated with disease susceptibility by intracellular parasites, respectively.

Язык: Английский

Процитировано

1