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1.
Metabolomics ; 17(6): 55, 2021 06 06.
Artigo em Inglês | MEDLINE | ID: mdl-34091802

RESUMO

BACKGROUND: Improvements in mass spectrometry (MS) technologies coupled with bioinformatics developments have allowed considerable advancement in the measurement and interpretation of lipidomics data in recent years. Since research areas employing lipidomics are rapidly increasing, there is a great need for bioinformatic tools that capture and utilize the complexity of the data. Currently, the diversity and complexity within the lipidome is often concealed by summing over or averaging individual lipids up to (sub)class-based descriptors, losing valuable information about biological function and interactions with other distinct lipids molecules, proteins and/or metabolites. AIM OF REVIEW: To address this gap in knowledge, novel bioinformatics methods are needed to improve identification, quantification, integration and interpretation of lipidomics data. The purpose of this mini-review is to summarize exemplary methods to explore the complexity of the lipidome. KEY SCIENTIFIC CONCEPTS OF REVIEW: Here we describe six approaches that capture three core focus areas for lipidomics: (1) lipidome annotation including a resolvable database identifier, (2) interpretation via pathway- and enrichment-based methods, and (3) understanding complex interactions to emphasize specific steps in the analytical process and highlight challenges in analyses associated with the complexity of lipidome data.


Assuntos
Biologia Computacional , Lipidômica , Bases de Dados Factuais , Lipídeos , Espectrometria de Massas
2.
Nucleic Acids Res ; 45(D1): D190-D199, 2017 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-27899635

RESUMO

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Domínios e Motivos de Interação entre Proteínas , Software , Humanos , Anotação de Sequência Molecular , Filogenia
3.
Nat Genet ; 34(3): 263-4, 2003 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-12796781

RESUMO

DNA vectors that express short hairpin RNAs (shRNAs) from RNA polymerase III (Pol III) promoters are a promising new tool to reduce gene expression in mammalian cells. shRNAs are processed to small interfering RNAs (siRNAs) of 21 nucleotides (nt) that guide the cleavage of the cognate mRNA by the RNA-induced silencing complex. Although siRNAs are thought to be too short to induce interferon expression, we report here that a substantial number of shRNA vectors can trigger an interferon response.


Assuntos
2',5'-Oligoadenilato Sintetase/metabolismo , Vetores Genéticos , Interferons/metabolismo , Lentivirus/genética , RNA Interferente Pequeno/metabolismo , RNA/química , RNA/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Indução Enzimática , Fibroblastos/metabolismo , Células HeLa , Humanos , Pulmão/metabolismo , Regiões Promotoras Genéticas , RNA Polimerase III/metabolismo , Fatores de Transcrição/antagonistas & inibidores , Transcrição Gênica , Transfecção
4.
Database (Oxford) ; 20222022 08 12.
Artigo em Inglês | MEDLINE | ID: mdl-35961013

RESUMO

Over the last 25 years, biology has entered the genomic era and is becoming a science of 'big data'. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3-4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.


Assuntos
Genômica , Proteínas , Sequência de Bases , Biologia Computacional , Genoma , Anotação de Sequência Molecular
5.
Genetics ; 176(1): 73-83, 2007 May.
Artigo em Inglês | MEDLINE | ID: mdl-17409062

RESUMO

Cdc25 phosphatase primes entry to mitosis by removing the inhibitory phosphate that is transferred to mitosis promoting factor (MPF) by Wee1 related kinases. A positive feedback loop then boosts Cdc25 and represses Wee1 activities to drive full-scale MPF activation and commitment to mitosis. Dominant mutations in the Schizosaccharomyces pombe spindle pole body (SPB) component Cut12 enable cdc25.22 mutants to overcome a G2 arrest at 36 degrees and enter mitosis. The recessive temperature-sensitive cut12.1 mutation results in the formation of monopolar spindles in which the spindle pole marker Sad1 is enriched on the nonfunctional SPB at 36 degrees . We identified mutations at five loci that suppressed the lethality of the recessive cut12.1 mutation at 36 degrees and conferred lethality at 20 degrees . Three of the five mutations led to the formation of monopolar spindles at restrictive temperatures, affected cell size at commitment to mitosis, and generated multiple Sad1 foci at nuclear periphery. The five loci, tfb2.rt1, tfb5.rt5, pla1.rt3, rpl4301.rt4, and rot2.1, and multicopy suppressors, including tfb1(+) and dbp10(+), are involved in transcription, translation, or RNA processing, prompting us to establish that elevating Cdc25 levels with the dominant cdc25.d1 allele, suppressed cut12.1. Thus, rot mutants provide a further link between protein production and cell-cycle progression.


Assuntos
Ciclo Celular , Regulação Fúngica da Expressão Gênica , Genes Fúngicos , Proteínas Associadas aos Microtúbulos/metabolismo , Fosfoproteínas/metabolismo , Proteínas de Schizosaccharomyces pombe/metabolismo , Schizosaccharomyces/citologia , Supressão Genética , Transcrição Gênica , Clonagem Molecular , Proteínas Mutantes/isolamento & purificação , Fenótipo , Biossíntese de Proteínas , Schizosaccharomyces/genética , Fuso Acromático/metabolismo , Fosfatases cdc25/genética
6.
Methods Mol Biol ; 1374: 23-54, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-26519399

RESUMO

The Universal Protein Resource (UniProt, http://www.uniprot.org ) consortium is an initiative of the SIB Swiss Institute of Bioinformatics (SIB), the European Bioinformatics Institute (EBI) and the Protein Information Resource (PIR) to provide the scientific community with a central resource for protein sequences and functional information. The UniProt consortium maintains the UniProt KnowledgeBase (UniProtKB), updated every 4 weeks, and several supplementary databases including the UniProt Reference Clusters (UniRef) and the UniProt Archive (UniParc).The Swiss-Prot section of the UniProt KnowledgeBase (UniProtKB/Swiss-Prot) contains publicly available expertly manually annotated protein sequences obtained from a broad spectrum of organisms. Plant protein entries are produced in the frame of the Plant Proteome Annotation Program (PPAP), with an emphasis on characterized proteins of Arabidopsis thaliana and Oryza sativa. High level annotations provided by UniProtKB/Swiss-Prot are widely used to predict annotation of newly available proteins through automatic pipelines.The purpose of this chapter is to present a guided tour of a UniProtKB/Swiss-Prot entry. We will also present some of the tools and databases that are linked to each entry.


Assuntos
Biologia Computacional/métodos , Bases de Dados de Proteínas , Animais , Humanos , Navegador
7.
PLoS One ; 9(5): e97683, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24848109

RESUMO

Targeted alteration of the genome lies at the heart of the exploitation of S. pombe as a model system. The rate of analysis is often determined by the efficiency with which a target locus can be manipulated. For most loci this is not a problem, however for some loci, such as fin1+, rates of gene targeting below 5% can limit the scope and scale of manipulations that are feasible within a reasonable time frame. We now describe a simple modification of transformation procedure for directing integration of genomic sequences that leads to a 5-fold increase in the transformation efficiency when antibiotic based dominant selection markers are used. We also show that removal of the pku70+ and pku80+ genes, which encode DNA end binding proteins required for the non-homologous end joining DNA repair pathway, increases the efficiency of gene targeting at fin1+ to around 75-80% (a 16-fold increase). We describe how a natMX6/rpl42+ cassette can be used for positive and negative selection for integration at a targeted locus. To facilitate the evaluation of the impact of a series of mutations on the function of a gene of interest we have generated three vector series that rely upon different selectable markers to direct the expression of tagged/untagged molecules from distinct genomic integration sites. pINTL and pINTK vectors use ura4+ selection to direct disruptive integration of leu1+ and lys1+ respectively, while pINTH vectors exploit nourseothricin resistance to detect the targeted disruption of a hygromycin B resistance conferring hphMX6 cassette that has been integrated on chromosome III. Finally, we have generated a series of multi-copy expression vectors that use resistance to nourseothricin or kanamycin/G418 to select for propagation in prototrophic hosts. Collectively these protocol modifications and vectors extend the versatility of this key model system.


Assuntos
Engenharia Genética/métodos , Schizosaccharomyces/genética , Antibacterianos/farmacologia , Farmacorresistência Bacteriana/genética , Vetores Genéticos/genética , Genoma Bacteriano/genética , Schizosaccharomyces/efeitos dos fármacos , Homologia de Sequência do Ácido Nucleico , Estreptotricinas/farmacologia , Transformação Genética
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