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1.
Methods Mol Biol ; 2774: 1-13, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38441754

RESUMO

Directed evolution is an efficient strategy for obtaining desired biomolecules. Since the 1990s, the emergence of display techniques has enabled high-throughput screening of functional proteins. However, classical methods require library construction by plasmid cloning and are limited by transformation efficiencies, typically limiting library sizes to ~106-107 variants. More recently, in vitro techniques have emerged that avoid cloning, allowing library sizes of >1012 members. One of these, CIS display, is a DNA-based display technique which allows high-throughput selection of biomolecules in vitro. CIS display creates the genotype-phenotype link required for selection by a DNA replication initiator protein, RepA, that binds exclusively to the template from which it has been expressed. This method has been successfully used to evolve new protein-protein interactions but has not been used before to select DNA-binding proteins, which are major components in mammalian synthetic biology. In this chapter, we describe a directed evolution method using CIS display to efficiently select functional DNA-binding proteins from pools of nonbinding proteins. The method is illustrated by enriching the minimal transcription factor Cro from a low starting frequency (1 in 109). This protocol is also applicable to engineering other DNA-binding proteins or transcription factors from combinatorial libraries.


Assuntos
Proteínas de Ligação a DNA , Fatores de Transcrição , Animais , Fatores de Transcrição/genética , Biblioteca Gênica , Proteínas de Ligação a DNA/genética , Clonagem Molecular , DNA/genética , Mamíferos
2.
Methods Mol Biol ; 2774: 135-152, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38441763

RESUMO

Sequencing-based, massively parallel genetic assays have enabled simultaneous characterization of the genotype-phenotype relationships for libraries encoding thousands of unique protein variants. Since plasmid transfection and lentiviral transduction have characteristics that limit multiplexing with pooled libraries, we developed a mammalian synthetic biology platform that harnesses the Bxb1 bacteriophage DNA recombinase to insert single promoterless plasmids encoding a transgene of interest into a pre-engineered "landing pad" site within the cell genome. The transgene is expressed behind a genomically integrated promoter, ensuring only one transgene is expressed per cell, preserving a strict genotype-phenotype link. Upon selecting cells based on a desired phenotype, the transgene can be sequenced to ascribe each variant a phenotypic score. We describe how to create and utilize landing pad cells for large-scale, library-based genetic experiments. Using the provided examples, the experimental template can be adapted to explore protein variants in diverse biological problems within mammalian cells.


Assuntos
Bacteriófagos , Genômica , Animais , Sequenciamento de Nucleotídeos em Larga Escala , Biblioteca Gênica , Bioensaio , Proteínas Mutantes , Mamíferos
3.
BMC Genomics ; 25(1): 227, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38429743

RESUMO

BACKGROUND: Hybridization capture-based targeted next generation sequencing (NGS) is gaining importance in routine cancer clinical practice. DNA library preparation is a fundamental step to produce high-quality sequencing data. Numerous unexpected, low variant allele frequency calls were observed in libraries using sonication fragmentation and enzymatic fragmentation. In this study, we investigated the characteristics of the artifact reads induced by sonication and enzymatic fragmentation. We also developed a bioinformatic algorithm to filter these sequencing errors. RESULTS: We used pairwise comparisons of somatic single nucleotide variants (SNVs) and insertions and deletions (indels) of the same tumor DNA samples prepared using both ultrasonic and enzymatic fragmentation protocols. Our analysis revealed that the number of artifact variants was significantly greater in the samples generated using enzymatic fragmentation than using sonication. Most of the artifacts derived from the sonication-treated libraries were chimeric artifact reads containing both cis- and trans-inverted repeat sequences of the genomic DNA. In contrast, chimeric artifact reads of endonuclease-treated libraries contained palindromic sequences with mismatched bases. Based on these distinctive features, we proposed a mechanistic hypothesis model, PDSM (pairing of partial single strands derived from a similar molecule), by which these sequencing errors derive from ultrasonication and enzymatic fragmentation library preparation. We developed a bioinformatic algorithm to generate a custom mutation "blacklist" in the BED region to reduce errors in downstream analyses. CONCLUSIONS: We first proposed a mechanistic hypothesis model (PDSM) of sequencing errors caused by specific structures of inverted repeat sequences and palindromic sequences in the natural genome. This new hypothesis predicts the existence of chimeric reads that could not be explained by previous models, and provides a new direction for further improving NGS analysis accuracy. A bioinformatic algorithm, ArtifactsFinder, was developed and used to reduce the sequencing errors in libraries produced using sonication and enzymatic fragmentation.


Assuntos
Artefatos , Genoma Humano , Humanos , Biblioteca Gênica , Análise de Sequência de DNA/métodos , DNA de Neoplasias , Sequenciamento de Nucleotídeos em Larga Escala/métodos
4.
Eur Rev Med Pharmacol Sci ; 28(5): 1976-1986, 2024 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-38497880

RESUMO

OBJECTIVE: Leaving Against Medical Advice (LAMA) is a prevalent issue in healthcare settings that may lead to negative patient outcomes. We conducted a systematic review and meta-analysis to assess the impact of LAMA on patient outcomes. MATERIALS AND METHODS: A comprehensive literature search was performed across PubMed, MEDLINE, Embase, Cochrane Library, CINAHL, PsycINFO, Web of Science, and Scopus. Studies reporting adverse outcomes, including mortality and hospital readmission rates, in patients who underwent LAMA were included. The odds ratios (ORs) with 95% confidence intervals (CIs) were pooled using a random-effects model. RESULTS: Eight studies were included in the review, with four contributing to the meta-analysis on 1-year mortality and five to the meta-analysis on hospital readmission rates. LAMA was not significantly associated with higher 1-year mortality [OR = 0.66, 95% CI (0.38, 1.16), p = 0.15] or hospital readmission rates [OR = 0.61, 95% CI (0.30, 1.23), p = 0.16] across the studies. However, there was substantial heterogeneity in the results (I2 = 91% for mortality; I2 = 99% for readmissions). CONCLUSIONS: While individual studies reported varying outcomes, the pooled results did not show a significant association between LAMA and increased 1-year mortality or hospital readmission rates. However, the high degree of heterogeneity suggests the influence of diverse patient populations, healthcare settings, and study methodologies on these outcomes. Further research is needed to better understand the factors contributing to the adverse outcomes associated with LAMA and to develop targeted interventions to mitigate them.


Assuntos
Readmissão do Paciente , Pacientes , Humanos , Biblioteca Gênica , Razão de Chances
5.
STAR Protoc ; 5(1): 102908, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38461411

RESUMO

Processing dissociated cells for transcriptomics is challenging when targeting small brain structures, like brainstem nuclei, where cell yield may be low. Here, we present a protocol for dissecting, dissociating, and cryopreserving mouse brainstem that allows asynchronous sample collection and downstream processing of cells obtained from brainstem tissue in neonatal mice. Although we demonstrate this protocol with the isolated preBötzinger complex and downstream SmartSeq3 cDNA library preparation, it could be readily adapted for other brainstem areas and library preparation approaches.


Assuntos
Tronco Encefálico , Análise da Expressão Gênica de Célula Única , Camundongos , Animais , Núcleo Celular , Perfilação da Expressão Gênica/métodos , Biblioteca Gênica
6.
Methods Mol Biol ; 2776: 243-257, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38502509

RESUMO

Global understanding of plastid gene expression has always been impaired by its complexity. RNA splicing, editing, and intercistronic processing create multiple transcripts isoforms that can hardly be resolved using traditional molecular biology techniques. During the last decade, the wide adoption of RNA-seq-based techniques has, however, allowed an unprecedented understanding of all the different steps of chloroplast gene expression, from transcription to translation. Current strategies are nonetheless unable to identify and quantify full length transcripts isoforms, a limitation that can now be overcome using Nanopore Sequencing. We here provide a complete protocol to produce, from total leaf RNA, cDNA libraries ready for Nanopore sequencing. While most Nanopore protocols take advantage of the mRNA polyA tail we here first ligate an RNA adapter to the 3' ends of the RNAs and use it to initiate the template switching reverse transcription. The cDNA is then prepared and indexed for use with the regular Oxford Nanopore v14 chemistry. This protocol is of particular interest to researchers willing to simultaneously study the multiple post-transcriptional processes prevalent in the chloroplast.


Assuntos
Sequenciamento por Nanoporos , Transcriptoma , Sequenciamento por Nanoporos/métodos , Biblioteca Gênica , RNA/genética , Isoformas de Proteínas/genética , Cloroplastos/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Análise de Sequência de RNA/métodos
7.
Methods Mol Biol ; 2754: 131-146, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38512665

RESUMO

Tau protein was extensively studied using nuclear magnetic resonance spectroscopy, providing a powerful way to determine interaction sites between Tau and partner proteins. Here we used this analytical tool to describe the epitopes of Tau-specific VHHs (variable domain of the heavy chain of the heavy chain-only antibodies, aka nanobodies) selected from a synthetic library. An in vitro Tau aggregation assay was subsequently used as a functional screen to check VHH efficacy as aggregation inhibitors. We have observed a correlation between the targeted epitope and the aggregation-inhibition capacity of a series of Tau-specific VHHs.


Assuntos
Anticorpos de Domínio Único , Anticorpos de Domínio Único/genética , Anticorpos de Domínio Único/química , Proteínas tau/genética , Epitopos , Cadeias Pesadas de Imunoglobulinas/química , Biblioteca Gênica
8.
Sci Rep ; 14(1): 6756, 2024 03 21.
Artigo em Inglês | MEDLINE | ID: mdl-38514891

RESUMO

Transposon directed insertion-site sequencing (TraDIS), a variant of transposon insertion sequencing commonly known as Tn-Seq, is a high-throughput assay that defines essential bacterial genes across diverse growth conditions. However, the variability between laboratory environments often requires laborious, time-consuming modifications to its protocol. In this technical study, we aimed to refine the protocol by identifying key parameters that can impact the complexity of mutant libraries. Firstly, we discovered that adjusting electroporation parameters including transposome concentration, transposome assembly conditions, and cell densities can significantly improve the recovery of viable mutants for different Escherichia coli strains. Secondly, we found that post-electroporation conditions, such as recovery time and the use of different mediums for selecting mutants may also impact the complexity of viable mutants in the library. Finally, we developed a simplified sequencing library preparation workflow based on a Nextera-TruSeq hybrid design where ~ 80% of sequenced reads correspond to transposon-DNA junctions. The technical improvements presented in our study aim to streamline TraDIS protocols, making this powerful technique more accessible for a wider scientific audience.


Assuntos
Elementos de DNA Transponíveis , Genes Bacterianos , Mutagênese Insercional , Elementos de DNA Transponíveis/genética , Análise Custo-Benefício , Sequência de Bases , Escherichia coli/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Biblioteca Gênica
9.
Proc Natl Acad Sci U S A ; 121(11): e2311726121, 2024 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-38451939

RESUMO

Proteins are a diverse class of biomolecules responsible for wide-ranging cellular functions, from catalyzing reactions to recognizing pathogens. The ability to evolve proteins rapidly and inexpensively toward improved properties is a common objective for protein engineers. Powerful high-throughput methods like fluorescent activated cell sorting and next-generation sequencing have dramatically improved directed evolution experiments. However, it is unclear how to best leverage these data to characterize protein fitness landscapes more completely and identify lead candidates. In this work, we develop a simple yet powerful framework to improve protein optimization by predicting continuous protein properties from simple directed evolution experiments using interpretable, linear machine learning models. Importantly, we find that these models, which use data from simple but imprecise experimental estimates of protein fitness, have predictive capabilities that approach more precise but expensive data. Evaluated across five diverse protein engineering tasks, continuous properties are consistently predicted from readily available deep sequencing data, demonstrating that protein fitness space can be reasonably well modeled by linear relationships among sequence mutations. To prospectively test the utility of this approach, we generated a library of stapled peptides and applied the framework to predict affinity and specificity from simple cell sorting data. We then coupled integer linear programming, a method to optimize protein fitness from linear weights, with mutation scores from machine learning to identify variants in unseen sequence space that have improved and co-optimal properties. This approach represents a versatile tool for improved analysis and identification of protein variants across many domains of protein engineering.


Assuntos
Aprendizado de Máquina , Proteínas , Proteínas/metabolismo , Engenharia de Proteínas/métodos , Mutação , Biblioteca Gênica
10.
Genome Biol ; 25(1): 72, 2024 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-38504331

RESUMO

DANCE is the first standard, generic, and extensible benchmark platform for accessing and evaluating computational methods across the spectrum of benchmark datasets for numerous single-cell analysis tasks. Currently, DANCE supports 3 modules and 8 popular tasks with 32 state-of-art methods on 21 benchmark datasets. People can easily reproduce the results of supported algorithms across major benchmark datasets via minimal efforts, such as using only one command line. In addition, DANCE provides an ecosystem of deep learning architectures and tools for researchers to facilitate their own model development. DANCE is an open-source Python package that welcomes all kinds of contributions.


Assuntos
Benchmarking , Aprendizado Profundo , Humanos , Algoritmos , Biblioteca Gênica , Análise de Célula Única
11.
PLoS One ; 19(3): e0300865, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38517905

RESUMO

Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.


Assuntos
DNA , Sequenciamento de Nucleotídeos em Larga Escala , Transposases , DNA/genética , Biblioteca Gênica , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Etanol , Análise de Sequência de DNA/métodos
12.
J Vis Exp ; (204)2024 Feb 23.
Artigo em Inglês | MEDLINE | ID: mdl-38465925

RESUMO

Transcriptomics allows to obtain comprehensive insights into cellular programs and their responses to perturbations. Despite a significant decrease in the costs of library production and sequencing in the last decade, applying these technologies at the scale necessary for drug screening remains prohibitively expensive, obstructing the immense potential of these methods. Our study presents a cost-effective system for transcriptome-based drug screening, combining miniaturized perturbation cultures with mini-bulk transcriptomics. The optimized mini-bulk protocol provides informative biological signals at cost-effective sequencing depth, enabling extensive screening of known drugs and new molecules. Depending on the chosen treatment and incubation time, this protocol will result in sequencing libraries within approximately 2 days. Due to several stopping points within this protocol, the library preparation, as well as the sequencing, can be performed time-independently. Processing simultaneously a high number of samples is possible; measurement of up to 384 samples was tested without loss of data quality. There are also no known limitations to the number of conditions and/or drugs, despite considering variability in optimal drug incubation times.


Assuntos
Perfilação da Expressão Gênica , Transcriptoma , Avaliação Pré-Clínica de Medicamentos , Biblioteca Gênica , Custos e Análise de Custo
13.
Angew Chem Int Ed Engl ; 63(12): e202319836, 2024 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-38330151

RESUMO

DNA encoded library (DEL) synthesis represents a convenient means to produce, annotate and store large collections of compounds in a small volume. While DELs are well suited for drug discovery campaigns, the chemistry used in their production must be compatible with the DNA tag, which can limit compound class accessibility. As a result, most DELs are heavily populated with peptidomimetic and sp2 -rich molecules. Herein, we show that sp3 -rich mono- and bicyclic heterocycles can be made on DNA from ketochlorohydrin aldol products through a reductive amination and cyclization process. The resulting hydroxypyrrolidines possess structural features that are desirable for DELs and target a distinct region of pharmaceutically relevant chemical space.


Assuntos
DNA , Bibliotecas de Moléculas Pequenas , Bibliotecas de Moléculas Pequenas/química , DNA/química , Biblioteca Gênica , Descoberta de Drogas/métodos , Aminação
14.
Sci Rep ; 14(1): 3130, 2024 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-38326509

RESUMO

The Tambaqui is one of the most representative Amazon fish species, being highly exploited in fisheries, aquaculture and as a research model. Nonetheless, data about functional genome are still required to evaluate reproductive and nutrition parameters as well as resistance to pathogens. The of next-generation sequencing has allows assessing the transcriptional processes in non-model species by providing comprehensive gene collections to be used as a database in further genomic applications and increased performance of captive populations. In this study, we relied on RNAseq approach to generate the first transcriptome of the telencephalon from adult males and females of Colossoma macropomum, resulting in a reference dataset for future functional studies. We retrieved 896,238 transcripts, including the identification of 267,785 contigs and 203,790 genes. From this total, 91 transcripts were differentially expressed, being 63 and 28 of them positively regulated for females and males, respectively. The functional annotation resulted in a library of 40 candidate genes for females and 20 for males. The functional enrichment classes comprised reproductive processes (GO:0,048,609; GO:0,003,006; GO:0,044,703; GO:0,032,504; GO:0,019,953) being related to sex differentiation (e.g., SAFB) and immune response (e.g., SLC2A6, AHNAK, NLRC3, NLRP3 and IgC MHC I alpha3), thus indicating that the genes in the neurotranscriptome of Tambaqui participate in sex differentiation and homeostasis of captive specimens. These data are useful to design the selection of genes related to sex determination and animal welfare in raising systems of Tambaqui.


Assuntos
Caraciformes , Animais , Masculino , Feminino , Caraciformes/genética , Aquicultura , Pesqueiros , Genômica , Biblioteca Gênica
15.
J Vis Exp ; (204)2024 Feb 02.
Artigo em Inglês | MEDLINE | ID: mdl-38372376

RESUMO

AQRNA-seq provides a direct linear relationship between sequencing read counts and small RNA copy numbers in a biological sample, thus enabling accurate quantification of the pool of small RNAs. The AQRNA-seq library preparation procedure described here involves the use of custom-designed sequencing linkers and a step for reducing methylation RNA modifications that block reverse transcription processivity, which results in an increased yield of full-length cDNAs. In addition, a detailed implementation of the accompanying bioinformatics pipeline is presented. This demonstration of AQRNA-seq was conducted through a quantitative analysis of the 45 tRNAs in Mycobacterium bovis BCG harvested on 5 selected days across a 20-day time course of nutrient deprivation and 6 days of resuscitation. Ongoing efforts to improve the efficiency and rigor of AQRNA-seq will also be discussed here. This includes exploring methods to obviate gel purification for mitigating primer dimer issues after PCR amplification and to increase the proportion of full-length reads to enable more accurate read mapping. Future enhancements to AQRNA-seq will be focused on facilitating automation and high-throughput implementation of this technology for quantifying all small RNA species in cell and tissue samples from diverse organisms.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala , RNA , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA/genética , RNA de Transferência/genética , Biblioteca Gênica , DNA Complementar/genética , Análise de Sequência de RNA/métodos
16.
J Chem Inf Model ; 64(4): 1123-1133, 2024 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-38335055

RESUMO

DNA-encoded library (DEL) has proven to be a powerful tool that utilizes combinatorially constructed small molecules to facilitate highly efficient screening experiments. These selection experiments, involving multiple stages of washing, elution, and identification of potent binders via unique DNA barcodes, often generate complex data. This complexity can potentially mask the underlying signals, necessitating the application of computational tools, such as machine learning, to uncover valuable insights. We introduce a compositional deep probabilistic model of DEL data, DEL-Compose, which decomposes molecular representations into their monosynthon, disynthon, and trisynthon building blocks and capitalizes on the inherent hierarchical structure of these molecules by modeling latent reactions between embedded synthons. Additionally, we investigate methods to improve the observation models for DEL count data, such as integrating covariate factors to more effectively account for data noise. Across two popular public benchmark data sets (CA-IX and HRP), our model demonstrates strong performance compared to count baselines, enriches the correct pharmacophores, and offers valuable insights via its intrinsic interpretable structure, thereby providing a robust tool for the analysis of DEL data.


Assuntos
DNA , Bibliotecas de Moléculas Pequenas , Bibliotecas de Moléculas Pequenas/química , DNA/química , Modelos Estatísticos , Biblioteca Gênica
17.
Mol Biol Rep ; 51(1): 367, 2024 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-38411701

RESUMO

BACKGROUND: Recombinase uvsY from bacteriophage T4, along with uvsX, is a key enzyme for recombinase polymerase amplification (RPA), which is used to amplify a target DNA sequence at a constant temperature. uvsY, though essential, poses solubility challenges, complicating the lyophilization of RPA reagents. This study aimed to enhance uvsY solubility. METHODS: Our hypothesis centered on the C-terminal region of uvsY influencing solubility. To test this, we generated a site-saturation mutagenesis library for amino acid residues Lys91-Glu134 of the N-terminal (His)6-tagged uvsY. RESULTS: Screening 480 clones identified A116H as the variant with superior solubility. Lyophilized RPA reagents featuring the uvsY variant A116H demonstrated enhanced performance compared to those with wild-type uvsY. CONCLUSIONS: The uvsY variant A116H emerges as an appealing choice for RPA applications, offering improved solubility and heightened lyophilization feasibility.


Assuntos
Aminoácidos , Recombinases , Recombinases/genética , Solubilidade , Biblioteca Gênica , Mutagênese
18.
Org Lett ; 26(8): 1688-1693, 2024 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-38385779

RESUMO

Using a novel homologation-heterocyclization cascade, the on-DNA synthesis of benzofurans from aldehydes has been developed. The methodology, based on an innovative use of the Seyferth-Gilbert homologation, followed by a high yielding Sonogashira coupling in situ intramolecular cyclization one-pot, two-step reaction, provides a powerful and unique pathway for DNA-encoded library (DEL) synthesis of a wide array of pharmaceutically relevant benzofuran-based scaffolds.


Assuntos
Benzofuranos , Biblioteca Gênica , Ciclização , DNA
19.
Bioinformatics ; 40(2)2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38402507

RESUMO

MOTIVATION: Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments. RESULTS: Bioframe is a library to enable flexible and performant operations on genomic interval dataframes in Python. Bioframe extends the Python data science stack to use cases for computational genome biology by building directly on top of two of the most commonly-used Python libraries, NumPy and Pandas. The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians. Bioframe achieves these goals while maintaining high performance and a rich set of features. AVAILABILITY AND IMPLEMENTATION: Bioframe is open-source under MIT license, cross-platform, and can be installed from the Python Package Index. The source code is maintained by Open2C on GitHub at https://github.com/open2c/bioframe.


Assuntos
Biologia Computacional , Genômica , Biblioteca Gênica , Sítios de Ligação , Ciência de Dados
20.
Sci Data ; 11(1): 193, 2024 Feb 13.
Artigo em Inglês | MEDLINE | ID: mdl-38351090

RESUMO

Oxylipins, small polar molecules derived from the peroxidation of polyunsaturated fatty acids (PUFAs), serve as biomarkers for many diseases and play crucial roles in human physiology and inflammation. Despite their significance, many non-enzymatic oxygenated metabolites of PUFAs (NEO-PUFAs) remain poorly reported, resulting in a lack of public datasets of experimental data and limiting their dereplication in further studies. To overcome this limitation, we constructed a high-resolution tandem mass spectrometry (MS/MS) dataset comprising pure NEO-PUFAs (both commercial and self-synthesized) and in vitro free radical-induced oxidation of diverse PUFAs. By employing molecular networking techniques with this dataset and the existent ones in public repositories, we successfully mapped a wide range of NEO-PUFAs, expanding the strategies for annotating oxylipins, and NEO-PUFAs and offering a novel workflow for profiling these molecules in biological samples.


Assuntos
Oxilipinas , Espectrometria de Massas em Tandem , Humanos , Ácidos Graxos Insaturados/análise , Ácidos Graxos Insaturados/química , Biblioteca Gênica , Inflamação , Oxilipinas/análise , Espectrometria de Massas em Tandem/métodos
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