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1.
Sci Data ; 11(1): 355, 2024 Apr 08.
Artículo en Inglés | MEDLINE | ID: mdl-38589415

RESUMEN

Chronic hepatitis B (CHB) is a major global health challenge. CHB can be controlled by antivirals but a therapeutic cure is lacking. CHB is characterized by limited HBV-specific T cell reactivity and functionality and expression of inhibitory receptors. The mechanisms driving these T cell phenotypes are only partially understood. Here, we created a single-cell RNA-sequencing dataset of HBV immune responses in patients to contribute to a better understanding of the dysregulated immunity. Blood samples of a well-defined cohort of 21 CHB and 10 healthy controls, including a subset of 5 matched liver biopsies, were collected. scRNA-seq data of total immune cells (55,825) plus sorted HBV-specific (1,963), non-naive (32,773) and PD1+ T cells (96,631) was generated using the 10X Genomics platform (186,123 cells) or the full-length Smart-seq2 protocol (1,069 cells). The shared transcript count matrices of single-cells serve as a valuable resource describing transcriptional changes underlying dysfunctional HBV-related T cell responses in blood and liver tissue and offers the opportunity to identify targets or biomarkers for HBV-related immune exhaustion.


Asunto(s)
Hepatitis B Crónica , Inmunidad Celular , Humanos , Virus de la Hepatitis B , Hepatitis B Crónica/genética , Hepatitis B Crónica/inmunología , ARN , Análisis de la Célula Individual , Análisis de Secuencia de ARN , Linfocitos T/inmunología , Hígado/virología
2.
NPJ Syst Biol Appl ; 9(1): 62, 2023 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-38102122

RESUMEN

Systemic lupus erythematosus (SLE) and primary Sjögren's syndrome (pSS) share clinical as well as pathogenic similarities. Although previous studies suggest various abnormalities in different immune cell compartments, dedicated cell-type specific transcriptomic signatures are often masked by patient heterogeneity. Here, we performed transcriptional profiling of isolated CD4, CD8, CD16 and CD19 lymphocytes from pSS and SLE patients upon T cell stimulation, in addition to a steady-state condition directly after blood drawing, in total comprising 581 sequencing samples. T cell stimulation, which induced a pronounced inflammatory response in all four cell types, gave rise to substantial re-modulation of lymphocyte subsets in the two autoimmune diseases compared to healthy controls, far exceeding the transcriptomic differences detected at steady-state. In particular, we detected cell-type and disease-specific down-regulation of a range of pro-inflammatory cytokine and chemokine pathways. Such differences between SLE and pSS patients are instrumental for selective immune targeting by future therapies.


Asunto(s)
Enfermedades Autoinmunes , Lupus Eritematoso Sistémico , Síndrome de Sjögren , Humanos , Síndrome de Sjögren/genética , Síndrome de Sjögren/metabolismo , Linfocitos T/metabolismo , Regulación hacia Abajo/genética , Lupus Eritematoso Sistémico/genética , Lupus Eritematoso Sistémico/metabolismo
3.
J Immunother Cancer ; 10(11)2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36319064

RESUMEN

BACKGROUND: Next-generation cancer immunotherapies are designed to broaden the therapeutic repertoire by targeting new immune checkpoints including lymphocyte-activation gene 3 (LAG-3) and T cell immunoglobulin and mucin-domain containing-3 (TIM-3). Yet, the molecular and cellular mechanisms by which either receptor functions to mediate its inhibitory effects are still poorly understood. Similarly, little is known on the differential effects of dual, compared with single, checkpoint inhibition. METHODS: We here performed in-depth characterization, including multicolor flow cytometry, single cell RNA sequencing and multiplex supernatant analysis, using tumor single cell suspensions from patients with cancer treated ex vivo with novel bispecific antibodies targeting programmed cell death protein 1 (PD-1) and TIM-3 (PD1-TIM3), PD-1 and LAG-3 (PD1-LAG3), or with anti-PD-1. RESULTS: We identified patient samples which were responsive to PD1-TIM3, PD1-LAG3 or anti-PD-1 using an in vitro approach, validated by the analysis of 659 soluble proteins and enrichment for an anti-PD-1 responder signature. We found increased abundance of an activated (HLA-DR+CD25+GranzymeB+) CD8+ T cell subset and of proliferating CD8+ T cells, in response to bispecific antibody or anti-PD-1 treatment. Bispecific antibodies, but not anti-PD-1, significantly increased the abundance of a proliferating natural killer cell subset, which exhibited enrichment for a tissue-residency signature. Key phenotypic and transcriptional changes occurred in a PD-1+CXCL13+CD4+ T cell subset, in response to all treatments, including increased interleukin-17 secretion and signaling toward plasma cells. Interestingly, LAG-3 protein upregulation was detected as a unique pharmacodynamic effect mediated by PD1-LAG3, but not by PD1-TIM3 or anti-PD-1. CONCLUSIONS: Our in vitro system reliably assessed responses to bispecific antibodies co-targeting PD-1 together with LAG-3 or TIM-3 using patients' tumor infiltrating immune cells and revealed transcriptional and phenotypic imprinting by bispecific antibody formats currently tested in early clinical trials.


Asunto(s)
Anticuerpos Biespecíficos , Neoplasias , Humanos , Linfocitos T CD8-positivos , Receptor 2 Celular del Virus de la Hepatitis A , Neoplasias/metabolismo , Receptor de Muerte Celular Programada 1 , Proteína del Gen 3 de Activación de Linfocitos
4.
NAR Genom Bioinform ; 3(4): lqab102, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-34761219

RESUMEN

Single-cell RNA sequencing (scRNA-seq) revolutionized our understanding of disease biology. The promise it presents to also transform translational research requires highly standardized and robust software workflows. Here, we present the toolkit Besca, which streamlines scRNA-seq analyses and their use to deconvolute bulk RNA-seq data according to current best practices. Beyond a standard workflow covering quality control, filtering, and clustering, two complementary Besca modules, utilizing hierarchical cell signatures and supervised machine learning, automate cell annotation and provide harmonized nomenclatures. Subsequently, the gene expression profiles can be employed to estimate cell type proportions in bulk transcriptomics data. Using multiple, diverse scRNA-seq datasets, some stemming from highly heterogeneous tumor tissue, we show how Besca aids acceleration, interoperability, reusability and interpretability of scRNA-seq data analyses, meeting crucial demands in translational research and beyond.

5.
Sci Rep ; 11(1): 12439, 2021 06 14.
Artículo en Inglés | MEDLINE | ID: mdl-34127723

RESUMEN

Coiled-coil regions were among the first protein motifs described structurally and theoretically. The simplicity of the motif promises that coiled-coil regions can be detected with reasonable accuracy and precision in any protein sequence. Here, we re-evaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Bank, down to each amino acid and its secondary structure. Apart from the 30-fold difference in minimum and maximum number of coiled coils predicted the tools strongly vary in where they predict coiled-coil regions. Accordingly, there is a high number of false predictions and missed, true coiled-coil regions. The evaluation of the binary classification metrics in comparison with naïve coin-flip models and the calculation of the Matthews correlation coefficient, the most reliable performance metric for imbalanced data sets, suggests that the tested tools' performance is close to random. This implicates that the tools' predictions have only limited informative value. Coiled-coil predictions are often used to interpret biochemical data and are part of in-silico functional genome annotation. Our results indicate that these predictions should be treated very cautiously and need to be supported and validated by experimental evidence.


Asunto(s)
Secuencias de Aminoácidos , Modelos Moleculares , Estructura Secundaria de Proteína , Secuencia de Aminoácidos , Bases de Datos de Proteínas/estadística & datos numéricos , Programas Informáticos
6.
Front Immunol ; 12: 635615, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33777025

RESUMEN

Circulating CD11c+ B cells are a key phenomenon in certain types of autoimmunity but have also been described in the context of regular immune responses (i.e., infections, vaccination). Using mass cytometry to profile 46 different markers on individual immune cells, we systematically initially confirmed the presence of increased CD11c+ B cells in the blood of systemic lupus erythematosus (SLE) patients. Notably, significant differences in the expression of CD21, CD27, and CD38 became apparent between CD11c- and CD11c+ B cells. We observed direct correlation of the frequency of CD21-CD27- B cells and CD21-CD38- B cells with CD11c+ B cells, which were most pronounced in SLE compared to primary Sjögren's syndrome patients (pSS) and healthy donors (HD). Thus, CD11c+ B cells resided mainly within memory subsets and were enriched in CD27-IgD-, CD21-CD27-, and CD21-CD38- B cell phenotypes. CD11c+ B cells from all donor groups (SLE, pSS, and HD) showed enhanced CD69, Ki-67, CD45RO, CD45RA, and CD19 expression, whereas the membrane expression of CXCR5 and CD21 were diminished. Notably, SLE CD11c+ B cells showed enhanced expression of the checkpoint molecules CD86, PD1, PDL1, CD137, VISTA, and CTLA-4 compared to HD. The substantial increase of CD11c+ B cells with a CD21- phenotype co-expressing distinct activation and checkpoint markers, points to a quantitative increased alternate (extrafollicular) B cell activation route possibly related to abnormal immune regulation as seen under the striking inflammatory conditions of SLE which shows a characteristic PD-1/PD-L1 upregulation.


Asunto(s)
Autoinmunidad , Linfocitos B/inmunología , Antígeno CD11c/sangre , Citometría de Flujo , Inmunofenotipificación , Lupus Eritematoso Sistémico/inmunología , Activación de Linfocitos , Síndrome de Sjögren/inmunología , ADP-Ribosil Ciclasa 1/sangre , Linfocitos B/metabolismo , Antígeno B7-H1/sangre , Biomarcadores/sangre , Estudios de Casos y Controles , Humanos , Lupus Eritematoso Sistémico/sangre , Lupus Eritematoso Sistémico/diagnóstico , Glicoproteínas de Membrana/sangre , Fenotipo , Receptor de Muerte Celular Programada 1/sangre , Receptores de Complemento 3d/sangre , Síndrome de Sjögren/sangre , Síndrome de Sjögren/diagnóstico , Miembro 7 de la Superfamilia de Receptores de Factores de Necrosis Tumoral/sangre
7.
Sci Rep ; 10(1): 10542, 2020 06 29.
Artículo en Inglés | MEDLINE | ID: mdl-32601281

RESUMEN

Naïve human pluripotent stem cells (hPSC) resemble the embryonic epiblast at an earlier time-point in development than conventional, 'primed' hPSC. We present a comprehensive miRNA profiling of naïve-to-primed transition in hPSC, a process recapitulating aspects of early in vivo embryogenesis. We identify miR-143-3p and miR-22-3p as markers of the naïve state and miR-363-5p, several members of the miR-17 family, miR-302 family as primed markers. We uncover that miR-371-373 are highly expressed in naïve hPSC. MiR-371-373 are the human homologs of the mouse miR-290 family, which are the most highly expressed miRNAs in naïve mouse PSC. This aligns with the consensus that naïve hPSC resemble mouse naive PSC, showing that the absence of miR-371-373 in conventional hPSC is due to cell state rather than a species difference.


Asunto(s)
Perfilación de la Expresión Génica , Células Madre Pluripotentes Inducidas/metabolismo , MicroARNs/metabolismo , Células Madre Pluripotentes/metabolismo , Humanos , MicroARNs/genética
8.
Int J Mol Sci ; 21(13)2020 Jul 07.
Artículo en Inglés | MEDLINE | ID: mdl-32645954

RESUMEN

Tissue-resident macrophages are key players in inflammatory processes, and their activation and functionality are crucial in health and disease. Numerous diseases are associated with alterations in homeostasis or dysregulation of the innate immune system, including allergic reactions, autoimmune diseases, and cancer. Macrophages are a prime target for drug discovery due to their major regulatory role in health and disease. Currently, the main sources of macrophages used for therapeutic compound screening are primary cells isolated from blood or tissue or immortalized or neoplastic cell lines (e.g., THP-1). Here, we describe an improved method to employ induced pluripotent stem cells (iPSCs) for the high-yield, large-scale production of cells resembling tissue-resident macrophages. For this, iPSC-derived macrophage-like cells are thoroughly characterized to confirm their cell identity and thus their suitability for drug screening purposes. These iPSC-derived macrophages show strong cellular identity with primary macrophages and recapitulate key functional characteristics, including cytokine release, phagocytosis, and chemotaxis. Furthermore, we demonstrate that genetic modifications can be readily introduced at the macrophage-like progenitor stage in order to interrogate drug target-relevant pathways. In summary, this novel method overcomes previous shortcomings with primary and leukemic cells and facilitates large-scale production of genetically modified iPSC-derived macrophages for drug screening applications.


Asunto(s)
Células Madre Pluripotentes Inducidas/citología , Macrófagos/citología , Técnicas de Cultivo de Célula/métodos , Línea Celular , Quimiotaxis/fisiología , Citocinas/metabolismo , Evaluación Preclínica de Medicamentos/métodos , Humanos , Células Madre Pluripotentes Inducidas/metabolismo , Macrófagos/metabolismo , Fagocitosis/fisiología
9.
Stem Cell Res ; 46: 101852, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-32521498

RESUMEN

Gene editing in human pluripotent stem cells (hPSC) is a powerful tool for understanding biology, for drug discovery and gene therapy. Naïve hPSC have been suggested to be superior for gene editing compared to conventional 'primed' hPSC. Using droplet digital PCR, we uncover the kinetics of Cas9-induced double strand break repair in conventional hPSC. Cut but unrepaired alleles reach their maximum after 12-24 h. Homology directed repair plateaus after 24 h, whereas repair by non-homologous end joining continues until 48 h after Cas9 introduction. Using this method, we demonstrate that the rate of homology directed repair to resolve Cas9-induced double strand breaks is 40% lower in naïve hPSC compared to conventional hPSC, correlating with, and feasibly explained by, a higher number of cells in G1 phase of the cell cycle in naïve hPSC. Therefore, naïve hPSC are less efficient for CRISPR/Cas9-mediated homology directed repair.


Asunto(s)
Sistemas CRISPR-Cas , Células Madre Pluripotentes , Sistemas CRISPR-Cas/genética , Roturas del ADN de Doble Cadena , Reparación del ADN por Unión de Extremidades , Edición Génica , Humanos , Reparación del ADN por Recombinación
10.
Bioessays ; 41(11): e1900066, 2019 11.
Artículo en Inglés | MEDLINE | ID: mdl-31544971

RESUMEN

The major transcript variants of human protein-coding genes are annotated to a certain degree of accuracy combining manual curation, transcript data, and proteomics evidence. However, there is considerable disagreement on the annotation of about 2000 genes-they can be protein-coding, noncoding, or pseudogenes-and on the annotation of most of the predicted alternative transcripts. Pure transcriptome mapping approaches seem to be limited in discriminating functional expression from noise. These limitations have partially been overcome by dedicated algorithms to detect alternative spliced micro-exons and wobble splice variants. Recently, knowledge about splice mechanism and protein structure are incorporated into an algorithm to predict neighboring homologous exons, often spliced in a mutually exclusive manner. Predicted exons are evaluated by transcript data, structural compatibility, and evolutionary conservation, revealing hundreds of novel coding exons and splice mechanism re-assignments. The emerging human pan-genome is necessitating distinctive annotations incorporating differences between individuals and between populations.


Asunto(s)
Genoma Humano/genética , Proteínas/genética , Algoritmos , Empalme Alternativo/genética , Animales , Exones/genética , Genómica/métodos , Humanos , Empalme del ARN/genética , Transcriptoma/genética
11.
BMC Genomics ; 19(1): 558, 2018 07 30.
Artículo en Inglés | MEDLINE | ID: mdl-30060733

RESUMEN

After the publication of this work [1], a mistake was noticed in the Eq. 1. Given an m × n expression matrix with m genes and samples of n tissues, the correct definition of the Gini index for gene i is.

12.
Nat Commun ; 9(1): 2032, 2018 05 23.
Artículo en Inglés | MEDLINE | ID: mdl-29795225

RESUMEN

Modification of SMN2 exon 7 (E7) splicing is a validated therapeutic strategy against spinal muscular atrophy (SMA). However, a target-based approach to identify small-molecule E7 splicing modifiers has not been attempted, which could reveal novel therapies with improved mechanistic insight. Here, we chose as a target the stem-loop RNA structure TSL2, which overlaps with the 5' splicing site of E7. A small-molecule TSL2-binding compound, homocarbonyltopsentin (PK4C9), was identified that increases E7 splicing to therapeutic levels and rescues downstream molecular alterations in SMA cells. High-resolution NMR combined with molecular modelling revealed that PK4C9 binds to pentaloop conformations of TSL2 and promotes a shift to triloop conformations that display enhanced E7 splicing. Collectively, our study validates TSL2 as a target for small-molecule drug discovery in SMA, identifies a novel mechanism of action for an E7 splicing modifier, and sets a precedent for other splicing-mediated diseases where RNA structure could be similarly targeted.


Asunto(s)
Imidazoles/farmacología , Indoles/farmacología , Atrofia Muscular Espinal/tratamiento farmacológico , ARN Mensajero/metabolismo , Empalme Alternativo , Animales , Animales Modificados Genéticamente , Drosophila , Evaluación Preclínica de Medicamentos , Exones/genética , Células HeLa , Humanos , Imidazoles/química , Imidazoles/uso terapéutico , Indoles/química , Indoles/uso terapéutico , Terapia Molecular Dirigida/métodos , Atrofia Muscular Espinal/genética , Fenotipo , Sitios de Empalme de ARN , ARN Mensajero/química , ARN Mensajero/genética , Elementos Reguladores de la Transcripción/efectos de los fármacos , Proteína 2 para la Supervivencia de la Neurona Motora/genética
13.
Cancer Discov ; 8(4): 395-402, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29545369

RESUMEN

Checkpoint inhibitor therapy has been a breakthrough in cancer research, but only some patients with cancer derive substantial benefit. Although mechanisms underlying sensitivity and resistance to checkpoint inhibitors are being elucidated, the importance of organ-specific regulation of immunity is currently underappreciated. Here, we call for a greater understanding of tissue-specific immunoregulation, namely, "tissue-specific immunostats," to make advances in treatments for cancer. A better understanding of how individual organs at baseline regulate the immune system could enable an improved precision medicine approach to cancer immunotherapy. Cancer Discov; 8(4); 395-402. ©2018 AACR.


Asunto(s)
Sistema Inmunológico , Neoplasias/inmunología , Neoplasias/terapia , Animales , Humanos , Inmunoterapia , Ratones , Especificidad de Órganos , Medicina de Precisión
14.
Mol Syst Biol ; 13(12): 959, 2017 12 14.
Artículo en Inglés | MEDLINE | ID: mdl-29242366

RESUMEN

Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi-cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila Finally, MXEs are significantly enriched in pathogenic mutations and their spatio-temporal expression might predict human disease pathology.


Asunto(s)
Empalme del ARN/genética , Animales , Análisis por Conglomerados , Enfermedad/genética , Evolución Molecular , Exones/genética , Sitios Genéticos , Genoma Humano , Humanos , Mamíferos/genética , Mutación/genética , Pliegue de Proteína , ARN Mensajero/genética , ARN Mensajero/metabolismo
15.
PLoS One ; 12(5): e0177716, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28493992

RESUMEN

[This corrects the article DOI: 10.1371/journal.pone.0174639.].

16.
BMC Genomics ; 18(1): 277, 2017 04 04.
Artículo en Inglés | MEDLINE | ID: mdl-28376718

RESUMEN

BACKGROUND: Gene expression data can be compromised by cells originating from other tissues than the target tissue of profiling. Failures in detecting such tissue heterogeneity have profound implications on data interpretation and reproducibility. A computational tool explicitly addressing the issue is warranted. RESULTS: We introduce BioQC, a R/Bioconductor software package to detect tissue heterogeneity in gene expression data. To this end BioQC implements a computationally efficient Wilcoxon-Mann-Whitney test and provides more than 150 signatures of tissue-enriched genes derived from large-scale transcriptomics studies. Simulation experiments show that BioQC is both fast and sensitive in detecting tissue heterogeneity. In a case study with whole-organ profiling data, BioQC predicted contamination events that are confirmed by quantitative RT-PCR. Applied to transcriptomics data of the Genotype-Tissue Expression (GTEx) project, BioQC reveals clustering of samples and suggests that some samples likely suffer from tissue heterogeneity. CONCLUSIONS: Our experience with gene expression data indicates a prevalence of tissue heterogeneity that often goes unnoticed. BioQC addresses the issue by integrating prior knowledge with a scalable algorithm. We propose BioQC as a first-line tool to ensure quality and reproducibility of gene expression data.


Asunto(s)
Perfilación de la Expresión Génica , Programas Informáticos , Algoritmos , Animales , Perros , Humanos , Ratones , Especificidad de Órganos , Reproducibilidad de los Resultados , Transcriptoma
17.
PLoS One ; 12(4): e0174639, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28369123

RESUMEN

Stable single-alpha helices (SAHs) are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments. Although the function of the SAH-domains in human class-6 and class-10 myosins has well been characterised, the distribution of the SAH-domain in all myosin subfamilies and across the eukaryotic tree of life remained elusive. Here, we analysed the largest available myosin sequence dataset consisting of 7919 manually annotated myosin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification of SAH-domains. With this approach we identified SAH-domains in more than one third of the supposed 79 myosin subfamilies. Depending on the myosin class, the presence of SAH-domains can range from a few to almost all class members indicating complex patterns of independent and taxon-specific SAH-domain gain and loss.


Asunto(s)
Miosinas/metabolismo , Conformación Proteica en Hélice alfa/fisiología , Dominios Proteicos/fisiología , Algoritmos , Secuencia de Aminoácidos , Animales , Calmodulina/metabolismo , Drosophila , Humanos , Unión Proteica
18.
Bioinformatics ; 31(5): 767-9, 2015 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-25338722

RESUMEN

UNLABELLED: Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single α-helices (SAH domains). Overview schemes show the predicted coiled-coil regions found in the query sequence and provide sliders, which can be used to select segments for detailed helical wheel and helical net views. A window-based score has been developed to predict SAH domains. Export to several bitmap and vector graphics formats is supported. AVAILABILITY AND IMPLEMENTATION: http://waggawagga.motorprotein.de


Asunto(s)
Gráficos por Computador , Miosinas/química , Estructura Secundaria de Proteína , Programas Informáticos , Secuencia de Aminoácidos , Humanos , Datos de Secuencia Molecular
19.
Nucleic Acids Res ; 42(Web Server issue): W7-11, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-24829447

RESUMEN

In this article, we present a user-friendly web interface for two alignment-free sequence-comparison methods that we recently developed. Most alignment-free methods rely on exact word matches to estimate pairwise similarities or distances between the input sequences. By contrast, our new algorithms are based on inexact word matches. The first of these approaches uses the relative frequencies of so-called spaced words in the input sequences, i.e. words containing 'don't care' or 'wildcard' symbols at certain pre-defined positions. Various distance measures can then be defined on sequences based on their different spaced-word composition. Our second approach defines the distance between two sequences by estimating for each position in the first sequence the length of the longest substring at this position that also occurs in the second sequence with up to k mismatches. Both approaches take a set of deoxyribonucleic acid (DNA) or protein sequences as input and return a matrix of pairwise distance values that can be used as a starting point for clustering algorithms or distance-based phylogeny reconstruction. The two alignment-free programmes are accessible through a web interface at 'Göttingen Bioinformatics Compute Server (GOBICS)': http://spaced.gobics.de http://kmacs.gobics.de and the source codes can be downloaded.


Asunto(s)
Filogenia , Análisis de Secuencia de ADN/métodos , Análisis de Secuencia de Proteína/métodos , Programas Informáticos , Algoritmos , Internet , Alineación de Secuencia , Interfaz Usuario-Computador
20.
PLoS One ; 9(2): e88111, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24498429

RESUMEN

Multicellular animals possess two to three different types of muscle tissues. Striated muscles have considerable ultrastructural similarity and contain a core set of proteins including the muscle myosin heavy chain (Mhc) protein. The ATPase activity of this myosin motor protein largely dictates muscle performance at the molecular level. Two different solutions to adjusting myosin properties to different muscle subtypes have been identified so far: Vertebrates and nematodes contain many independent differentially expressed Mhc genes while arthropods have single Mhc genes with clusters of mutually exclusive spliced exons (MXEs). The availability of hundreds of metazoan genomes now allowed us to study whether the ancient bilateria already contained MXEs, how MXE complexity subsequently evolved, and whether additional scenarios to control contractile properties in different muscles could be proposed, By reconstructing the Mhc genes from 116 metazoans we showed that all intron positions within the motor domain coding regions are conserved in all bilateria analysed. The last common ancestor of the bilateria already contained a cluster of MXEs coding for part of the loop-2 actin-binding sequence. Subsequently the protostomes and later the arthropods gained many further clusters while MXEs got completely lost independently in several branches (vertebrates and nematodes) and species (for example the annelid Helobdella robusta and the salmon louse Lepeophtheirus salmonis). Several bilateria have been found to encode multiple Mhc genes that might all or in part contain clusters of MXEs. Notable examples are a cluster of six tandemly arrayed Mhc genes, of which two contain MXEs, in the owl limpet Lottia gigantea and four Mhc genes with three encoding MXEs in the predatory mite Metaseiulus occidentalis. Our analysis showed that similar solutions to provide different myosin isoforms (multiple genes or clusters of MXEs or both) have independently been developed several times within bilaterian evolution.


Asunto(s)
Artrópodos/genética , Drosophila melanogaster/genética , Exones/genética , Familia de Multigenes , Músculos/metabolismo , Cadenas Pesadas de Miosina/genética , Empalme del ARN/genética , Secuencia de Aminoácidos , Animales , Datos de Secuencia Molecular , Filogenia , Homología de Secuencia , Homología de Secuencia de Aminoácido
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