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1.
Cell Mol Life Sci ; 79(1): 22, 2022 Jan 03.
Artículo en Inglés | MEDLINE | ID: mdl-34981210

RESUMEN

The three-dimensional configuration of the genome ensures cell type-specific gene expression profiles by placing genes and regulatory elements in close spatial proximity. Here, we used in situ high-throughput chromosome conformation (in situ Hi-C), RNA sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) to characterize the high-order chromatin structure signature of female germline stem cells (FGSCs) and identify its regulating key factor based on the data-driven of multiple omics data. By comparison with pluripotent stem cells (PSCs), adult stem cells (ASCs), and somatic cells at three major levels of chromatin architecture, A/B compartments, topologically associating domains, and chromatin loops, the chromatin architecture of FGSCs was most similar to that of other ASCs and largely different from that of PSCs and somatic cells. After integrative analysis of the three-dimensional chromatin structure, active compartment-associating loops (aCALs) were identified as a signature of high-order chromatin organization in FGSCs, which revealed that CCCTC-binding factor was a major factor to maintain the properties of FGSCs through regulation of aCALs. We found FGSCs belong to ASCs at chromatin structure level and characterized aCALs as the high-order chromatin structure signature of FGSCs. Furthermore, CTCF was identified to play a key role in regulating aCALS to maintain the biological functions of FGSCs. These data provide a valuable resource for future studies of the features of chromatin organization in mammalian stem cells and further understanding of the fundamental characteristics of FGSCs.


Asunto(s)
Factor de Unión a CCCTC/metabolismo , Genoma , Imagenología Tridimensional , Células Madre Oogoniales/metabolismo , Células Madre Adultas/metabolismo , Animales , Secuencia de Bases , Forma de la Célula , Cromatina/metabolismo , Cromosomas de los Mamíferos/metabolismo , Femenino , Células Madre Pluripotentes Inducidas/metabolismo , Masculino , Ratones Endogámicos C57BL , Células Madre Oogoniales/citología
2.
BMC Bioinformatics ; 23(1): 18, 2022 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-34991448

RESUMEN

BACKGROUND: The function of non-coding RNA sequences is largely determined by their spatial conformation, namely the secondary structure of the molecule, formed by Watson-Crick interactions between nucleotides. Hence, modern RNA alignment algorithms routinely take structural information into account. In order to discover yet unknown RNA families and infer their possible functions, the structural alignment of RNAs is an essential task. This task demands a lot of computational resources, especially for aligning many long sequences, and it therefore requires efficient algorithms that utilize modern hardware when available. A subset of the secondary structures contains overlapping interactions (called pseudoknots), which add additional complexity to the problem and are often ignored in available software. RESULTS: We present the SeqAn-based software LaRA 2 that is significantly faster than comparable software for accurate pairwise and multiple alignments of structured RNA sequences. In contrast to other programs our approach can handle arbitrary pseudoknots. As an improved re-implementation of the LaRA tool for structural alignments, LaRA 2 uses multi-threading and vectorization for parallel execution and a new heuristic for computing a lower boundary of the solution. Our algorithmic improvements yield a program that is up to 130 times faster than the previous version. CONCLUSIONS: With LaRA 2 we provide a tool to analyse large sets of RNA secondary structures in relatively short time, based on structural alignment. The produced alignments can be used to derive structural motifs for the search in genomic databases.


Asunto(s)
ARN , Programas Informáticos , Algoritmos , Secuencia de Bases , Humanos , Conformación de Ácido Nucleico , ARN/genética , Alineación de Secuencia , Análisis de Secuencia de ARN
3.
BMC Bioinformatics ; 23(1): 25, 2022 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-34991450

RESUMEN

BACKGROUND: Sequencing technologies are prone to errors, making error correction (EC) necessary for downstream applications. EC tools need to be manually configured for optimal performance. We find that the optimal parameters (e.g., k-mer size) are both tool- and dataset-dependent. Moreover, evaluating the performance (i.e., Alignment-rate or Gain) of a given tool usually relies on a reference genome, but quality reference genomes are not always available. We introduce Lerna for the automated configuration of k-mer-based EC tools. Lerna first creates a language model (LM) of the uncorrected genomic reads, and then, based on this LM, calculates a metric called the perplexity metric to evaluate the corrected reads for different parameter choices. Next, it finds the one that produces the highest alignment rate without using a reference genome. The fundamental intuition of our approach is that the perplexity metric is inversely correlated with the quality of the assembly after error correction. Therefore, Lerna leverages the perplexity metric for automated tuning of k-mer sizes without needing a reference genome. RESULTS: First, we show that the best k-mer value can vary for different datasets, even for the same EC tool. This motivates our design that automates k-mer size selection without using a reference genome. Second, we show the gains of our LM using its component attention-based transformers. We show the model's estimation of the perplexity metric before and after error correction. The lower the perplexity after correction, the better the k-mer size. We also show that the alignment rate and assembly quality computed for the corrected reads are strongly negatively correlated with the perplexity, enabling the automated selection of k-mer values for better error correction, and hence, improved assembly quality. We validate our approach on both short and long reads. Additionally, we show that our attention-based models have significant runtime improvement for the entire pipeline-18[Formula: see text] faster than previous works, due to parallelizing the attention mechanism and the use of JIT compilation for GPU inferencing. CONCLUSION: Lerna improves de novo genome assembly by optimizing EC tools. Our code is made available in a public repository at: https://github.com/icanforce/lerna-genomics .


Asunto(s)
Algoritmos , Secuenciación de Nucleótidos de Alto Rendimiento , Secuencia de Bases , Genómica , Análisis de Secuencia de ADN , Programas Informáticos
4.
Acta Trop ; 225: 106196, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34687640

RESUMEN

Trichomoniasis is the most common nonviral sexually transmitted disease; it is caused by Trichomonas vaginalis and seriously threatens human reproductive health. Telomeres are specialised DNA-protein complexes at the ends of chromosomes that have a protective function. The aim of the present study was to identify and characterise the telomeric DNA of T. vaginalis-which has not been previously reported-by multiple molecular methods including sequencing, the Bal nuclease (BAL) 31 nuclease assay, fluorescence in situ hybridisation (FISH), and Southern blotting. We found numerous repeated units of TTTTAGGG in T. vaginalis genomic DNA digested with S1 nuclease in combination with XbaI restriction enzyme. The (TTTTAGGG)n tandem repeats were also highly sensitive to BAL 31 exonuclease digestion. We confirmed that the (TTTTAGGG)n repeats were located at the end of T. vaginalis chromosomes by FISH. Restriction enzyme digestion combined with Southern blotting using a digoxigenin-labelled (TTTTAGGG)5 probe showed that the T. vaginalis telomeric DNA length varied from 1.0 to 1.5 kb. This is the first report on the telomeric DNA sequence of T. vaginalis which includes the length and distribution on chromosomes; our findings lay a foundation for further study on telomere maintenance mechanisms in T. vaginalis.


Asunto(s)
Tricomoniasis , Trichomonas vaginalis , Secuencia de Bases , ADN , Humanos , Telómero/genética , Trichomonas vaginalis/genética
5.
Gene ; 808: 145974, 2022 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-34592348

RESUMEN

The mitochondrial genome (mitogenome) has been regarded as significant source of data to better understand the phylogenetic relationships within the Euphasmatodea, but no mitogenome in Aschiphasmatoidea has been sequenced to date. In this study, two mitogenomes of Orthomeria smaragdinum and Nanhuaphasma hamicercum of Aschiphasmatidae were sequenced and annotated for the first time. The same mitochondrial gene rearrangement structure was present in the two mitogenomes sequenced, showing as the translocation of tRNA-Arg and tRNA-Asn, which conformed to the tandem duplication-random loss and could be used as a possible synapomorphy for Aschiphasmatidae. The phylogenetic results based on the maximum likelihood (ML) and bayesian inference (BI) methods both showed that Aschiphasmatidae and Neophasmatodea in Euphasmatodea are sister taxa. Although the monophyly of Oriophasmata, Occidophasmata, Diapheromeridae, Phasmatidae, Lonchodidae and Bacilloidea has not been solved, the monophyly of Neophasmatodea and Phyllioidea was well supported.


Asunto(s)
Genoma Mitocondrial/genética , Mitocondrias/genética , Nematodos/genética , Animales , Secuencia de Bases/genética , Orden Génico/genética , Reordenamiento Génico/genética , Genómica/métodos , Neoptera/genética , Filogenia
6.
Gene ; 807: 145960, 2022 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-34509581

RESUMEN

Opsin is a fellow of the G protein-coupled receptors (GPCRs) superfamily. It can be divided into visual and non-visual opsin according to whether it is directly involved in visual imaging. Opsin plays an important role in visual image formation and the regulation of non-image forming functions such as circadian entrainment in the growth, development and evolution of fish. Crimson snapper belongs to Perciforme mainly found in the Indo-West Pacific and the South China Sea. It is one of the most influential economic fishes in the South China Sea. In order to study the existence and expression of opsin gene in Crimson snapper, we sequenced the genome and tissue sample transcriptome of Crimson snapper. In this study, 32 opsin genes were identified from the genome of Crimson snapper. The length of these genes ranged from 1061 bp to 86203 bp and were distributed on 15 different chromosomes. The analysis of opsin gene family of Crimson snapper showed that the sws2 had two extra copies as compared with that of Zebrafish. Domain and motif analysis revealed that all the 32 opsin genes have seven-(pass)-transmembrane domain receptors (7TM receptors) each, and the opsin family contained 10 common motifs. The expression level of opsin gene, confirmed by RT-qPCR, was analyzed by using nine tissues transcriptome databases of Crimson snapper. The results showed that almost all opsin genes were highly expressed in the retina and brain, except opn7a and opn7b which were expressed in intestine and red skin, and almost no expression in other tissues. Our results provide a comprehensive basic knowledge for the opsin gene family of Crimson snapper, which has significance for the study of the function of opsin in Lutjanidaes.


Asunto(s)
Opsinas/genética , Perciformes/genética , Animales , Secuencia de Bases/genética , China , Clonación Molecular/métodos , Enfermedades de los Peces/genética , Expresión Génica/genética , Opsinas/metabolismo , Perciformes/metabolismo , Receptores Acoplados a Proteínas G/genética , Transcriptoma/genética
7.
Methods Mol Biol ; 2391: 1-20, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34686972

RESUMEN

Fusarium ranks as the most important group of plant pathogens, responsible for a wide range of economically destructive diseases, including vascular wilts and root, crown, and stem rots. In addition, head blight and ear rot diseases are associated with the accumulation of mycotoxins in cereals. With over 300 phylogenetically distinct species, and a dearth of phenotypical characteristics, DNA sequence data in most instances is the only reliable means for obtaining an accurate species identification. Here we describe how to obtain single-spored pure cultures from symptomatic host tissue and a molecular identification by querying publicly accessible DNA sequence databases using a portion of translation elongation factor 1-α (TEF1), the largest subunit of RNA polymerase (RPB1), and/or the second largest subunit of RNA polymerase (RPB2).


Asunto(s)
Fusarium , Secuencia de Bases , ADN de Hongos/genética , ARN Polimerasas Dirigidas por ADN/genética , Fusarium/genética , Filogenia
8.
Methods Mol Biol ; 2404: 393-407, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34694622

RESUMEN

The ability to detect 2'-O-methylation sites (Nm) in high-throughput fashion is important, as increasing evidence points to a more diverse landscape for this RNA modification as well as the possibility of yet unidentified functions. Here we describe an optimized version of RibOxi-seq, which is built upon the original published method, that not only accurately profiles ribosomal RNA (rRNA) Nm sites with minimal RNA input but is also robust enough to identify mRNA intronic and exonic sites.


Asunto(s)
Transcriptoma , Secuencia de Bases , Metilación , ARN , ARN Ribosómico/metabolismo
9.
Methods Mol Biol ; 2257: 211-233, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-34432281

RESUMEN

MicroRNAs are important regulators in many eukaryotic lineages. Typical miRNAs have a length of about 22nt and are processed from precursors that form a characteristic hairpin structure. Once they appear in a genome, miRNAs are among the best-conserved elements in both animal and plant genomes. Functionally, they play an important role in particular in development. In contrast to protein-coding genes, miRNAs frequently emerge de novo. The genomes of animals and plants harbor hundreds of mutually unrelated families of homologous miRNAs that tend to be persistent throughout evolution. The evolution of their genomic miRNA complement closely correlates with important morphological innovation. In addition, miRNAs have been used as valuable characters in phylogenetic studies. An accurate and comprehensive annotation of miRNAs is required as a basis to understand their impact on phenotypic evolution. Since experimental data on miRNA expression are limited to relatively few species and are subject to unavoidable ascertainment biases, it is inevitable to complement miRNA sequencing by homology based annotation methods. This chapter reviews the state of the art workflows for homology based miRNA annotation, with an emphasis on their limitations and open problems.


Asunto(s)
Filogenia , Animales , Secuencia de Bases , Genoma de Planta , MicroARNs/genética , Plantas/genética
10.
Curr Microbiol ; 79(1): 10, 2021 Dec 14.
Artículo en Inglés | MEDLINE | ID: mdl-34905112

RESUMEN

Currently, over 190 species in family Vibrionaceae, including not-yet-cultured taxa, have been described and classified into over nine genera, in which the number of species has doubled compared to the previous vibrio evolutionary update (Vibrio Clade 2.0) (Sawabe et al. 2014). In this study, "Vibrio Clade 3.0," the second update of the molecular phylogenetic analysis was performed based on nucleotide sequences of eight housekeeping genes (8-HKGs) retrieved from genome sequences, including 22 newly determined genomes. A total of 51 distinct clades were observed, of which 21 clades are newly described. We further evaluated the delineation powers of the clade classification based on nucleotide sequences of 34 single-copy genes and 11 ribosomal protein genes (11-RPGs) retrieved from core-genome sequences; however, the delineation power of 8-HKGs is still high and that gene set can be reliably used for the classification and identification of Vibrionaceae. Furthermore, the 11-RPGs set proved to be useful in identifying uncultured species among metagenome-assembled genome (MAG) and/or single-cell genome-assembled genome (SAG) pools. This study expands the awareness of the diversity and evolutionary history of the family Vibrionaceae and accelerates the taxonomic applications in classifying as not-yet-cultured taxa among MAGs and SAGs.


Asunto(s)
Vibrio , Vibrionaceae , Secuencia de Bases , Genoma Bacteriano , Filogenia , Análisis de Secuencia de ADN , Vibrio/genética , Vibrionaceae/genética
11.
Int J Mol Sci ; 22(24)2021 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-34948288

RESUMEN

The killer phenotype of Torulaspora delbrueckii (Td) and Saccharomyces cerevisiae (Sc) is encoded in the genome of medium-size dsRNA viruses (V-M). Killer strains also contain a helper large size (4.6 kb) dsRNA virus (V-LA) which is required for maintenance and replication of V-M. Another large-size (4.6 kb) dsRNA virus (V-LBC), without known helper activity to date, may join V-LA and V-M in the same yeast. T. delbrueckii Kbarr1 killer strain contains the killer virus Mbarr1 in addition to two L viruses, TdV-LAbarr1 and TdV-LBCbarr1. In contrast, the T. delbrueckii Kbarr2 killer strain contains two M killer viruses (Mbarr1 and M1) and a LBC virus (TdV-LBCbarr2), which has helper capability to maintain both M viruses. The genomes of TdV-LBCbarr1 and TdV-LBCbarr2 were characterized by high-throughput sequencing (HTS). Both RNA genomes share sequence identity and similar organization with their ScV-LBC counterparts. They contain all conserved motifs required for translation, packaging, and replication of viral RNA. Their Gag-Pol amino-acid sequences also contain the features required for cap-snatching and RNA polymerase activity. However, some of these motifs and features are similar to those of LA viruses, which may explain that at least TdV-LBCbarr2 has a helper ability to maintain M killer viruses. Newly sequenced ScV-LBC genomes contained the same motifs and features previously found in LBC viruses, with the same genome location and secondary structure. Sequence comparison showed that LBC viruses belong to two clusters related to each species of yeast. No evidence for associated co-evolution of specific LBC with specific M virus was found. The presence of the same M1 virus in S. cerevisiae and T. delbrueckii raises the possibility of cross-species transmission of M viruses.


Asunto(s)
Virus ARN Bicatenario/genética , Genoma Viral/genética , Virus Helper/genética , ARN Bicatenario/genética , Torulaspora/genética , Vino/microbiología , Vino/virología , Secuencia de Aminoácidos , Secuencia de Bases , Cápside , ARN Viral/genética , Saccharomyces cerevisiae/genética
12.
Cells ; 10(12)2021 12 01.
Artículo en Inglés | MEDLINE | ID: mdl-34943889

RESUMEN

Phenobarbital (PB), a widely used antiepileptic drug, is known to upregulate the expression of numerous drug-metabolizing enzymes and transporters in the liver primarily via activation of the constitutive androstane receptor (CAR, NR1I3). The solute carrier family 13 member 5 (SLC13A5), a sodium-coupled citrate transporter, plays an important role in intracellular citrate homeostasis that is associated with a number of metabolic syndromes and neurological disorders. Here, we show that PB markedly elevates the expression of SLC13A5 through a pregnane X receptor (PXR)-dependent but CAR-independent signaling pathway. In human primary hepatocytes, the mRNA and protein expression of SLC13A5 was robustly induced by PB treatment, while genetic knockdown or pharmacological inhibition of PXR significantly attenuated this induction. Utilizing genetically modified HepaRG cells, we found that PB induces SLC13A5 expression in both wild type and CAR-knockout HepaRG cells, whereas such induction was fully abolished in the PXR-knockout HepaRG cells. Mechanistically, we identified and functionally characterized three enhancer modules located upstream from the transcription start site or introns of the SLC13A5 gene that are associated with the regulation of PXR-mediated SLC13A5 induction. Moreover, metformin, a deactivator of PXR, dramatically suppressed PB-mediated induction of hepatic SLC13A5 as well as its activation of the SLC13A5 luciferase reporter activity via PXR. Collectively, these data reveal PB as a potent inducer of SLC13A5 through the activation of PXR but not CAR in human primary hepatocytes.


Asunto(s)
/metabolismo , Hepatocitos/metabolismo , Fenobarbital/farmacología , Receptor X de Pregnano/metabolismo , Simportadores/genética , Secuencia de Bases , Células Cultivadas , Regulación de la Expresión Génica/efectos de los fármacos , Hepatocitos/efectos de los fármacos , Humanos , Intrones/genética , Metformina/farmacología , Modelos Biológicos , Receptor X de Pregnano/antagonistas & inhibidores , ARN Mensajero/genética , ARN Mensajero/metabolismo , Elementos de Respuesta/genética , Simportadores/metabolismo
13.
BMC Bioinformatics ; 22(1): 610, 2021 Dec 23.
Artículo en Inglés | MEDLINE | ID: mdl-34949163

RESUMEN

BACKGROUND: The interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats-normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently. RESULTS: We developed the GeneTonic software package, which serves as a comprehensive toolkit for streamlining the interpretation of functional enrichment analyses, by fully leveraging the information of expression values in a differential expression context. GeneTonic is implemented in R and Shiny, leveraging packages that enable HTML-based interactive visualizations for executing drilldown tasks seamlessly, viewing the data at a level of increased detail. GeneTonic is integrated with the core classes of existing Bioconductor workflows, and can accept the output of many widely used tools for pathway analysis, making this approach applicable to a wide range of use cases. Users can effectively navigate interlinked components (otherwise available as flat text or spreadsheet tables), bookmark features of interest during the exploration sessions, and obtain at the end a tailored HTML report, thus combining the benefits of both interactivity and reproducibility. CONCLUSION: GeneTonic is distributed as an R package in the Bioconductor project ( https://bioconductor.org/packages/GeneTonic/ ) under the MIT license. Offering both bird's-eye views of the components of transcriptome data analysis and the detailed inspection of single genes, individual signatures, and their relationships, GeneTonic aims at simplifying the process of interpretation of complex and compelling RNA-seq datasets for many researchers with different expertise profiles.


Asunto(s)
ARN , Programas Informáticos , Secuencia de Bases , Reproducibilidad de los Resultados , Análisis de Secuencia de ARN
14.
PLoS One ; 16(12): e0254466, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34972106

RESUMEN

Relaxin/insulin-like family peptide receptor 1 (RXFP1) mediates relaxin's antifibrotic effects and has reduced expression in the lung and skin of patients with fibrotic interstitial lung disease (fILD) including idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc). This may explain the failure of relaxin-based anti-fibrotic treatments in SSc, but the regulatory mechanisms controlling RXFP1 expression remain largely unknown. This study aimed to identify regulatory elements of RXFP1 that may function differentially in fibrotic fibroblasts. We identified and evaluated a distal regulatory region of RXFP1 in lung fibroblasts using a luciferase reporter system. Using serial deletions, an enhancer upregulating pGL3-promoter activity was localized to the distal region between -584 to -242bp from the distal transcription start site (TSS). This enhancer exhibited reduced activity in IPF and SSc lung fibroblasts. Bioinformatic analysis identified two clusters of activator protein 1 (AP-1) transcription factor binding sites within the enhancer. Site-directed mutagenesis of the binding sites confirmed that only one cluster reduced activity (-358 to -353 relative to distal TSS). Co-expression of FOS in lung fibroblasts further increased enhancer activity. In vitro complex formation with a labeled probe spanning the functional AP-1 site using nuclear proteins isolated from lung fibroblasts confirmed a specific DNA/protein complex formation. Application of antibodies against JUN and FOS resulted in the complex alteration, while antibodies to JUNB and FOSL1 did not. Analysis of AP-1 binding in 5 pairs of control and IPF lung fibroblasts detected positive binding more frequently in control fibroblasts. Expression of JUN and FOS was reduced and correlated positively with RXFP1 expression in IPF lungs. In conclusion, we identified a distal enhancer of RXFP1 with differential activity in fibrotic lung fibroblasts involving AP-1 transcription factors. Our study provides insight into RXFP1 downregulation in fILD and may support efforts to reevaluate relaxin-based therapeutics alongside upregulation of RXFP1 transcription.


Asunto(s)
Elementos de Facilitación Genéticos/genética , Fibroblastos/metabolismo , Pulmón/citología , Receptores Acoplados a Proteínas G/genética , Receptores de Péptidos/genética , Factor de Transcripción AP-1/metabolismo , Secuencia de Bases , Sitios de Unión , Mapeo Cromosómico , Regulación de la Expresión Génica/efectos de los fármacos , Genoma Humano , Humanos , Regiones Promotoras Genéticas/genética , Unión Proteica/efectos de los fármacos , Proteínas Proto-Oncogénicas c-fos/metabolismo , Proteínas Proto-Oncogénicas c-jun/metabolismo , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Receptores de Péptidos/metabolismo
15.
Cell Mol Life Sci ; 79(1): 5, 2021 Dec 22.
Artículo en Inglés | MEDLINE | ID: mdl-34936021

RESUMEN

BACKGROUND: Extracellular vesicles (EVs) are regulators of cell-cell interactions and mediators of horizontal transfer of bioactive molecules between cells. EV-mediated cell-cell interactions play roles in physiological and pathophysiological processes, which maybe modulated by exposure to pathogens and cocaine use. However, the effect of pathogens and cocaine use on EV composition and function are not fully understood. RESULTS: Here, we used systems biology and multi-omics analysis to show that HIV infection (HIV +) and cocaine (COC) use (COC +) promote the release of semen-derived EVs (SEV) with dysregulated extracellular proteome (exProtein), miRNAome (exmiR), and exmiR networks. Integrating SEV proteome and miRNAome revealed a significant decrease in the enrichment of disease-associated, brain-enriched, and HIV-associated miR-128-3p (miR-128) in HIV + COC + SEV with a concomitant increase in miR-128 targets-PEAK1 and RND3/RhoE. Using two-dimensional-substrate single cell haptotaxis, we observed that in the presence of HIV + COC + SEV, contact guidance provided by the extracellular matrix (ECM, collagen type 1) network facilitated far-ranging haptotactic cues that guided monocytes over longer distances. Functionalizing SEV with a miR-128 mimic revealed that the strategic changes in monocyte haptotaxis are in large part the result of SEV-associated miR-128. CONCLUSIONS: We propose that compositionally and functionally distinct HIV + COC + and HIV-COC- SEVs and their exmiR networks may provide cells relevant but divergent haptotactic guidance in the absence of chemotactic cues, under both physiological and pathophysiological conditions.


Asunto(s)
Quimiotaxis , Cocaína/farmacología , Vesículas Extracelulares/metabolismo , Infecciones por VIH/genética , MicroARNs/metabolismo , Monocitos/metabolismo , Proteoma/metabolismo , Semen/metabolismo , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Secuencia de Bases , Comorbilidad , Redes Reguladoras de Genes , Humanos , MicroARNs/genética , Persona de Mediana Edad , Adulto Joven
16.
Folia Parasitol (Praha) ; 682021 Oct 13.
Artículo en Inglés | MEDLINE | ID: mdl-34782490

RESUMEN

The Gram-negative, obligate intracellular tick-transmitted pathogen Anaplasma phagocytophilum can cause acute febrile diseases in humans and domestic animals. The expansion of the tick Ixodes ricinus (Linnaeus, 1758) in northern Europe due to climate change is of serious concern for animal and human health. The aim of the present study was to investigate the impact of A. phagocytophilum infection in moose Alces alces (Linnaeus) calves by evaluating the carcass weights of infected and non-infected animals and examining animal tissues samples for co-infections with either species of Babesia Starcovici, 1893 or bacteria of the genus Bartonella. The carcasses of 68 free-ranging moose calves were weighed by hunters during the hunting seasons from 2014 to 2017 in two regions in southern Norway and spleen samples were collected. Anaplasma phagocytophilum was detected in moose sampled from locations infected with ticks with a prevalence of 82% (n = 46). The carcass weights of A. phagocytophilum-infected calves (n = 46) and non-infected (n = 22) calves were compared. Although the average weight of infected calves (45.6 kg) was lower than that of non-infected calves (46.5 kg), the difference was not statistically significant. Three different variants of the bacterium 16S rRNA gene were identified. The average weight of animals infected with variant I was 49.9 kg, whereas that of animals infected with variant III was 42.0 kg, but the difference was not statistically significant (p = 0.077). Co-infections of A. phagocytophilum with Bartonella spp. or with Babesia spp. were found in 20 and two calves, respectively. A triple infection was found in two calves. Sequence analysis of the 18S rRNA gene of Babesia-positive samples revealed the presence of Babesia cf. odocoilei (Emerson et Wright, 1970). Strains of Bartonella closely related to Bartonella bovis (Bermond, Boulouis, Heller, Laere, Monteil, Chomel, Sander, Dehio et Piemont, 2002) were identified based on phylogenetic analysis of the gltA and rpoB genes. The loss of body mass in moose calves in the tick-infected site was probably influenced by multiple factors.


Asunto(s)
Anaplasma phagocytophilum , Ciervos , Ehrlichiosis/veterinaria , Anaplasma phagocytophilum/clasificación , Anaplasma phagocytophilum/genética , Anaplasma phagocytophilum/aislamiento & purificación , Animales , Babesia/genética , Bartonella/genética , Secuencia de Bases , Peso Corporal , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Bacteriano/aislamiento & purificación , Ehrlichiosis/complicaciones , Ehrlichiosis/epidemiología , Ehrlichiosis/patología , Noruega/epidemiología , Oligonucleótidos/química , Filogenia , Reacción en Cadena de la Polimerasa/veterinaria , Bazo/microbiología , Bazo/patología
17.
Zootaxa ; 5026(1): 59-70, 2021 Aug 24.
Artículo en Inglés | MEDLINE | ID: mdl-34810941

RESUMEN

A newly identified tardigrade species from China, Pilatobius nuominensis sp. nov., belongs to the group of species with cuticle of the dorsal and lateral caudal region with evident irregular polygonal sculpture. Nucleotide sequences of two nuclear (18S rRNA, 28S rRNA) and one mitochondrial (COI) DNA fragments of the new species are provided, which allows an independent verification of the taxonomic status of the new species. This is the first record of the genus Pilatobius in the Great Hinggan Mountains.


Asunto(s)
Tardigrada , Animales , Secuencia de Bases , China , Filogenia , ARN Ribosómico 18S , ARN Ribosómico 28S , Tardigrada/genética
18.
Zootaxa ; 5027(1): 127-135, 2021 Aug 30.
Artículo en Inglés | MEDLINE | ID: mdl-34811241

RESUMEN

The genera Teredorus and Systolederus belong to Tetriginae and Metrodorinae respectively. However, species within these two genera have strikingly similar features, made it difficult to identify clearly by morphological characteristics. In this study, we sequenced the mitochondrial genomes (mitogenomes) of two Teredorus species, and compared them with Systolederus mitochondrial sequences. The sequenced mitogenomes of T. hainanensis and T. bashanensis are 14,946 bp and 14,775 bp in size, respectively. The A+T content of mitogenomes is 76.2% (T. hainanensis) and 74.0% (T. bashanensis). Comparative analysis showed that mitochondrial sequences and structure were similar within these two genera. The results of K2P distances and phylogenetic analysis revealed that Systolederus and Teredorus might be likely considered as one genus of Teredorus. It will provide important resources for further understanding of the taxonomy and phylogenetic relationship of Systolederus and Teredorus.


Asunto(s)
Genoma Mitocondrial , Ortópteros , Animales , Secuencia de Bases , Ortópteros/genética , Filogenia
19.
PLoS One ; 16(10): e0258298, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-34637470

RESUMEN

Papaya ringspot virus biotype-P is a detrimental pathogen of economically important papaya and cucurbits worldwide. The mutation prone feature of this virus perhaps accounts for its geographical dissemination. In this study, investigations of the atypical PRSV-P strain was conducted based on phylogenetic, recombination and genetic differentiation analyses considering of it's likely spread across India and Bangladesh. Full length genomic sequences of 38 PRSV isolates and 35 CP gene sequences were subjected to recombination analysis. A total of 61 recombination events were detected in aligned complete PRSV genome sequences. 3 events were detected in complete genome of PRSV strain PK whereas one was in its CP gene sequence. The PRSV-PK appeared to be recombinant of a major parent from Bangladesh. However, the genetic differentiation based on full length genomic sequences revealed less frequent gene flow between virus PRSV-PK and the population from America, India, Colombia, other Asian Countries and Australia. Whereas, frequent gene flow exists between Pakistan and Bangladesh virus populations. These results provided evidence correlating geographical position and genetic distances. We speculate that the genetic variations and evolutionary dynamics of this virus may challenge the resistance developed in papaya against PRSV and give rise to virus lineage because of its atypical emergence where geographic spread is already occurring.


Asunto(s)
Carica/genética , Carica/virología , Evolución Molecular , Variación Genética , Enfermedades de las Plantas/genética , Potyvirus/genética , Regiones no Traducidas 3'/genética , Secuencia de Bases , Flujo Génico , Genoma Viral , Funciones de Verosimilitud , Filogenia , Recombinación Genética , Estadística como Asunto
20.
J Vis Exp ; (175)2021 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-34605821

RESUMEN

During gene expression, the vital step of pre-mRNA splicing involves accurate recognition of splice sites and efficient assembly of spliceosomal complexes to join exons and remove introns prior to cytoplasmic export of the mature mRNA. Splicing efficiency can be altered by the presence of mutations at splice sites, the influence of trans-acting splicing factors, or the activity of therapeutics. Here, we describe the protocol for a cellular assay that can be applied for monitoring the splicing efficiency of any given exon. The assay uses an adaptable plasmid encoded 3-exon/2-intron minigene reporter, which can be expressed in mammalian cells by transient transfection. Post-transfection, total cellular RNA is isolated, and the efficiency of exon splicing in the reporter mRNA is determined by either primer extension or semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). We describe how the impact of disease associated 5' splice-site mutations can be determined by introducing them in the reporter; and how the suppression of these mutations can be achieved by co-transfection with U1 small nuclear RNA (snRNA) construct carrying compensatory mutations in its 5' region that basepairs with the 5'-splice sites at exon-intron junctions in pre-mRNAs. Thus, the reporter can be used for the design of therapeutic U1 particles to improve recognition of mutant 5' splice-sites. Insertion of cis-acting regulatory sites, such as splicing enhancer or silencer sequences, into the reporter can also be used to examine the role of U1 snRNP in regulation mediated by a specific alternative splicing factor. Finally, reporter expressing cells can be incubated with small molecules to determine the effect of potential therapeutics on constitutive pre-mRNA splicing or on exons carrying mutant 5' splice sites. Overall, the reporter assay can be applied to monitor splicing efficiency in a variety of conditions to study fundamental splicing mechanisms and splicing-associated diseases.


Asunto(s)
Empalme Alternativo , Empalme del ARN , Animales , Secuencia de Bases , Intrones/genética , Precursores del ARN/genética , Precursores del ARN/metabolismo , Sitios de Empalme de ARN , Empalme del ARN/genética
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