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1.
Nat Commun ; 12(1): 4809, 2021 08 10.
Artigo em Inglês | MEDLINE | ID: mdl-34376689

RESUMO

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.


Assuntos
COVID-19/epidemiologia , COVID-19/virologia , Genoma Viral , SARS-CoV-2/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , COVID-19/diagnóstico , COVID-19/transmissão , Criança , Pré-Escolar , Feminino , Variação Genética , Humanos , Lactente , Quênia/epidemiologia , Masculino , Pessoa de Meia-Idade , Pandemias , Filogenia , Saúde Pública , SARS-CoV-2/classificação , SARS-CoV-2/isolamento & purificação , Análise de Sequência , Tanzânia , Viagem , Adulto Jovem
2.
BMC Plant Biol ; 21(1): 400, 2021 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-34454435

RESUMO

BACKGROUNDS: Pomegranate is an excellent tree species with nutritional, medicinal, ornamental and ecological values. Studies have confirmed that SPL factors play an important role in floral transition and flower development. RESULTS: Used bioinformatics methods, 15 SPL (SQUAMOSA promoter-binding protein-like) genes were identified and analyzed from the 'Taishanhong' pomegranate (P. granatum L.) genome. Phylogenetic analysis showed that PgSPLs were divided into six subfamilies (G1 ~ G6). PgSPL promoter sequences contained multiple cis-acting elements associated with abiotic stress or hormonal response. Based on the transcriptome data, expression profiles of different tissues and different developmental stages showed that PgSPL genes had distinct temporal and spatial expression characteristics. The expression analysis of miR156 in small RNA sequencing results showed that miR156 negatively regulated the expression of target genes. qRT-PCR analysis showed that the expression levels of PgSPL2, PgSPL3, PgSPL6, PgSPL11 and PgSPL14 in leaves were significantly higher than those in buds and stems (p < 0.05). The expression levels of PgSPL5, PgSPL12 and PgSPL13 in flower buds were significantly higher than that in leaves and stems (p < 0.05). The full-length of coding sequence of PgSPL5 and PgSPL13 were obtained by homologous cloning technology. The full length of PgSPL5 is 1020 bp, and PgSPL13 is 489 bp, which encodes 339 and 162 amino acids, respectively. Further investigation revealed that PgSPL5 and PgSPL13 proteins were located in the nucleus. Exogenous plant growth regulator induction experiments showed that PgSPL5 was up-regulated in leaves and stems. PgSPL13 was up-regulated in leaves and down-regulated in stems. When sprayed with 6-BA, IBA and PP333 respectively, PgSPL5 and PgSPL13 were up-regulated most significantly at P2 (bud vertical diameter was 5.1 ~ 12.0 mm) stage of bisexual and functional male flowers. CONCLUSIONS: Our findings suggested that PgSPL2, PgSPL3, PgSPL6, PgSPL11 and PgSPL14 played roles in leaves development of pomegranate. PgSPL5, PgSPL12 and PgSPL13 played roles in pomegranate flower development. PgSPL5 and PgSPL13 were involved in the response process of different plant hormone signal transduction in pomegranate development. This study provided a robust basis for further functional analyses of SPL genes in pomegranate.


Assuntos
Flores/crescimento & desenvolvimento , Flores/genética , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/genética , Romã (Fruta)/crescimento & desenvolvimento , Romã (Fruta)/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Genoma de Planta , Estudo de Associação Genômica Ampla , Família Multigênica , Filogenia , Análise de Sequência
3.
BMC Genomics ; 22(1): 626, 2021 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-34425749

RESUMO

BACKGROUND: Long-read sequencing has great promise in enabling portable, rapid molecular-assisted cancer diagnoses. A key challenge in democratizing long-read sequencing technology in the biomedical and clinical community is the lack of graphical bioinformatics software tools which can efficiently process the raw nanopore reads, support graphical output and interactive visualizations for interpretations of results. Another obstacle is that high performance software tools for long-read sequencing data analyses often leverage graphics processing units (GPU), which is challenging and time-consuming to configure, especially on the cloud. RESULTS: We present a graphical cloud-enabled workflow for fast, interactive analysis of nanopore sequencing data using GPUs. Users customize parameters, monitor execution and visualize results through an accessible graphical interface. The workflow and its components are completely containerized to ensure reproducibility and facilitate installation of the GPU-enabled software. We also provide an Amazon Machine Image (AMI) with all software and drivers pre-installed for GPU computing on the cloud. Most importantly, we demonstrate the potential of applying our software tools to reduce the turnaround time of cancer diagnostics by generating blood cancer (NB4, K562, ME1, 238 MV4;11) cell line Nanopore data using the Flongle adapter. We observe a 29x speedup and a 93x reduction in costs for the rate-limiting basecalling step in the analysis of blood cancer cell line data. CONCLUSIONS: Our interactive and efficient software tools will make analyses of Nanopore data using GPU and cloud computing accessible to biomedical and clinical scientists, thus facilitating the adoption of cost effective, fast, portable and real-time long-read sequencing.


Assuntos
Biologia Computacional , Software , Reprodutibilidade dos Testes , Análise de Sequência , Fluxo de Trabalho
4.
Arch Virol ; 166(10): 2779-2787, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34363535

RESUMO

Feline infectious peritonitis (FIP) is a lethal infectious disease of domestic cats caused by feline coronavirus (FCoV) infection. Feline infectious peritonitis virus (FIPV) is a mutant type of FCoV that is characterized by causing fibrinous serositis with effusions in the pleural and abdominal cavities (wet form) and/or granulomatous-necrotizing inflammatory lesions in several organs (dry form). There have been numerous studies on FIP worldwide, whereas information about this disease in Thailand is still limited. Most studies involving molecular surveillance and evaluation of FCoV field strains have examined the genetic diversity of the spike and accessory ORF3c coding regions. Of these, the S gene is more divergent and is responsible for the two FCoV serotypes, while ORF3c harbors mutations that result either in early termination or destruction of the protein. In this study, we investigated the genetic diversity and genetic relationships among the current Thai and global FCoV strains in the accessory and nucleocapsid genes using a virus-specific PCR method. Comparative sequence analysis suggested that the Thai FCoV isolates were most closely related to strains reported in the Netherlands, the USA, and China. In the ORF3ab sequences, some Thai strains were more than 99% identical to the DF-2 prototype strain. Truncation of the 3a gene product was found in Thai FCoV strains of group 2. Amino acid deletions were observed in the N, ORF3c, and ORF7b proteins of Thai FCoV sequences. The accessory gene sequence divergence may be responsible for driving the periodic emergence and continued persistence of FCoVs in Thai domestic cat populations. Our findings provide updated information about the molecular characteristics of the accessory and nucleocapsid genes of FCoV strains in circulation that were not previously documented in this country.


Assuntos
Proteínas do Nucleocapsídeo de Coronavírus/genética , Coronavirus Felino/genética , Peritonite Infecciosa Felina/virologia , Proteínas Virais Reguladoras e Acessórias/genética , Sequência de Aminoácidos , Animais , Gatos , Coronavirus Felino/classificação , Coronavirus Felino/isolamento & purificação , Peritonite Infecciosa Felina/diagnóstico , Variação Genética , Mutação , Fases de Leitura Aberta/genética , Filogenia , RNA Viral/genética , Análise de Sequência , Tailândia/epidemiologia
5.
Zhonghua Yi Xue Yi Chuan Xue Za Zhi ; 38(8): 809-811, 2021 Aug 10.
Artigo em Chinês | MEDLINE | ID: mdl-34365632

RESUMO

OBJECTIVE: To explore the molecular basis for a rare case with Para-Bombay AB blood type. METHODS: Serological method was used to determine the blood type of the proband. Exons 6 and 7 of the ABO gene and the coding regions of FUT1 and FUT2 genes were analyzed by direct sequencing. RESULTS: Serological results showed that the proband was a Para-Bombay AB subtype. His genotype was determined as ABO*A1.02/B.01. The proband was also found to harbor c.551-552delAG and c.881-882delTT of the FUT1 gene. For his four children, there were three type B and one type A, though the expression of the H type was normal. CONCLUSION: The double deletions in the coding region of the FUT1 gene probably underlay the Para-Bombay blood type in the proband. Carrier of single-strand deletions may have a normal ABO phenotype.


Assuntos
Sistema ABO de Grupos Sanguíneos , Fucosiltransferases , Sistema ABO de Grupos Sanguíneos/genética , Alelos , Fucosiltransferases/genética , Genótipo , Humanos , Masculino , Fenótipo , Análise de Sequência
6.
Arch Virol ; 166(9): 2521-2527, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34240278

RESUMO

Feline calicivirus (FCV) is a contagious cat pathogen that causes oral ulceration and/or upper respiratory disease. In this study, we collected 61 samples from a pet hospital in Beijing and used PCR or RT-PCR to detect FCV and feline herpesvirus 1 (FHV-1). Approximately 44.3% (27/61) of the samples were FCV positive, and 23.0% (14/61) were coinfected with FCV and FHV-1. FCV was isolated from 15 samples. One isolate was from a cat with virulent systemic disease (VSD) signs, and 14 isolates were from cats with stomatitis or upper respiratory diseases. The range of genome sequence identity among these isolates was 76.1-100.0%. Four of the isolates were considered to be of the same strain, with sequence identity ranging from 99.5 to 99.7%, and two isolates, BJ-280 and BJ-288, had completely identical sequences. The genomic sequence identity ranged from 76.0 to 88.5% between the 15 isolates and several reference strains, including the F4 and F9 vaccine strains. These results demonstrate that many FCV strains are co-circulating in Beijing. Due to the diversity of FCV in Beijing, it is necessary to monitor the current prevalence of the virus. This study provides more information for the development of effective measures to control FCV.


Assuntos
Infecções por Caliciviridae/virologia , Calicivirus Felino/classificação , Calicivirus Felino/isolamento & purificação , Doenças do Gato/virologia , Filogenia , Animais , Pequim , Infecções por Caliciviridae/imunologia , Infecções por Caliciviridae/veterinária , Calicivirus Felino/genética , Doenças do Gato/imunologia , Gatos , Mutação , Análise de Sequência , Varicellovirus
7.
Bioinformatics ; 37(Suppl_1): i111-i119, 2021 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-34252944

RESUMO

MOTIVATION: The standard bootstrap method is used throughout science and engineering to perform general-purpose non-parametric resampling and re-estimation. Among the most widely cited and widely used such applications is the phylogenetic bootstrap method, which Felsenstein proposed in 1985 as a means to place statistical confidence intervals on an estimated phylogeny (or estimate 'phylogenetic support'). A key simplifying assumption of the bootstrap method is that input data are independent and identically distributed (i.i.d.). However, the i.i.d. assumption is an over-simplification for biomolecular sequence analysis, as Felsenstein noted. RESULTS: In this study, we introduce a new sequence-aware non-parametric resampling technique, which we refer to as RAWR ('RAndom Walk Resampling'). RAWR consists of random walks that synthesize and extend the standard bootstrap method and the 'mirrored inputs' idea of Landan and Graur. We apply RAWR to the task of phylogenetic support estimation. RAWR's performance is compared to the state-of-the-art using synthetic and empirical data that span a range of dataset sizes and evolutionary divergence. We show that RAWR support estimates offer comparable or typically superior type I and type II error compared to phylogenetic bootstrap support. We also conduct a re-analysis of large-scale genomic sequence data from a recent study of Darwin's finches. Our findings clarify phylogenetic uncertainty in a charismatic clade that serves as an important model for complex adaptive evolution. AVAILABILITY AND IMPLEMENTATION: Data and software are publicly available under open-source software and open data licenses at: https://gitlab.msu.edu/liulab/RAWR-study-datasets-and-scripts.


Assuntos
Software , Filogenia , Análise de Sequência
8.
Arch Virol ; 166(9): 2627-2632, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34255185

RESUMO

In this study, a novel picornavirus (perchPV/M9/2015/HUN, GenBank accession no. MW590713) was detected in eight (12.9%) out of 62 faecal samples collected from three (Perca fluviatilis, Sander lucioperca, and Ameiurus melas) out of 13 freshwater fish species tested and genetically characterized using viral metagenomics and RT-PCR methods. The complete genome of perchPV/M9/2015/HUN is 7,741 nt long, excluding the poly(A) tail, and has the genome organization 5'UTRIRES-?/P1(VP0-VP3-VP1)/P2(2A1NPG↓P-2A2H-box/NC-2B-2C)/P3(3A-3BVPg-3CPro-3DPol)/3'UTR-poly(A). The P1, 2C, and 3CD proteins had 41.4%, 38.1%, and 47.3% amino acid sequence identity to the corresponding proteins of Wenling lepidotrigla picornavirus (MG600079), eel picornavirus (NC_022332), and Wenling pleuronectiformes picornavirus (MG600098), respectively, as the closest relatives in the genus Potamipivirus. PerchPV/M9/2015/HUN represents a potential novel fish-origin species in an unassigned genus in the family Picornaviridae.


Assuntos
Ictaluridae/virologia , Percas/virologia , Filogenia , Infecções por Picornaviridae/veterinária , Infecções por Picornaviridae/virologia , Picornaviridae/classificação , Picornaviridae/isolamento & purificação , Regiões 3' não Traduzidas , Regiões 5' não Traduzidas , Sequência de Aminoácidos , Animais , Fezes/virologia , Água Doce , Genoma Viral , Hungria , Picornaviridae/genética , RNA Viral/genética , Análise de Sequência , Proteínas Virais/genética
9.
Nat Commun ; 12(1): 4064, 2021 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-34210966

RESUMO

The intrinsically disordered region (IDR) is a preserved signature of phytobacterial type III effectors (T3Es). The T3E IDR is thought to mediate unfolding during translocation into the host cell and to avoid host defense by sequence diversification. Here, we demonstrate a mechanism of host subversion via the T3E IDR. We report that the Xanthomonas campestris T3E XopR undergoes liquid-liquid phase separation (LLPS) via multivalent IDR-mediated interactions that hijack the Arabidopsis actin cytoskeleton. XopR is gradually translocated into host cells during infection and forms a macromolecular complex with actin-binding proteins at the cell cortex. By tuning the physical-chemical properties of XopR-complex coacervates, XopR progressively manipulates multiple steps of actin assembly, including formin-mediated nucleation, crosslinking of F-actin, and actin depolymerization, which occurs through competition for actin-depolymerizing factor and depends on constituent stoichiometry. Our findings unravel a sophisticated strategy in which bacterial T3E subverts the host actin cytoskeleton via protein complex coacervation.


Assuntos
Citoesqueleto de Actina/metabolismo , Proteínas de Bactérias/metabolismo , Xanthomonas/metabolismo , Agrobacterium , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Bactérias/genética , Proteínas Intrinsicamente Desordenadas/metabolismo , Cinética , Plantas Geneticamente Modificadas , Análise de Sequência , Tabaco , Xanthomonas/genética , Xanthomonas campestris/metabolismo
10.
J Cardiothorac Surg ; 16(1): 167, 2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34099002

RESUMO

BACKGROUND: Cystic echinococcosis (CE)/hydatidosis is an important neglected parasitic zoonotic disease caused by the metacestode of Echinococcus granulosus s.l. The present study was designed to identify the pulmonary CE species/genotypes in isolated human underwent to surgery in our center in Southern Iran. METHODS: The study population of this study were all patients in Fars province who were admitted to Namazi Hospitals for pulmonary hydatid cyst surgery. Thoracic surgery was performed in the thoracic ward and the cyst/s was removed by open surgery via posterolateral or lateral thoracotomy. DNA was extracted from the germinal layer or the protoscoleces. PCR technique was performed using the cytochrome C oxidase subunit1 (cox1) gene, and the products were sequenced. RESULTS: A total of 32 pulmonary hydatid cyst samples were collected from 9 (28%) female and 23 (72%) male aged from 4 to 74 years old. A total of 18(56%) cyst/s were in the left lobe and 14 (44%) cysts in the right lobe. Sequence analysis of the cysts showed that 24 samples (75%) were E. granulosus s.s (G1-G3) genotype and 8 (25%) were E. canadensis (G6/G7) genotype. CONCLUSION: E.granulosus s.s genotype was the most prevalent genotype followed by E. canadensis (G6/G7) genotype. There was no significant statistical correlation between cysts' size, location, genotype strain, and patients' age and gender.


Assuntos
DNA de Helmintos/análise , Equinococose Pulmonar/parasitologia , Echinococcus granulosus/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Genes Mitocondriais , Genótipo , Adolescente , Adulto , Idoso , Animais , Criança , Pré-Escolar , Equinococose Pulmonar/diagnóstico , Echinococcus granulosus/classificação , Echinococcus granulosus/isolamento & purificação , Feminino , Marcadores Genéticos , Humanos , Irã (Geográfico) , Masculino , Pessoa de Meia-Idade , Análise de Sequência , Análise de Sequência de DNA , Adulto Jovem
11.
Curr Opin Virol ; 49: 111-116, 2021 08.
Artigo em Inglês | MEDLINE | ID: mdl-34116392

RESUMO

The COVID-19 pandemic has entailed simultaneous revolutions in virology diagnostics, clinical trials management, and antiviral therapy and vaccinology. Over the past year, SARS-CoV-2 diagnostic testing has moved from highly centralized laboratories to at-home and even over the-counter. This transition has been lionized for its potential public health impact via isolation, but has been less examined for its effect on individual health and therapeutics. Since early initiation of antiviral therapy routinely has been associated with greater treatment efficacy for viral infections, these diagnostic testing innovations offer new opportunities for both clinical testing as well as clinical trials for antiviral therapy. Given a rapidly growing antiviral therapeutic pipeline and the profound impact of individual beneficiary outcomes on sculpting reimbursement policy, the therapeutic benefits associated with rapid viral testing may lead to significant adoption beyond potential public health impacts.


Assuntos
Teste para COVID-19 , COVID-19/diagnóstico , COVID-19/terapia , Testes Imediatos , Antivirais/uso terapêutico , Teste para COVID-19/economia , Teste para COVID-19/normas , Teste para COVID-19/estatística & dados numéricos , Ensaios Clínicos como Assunto , Diagnóstico Precoce , Humanos , Testes Imediatos/economia , Testes Imediatos/normas , Testes Imediatos/estatística & dados numéricos , SARS-CoV-2/genética , SARS-CoV-2/imunologia , SARS-CoV-2/isolamento & purificação , Análise de Sequência , Carga Viral
12.
Nucleic Acids Res ; 49(W1): W193-W198, 2021 07 02.
Artigo em Inglês | MEDLINE | ID: mdl-34104972

RESUMO

Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the difficulty in selecting an optimal sequence for exon skipping. The efficacy of ASOs is often unpredictable, because of the numerous factors involved in exon skipping. To address this gap, we have developed a computational method using machine-learning algorithms that factors in many parameters as well as experimental data to design highly effective ASOs for exon skipping. eSkip-Finder (https://eskip-finder.org) is the first web-based resource for helping researchers identify effective exon skipping ASOs. eSkip-Finder features two sections: (i) a predictor of the exon skipping efficacy of novel ASOs and (ii) a database of exon skipping ASOs. The predictor facilitates rapid analysis of a given set of exon/intron sequences and ASO lengths to identify effective ASOs for exon skipping based on a machine learning model trained by experimental data. We confirmed that predictions correlated well with in vitro skipping efficacy of sequences that were not included in the training data. The database enables users to search for ASOs using queries such as gene name, species, and exon number.


Assuntos
Bases de Dados de Ácidos Nucleicos , Éxons , Aprendizado de Máquina , Oligonucleotídeos Antissenso/química , Software , Internet , Íntrons , Splicing de RNA , Análise de Sequência
13.
Comp Immunol Microbiol Infect Dis ; 77: 101675, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-34098505

RESUMO

INTRODUCTION: Dogs are known as asymptomatic carriers forCampylobacter jejuni. The number of pet dogs is increasing in Egypt in the last decade. OBJECTIVE: This study aimed to investigate the frequency ofC. jejuni infection in dogs and humans, molecular typing of associated virulence genes, and flaA-SVR gene using sequencing. METHODOLOGY: 152 unpaired fecal swabs from dogs (n = 72) and humans (80) were examined for the presence of C. jejuni and Campylobacter 23S rRNA, and the pathogenicity genes including mapA genes, virB11, flaA, wlaN, iam, tetO, and aadA genes. Sequencing of the flaA- amplicon was also performed for the representative isolates. RESULTS: The isolation rate ofC. jejuni was 20.8 % and 31.2 %, respectively in dogs and humans, and all isolates were tested positive for 23S rRNA and mapA genes. C. jejuni harbor virB11 and wlaN (20 %, 0%), iam (10 %, 20 %), tetO and aadA1 (40 %, both), and flaA (40 %, 20 %) in human and dog strains, respectively. The flaA-SVR sequences revealed high identity between human and dog isolates (94.8 %), but revealed 18 substitutions in the amino acid sequence, and showed that the dog and human C. jejuni were close to strains isolated from human and poultry sources. CONCLUSION: this study demonstrated the comparative sequence analysis ofC. jejuni flaA-SVR fragment in dogs and some Egyptians, which indicated a high identity percentage between them. The results suggest that C. jejuni reservoirs dogs is an alarming public health concern and effective hygienic measures are necessary for house-holding pets to prevent C. jejuni zoonosis in Egypt's community.


Assuntos
Infecções por Campylobacter , Campylobacter jejuni , Campylobacter , Doenças do Cão , Animais , Campylobacter/genética , Infecções por Campylobacter/epidemiologia , Infecções por Campylobacter/veterinária , Campylobacter jejuni/genética , Doenças do Cão/epidemiologia , Cães , Egito/epidemiologia , Flagelina/genética , Humanos , Análise de Sequência/veterinária
14.
Nat Protoc ; 16(6): 2802-2825, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33953394

RESUMO

Several essential components of the electron transport chain, the major producer of ATP in mammalian cells, are encoded in the mitochondrial genome. These 13 proteins are translated within mitochondria by 'mitoribosomes'. Defective mitochondrial translation underlies multiple inborn errors of metabolism and has been implicated in pathologies such as aging, metabolic syndrome and cancer. Here, we provide a detailed ribosome profiling protocol optimized to interrogate mitochondrial translation in mammalian cells (MitoRiboSeq), wherein mitoribosome footprints are generated with micrococcal nuclease and mitoribosomes are separated from cytosolic ribosomes and other RNAs by ultracentrifugation in a single straightforward step. We highlight critical steps during library preparation and provide a step-by-step guide to data analysis accompanied by open-source bioinformatic code. Our method outputs mitoribosome footprints at single-codon resolution. Codons with high footprint densities are sites of mitoribosome stalling. We recently applied this approach to demonstrate that defects in mitochondrial serine catabolism or in mitochondrial tRNA methylation cause stalling of mitoribosomes at specific codons. Our method can be applied to study basic mitochondrial biology or to characterize abnormalities in mitochondrial translation in patients with mitochondrial disorders.


Assuntos
Perfilação da Expressão Gênica , Ribossomos Mitocondriais/metabolismo , Biossíntese de Proteínas , Análise de Sequência/métodos , Células HCT116 , Humanos
15.
BMC Psychiatry ; 21(1): 245, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33975564

RESUMO

BACKGROUND: Understanding the long-term inpatient service cost and utilization of psychiatric patients may provide insight into service demand for these patients and guide the design of targeted mental health programs. This study assesses 3-year hospitalization patterns and quantifies service utilization intensity of psychiatric patients in Beijing, China. METHODS: We identified patients admitted for one of three major psychiatric disorders (schizophrenia, bipolar and depressive disorders) between January 1 and December 31, 2013 in Beijing, China. Inpatient admissions during the following 3 years were extracted and analyzed using sequence analysis. Clinical characteristics, psychiatric and non-psychiatric service use of included patients were analyzed. RESULTS: The study included 3443 patients (7657 hospitalizations). The patient hospitalization sequences were grouped into 4 clusters: short stay (N = 2741 (79.61% of patients), who had 126,911 or 26.82% of the hospital days within the sample), repeated long stay (N = 404 (11.73%), 76,915 (16.26%) days), long-term stay (N = 101 (2.93%), 59,909 (12.66%) days) and permanent stay (N = 197 (5.72%), 209,402 (44.26%) days). Length and frequency of hospitalization, as well as readmission rates were significantly different across the 4 clusters. Over the 3-year period, hospitalization days per year decreased for patients in the short stay and repeated long stay clusters. Patients with schizophrenia (1705 (49.52%)) had 78.4% of cumulative psychiatric stays, with 11.14% of them in the permanent stay cluster. Among patients with depression, 23.11% had non-psychiatric hospitalizations, and on average 46.65% of their total inpatient expenses were for non-psychiatric care, the highest among three diagnostic groups. CONCLUSION: Hospitalization patterns varied significantly among psychiatric patients and across diagnostic categories. The high psychiatric care service use of the long-term and permanent stay patients underlines the need for evidence-based interventions to reduce cost and improve care quality.


Assuntos
Hospitalização , Transtornos Mentais , Pequim , China , Humanos , Tempo de Internação , Transtornos Mentais/epidemiologia , Transtornos Mentais/terapia , Análise de Sequência
16.
Curr Protoc ; 1(5): e136, 2021 May.
Artigo em Inglês | MEDLINE | ID: mdl-34043288

RESUMO

The use of genome editing tools is expanding our understanding of various human diseases by providing insight into gene-disease interactions. Despite the recognized role of toxicants in the development of human health issues and conditions, there is currently limited characterization of their mechanisms of action, and the application of CRISPR-based genome editing to the study of toxicants could help in the identification of novel gene-environment interactions. CRISPR-based functional screens enable identification of cellular mechanisms fundamental for response and susceptibility to a given toxicant. The aim of this review is to inform future directions in the application of CRISPR technologies in toxicological studies. We review and compare different types of CRISPR-based methods including pooled, anchored, combinatorial, and perturb-sequencing screens in vitro, in addition to pooled screenings in model organisms. © 2021 Wiley Periodicals LLC.


Assuntos
Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Edição de Genes , Interação Gene-Ambiente , Humanos , Análise de Sequência
17.
Viruses ; 13(3)2021 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-33804215

RESUMO

Ross River virus (RRV) is the most medically significant mosquito-borne virus of Australia, in terms of human morbidity. RRV cases, characterised by febrile illness and potentially persistent arthralgia, have been reported from all Australian states and territories. RRV was the cause of a large-scale epidemic of multiple Pacific Island countries and territories (PICTs) from 1979 to 1980, involving at least 50,000 cases. Historical evidence of RRV seropositivity beyond Australia, in populations of Papua New Guinea (PNG), Indonesia and the Solomon Islands, has been documented. We describe the genomic characterisation and timescale analysis of the first isolate of RRV to be sampled from PNG to date. Our analysis indicates that RRV has evolved locally within PNG, independent of Australian lineages, over an approximate 40 year period. The mean time to most recent common ancestor (tMRCA) of the unique PNG clade coincides with the initiation of the PICTs epidemic in mid-1979. This may indicate that an ancestral variant of the PNG clade was seeded into the region during the epidemic, a period of high RRV transmission. Further epidemiological and molecular-based surveillance is required in PNG to better understand the molecular epidemiology of RRV in the general Australasian region.


Assuntos
Culicidae/virologia , Evolução Molecular , Genoma Viral , Vírus do Rio Ross/genética , Análise de Sequência , Infecções por Alphavirus/virologia , Animais , Humanos , Papua Nova Guiné , Filogenia , Vírus do Rio Ross/classificação , Vírus do Rio Ross/isolamento & purificação
18.
Viruses ; 13(5)2021 04 23.
Artigo em Inglês | MEDLINE | ID: mdl-33922604

RESUMO

Swine enteric viral infections are responsible for substantial economic losses in the pork industry worldwide. Porcine epidemic diarrhea (PEDV) is one of the main causative agents of diarrhea in lactating pigs, and reports of PEDV coinfection with other enteric viruses highlight the importance of viral interactions for disease presentation and outcomes. Using next-generation sequencing (NGS) and sequence analyses from samples taken from piglets with acute diarrhea, we explored the possible interactions between PEDV and other less reported pathogens. PEDV coinfection with porcine kobuvirus (PKV) was detected in 36.4% (27/74) of samples. Full genomes from porcine coronavirus and kobuvirus were obtained, as was a partial porcine sapovirus genome (PSaV). The phylogenetic results show the clustering of these strains corresponding to the geographical relationship. To our knowledge, this is the first full genome and isolation report for porcine kobuvirus in México, as well as the first phylogenetic analysis for porcine sapovirus in the country. The NGS approach provides a better perspective of circulating viruses and other pathogens in affected production units.


Assuntos
Coinfecção/virologia , Infecções por Coronavirus/virologia , Kobuvirus/genética , Kobuvirus/isolamento & purificação , Vírus da Diarreia Epidêmica Suína/genética , Vírus da Diarreia Epidêmica Suína/isolamento & purificação , Animais , Coinfecção/epidemiologia , Infecções por Coronavirus/epidemiologia , Diarreia/virologia , Fezes/virologia , Genoma Viral , Kobuvirus/classificação , México/epidemiologia , Técnicas de Diagnóstico Molecular , Filogenia , Vírus da Diarreia Epidêmica Suína/classificação , Sapovirus/genética , Análise de Sequência , Suínos , Doenças dos Suínos/virologia
19.
Viruses ; 13(5)2021 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-33925388

RESUMO

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the ongoing global COVID-19 pandemic that began in late December 2019. The rapid spread of SARS-CoV-2 is primarily due to person-to-person transmission. To understand the epidemiological traits of SARS-CoV-2 transmission, we conducted phylogenetic analysis on genome sequences from >54K SARS-CoV-2 cases obtained from two public databases. Hierarchical clustering analysis on geographic patterns in the resulting phylogenetic trees revealed a co-expansion tendency of the virus among neighboring countries with diverse sources and transmission routes for SARS-CoV-2. Pairwise sequence similarity analysis demonstrated that SARS-CoV-2 is transmitted locally and evolves during transmission. However, no significant differences were seen among SARS-CoV-2 genomes grouped by host age or sex. Here, our identified epidemiological traits provide information to better prevent transmission of SARS-CoV-2 and to facilitate the development of effective vaccines and therapeutics against the virus.


Assuntos
COVID-19/epidemiologia , COVID-19/virologia , SARS-CoV-2/classificação , Sequência de Bases , COVID-19/transmissão , Bases de Dados de Ácidos Nucleicos , Genoma Viral , Humanos , Pandemias , Filogenia , SARS-CoV-2/genética , SARS-CoV-2/isolamento & purificação , Análise de Sequência
20.
Mol Biol Rep ; 48(4): 3629-3635, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33893925

RESUMO

PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.


Assuntos
Reação em Cadeia da Polimerase/métodos , Polimorfismo Conformacional de Fita Simples , Animais , Coronavirus/classificação , Coronavirus/genética , Coronavirus/isolamento & purificação , Humanos , Tipagem Molecular/métodos , Patologia Molecular/métodos , Polimorfismo de Fragmento de Restrição , Análise de Sequência/métodos
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