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1.
Data Brief ; 47: 109005, 2023 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36915641

RESUMO

Salmonella enterica serovar Rissen is an emerging and important Salmonella serovar prevalent in live animals and foods from retail markets worldwide. Here, we describe the whole-genome sequence of Salmonella enterica Serovar Rissen Sequence Type 8877 isolated from a cracked table egg in Sudan. The whole-genome sequencing was obtained using Illumina Miseq platform. The quality of the sequenced read, the De novo assembly, and the sequencing typing was conducted by JEKESA pipeline (https://github.com/stanikae/jekesa). The assembled genome was also uploaded to the Center for Genomic Epidemiology web server to determine acquired antibiotic resistance genes, predict the serovar, and the antigenic profile. The genome of Salmonella enterica serovar Rissen 1-M1 was found to harbor 4,689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by NCBI Prokaryotic Genome Annotation Pipeline. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession JAPSFB000000000.

2.
PLoS Comput Biol ; 17(10): e1009462, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34673773

RESUMO

The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computational tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on specific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the development of bioinformatics in the country.


Assuntos
Biologia Computacional , Universidades/organização & administração , Biologia Computacional/educação , Biologia Computacional/organização & administração , Países em Desenvolvimento , Humanos , Sudão
3.
Infect Dis (Auckl) ; 13: 1178633720930711, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32595278

RESUMO

Recently, Coronavirus has been given considerable attention from the biomedical community based on the emergence and isolation of a deadly coronavirus infecting human. To understand the behavior of the newly emerging MERS-CoV requires knowledge at different levels (epidemiologic, antigenic, and pathogenic), and this knowledge can be generated from the most related viruses. In this study, we aimed to compare between 3 species of Coronavirus, namely Middle East Respiratory Syndrome (MERS-CoV), Severe Acute Respiratory Syndrome (SARS-CoV), and NeoCoV regarding whole genomes and 6 similar proteins (E, M, N, S, ORF1a, and ORF1ab) using different bioinformatics tools to provide a better understanding of the relationship between the 3 viruses at the nucleotide and amino acids levels. All sequences have been retrieved from National Center for Biotechnology Information (NCBI). Regards to target genomes' phylogenetic analysis showed that MERS and SARS-CoVs were closer to each other compared with NeoCoV, and the last has the longest relative time. We found that all phylogenetic methods in addition to all parameters (physical and chemical properties of amino acids such as the number of amino acid, molecular weight, atomic composition, theoretical pI, and structural formula) indicated that NeoCoV proteins were the most related to MERS-CoV one. All phylogenetic trees (by both maximum-likelihood and neighbor-joining methods) indicated that NeoCoV proteins have less evolutionary changes except for ORF1a by just maximum-likelihood method. Our results indicated high similarity between viral structural proteins which are responsible for viral infectivity; therefore, we expect that NeoCoV sooner may appear in human-related infection.

4.
Int J Infect Dis ; 97: 126-130, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32497807

RESUMO

OBJECTIVE: The aim of this study was to determine the OBI in plasma and urine samples from renal transplant patients using Multiplex Nested PCR. METHOD: A total of 100 samples (plasma and urine) were collected from renal transplant patients admitted to the renal transplant center in Khartoum north, Sudan in 2019. For each sample, HBsAg, HBeAg and anti HBcAg were detected using Enzyme linked Immune sorbent assay (ELISA). The viral DNA was then extracted using viral DNA extraction kit and were then tested for HBV DNA by using multiplex nested PCR. Statistical analysis was done using statistical package of social science (IBM SPSS version 20.0) considering a P value ≤ 0.05 as a level of significance. RESULTS: HBsAg were not detected in al patient but, HBeAg were 14 (14%) and anti HBcAg were 36 (36%)were detect by using ELISA. A total 18 (18%) and 3 out of 100 were found positive in plasma and urine samples, respectively. Regarding the virus genotypes, D, E and mixed D/E genotypes were detected in all positive samples. Females were significantly (P value=0.013) higher detectable with HBV than males in plasma samples CONCLUSION: OBI incidence in renal transplant patients is high in Sudan. The multiplex nested PCR had identified OBI with a high rate supporting the efficiency of using molecular techniques in detecting of HBV. This will lead to an appropriate diagnosis and minimizing the risk to be infected by HBV.


Assuntos
Vírus da Hepatite B/isolamento & purificação , Hepatite B/virologia , Transplante de Rim , Adulto , Estudos Transversais , DNA Viral/sangue , Feminino , Genótipo , Hepatite B/sangue , Hepatite B/urina , Antígenos do Núcleo do Vírus da Hepatite B/imunologia , Antígenos de Superfície da Hepatite B/sangue , Antígenos E da Hepatite B/imunologia , Vírus da Hepatite B/genética , Humanos , Masculino , Pessoa de Meia-Idade , Reação em Cadeia da Polimerase , Sudão
5.
Microbiol Resour Announc ; 9(11)2020 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-32165387

RESUMO

We report here the whole-genome sequence of Escherichia coli NUBRI-E, a representative of E. coli clone O25:H4 sequence type 131 with bla CTX-M-15, which was obtained from a Sudanese patient with a urinary tract infection.

6.
Microbiol Resour Announc ; 8(40)2019 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-31582453

RESUMO

Pseudomonas aeruginosa is a common nosocomial pathogen often associated with a high mortality rate in vulnerable populations. Here, we describe the genomic sequence of a pan-resistant, high-risk clone of P. aeruginosa sequence type 111 (ST111) isolated from a hospital patient in Sudan.

7.
Biomark Cancer ; 11: 1179299X19861957, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31555051

RESUMO

AIM: Verrucous carcinoma (VC) is a low-grade rare variant of squamous cell carcinoma (SCC). Syndecan-1 (CD138) is a heparan sulfate proteoglycan which participates in cell-to-cell adhesion and cell-matrix interaction. Being misled by the apparent non-aggressive nature of VC, some clinicians and pathologists believe that this tumor is not an aggressive tumor, not realizing the fact that some of these lesions may contain nests or foci of well-differentiated SCC. This study aimed to assess syndecan-1 expression of VC and detection of micro-invasion in VC using syndecan-1 immunohistochemical (IHC) stain. METHODS: Observational analytical study of 34 paraffin block of VC cases and 24 cases of variable grades of oral epithelial dysplasia. Cases were stained by hematoxylin and eosin (H&E) and then IHC stain for syndecan-1 was applied. Nine paraffin blocks from specimens of normal oral mucosa were used as the reference group for syndecan-1 stain positivity. RESULTS: In this study, we found that 32 (94.1%) out of 34 of verrucous carcinoma cases showed loss of syndecan-1 expression. Moreover, highly statistically significant association was found between the presence of suggestive micro-invasion in H&E and loss of syndecan-1 expression in micro-invasive area in the same case. CONCLUSIONS: In conclusion, syndecan-1 stain can be used as a biomarker in detection of micro-invasion in verrucous carcinoma.

8.
Microbiol Resour Announc ; 8(32)2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31395632

RESUMO

Acinetobacter baumannii has emerged as an important pathogen leading to multiple nosocomial outbreaks. Here, we describe the genomic sequence of a multidrug-resistant Acinetobacter baumannii sequence type 164 (ST164) isolate from a hospital patient in Sudan. To our knowledge, this is the first reported draft genome of an A. baumannii strain isolated from Sudan.

9.
Microbiol Resour Announc ; 8(32)2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31395633

RESUMO

Klebsiella pneumoniae is an opportunistic pathogen that accounts for a significant proportion of hospital-acquired infections and is a leading cause of nosocomial outbreaks. Here, we describe the genomic sequence of a highly resistant K. pneumoniae sequence type 14 (ST14) strain isolated from Sudan.

10.
Evol Bioinform Online ; 15: 1176934319864945, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31360059

RESUMO

Whole genome sequencing of methicillin-resistant Staphylococcus aureus (MRSA) strain isolated from Sudan has led to a great deal of information, which allows the identification and characterization of some pivotal proteins. The objective of this study was to investigate the penicillin-binding proteins, PBP and PBP2a, of SO-1977 strain to have insights about their physicochemical properties and to assess and describe the interaction of some phytochemicals against them in silico. PBP and PBP2a from MRSA's Sudan strain were found to be of great resemblance with some other strains. G246E single-nucleotide polymorphism was reported and identified in the allosteric binding site positioned in the non-penicillin-binding domain. The docked compounds demonstrated good binding energies and hydrogen bond interactions with residue Ser404 which plays crucial roles in ß-lactam activity. This finding would contribute significantly to designing effective ß-lactam drugs, to combat and treat ß-lactam-resistant bacteria in the future.

11.
Bioinformation ; 15(3): 160-164, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31354190

RESUMO

This study aims to describe the global detection and functional inference of hypothetical protein CA803_03125 from Staphylococcus aureus SO-1977. Computational methods were utilized to study this protein based on sequence similarity and presence of known protein domains. The BLASTp result revealed a significant similarity between the hypothetical protein (CA803_03125) and ADP-ribose hydrolase protein from four S. aureus strains (MW2, MRSA252, COL, and N315). Evolutionary tree diagram revealed a close relationship between the hypothetical protein and proteins of MW2 and COL strains. The physicochemical characterization revealed that all proteins were found to be stable, soluble, hydrophilic and acidic in their nature. The Macro domain was found to exist within all proteins. Moreover, the proteins were of pronounced similarity in terms of primary, secondary and tertiary organization. The protein CA803_03125 (SO-1977) is already known and well characterized as ADP-ribose hydrolase; therefore, we would recommend that its NCBI data has to be updated to be submitted under the name of ADP-ribose hydrolase.

12.
BMC Microbiol ; 19(1): 126, 2019 06 11.
Artigo em Inglês | MEDLINE | ID: mdl-31185900

RESUMO

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA's virulence and resistance mechanisms is a continuing concern toward controlling such burdens through using high throughput whole Genome Sequencing (WGS) and molecular diagnostic assays. The objective of the present study is to perform whole-genome sequencing of MRSA isolated from Sudan using Illumina Next Generation Sequencing (NGS) platform. RESULTS: The genome of MRSA strain SO-1977 consists of 2,827,644 bp with 32.8% G + C, 59 RNAs and 2629 predicted coding sequences (CDSs). The genome has 26 systems, one of which is the major class in the disease virulence and defence. A total of 83 genes were annotated to virulence disease and defence category some of these genes coding as functional proteins. Based on genome analysis, it is speculated that the SO-1977 strain has resistant genes to Teicoplanin, Fluoroquinolones, Quinolone, Cephamycins, Tetracycline, Acriflavin and Carbapenems. The results revealed that the SO-1977, strain isolated from Sudan has a wide range of antibiotic resistance compared to related strains. CONCLUSION: The study reports for the first time the whole genome sequence of Sudan MRSA isolates. The release of the genome sequence of the strain SO-1977 will avail MRSA in public databases for further investigations on the evolution of resistant mechanism and dissemination of the -resistant genes of MRSA.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Staphylococcus aureus Resistente à Meticilina/genética , Infecções Estafilocócicas/microbiologia , Sequenciamento Completo do Genoma/métodos , Antibacterianos , Composição de Bases , Farmacorresistência Bacteriana , Tamanho do Genoma , Genoma Bacteriano , Humanos , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Testes de Sensibilidade Microbiana , Anotação de Sequência Molecular , Sudão , Fatores de Virulência/genética
13.
Parasitol Res ; 117(4): 1271-1276, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29516215

RESUMO

Tropical theileriosis is a serious animal disease transmitted by tick vectors. The agents of theileriosis are obligate intracellular parasites that cause mild to severe disease in the mammalian host. Tropical theileriosis has been recognized as a burden to the development of the dairy industry in Sudan and causes major economic losses. However, knowledge about the distribution of Theileria spp. in Sudan and the extent of sequence variation within the 18S rRNA gene is currently unknown. The aim of this study was to determine the diversity of Theileria spp. using 18S rRNA-based PCR to detect parasites in cattle followed by cloning and sequencing. We observed an overall prevalence rate of 63% hemoparasite infection in cattle from Sennar state. A subset of samples was used for cloning and sequencing of the 18S rRNA gene. Nineteen of 44 animals were co-infected with more than one species of Theilera. Phylogenetic analysis revealed three Theileria spp. that were predominant in cattle including pathogenic T. annulata and apathogenic T. velifera and T. mutans. The present study provides information regarding the prevalence of theileriosis in Sudan and will help to design strategies to control it. Additionally, more study is needed to determine tick vector competence and degree of coinfection with multiple Theileria spp. in Sudan. This represents the first molecular phylogeny report to identify Theileria spp. in cattle from Sudan.


Assuntos
Doenças dos Bovinos/epidemiologia , Bovinos/parasitologia , Theileria/classificação , Theileria/genética , Theileriose/epidemiologia , Doenças Transmitidas por Carrapatos/epidemiologia , Animais , Doenças dos Bovinos/parasitologia , Variação Genética , Filogenia , RNA Ribossômico 18S/genética , Sudão/epidemiologia , Theileria/isolamento & purificação , Theileriose/parasitologia , Doenças Transmitidas por Carrapatos/parasitologia
14.
Genome Announc ; 5(42)2017 Oct 19.
Artigo em Inglês | MEDLINE | ID: mdl-29051236

RESUMO

Methicillin-resistant Staphylococcus aureus is increasingly becoming resistant to most antibiotics and consequently has become a challenging public health problem in Sudan. The present study documented the first complete genome sequence of strain SO-1977, isolated from a contaminated wound in Sudan.

15.
Adv Bioinformatics ; 2016: 2632917, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27478437

RESUMO

This study was carried out for Homo sapiens single variation (SNPs/Indels) in BRAF gene through coding/non-coding regions. Variants data was obtained from database of SNP even last update of November, 2015. Many bioinformatics tools were used to identify functional SNPs and indels in proteins functions, structures and expressions. Results shown, for coding polymorphisms, 111 SNPs predicted as highly damaging and six other were less. For UTRs, showed five SNPs and one indel were altered in micro RNAs binding sites (3' UTR), furthermore nil SNP or indel have functional altered in transcription factor binding sites (5' UTR). In addition for 5'/3' splice sites, analysis showed that one SNP within 5' splice site and one Indel in 3' splice site showed potential alteration of splicing. In conclude these previous functional identified SNPs and indels could lead to gene alteration, which may be directly or indirectly contribute to the occurrence of many diseases.

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