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Fulltext Genome analysis of streptococcus gordonii sk12

Khairuldin AM, Ibrahim IK, Wakiyuddin SB, Z, Wenning, AO, Lesley, SJ, Nicholas, et al.

Ann Dent, 2014;21(2):17-26.
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The gram-positive, mesophilic and non-motile coccus Streptococcus gordonii is an important causative agent of infective endocarditis (IE). This pioneer species of dental plaque also causes bacteraemia in immune-supressed patients. In this study, we analysed the genome of a representative strain, Streptococcus gordonii SK12 that was originally isolated from the oral cavity. To gain a better understanding of the biology, virulence and phylogeny, of this potentially pathogenic organism, high-throughput Illumina HiSeq technology and different bioinformatics approaches were performed. Genome assembly of SK12 was performed using CLC Genomic Workbench 5.1.5 while RAST annotation revealed the key genomic features. The assembled draft genome of Streptococcus gordonii SK12 consists of 27 contigs, with a genome size of 2,145,851 bp and a G+C content of 40.63%. Phylogenetic inferences have confirmed that SK12 is closely related to the widely studied strain Streptococcus gordonii Challis. Interestingly, we predicted 118 potential virulence genes in SK12 genome which may contribute to bacterial pathogenicity in infective endocarditis. We also discovered an intact prophage which might be recently integrated into the SK12 genome. Examination of genes present in genomic islands revealed that this oral strain
might has potential to acquire new phenotypes/traits including strong defence system, bacitracin
resistance and collateral detergent sensitivity. This detailed analysis of S. gordonii SK12 further improves our understanding of the genetic make-up of S. gordonii as a whole and may help to elucidate how this species is able to transition between living as an oral commensal and potentially causing the lifethreatening condition infective endocarditis.
Fulltext Evaluation of maxillary anterior teeth and their relation to the golden proportion in Malaysian population

Al-Marzok MI, Majeed KR, Ibrahim IK

BMC Oral Health, 2013;13:9.
PMID: 23347800 DOI: 10.1186/1472-6831-13-9

The maxillary anterior teeth are important in achieving pleasing dental aesthetics. Various methods are used to measure the size and form of them, including the golden proportion between their perceived widths, and the width-to-height ratio, referred to as the golden standard. The purpose of this study was conducted to evaluate whether consistent relationships exist between tooth width and height of the clinical crown dimensions; and to investigate the occurrence of the golden proportion of the maxillary anterior teeth.
Polycythaemia Vera among Sudanese Patients with Special Emphasis on JAK2 Mutations

Ibrahim IK, Hassan R, Ali EW, Omer A

Asian Pac J Cancer Prev, 2019 Jan 25;20(1):41-44.
PMID: 30677867

Background: In recent years, a somatic point mutation in the Janus Kinase 2 (JAK2) gene (1849 G→T, V617F)
has been reported to occur in over 90% of patients with polycythemia vera (PV). Another JAK2 mutation in exon 12
had been described and shown capable of activating erythropoietin signaling pathways. Objective: In this study, we
aimed to determine the frequency of Jak2 mutations (JAK2V617F and JAK2 exon 12) as well as their relationships
with hematological parameters in Sudanese patients with myeloproliferative disorders (MPD). A comparison with
findings of published studies from other geographic regions was included. Materials and Methods: From each of
a total of 83 polycythaemia patients, six milliliters (ml) of venous blood were collected and processed for molecular
analysis and measurement of serum erythropoietin level by enzyme-linked immunoassay (ELISA). The JAK2 V617F
mutation was determined using an allele-specific competitive blocker (ACB) -PCR assay and High Resolution Melting
(HRM) analysis was applied for the JAK2 exon 12 mutation. Results: According to patients’ history and the results
for EPO levels, nine (10.7 %) out of 83 patients were found to have secondary polycythaemia and 74 (89.3%) PV. The
overall frequency of the 2 JAK2 mutations was 94.6% in our Sudanese PV patients, JAK2V617F being found in 91%
and JAK2 exon 12 mutations in 8.1%.Conclusion: In summary JAK2 V617F and JAK2 exon 12 mutations are very
common in Sudanese PC cases.
Alpha-hemoglobin-stabilizing protein (AHSP): a modulatory factor in β-thalassemia

Che Yaacob NS, Islam MA, Alsaleh H, Ibrahim IK, Hassan R

Int J Hematol, 2020 Mar;111(3):352-359.
PMID: 31894534 DOI: 10.1007/s12185-019-02806-8

Hemoglobin (Hb) is an iron-containing metalloprotein that transports oxygen molecules from the lungs to the rest of the human body. Among the different variants of Hb, HbA1 is the most common and is composed of two alpha (αHb) and two beta globin chains (βHb) constructing a heterotetrameric protein complex (α2β2). Due to the higher number of AHSP genes, there is a tendency to produce approximately twice as much of α subunit as β subunit. Therefore, there is a chance of presenting excess α subunit leftover in human blood plasma; excess subunits subsequently bind with each other and aggregates β-thalassemia occurs due to lack of or reduced numbers of βHb subunit. Alpha-hemoglobin-stabilizing protein (AHSP) is a scavenger protein which acts as a molecular chaperon by reversibly binding with free αHb forming a complex (AHSP-αHb) that prevents aggregation and precipitation preventing deleterious effects towards developing serious human diseases including β-thalassemia. Clinical severity worsens if mutations in AHSP gene co-occur in patients with β-thalassemia. Considering the mechanism of action of AHSP and its contribution to ameliorating β-thalassemia severity, it could potentially be used as a modulatory agent in the treatment of β-thalassemia.
Fulltext Interleukin-10 (1082G/A) Polymorphism is Associated with Susceptibility of Acute Myeloid Leukemia Patients in Sudanese Population

Sharif OM, Hassan R, Mohammed Basbaeen AA, Mohmed AH, Ibrahim IK

Asian Pac J Cancer Prev, 2019 07 01;20(7):1939-1943.
PMID: 31350948 DOI: 10.31557/APJCP.2019.20.7.1939

Background: Interleukin-10 (IL-10) is a multifunctional cytokine with both immunosuppressive and antiangiogenicfunctions
and may have both tumor-promoting and -inhibiting properties. We examined the association
between a single nucleotide polymorphism (SNP) in IL-10 -1082G/A (rs1800896) in Sudanese acute myeloid leukemia
(AML) patients and to assess the association between polymorphisms in IL-10 -1082G/A (rs1800896) and the
hematological profile in Sudanese patients with AML. Methods: A total of 30 patients with acute myeloid leukemia
and 30 control subjects were enrolled in this study. Blood samples were collected from all patients in EDTA containing
tubes. Genomic DNA was extracted from all blood samples using salting out method. The genotypic variants of
IL-10 (-1082G/A) polymorphism were detected by allele specific-PCR. Results: We found that (36.7%) of patients have
homogenous GG genotype, (43.3%) have heterogeneous GA genotype and (20.0%) have AA genotype. GA genotype
was significantly associated with higher risk of AML compared with the homozygous Genotypes (GG and AA), there is
no association between IL-10 (-1082G/A) polymorphism and AML sub-type, gender, age group, mean of hematological
parameters. Conclusion: Our study concluded that GA genotype of IL-10 -1082G/A (rs1800896) polymorphism is a
risk factor for AML and G allele is insignificantly higher than A allele in AML patient. No association between IL-10
(-1082G/A) polymorphism and AML sub-type, gender, age group, mean of hematological parameters.
TP53 Gene 72 Arg/Pro (rs1042522) Single Nucleotide Polymorphism Contribute to Increase the Risk of B-Chronic Lymphocytic Leukemia in the Sudanese Population

Mohammed Basabaeen AA, Abdelgader EA, Babekir EA, Abdelrahim SO, Eltayeb NH, Altayeb OA, et al.

Asian Pac J Cancer Prev, 2019 May 25;20(5):1579-1585.
PMID: 31128065

Objective: This study aimed at exploring the association of TP53 72Arg/Pro polymorphism and Risk of Chronic
Lymphocytic Leukemia and to assess the correlation between TP53 72Arg/Pro polymorphism and clinical parameter,
hematological profile and some biological prognostic markers among Sudanese patients with chronic lymphocytic
leukemia. Methods: A case-control study was conducted in Khartoum state, Sudan, during the period from April 2017 to
April 2018, involved 110 B-CLL patients and 80 healthy volunteers as a control group. Physical examination, Complete
Blood Count and Immunophenotype were performed in all patients to confirm the diagnosis. Clinical staging such as
Rai and Binet were studied. CD38 and ZAP70 were performed by Flow Cytometry. Blood samples were collected from
all participants; DNA was extracted by using ANALYTIKJENA Blood DNA Extraction Kit (Germany) and analyzed
TP53 codon 72Arg/Pro Polymorphism by using AS-PCR. The statistical analysis was performed using SPSS version
23.0 software (Chicago, IL, USA). Results: the Arg/Pro was the most frequent genotype in B-CLL patients(50%),
followed by Arg/Arg (25.5%) and Pro/Pro (24.5%), whereas in healthy control group Arg/Pro was the most frequent
(47.5%), followed by Arg/Arg (45%) and Pro/Pro (7.5%). Our data indicate a higher frequency of homozygous Pro/
Pro in the B-CLL patients as compared to controls with an OR of 4.01 for the Pro/Pro genotype and lower frequency
of Arg/Arg genotype in CLL patients as compared to controls with an OR of .42 for the Arg/Arg genotype. Also, the
Pro allele showed higher risk than Arg allele (P value=0.000, OR 2.23, 95% CI=1.45-3.41). No significant association
between gender, clinical staging systems (Rai, Binet), biological prognostic markers (CD38 expression or ZAP70
expression), and TP53 codon 72Arg/Pro polymorphisms, except Arg/Arg genotype tended to be associated with younger
age (P =0.04). Conclusion: Our data suggested that Pro/Pro genotype contribute to increased susceptibility to B-Chronic
Lymphocytic Leukemia risk in our population tenfold higher than those had Arg/Arg genotype.
Fulltext Combined analysis of ZAP-70 and CD38 expression in sudanese patients with B-cell chronic lymphocytic leukemia

Basabaeen AA, Abdelgader EA, BaHashwan OS, Babekir EA, Abdelateif NM, Bamusa SA, et al.

BMC Res Notes, 2019 May 23;12(1):282.
PMID: 31122288 DOI: 10.1186/s13104-019-4319-8

OBJECTIVE: To investigate the ZAP-70 and CD38 expressions and their combined expressions in Sudanese B-CLL patients and their relationships with clinical and hematological characteristics as well as the disease staging at presentation.
RESULTS: In the present cross-sectional descriptive study, analysis of ZAP-70 expression showed that 36/110 (32.7%) patients positively expressed ZAP-70 and insignificant higher presentation in intermediate and at advanced stages as well as no correlation was seen with hematological parameters and clinical features compared with negatively ZAP-70, on the other hand, 41/110 (37.3%) were CD38+ and no significant correlation was shown with the stage at presentation, clinical characteristics (except Splenomegaly, P = 0.02) and hematological parameters. However, in combined expressions of both ZAP-70 and CD38 together, 20/110 (18.2%) were concordantly ZAP-70+/CD38+, 53/110 (48.2%) concordantly ZAP-70-/CD38- and 37/110 (33.6%) either ZAP-70+ or CD38+, and these three groups showed insignificant correlation with clinical (except Splenomegaly, P = 0.03) and hematological parameters, and the stage at presentation. Our data showed the combined analysis of these two markers, lead to classify our patients into three subgroups (either concordant positive, negative or discordant expressions) with statistically insignificant correlation with clinical presentation (except Splenomegaly), hematological parameters and stage at presentation of B-CLL patients.
Fulltext Molecular epidemiology of malaria parasite amongst patients in a displaced people's camp in Sudan

Eshag HA, Elnzer E, Nahied E, Talib M, Mussa A, Muhajir AEMA, et al.

Trop Med Health, 2020;48:3.
PMID: 32015668 DOI: 10.1186/s41182-020-0192-3

Background: Despite the importance of epidemiological studies in the development of effective control strategies and provision of basic health services for refugees and internally displaced persons (IDPs), data on the prevalence of malaria are limited. Thus, this study was conducted to estimate the molecular prevalence of malaria amongst the displaced population in Ardamata IDP camp in Al-Geneina City, Sudan.
Methods: A cross-sectional study was conducted from July 2018 to December 2018 to estimate malaria prevalence amongst the displaced population in Ardamata IDP camp in Al-Geneina City, Sudan. A total of 380 patients with suspected malaria were recruited. Nested polymerase chain reaction (nPCR) assays were performed to detect the Plasmodium genus and species.
Results: Of 380 patients, 232 (61.1%) were positive for malaria. Plasmodium falciparum was the only prevalent species detected amongst the study population. nPCR analysis revealed that none of the samples had Plasmodium vivax, Plasmodium ovale or Plasmodium malariae. The malaria prevalence rate was higher amongst males (67.1%) than in females (56.8%), and gender was the only risk factor that was significantly associated with malaria infection (p = .042).
Conclusions: Despite control programmes, malaria remains a significant cause of illness amongst a displaced population. The high prevalence of malaria infection in this study indicates that additional health facilities and control strategies should be implemented in displaced camps and the surrounding areas.
Conformation sensitive gel electrophoresis for the detection of calreticulin mutations in BCR-ABL1-negative myeloproliferative neoplasms

Zakaria NA, Rosle NA, Siti Asmaa MJ, Aziee S, Haiyuni MY, Samat NA, et al.

Int J Lab Hematol, 2021 Dec;43(6):1451-1457.
PMID: 34125992 DOI: 10.1111/ijlh.13628

INTRODUCTION: Calreticulin (CALR) mutations in myeloproliferative neoplasms (MPN) have been reported to be key markers in the molecular diagnosis, particularly in patients lacking JAK2 V617F mutation. In most current reports, CALR mutations were analysed by either allele-specific PCR (AS-PCR), or the more expensive quantitative real-time PCR, pyrosequencing and next-generation sequencing. Hence, we report the use of an alternative method, the conformation sensitive gel electrophoresis (CSGE) for the detection of CALR mutations in BCR-ABL1-negative MPN patients.
METHODS: Forty BCR-ABL1-negative MPN patients' DNA: 19 polycythemia vera (PV), 7 essential thrombocytosis (ET) and 14 primary myelofibrosis (PMF), were screened for CALR mutations by CSGE. PCR primers were designed to amplify sequences spanning between exons 8 and 9 to target the mutation hotspots in CALR. Amplicons displaying abnormal CSGE profiles by electrophoresis were directly sequenced, and results were analysed by BioEdit Sequence Alignment Editor v7.2.6. CSGE results were compared with AS-PCR and confirmed by Sanger sequencing.
RESULTS: CSGE identified 4 types of mutations; 2 PMF patients with either CALR type 1 (c.1099_1150del52) or type 2 (c.1155_1156insTTGTC), 1 ET patient with nucleotide deletion (c.1121delA) and insertion (c.1190insA) and 1 PV patient with p.K368del (c.1102_1104delAAG) and insertion (c.1135insA) inframe mutations. Three patients have an altered KDEL motif at the C-terminal of CALR protein. In comparison, AS-PCR only able to detect two PMF patients with mutations, either type 1 and type 2.
CONCLUSION: CSGE is inexpensive, sensitive and reliable alternative method for the detection of CALR mutations in BCR-ABL1-negative MPN patients.