MyMedR

Displaying all 9 publications

Abstract:

Sort:

Optimization of Salmonella Typhi biofilm assay on polypropylene microtiter plates using response surface methodology

Ganjali Dashti M, Abdeshahian P, Sudesh K, Phua KK

Biofouling, 2016;32(4):477-87.
PMID: 26963754 DOI: 10.1080/08927014.2015.1135328

The objective of this study was to develop an optimized assay for Salmonella Typhi biofilm that mimics the environment of the gallbladder as an experimental model for chronic typhoid fever. Multi-factorial assays are difficult to optimize using traditional one-factor-at-a-time optimization methods. Response surface methodology (RSM) was used to optimize six key variables involved in S. Typhi biofilm formation on cholesterol-coated polypropylene 96-well microtiter plates. The results showed that bile (1.22%), glucose (2%), cholesterol (0.05%) and potassium chloride (0.25%) were critical factors affecting the amount of biofilm produced, but agitation (275 rpm) and sodium chloride (0.5%) had antagonistic effects on each other. Under these optimum conditions the maximum OD reading for biofilm formation was 3.4 (λ600 nm), and the coefficients of variation for intra-plate and inter-plate assays were 3% (n = 20) and 5% (n = 8), respectively. These results showed that RSM is an effective approach for biofilm assay optimization.
Fulltext Repeated batch fermentation biotechnology for the biosynthesis of lipid and gamma-linolenic acid by Cunninghamella bainieri 2A1

Ganjali Dashti M, Abdeshahian P, Wan Yusoff WM, Kalil MS, Abdul Hamid A

Biomed Res Int, 2014;2014:831783.
PMID: 25147817 DOI: 10.1155/2014/831783

The biosynthesis of biomedical products including lipid and gamma-linolenic acid (GLA) by Cunninghamella bainieri 2A1 was studied in repeated batch fermentation. Three key process variables, namely, glucose concentration, ammonium tartrate concentration, and harvesting time, were optimized using response surface methodology. Repeated batch fermentation was carried out by the cultivation of Cunninghamella bainieri 2A1 in nitrogen-limited medium with various nitrogen concentration (1-4 g/L) and glucose concentration (20-40 g/L) at three time intervals (12 h, 24 h, and 48 h). Experimental results showed that the highest lipid concentration of 6.2 g/L and the highest GLA concentration of 0.4 g/L were obtained in optimum conditions, where 20.2 g/L glucose, 2.12 g/L ammonium tartrate, and 48 h harvesting time were utilized. Statistical results showed that the interaction between glucose and ammonium tartrate concentration had highly significant effects on lipid and GLA biosynthesis (P < 0.01). Moreover, harvesting time had a significant interaction effect with glucose and ammonium tartrate concentration on lipid production (P < 0.05).
Fulltext Can the BASNEF Model Help to Develop Self-Administered Healthy Behavior in Iranian Youth?

Shahnazi H, Bee Koon P, Abd Talib R, Lubis SH, Ganjali Dashti M, Khatooni E, et al.

Iran Red Crescent Med J, 2016 Mar;18(3):e23847.
PMID: 27231582 DOI: 10.5812/ircmj.23847

The stage of youth is critical for human development in several ways. On the one hand, it can lead people towards the adoption of a healthy lifestyle during adulthood based on these earlier practices. On the other hand, it can comprise the development of healthy living practices later on in live, an outcome which is often caused by the youth adopting a risky lifestyle early on.
Dietary predictors of overweight and obesity in Iranian adolescents

Bahreini Esfahani N, Ganjali Dashti N, Ganjali Dashti M, Noorv MI, Koon PB, Talib RA, et al.

Iran Red Crescent Med J, 2016 Sep;18(9):e25569.
PMID: 28144452 DOI: 10.5812/ircmj.25569

BACKGROUND: Considering both diet and energy expenditures possess some influence on weight status, research into dietary determinants of obesity is challenging but essential to rational planning of well-organized interventions to avoid obesity.
OBJECTIVES: This study aimed to determine whether dietary factors were predictive of overweight and obesity in adolescents in the Iranian population.
PATIENTS AND METHODS: A total of 840 students, ages 15 - 17, from six schools were enrolled in this cross-sectional study. A diet-patterns approach often has been used to describe the eating patterns in adolescents. Height, weight, and waist circumference anthropometric indices, physical activity, waist hip ratio, and BMI measurements were determined. Daily dietary data and weighed food records were collected in 2010 and 2011. Abdominal obesity was defined according to world health organization guidelines, and the relationship between dietary predictor variables and the measures of adiposity were determined by using linear regression. Usual dietary intakes were assessed in an experimental study of Esfahani students.
RESULTS: In total, 38.5% of girls and 32.2% of boys had a Western dietary pattern as the more prevalent pattern. The diet quality of adolescents with the lowest score on each dietary pattern was compared with those recording the highest scores. Those with the Western dietary pattern score were less likely to exercise and had a higher prevalence of general obesity. Adolescents in the greater quartile of the Mediterranean dietary patterns had the lowest odds of being overweight (OR 0.50, 95%; CI 0.27 - 0.73) and obese (OR 0.48, 95%; CI 0.15 - 0.80) than those in the lower quartile, whereas those in the greater quartile of the Western dietary pattern had the highest odds of being overweight (OR 1.69, 95%; CI 1.10 - 2.04) and obese (OR 1.44, 95% CI 1.05 - 1.84). Higher consumption of a Western dietary pattern and a salty dietary pattern were associated significantly with obesity (P < 0.05). Intake of a Western dietary pattern and a salty-sweet dietary pattern were associated positively with measures of adiposity, namely body mass index and waist circumference.
CONCLUSIONS: This study showed significant associations between the seven dietary patterns and overweight and obesity among adolescents. Using dietary patterns within adolescents can provide important information on dietary consumption, and this approach is clearer and much easier to follow.
KEYWORDS: Adolescent; Dietary Patterns; Food Habits; Obesity; Overweight; Predictors
Fulltext Enhancement of bioplastic polyhydroxybutyrate P(3HB) production from glucose by newly engineered strain Cupriavidus necator NSDG-GG using response surface methodology

Biglari N, Ganjali Dashti M, Abdeshahian P, Orita I, Fukui T, Sudesh K

3 Biotech, 2018 Aug;8(8):330.
PMID: 30073115 DOI: 10.1007/s13205-018-1351-7

This study aimed to enhance production of polyhydroxybutyrate P(3HB) by a newly engineered strain of Cupriavidus necator NSDG-GG by applying response surface methodology (RSM). From initial experiment of one-factor-at-a-time (OFAT), glucose and urea were found to be the most significant substrates as carbon and nitrogen sources, respectively, for the production of P(3HB). OFAT experiment results showed that the maximum biomass, P(3HB) content, and P(3HB) concentration of 8.95 g/L, 76 wt%, and 6.80 g/L were achieved at 25 g/L glucose and 0.54 g/L urea with an agitation rate of 200 rpm at 30 °C after 48 h. In this study, RSM was applied to optimize the three key variables (glucose concentration, urea concentration, and agitation speed) at a time to obtain optimal conditions in a multivariable system. Fermentation experiments were conducted in shaking flask by cultivation of C. necator NSDG-GG using various glucose concentrations (10-50 g/L), urea concentrations (0.27-0.73 g/L), and agitation speeds (150-250 rpm). The interaction between the variables studied was analyzed by ANOVA analysis. The RSM results indicated that the optimum cultivation conditions were 37.70 g/L glucose, 0.73 g/L urea, and 200 rpm agitation speed. The validation experiments under optimum conditions produced the highest biomass of 12.84 g/L, P(3HB) content of 92.16 wt%, and P(3HB) concentration of 11.83 g/L. RSM was found to be an efficient method in enhancing the production of biomass, P(3HB) content, and P(3HB) concentration by 43, 21, and 74%, respectively.
Fulltext LEMABE: a novel framework to improve analogy-based software cost estimation using learnable evolution model

Dashti M, Javdani Gandomani T, Hasanpoor Adeh D, Zulzalil H, Md Sultan AB

PeerJ Comput Sci, 2022;8:e800.
PMID: 35111910 DOI: 10.7717/peerj-cs.800

One of the most important and critical factors in software projects is the proper cost estimation. This activity, which has to be done prior to the beginning of a project in the initial stage, always encounters several challenges and problems. However, due to the high significance and impact of the proper cost estimation, several approaches and methods have been proposed regarding how to perform cost estimation, in which the analogy-based approach is one of the most popular ones. In recent years, many attempts have been made to employ suitable techniques and methods in this approach in order to improve estimation accuracy. However, achieving improved estimation accuracy in these techniques is still an appropriate research topic. To improve software development cost estimation, the current study has investigated the effect of the LEM algorithm on optimization of features weighting and proposed a new method as well. In this research, the effectiveness of this algorithm has been examined on two datasets, Desharnais and Maxwell. Then, MMRE, PRED (0.25), and MdMRE criteria have been used to evaluate and compare the proposed method against other evolutionary algorithms. Employing the proposed method showed considerable improvement in estimating software cost estimation.
Fulltext Association between alleles, haplotypes, and amino acid variations in HLA class II genes and type 1 diabetes in Kuwaiti children

Dashti M, Nizam R, Jacob S, Al-Kandari H, Al Ozairi E, Thanaraj TA, et al.

Front Immunol, 2023;14:1238269.
PMID: 37638053 DOI: 10.3389/fimmu.2023.1238269

Type 1 diabetes (T1D) is a complex autoimmune disorder that is highly prevalent globally. The interactions between genetic and environmental factors may trigger T1D in susceptible individuals. HLA genes play a significant role in T1D pathogenesis, and specific haplotypes are associated with an increased risk of developing the disease. Identifying risk haplotypes can greatly improve the genetic scoring for early diagnosis of T1D in difficult to rank subgroups. This study employed next-generation sequencing to evaluate the association between HLA class II alleles, haplotypes, and amino acids and T1D, by recruiting 95 children with T1D and 150 controls in the Kuwaiti population. Significant associations were identified for alleles at the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci, including DRB1*03:01:01, DQA1*05:01:01, and DQB1*02:01:01, which conferred high risk, and DRB1*11:04:01, DQA1*05:05:01, and DQB1*03:01:01, which were protective. The DRB1*03:01:01~DQA1*05:01:01~DQB1*02:01:01 haplotype was most strongly associated with the risk of developing T1D, while DRB1*11:04-DQA1*05:05-DQB1*03:01 was the only haplotype that rendered protection against T1D. We also identified 66 amino acid positions across the HLA-DRB1, HLA-DQA1, and HLA-DQB1 genes that were significantly associated with T1D, including novel associations. These results validate and extend our knowledge on the associations between HLA genes and T1D in Kuwaiti children. The identified risk alleles, haplotypes, and amino acid variations may influence disease development through effects on HLA structure and function and may allow early intervention via population-based screening efforts.
Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius)

Bahbahani H, Al-Zoubi S, Ali F, Afana A, Dashti M, Al-Ateeqi A, et al.

Mitochondrion, 2023 Mar;69:36-42.
PMID: 36690316 DOI: 10.1016/j.mito.2023.01.004

The two species of the Old World Camelini tribe, dromedary and Bactrian camels, show superior adaptability to the different environmental conditions they populate, e.g. desert, mountains and coastal areas, which might be associated with adaptive variations on their mitochondrial DNA. Here, we investigate signatures of natural selection in the 13-mitochondrial protein-coding genes of different dromedary camel populations from the Arabian Peninsula, Africa and southwest Asia. The full mitogenome sequences of 42 dromedaries, 38 domestic Bactrian, 29 wild Bactrian camels and 31 samples representing the New World Lamini tribe reveal species-wise genetic distinction among Camelidae family species, with no evidence of geographic distinction among dromedary camels. We observe gene-wide signals of adaptive divergence between the Old World and New World camels, with evidence of purifying selection among Old World camel species. Upon comparing the different Camelidae tribes, 27 amino acid substitutions across ten mtDNA protein-coding genes were found to be under positive selection, in which, 24 codons were defined to be under positive adaptive divergence between Old World and New World camels. Seven codons belonging to three genes demonstrated positive selection in dromedary lineage. A total of 89 codons were found to be under positive selection in Camelidae family based on investigating the impact of amino acid replacement on the physiochemical properties of proteins, including equilibrium constant and surrounding hydrophobicity. These mtDNA variants under positive selection in the Camelidae family might be associated with their adaptation to their contrasting environments.
Fulltext Genetic insights into MIS-C Post-COVID-19 in Kuwaiti children: investigating monogenic factors

Dashti M, AlKandari H, Malik MZ, Nizam R, John SE, Jacob S, et al.

Front Cell Infect Microbiol, 2024;14:1444216.
PMID: 39844836 DOI: 10.3389/fcimb.2024.1444216

BACKGROUND: Multisystem inflammatory syndrome in children (MIS-C) is a severe complication arising from SARS-CoV-2 infection, with indications that rare inborn errors of immunity may play a role in its pathogenesis. Recent studies suggest that genetic predispositions, particularly monogenic forms, could significantly influence the immune responses to SARS-CoV-2 in MIS-C.
METHODS: We analysed 24 children under 12 years old, all of whom met the criteria provided by the World Health Organization, 2020 for MIS-C diagnosis, from the Paediatric COVID-19 Registry in Kuwait (PCR-Q8). Demographic and clinical data were collected from medical records, and exome sequencing was performed on the children and their parents to identify rare exonic variants. These variants were prioritized using two approaches: a candidate genes approach employing trio segregation analysis, and a candidate variants approach using a gene panel informed by previous studies on MIS-C-related genetic variants and datasets of differentially expressed genes in MIS-C patients.
RESULTS: The candidate genes approach identified 53 unique genes in 20 of the 24 probands, including DDX60 and TMEM154, which were also differentially expressed between MIS-C and control groups. The candidate variants approach identified 33 rare, predicted deleterious heterozygous variants across 19 unique genes in 19 of the 24 probands, including both previously described and novel candidate variants for MIS-C. Pathway analysis of the identified genes from both approaches revealed significant involvement in immune response, viral defence, and inflammatory pathways.
CONCLUSION: This study underscores the monogenic susceptibility to MIS-C, enhancing the evidence base through comprehensive genetic analysis. The findings highlight the critical role of genetic predispositions in MIS-C and suggest that further functional genomics work is necessary to explore the mechanistic contributions of these genes, facilitating the development of targeted diagnostic strategies.