Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective.

BACKGROUND: The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Moreover, manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. RESULTS: Here, we present an example of a crowd-sourcing effort aimed at curating and annotating TE libraries of two non-model species built around a collaborative, peer-reviewed teaching process. Manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd-sourcing efforts could therefore offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. CONCLUSIONS: The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs in a reasonable time frame. Our crowd-sourcing setting can be used as a teaching reference guide for similar projects: A hidden treasure awaits discovery within non-model organisms.

High-resolution melt curve analysis: An approach for variant detection in the TPO gene of congenital hypothyroid patients in Bangladesh.

TPO (Thyroid Peroxidase) is known to be one of the major genes involved in congenital hypothyroid patients with thyroid dyshormonogenesis. The present study aims to validate high-resolution melting (HRM) curve analysis as a substitute method for Sanger sequencing, focusing on the frequently observed non-synonymous mutations c.1117G>T, c.1193G>C, and c.2173A>C in the TPO gene in patients from Bangladesh. We enrolled 36 confirmed cases of congenital hypothyroid patients with dyshormonogenesis to establish the HRM method. Blood specimens were collected, and DNA was extracted followed by PCR and Sanger sequencing. Among the 36 specimens, 20 were pre-sequenced, and variants were characterized through Sanger sequencing. Following pre-sequencing, the 20 pre-sequenced specimens underwent real-time PCR-HRM curve analysis to determine the proper HRM condition for separating the three variations from the wild-type state into heterozygous and homozygous states. Furthermore, 16 unknown specimens were subjected to HRM analysis to validate the method. This method demonstrated a sensitivity and specificity of 100 percent in accurately discerning wild-type alleles from both homozygous and heterozygous states of c.1117G>T (23/36; 63.8%), c.1193G>C (30/36; 83.3%), and c.2173A>C (23/36; 63.8%) variants frequently encountered among 36 Bangladeshi patients. The HRM data was found to be similar to the sequencing result, thus confirming the validity of the HRM approach for TPO gene variant detection. In conclusion, HRM-based molecular technique targeting variants c.1117G>T, c.1193G>C, and c.2173A>C could be used as a high throughput, rapid, reliable, and cost-effective screening approach for the detection of all common mutations in TPO gene in Bangladeshi patients with dyshormonogenesis.

Real-world evidence on the effectiveness and safety of gliclazide MR 60 mg in Bangladeshi patients with Type II diabetes during fasting: a sub-analysis from the global DIA-RAMADAN study.

Aim: Many Muslims with Type II diabetes (T2DM) fast during Ramadan, which can put them at increased risk of hypoglycemia. This sub-analysis of the global DIA-RAMADAN study assessed the effectiveness and safety of gliclazide modified release (MR) 60 mg in the Bangladeshi cohort. Materials & methods: DIA-RAMADAN was an international, prospective, observational study conducted in adult T2DM patients intending to fast and receiving gliclazide MR 60 mg once daily for ≥90 days before Ramadan. Dosing was switched from morning to evening at the start of Ramadan. The primary outcome was the proportion of patients with ≥1 symptomatic hypoglycemic event. Secondary outcomes included changes between inclusion (V0) and end of study visit (V1) in glycated hemoglobin (HbA1c), body weight and fasting plasma glucose (FPG). Results: Among the 98 Bangladeshi patients, 80 (81.6%) were at moderate/low-risk (category 3) for fasting and 18 (18.4%) were high-risk (category 2), as per International Diabetes Federation and Diabetes and Ramadan International Alliance (IDF-DAR) guidelines. Gliclazide MR was being prescribed as monotherapy to 59 (60.2%) patients and in combination with metformin to 39 (39.8%). There was no incidence of severe hypoglycemic events. Mean (±SD) HbA1c change from V0 was -0.1 ± 0.8% (p = 0.159). Mean (±SD) changes in FPG and body weight were -0.8 ± 39.7 mg/dl (p = 0.876) and -0.0 ± 1.5 kg (p = 0.810), respectively. Conclusion: In a real-world setting, this sub-analysis in Bangladeshi patients shows that patients with T2DM treated with gliclazide MR 60 mg can fast safely during Ramadan with a very low risk of hypoglycemia, while maintaining glycemic control and body weight.

Hypothalamic-Pituitary-Adrenal Axis Activity in SARS-CoV-2 Infected Noncritically Ill Hospitalized Patients.

Objectives: This study determined the baseline hypothalamic-pituitary-adrenal axis hormonal levels and their associated factors in noncritically ill hospitalized patients with coronavirus disease 2019 (COVID-19). Methodology: This cross-sectional study was carried out in 91 noncritical RT-PCR-confirmed COVID-19 patients (aged 18 to 65 years) recruited consecutively from the COVID unit of two tertiary care hospitals over a period of six months. After the screening, relevant history and physical examinations were done, and blood was drawn between 07:00 am to 09:00 am in a fasting state to measure serum cortisol and plasma adrenocorticotropic hormone (ACTH) by chemiluminescent microparticle immunoassay. Results: Of 91 patients, 54, 26, and 11 had mild, moderate, and severe COVID-19, respectively. Median values of serum cortisol (p = 0.057) and plasma ACTH (p = 0.910) were statistically similar among the severity groups. Considering a cortisol cut-off of 276 nmol/L (<10 µg/dL), the highest percent of adrenal insufficiency was present in severe (27.3%), followed by mild (25.9%) and least in the moderate (3.8%) COVID-19 cases. Using the cortisol/ACTH ratio >15, only 6.6% had enough reserve. Conclusions: The adrenocortical response was compromised in a significant percentage of noncritically ill hospitalized patients with COVID-19, with the highest percentage of adrenal insufficiency present in severely infected cases. The HPA axis parameters of serum cortisol, plasma ACTH and cortisol/ACTH were similar across the severity of noncritical patients with COVID-19.

Sex-Specific Total Testosterone and Dehydroepiandrosterone Sulfate Status in Noncritically Ill Hospitalized Patients with Coronavirus Disease 2019: A Cross-Sectional Study.

BACKGROUND: In individuals with coronavirus disease 2019 (COVID-19), male subjects have consistently been linked to poor severity and prognosis. Data on sex hormones in non-critical COVID-19-infected patients are scarce. The aim of this study was to assess the status of total testosterone (TT) and dehydroepiandrosterone sulfate (DHEAS) among noncritical patients with COVID-19 according to sex and their associations with clinical and biochemical features. MATERIALS AND METHODS: This cross-sectional observational study was done in the COVID-19 unit of a University hospital during the period of September 2021 to February 2022 among 91 adults (18-65 years) with reverse transcriptase- polymerase chain reaction confirmed noncritical COVID-19 patients. Blood was drawn by venipuncture before receiving steroids between 07:00 to 09:00 a.m. in a fasting state to measure serum TT and DHEAS by chemiluminescent microparticle immunoassay. Diagnosis and classification of COVID-19 were done according to World Health Organization's interim guidance. Age- and sex-specific laboratory reference values were used to classify the TT and DHEAS status of the patients. RESULTS: Only three males (8.1%) had low TT and the rest had normal TT. On the other hand, 15 (27.8%) of the females had high TT with normal levels in the rest. Similarly, 11 (29.7%) males had low DHEAS. Females had low, normal, and high DHEAS in four (7.4%), 48 (88.9%), and two (3.7%) cases respectively. Males with moderate severity of COVID-19 had significantly lower DHEAS (post hoc P=0.038) than the mild group. Both TT (P=0.008) and DHEAS (P=0.023) significantly correlated with neutrophils/lymphocytes ratio and only DHEAS with platelets/lymphocytes ratio (P=0.044) in males. In females, TT significantly correlated with serum sodium (P=0.034). CONCLUSION: In noncritical COVID-19 patients, substantial gender variations in TT and DHEAS were detected and correlated with severity markers in males.

Serum homocysteine level in newly diagnosed young patients with abnormal glucose tolerance.

Background: Hyperhomocysteinemia is an emerging risk factor causing early-onset cardiovascular events. The objective of the study was to assess serum homocysteine levels in newly diagnosed young persons (age < 30 years) with abnormal glucose tolerance. Methodology: This cross-sectional study included 40 young participants with newly diagnosed abnormal glucose tolerance (including prediabetes and diabetes mellitus) and an equal number of young persons with normal glucose tolerance (normal glucose tolerance vs prediabetes vs. diabetes mellitus-age (years): 25.0 (22.0, 28.0) vs 25.50 (21.50, 27.0) vs 28.0 (25.0, 29.0), median (interquartile range)). Glycemic status was diagnosed by American Diabetes Association, 2021 criteria. After taking clinical information, fasting blood was collected to measure homocysteine by chemiluminescent immunoassay. Results: Homocysteine level was different across the spectrum of glycemic status (normal glucose tolerance vs. prediabetes vs. diabetes mellitus: 15.57 (13.89-20.71) vs 13.19 (11.40-18.11) vs 12.27 (9.97-14.42) µmol/L; median (interquartile range); p = 0.006). Serum homocysteine was significantly elevated in participants with normal glucose tolerance than diabetes mellitus (p = 0.006) but statistically similar in prediabetes in comparison to both normal glucose tolerance and diabetes mellitus (p = NS for both). Homocysteine level was above the normal level in 47.5% of participants with normal glucose tolerance and in 22.5% with abnormal glucose tolerance (p = 0.019). Conclusions: Patients under 30 years with diabetes mellitus had lower homocysteine levels than those with normal glucose tolerance.

Turner Syndrome With Isochromosome Structural Abnormalities: A Case Report.

Turner syndrome (TS) is the most common cause of short stature and delayed puberty in females. Approximately half of the patients have the classic form with a genotype of 45,XO, one-fourth of patients have different mosaic forms, and the remaining one-fourth have structural abnormalities on the X chromosome. Among the structural abnormalities, the most common is isochromosome Xq. Females with structural variants of TS can present with delayed menarche, amenorrhea, and infertility rather than classic manifestations of TS. This study describes two rare variants of TS. One was a structural abnormality on the X chromosome, 46X,iso(Xq), and the other involves a mosaic variety of TS, including isochromosome X in the form of 45,XO/46X,iso(Xq). Both patients presented with short stature and secondary amenorrhea without classic manifestations of TS. In TS with or without mosaicism, the frequency of isochromosomes is reported to be about 15% to 18%. Owing to the absence of classical manifestations of TS, diagnosis may be delayed or missed. Therefore, females of short stature with secondary amenorrhea should be evaluated for rare variants of TS by chromosomal analysis.

A dataset for successful recognition of cucumber diseases.

Plant disease is a common impediment to the productivity of the world's agricultural production, which adversely affects the quality and yield of crops and causes heavy economic losses to farmers. The cucumber is a frequently grown creeping vine plant that has few calories but is high in water and several vital vitamins and minerals. Due to the unfavorable ecological environment and non-biological circumstances, cucumber diseases will adversely harm the quality of cucumber and cause heavy financial loss. Early identification and protection of crop diseases are essential for disease management, crop yield enhancement, cost reduction, and boosting agricultural production. The traditional diagnosis of crop diseases is often time-consuming, laborious, ineffective, and subjective. To cope with this scenario, the development of a machine-based model which can detect cucumber diseases is a demand of time for increasing agricultural production. This article offers a major cucumber dataset to build an effective machine vision-based model which can detect more variety of cucumber diseases. The dataset includes eight different types of classes containing disease-affected and disease-free cucumber images (Anthracnose, Bacterial Wilt, Belly Rot, Downy Mildew, Pythium Fruit Rot, Gummy Stem Blight, Fresh leaves, and Fresh cucumber) which were collected from the 6th to 30th of May 2022 from real fields with the cooperation of an expert from an agricultural institution. The dataset is hosted by the Department of Computer Science and Engineering, Jahangirnagar University, and is freely accessible at https://data.mendeley.com/datasets/y6d3z6f8z9/1.

An extensive dataset for successful recognition of fresh and rotten fruits.

Detection of rotten fruits is very crucial for agricultural productions and fruit processing as well as packaging industries. Usually, the detection of fresh and rotten fruits is done manually which is an ineffective and lengthy process for farmers. For this reason, the development of a new classification model is required which will reduce human effort, cost, and production time in the agriculture industry by recognizing defects in the fruits. This article offers a major dataset to the researchers to develop effective algorithms for recognizing more variety of fruits and overcome the limitations by increasing accuracy as well as decreasing computation time. This dataset contains sixteen types of fruit classes, namely fresh grape, rotten grape, fresh guava, rotten guava, fresh jujube, rotten jujube, fresh pomegranate, rotten pomegranate, fresh strawberry, rotten strawberry, fresh apple, rotten apple, fresh banana, rotten banana, fresh orange, rotten orange. We collected various fresh and rotten fruit images from 16th to 31st March 2022 from different fruit shops and real fields with the help of a domain specialist from an agricultural organization. The dataset is hosted by the Department of Computer Science and Engineering, Jahangirnagar University, and is freely available at https://data.mendeley.com/datasets/bdd69gyhv8/1.

The Current Situation Regarding Long-Acting Insulin Analogues Including Biosimilars Among African, Asian, European, and South American Countries; Findings and Implications for the Future.

Background: Diabetes mellitus rates continue to rise, which coupled with increasing costs of associated complications has appreciably increased global expenditure in recent years. The risk of complications are enhanced by poor glycaemic control including hypoglycaemia. Long-acting insulin analogues were developed to reduce hypoglycaemia and improve adherence. Their considerably higher costs though have impacted their funding and use. Biosimilars can help reduce medicine costs. However, their introduction has been affected by a number of factors. These include the originator company dropping its price as well as promoting patented higher strength 300 IU/ml insulin glargine. There can also be concerns with different devices between the manufacturers. Objective: To assess current utilisation rates for insulins, especially long-acting insulin analogues, and the rationale for patterns seen, across multiple countries to inform strategies to enhance future utilisation of long-acting insulin analogue biosimilars to benefit all key stakeholders. Our approach: Multiple approaches including assessing the utilisation, expenditure and prices of insulins, including biosimilar insulin glargine, across multiple continents and countries. Results: There was considerable variation in the use of long-acting insulin analogues as a percentage of all insulins prescribed and dispensed across countries and continents. This ranged from limited use of long-acting insulin analogues among African countries compared to routine funding and use across Europe in view of their perceived benefits. Increasing use was also seen among Asian countries including Bangladesh and India for similar reasons. However, concerns with costs and value limited their use across Africa, Brazil and Pakistan. There was though limited use of biosimilar insulin glargine 100 IU/ml compared with other recent biosimilars especially among European countries and Korea. This was principally driven by small price differences in reality between the originator and biosimilars coupled with increasing use of the patented 300 IU/ml formulation. A number of activities were identified to enhance future biosimilar use. These included only reimbursing biosimilar long-acting insulin analogues, introducing prescribing targets and increasing competition among manufacturers including stimulating local production. Conclusions: There are concerns with the availability and use of insulin glargine biosimilars despite lower costs. This can be addressed by multiple activities.

Current utilization patterns for long-acting insulin analogues including biosimilars among selected Asian countries and the implications for the future.

INTRODUCTION: Prevalence rates for diabetes mellitus continue to rise, which, coupled with increasing costs of complications, has appreciably increased expenditure in recent years. Poor glycaemic control including hypoglycaemia enhances complication rates and associated morbidity, mortality and costs. Consequently, this needs to be addressed. Whilst the majority of patients with diabetes have type-2 diabetes, a considerable number of patients with diabetes require insulin to help control their diabetes. Long-acting insulin analogues were developed to reduce hypoglycaemia associated with insulin and help improve adherence, which can be a concern. However, their considerably higher costs have impacted on their funding and use, especially in countries with affordability issues. Biosimilars can help reduce the costs of long-acting insulin analogues thereby increasing available choices. However, the availability and use of long-acting insulin analogues can be affected by limited price reductions versus originators and limited demand-side initiatives to encourage their use. Consequently, we wanted to assess current utilisation rates for long-acting insulin analogues, especially biosimilars, and the rationale for patterns seen, across multiple Asian countries ranging from Japan (high-income) to Pakistan (lower-income) to inform future strategies. METHODOLOGY: Multiple approaches including assessing utilization and prices of insulins including biosimilars among six Asian countries and comparing the findings especially with other middle-income countries. RESULTS: Typically, there was increasing use of long-acting insulin analogues among the selected Asian countries. This was especially the case enhanced by biosimilars in Bangladesh, India, and Malaysia reflecting their perceived benefits. However, there was limited use in Pakistan due to issues of affordability similar to a number of African countries. The high use of biosimilars in Bangladesh, India and Malaysia was helped by issues of affordability and local production. The limited use of biosimilars in Japan and Korea reflects limited price reductions and demand-side initiatives similar to a number of European countries. CONCLUSIONS: Increasing use of long-acting insulin analogues across countries is welcomed, adding to the range of insulins available, which increasingly includes biosimilars. A number of activities are needed to enhance the use of long-acting insulin analogue biosimilars in Japan, Korea and Pakistan.

Ongoing efforts to improve the management of patients with diabetes in Bangladesh and the implications.

BACKGROUND: Prevalence rates of patients with diabetes are growing across countries, and Bangladesh is no exception. Associated costs are also increasing, driven by costs associated with the complications of diabetes including hypoglycemia. Long-acting insulin analogues were developed to reduce hypoglycemia as well as improve patient comfort and adherence. However, they have been appreciably more expensive, reducing their affordability and use. Biosimilars offer a way forward. Consequently, there is a need to document current prescribing and dispensing rates for long-acting insulin analogues across Bangladesh, including current prices and differences, as a result of affordability and other issues. METHODS: Mixed method approach including surveying prescribing practices in hospitals coupled with dispensing practices and prices among community pharmacies and drug stores across Bangladesh. This method was adopted since public hospitals only dispense insulins such as soluble insulins free-of-charge until funds run out and all long-acting insulin analogues have to be purchased from community stores. RESULTS: There has been growing prescribing and dispensing of long-acting insulins in Bangladesh in recent years, now accounting for over 80% of all insulins dispensed in a minority of stores. This increase has been helped by growing prescribing and dispensing of biosimilar insulin glargine at lower costs than the originator, with this trend likely to continue with envisaged growth in the number of patients. Consequently, Bangladesh can serve as an exemplar to other low- and middle-income countries struggling to fund long-acting insulin analogues for their patients. CONCLUSIONS: It was encouraging to see continued growth in the prescribing and dispensing of long-acting insulin analogues in Bangladesh via the increasing availability of biosimilars. This is likely to continue benefitting all key stakeholder groups.

Frequency of Hepatitis B, C and HIV Infections among Transfusion-Dependent Beta Thalassemia Patients in Dhaka.

Transfusion transmitted infections have remained a major deterrent to public health, particularly among the patients with transfusion-dependent Beta thalassemia in developing countries. Although proper donor selection through adoption of WHO-advised infection panel has lowered the rate of infections, the multi-transfused patients are not free of risk. In this study, we screened 148 transfusion-dependent Beta thalassemia patients to determine the frequency of Hepatitis C Virus (HCV), Hepatitis B Virus (HBV) and Human Immunodeficiency Virus (HIV) using the ELISA method. Among them, infected cases with HCV, HBV and HIV were 13.51%, 3.37% and 0%, respectively. Moreover, 2% of the patients were found to be co-infected with both HBV and HCV. The percentage of infections in the patients with frequent transfusion interval (≤30 days) was significantly higher (p < 0.0005) than that in the patients with less frequent transfusion intervals (>30 days). Immunochromatography (ICT)-based rapid test kits are usually used to screen and confirm these infections in the blood of the patients. However, ICT-based tests are not sensitive enough to detect the infections. So, a combination of both Nucleic Acid testing (NAT) and serological testing are suggested to significantly reduce the risk of viral infections during blood transfusion.

Bioinformatic and Molecular Analysis of Satellite Repeat Diversity in Vaccinium Genomes.

Bioinformatic and molecular characterization of satellite repeats was performed to understand the impact of their diversification on Vaccinium genome evolution. Satellite repeat diversity was evaluated in four cultivated and wild species, including the diploid species Vaccinium myrtillus and Vaccinium uliginosum, as well as the tetraploid species Vaccinium corymbosum and Vaccinium arctostaphylos. We comparatively characterized six satellite repeat families using in total 76 clones with 180 monomers. We observed that the monomer units of VaccSat1, VaccSat2, VaccSat5, and VaccSat6 showed a higher order repeat (HOR) structure, likely originating from the organization of two adjacent subunits with differing similarity, length and size. Moreover, VaccSat1, VaccSat3, VaccSat6, and VaccSat7 were found to have sequence similarity to parts of transposable elements. We detected satellite-typical tandem organization for VaccSat1 and VaccSat2 in long arrays, while VaccSat5 and VaccSat6 distributed in multiple sites over all chromosomes of tetraploid V. corymbosum, presumably in long arrays. In contrast, very short arrays of VaccSat3 and VaccSat7 are dispersedly distributed over all chromosomes in the same species, likely as internal parts of transposable elements. We provide a comprehensive overview on satellite species specificity in Vaccinium, which are potentially useful as molecular markers to address the taxonomic complexity of the genus, and provide information for genome studies of this genus.

Nationwide carrier detection and molecular characterization of ß-thalassemia and hemoglobin E variants in Bangladeshi population.

BACKGROUND: ß-thalassemia is one of the most common inherited blood disorders in the world and a major deterrent to the public health of Bangladesh. The management of thalassemia patients requires lifelong frequent blood transfusion and the available treatment options are unsatisfactory. A national policy on thalassemia prevention is mandatory in Bangladesh. However, precise and up-to-date information on the frequency of ß-thalassemia carriers are missing due to lack of accurate diagnostic approaches, limited access to information and absence of national screening program. This study aims to determine the nationwide carrier frequency of hemoglobin E (HbE) and ß- thalassemia and mutation spectrum among the carriers using molecular, hematological and biochemical methods. METHODS: The study enrolled a total of 1877 individuals (60.1% male and 39.9% female) aged between 18 and 35 years. Total sample size and its division-wise breakdown were calculated in proportion to national and division-wise population. Venous blood was collected and subjected to CBC analysis and Hb-electrophoresis for each participant. Serum ferritin was measured to detect coexistence of iron deficiency anemia with thalassemia carrier. DNA-based High Resolution Melting (HRM) curve analysis was performed for confirmation of carrier status by mutation detection. RESULTS: Of 11.89% (95% CI, 10.43-13.35) carriers of ß-globin gene mutations, 8.68% (95% CI, 7.41-9.95) had HbE trait (ETT) and 2.24% (95% CI, 1.57-2.91) had beta-thalassemia trait (BTT). Among eight divisions, Rangpur had the highest carrier frequency of 27.1% (ETT-25%, BTT-2.1%), whereas Khulna had the lowest frequency of 4.2% (ETT-4.2% only). Moreover, α- thalassemia, HbD trait, HbE disease, hereditary persistence of HbF were detected in 0.11, 0.16, 0.43 and 0.16% participants, respectively. HRM could identify two individuals with reported pathogenic mutations in both alleles who were erroneously interpreted as carriers by hematological indices. Finally, a total of nine different mutations including a novel mutation (c.151A > G) were detected in the ß-globin gene. CONCLUSIONS: Since carrier frequency for both HbE and ß-thalassemia is alarmingly high in Bangladesh, a nationwide awareness and prevention program should be made mandatory to halt the current deteriorating situations. Mutation-based confirmation is highly recommended for the inconclusive cases with conventional carrier screening methods to avoid any faulty detection of thalassemia carriers.

A Hospital-Based Study of Iodine Nutrition Status of Breastfeeding Mothers in Bangladesh.

Adequacy of iodine nutrition status in breastfeeding mothers is vital in preventing iodine deficiency disorder (IDD) in neonates and children. The aim of the study was to assess urinary iodine status in breastfeeding mothers attending Bangabandhu Sheikh Mujib Medical University (BSMMU) hospital in Bangladesh. In this cross-sectional study carried out from January 2014 to January 2015, urinary iodine (UI; µgm/L) level of 266 mothers (age 26.6 ± 4.7 years (mean ± SD), exclusively breastfeeding: 132 and nonexclusively breastfeeding: 134), recruited on consecutive basis from BSMMU outdoor and indoor, were measured in spot urine following the wet digestion method. Median UI in the participants was 298.6 (interquartile range, IQR 206.6-454.9) µgm/L and only 6.4% lactating mother had low UI (i.e. <100 µgm/L). There was no difference of median UI in relation to exclusive or nonexclusive breast feeding, presence of goiter, parity, and age of breastfed baby (p=ns for all). But median UI was higher in older subjects (≥30 years vs. <30 years: 364.4 (228.4-529.9) vs. 283.7 (205.4-434.0); median (IQR) p=0.040)), with good socioeconomic condition (good vs. average or less: 328.2 (243.8-510.0) vs. 274.4 (200.0-433.3); median (IQR); p=0.020), and in those who are aware regarding the importance of iodine (aware vs. unaware: 316.6 (225.2-506.3) vs. 270.1 (196.0-407.2); median (IQR); p=0.018). The proportion of participants with UI < 100 µgm/L was similar in all the groups. Logistic regressions to predict deficient UI status revealed none of the variables to be an independent predictor. This study indicates that deficient iodine nutrition status in Bangladeshi breastfeeding mothers is not frequent at present.

Age-Specific Cut-off Values of Amino Acids and Acylcarnitines for Diagnosis of Inborn Errors of Metabolism Using Liquid Chromatography Tandem Mass Spectrometry.

Liquid Chromatography tandem mass spectrometry (LC-MS/MS) is used for the diagnosis of more than 30 inborn errors of metabolisms (IEMs). Accurate and reliable diagnosis of IEMs by quantifying amino acids (AAs) and acylcarnitines (ACs) using LC-MS/MS systems depend on the establishment of age-specific cut-offs of the analytes. This study aimed to (1) determine the age-specific cut-off values of AAs and ACs in Bangladesh and (2) validate the LC-MS/MS method for diagnosis of the patients with IEMs. A total of 570 enrolled healthy participants were divided into 3 age groups, namely, (1) newborns (1-7 days), (2) 8 days-7 years, and (3) 8-17 years, to establish the age-specific cut-offs for AAs and ACs. Also, 273 suspected patients with IEMs were enrolled to evaluate the reliability of the established cut-off values. Quantitation of AAs and ACs was performed on an automated LC-MS/MS system using dried blood spot (DBS) cards. Then the specimens of the enrolled clinically suspected patients were analyzed by the established method. Nine patients came out as screening positive for different IEMs, including two borderline positive cases of medium-chain acyl-CoA dehydrogenase deficiency (MCAD). A second-tier test for confirmation of the screening positive cases was conducted by urinary metabolic profiling using gas chromatography- mass spectrometry (GC-MS). Out of 9 cases that came out as screening positive by LC-MS/MS, seven cases were confirmed by urinary GC-MS analysis including 3 cases with phenylketonuria, 1 with citrullinemia type II, 1 with methylmalonic acidemia, 1 with isovaleric acidemia and 1 with carnitine uptake defect. Two borderline positive cases with MCAD were found negative by urinary GC-MS analysis. In conclusion, along with establishment of a validated LC-MS/MS method for quantitation of AAs and ACs from the DBS cards, the study also demonstrates the presence of predominantly available IEMs in Bangladesh.

Impaired acylcarnitine profile in transfusion-dependent beta-thalassemia major patients in Bangladesh.

Patients with beta-thalassemia major (BTM) suffer from fatigue, poor physical fitness, muscle weakness, lethargy, and cardiac complications which are related to an energy crisis. Carnitine and acylcarnitine derivatives play important roles in fatty acid oxidation, and deregulation of carnitine and acylcarnitine metabolism may lead to an energy crisis. The present study aimed to investigate carnitine and acylcarnitine metabolites to gain an insight into the pathophysiology of BTM. Dried blood spots of 45 patients with BTM and 96 age-matched healthy controls were analyzed for free carnitine and 24 acylcarnitines by using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Although medium chain acylcarnitine levels were similar in the patients with BTM and healthy controls, free carnitine, short chain acylcarnitines, long chain acylcarnitines, and total acylcarnitine levels were significantly lower in patients with BTM than in the healthy controls (P < 0.05). Moreover, an impaired fatty acid oxidation rate was observed in the patients with BTM, as manifested by decreased fatty acid oxidation indicator ratios, namely C2/C0 and (C2 + C3)/C0. Furthermore, an increase in the C0/(C16 + C18) ratio indicated reduced carnitine palmitoyltransferase-1 (CPT-1) activity in the patients with BTM compared with that in the healthy controls. Thus, a low level of free carnitine and acylcarnitines together with impaired CPT-1 activity contribute to energy crisis-related complications in the patients with BTM.

High resolution melting curve analysis targeting the HBB gene mutational hot-spot offers a reliable screening approach for all common as well as most of the rare beta-globin gene mutations in Bangladesh.

BACKGROUND: Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c.1 - c.92), intron-1 (c.92 + 1 - c.92 + 130) and a portion of exon-2 (c.93 - c.217) of the HBB gene which harbors more than 95% of mutant alleles responsible for beta-thalassemia in Bangladesh. RESULTS: Our HRM approach could successfully differentiate ten beta-globin gene mutations, namely c.79G > A, c.92 + 5G > C, c.126_129delCTTT, c.27_28insG, c.46delT, c.47G > A, c.92G > C, c.92 + 130G > C, c.126delC and c.135delC in heterozygous states from the wild type alleles, implying the significance of the approach for carrier screening as the first three of these mutations account for ~85% of total mutant alleles in Bangladesh. Moreover, different combinations of compound heterozygous mutations were found to generate melt curves that were distinct from the wild type alleles and from one another. Based on the findings, sixteen reference samples were run in parallel to 41 unknown specimens to perform direct genotyping of the beta-thalassemia specimens using HRM. The HRM-based genotyping of the unknown specimens showed 100% consistency with the sequencing result. CONCLUSIONS: Targeting the mutational hot-spot, the HRM approach could be successfully applied for screening of beta-thalassemia carriers in Bangladesh as well as in other countries of South Asia and Southeast Asia. The approach could be a useful supplement of hematological and electrophortic indices in order to avoid false positive and false negative results.