Computational insights into diverse aspects of glutathione S-transferase gene family in Papaver somniferum

Plant glutathione S-transferases are an ancient protein superfamily having antioxidant activity. These proteins are primarily involved in diverse plant functions such as plant growth and development, secondary metabolism, signaling pathways and defense against biotic and abiotic stresses. The current study aimed to comprehensively identify and characterize the GST gene family in the medicinally important crop Papaver somniferum. A total of 93 GST proteins were identified belonging to eight GST classes and found to be majorly localized in the cytoplasm. All GST genes were found on eleven opium chromosomes. Gene duplication analysis showed segmental duplication as a key factor for opium GST gene family expansion under strong purifying selection. Phylogenetic analysis with gymnosperm, angiosperm and bryophyte revealed the evolution of GSTs earlier than their division into separate groups and also prior to the divergence of monocot and dicot. The secondary structure prediction showed the dominance of α-helices indicative of PsomGSTs as structurally stable and elastic proteins. Gene architecture showed the conservation of number of exons across the classes. MEME analysis revealed only a few class specific and many across class conserved motifs. Ser was found to be the active site residue of tau, phi, theta and zeta class and Cys was catalytic residue of DHAR, lambda and GHR class. Promoter analyses identified many cis-acting regulatory elements related to hormonal, cellular, stress and light response functions. Ser was the key phosphorylation site. Only three glycosylation sites were found across the 93 PsomGSTs. 3D structure prediction was also performed and was validated. Interactome analyses revealed the correlation of PsomGSTs with glutathione metabolizing proteins. Gene enrichment analysis and KEGG pathway analyzed the involvement of PsomGSTs in three major pathways i.e. glutathione metabolism, tyrosine metabolism and ascorbate metabolism. The outcome revealed high model quality of PsomGSTs. The results of the current study will be of potential significance to understand the functional and structural importance of the GST gene family in opium, a medicinally important crop.

Genome-wide identification and characterization of glutathione S-transferase gene family in Musa acuminata L. AAA group and gaining an insight to their role in banana fruit development

Glutathione S-transferases are a multifunctional protein superfamily that is involved in diverse plant functions such as defense mechanisms, signaling, stress response, secondary metabolism, and plant growth and development. Although the banana whole-genome sequence is available, the distribution of GST genes on banana chromosomes, their subcellular localization, gene structure, their evolutionary relation with each other, conserved motifs, and their roles in banana are still unknown. A total of 62 full-length GST genes with the canonical thioredoxin fold have been identified belonging to nine GST classes, namely tau, phi, theta, zeta, lambda, DHAR, EF1G, GHR, and TCHQD. The 62 GST genes were distributed into 11 banana chromosomes. All the MaGSTs were majorly localized in the cytoplasm. Gene architecture showed the conservation of exon numbers in individual GST classes. Multiple Em for Motif Elicitation analyses revealed few class-specific motifs and many motifs were found in all the GST classes. Multiple sequence alignment of banana GST amino acid sequences with rice, Arabidopsis, and soybean sequences revealed the Ser and Cys as conserved catalytic residues. Gene duplication analyses showed the tandem duplication as a driving force for GST gene family expansion in banana. Cis-regulatory element analysis showed the dominance of light-responsive element followed by stress- and hormone-responsive elements. Expression profiling analyses were also done by RNA-seq data. It was observed that MaGSTs are involved in various stages of fruit development. MaGSTU1 was highly upregulated. The comprehensive and organized studies of MaGST gene family provide groundwork for further functional analysis of MaGST genes in banana at molecular level and further for plant breeding approaches.

Tuberculosis of Cystic Lymph Node of Lund-A Rare Presentation

Tuberculosis is one of the major infectious diseases in Bangladesh. After respiratory system, lymphatic and gastrointestinal tracts are the commonest sites of development of this pathology. However, hepatobiliary tuberculosis is rare, seen in approximately 1% of all abdominal cases. Reporting of tuberculosis of the cystic duct lymph node is very uncommon. Its diagnosis is difficult because of the absence of characteristic symptoms and signs. In this case report, we present a case of tuberculosis of cystic duct lymph node. Journal of Surgical Sciences (2013) Vol. 17 (1) : 62-63

Association between Serum Apolipoprotein-B and Acute Ischaemic Stroke

Stroke is one of the leading causes of death and disability in developed as well as developing countries like Bangladesh. There is a crucial need to identify additional risk factors that are easily measurable and treatable in general population. Role of serum lipids, lipoproteins and lipoprotein related variables in the prediction of stroke is less clear. Abnormalities in plasma lipoproteins are the most firmly established and best understood risk factors for atherosclerosis and they are probable risk factors for ischaemic stroke, largely by their link to atherosclerosis. High serum apolipoprotein-B (Apo-B) levels may predict an increased risk for ischaemic stroke. Aim of the study was to evaluate the association between serum Apo-B level and acute ischaemic stroke and to measure and compare serum Apo-B level in ischaemic stroke and normal subjects. A cross-sectional comparative study was carried out in the department of Neurology, Mymensingh Medical College Hospital, Mymensingh, Bangladesh from July 2013 to June 2015. A total number of 100 subjects within 18-70 years were considered for the study. Fifty (50) subjects with stroke (both clinically as well as CT scan of head or MRI of brain proven) were taken as the cases and 50 age and sex matched nearly healthy individuals without stroke were taken as the controls by using non-probability sampling procedure. Total cholesterol, HDL cholesterol and triglycerides were estimated by enzymatic method using Semiautoanalyser. LDL cholesterol was estimated by Friedewald formula. Apo-B was estimated by immunoturbidimetric method using Semiautoanalyser. Finally collected data were analyzed by using SPSS software Version 20. Student 't' test was used to compare the data between cases and controls. P value was set <0.05. Diagnostic validity tests were conducted to assess the diagnostic efficiency of Apo-B. Total cholesterol, LDL cholesterol and triglycerides are significantly increased in cases compared to controls. HDL-cholesterol was significantly decreased in cases compared to controls. Apo-B was significantly increased in cases compared to controls. The result was statistically significant. Apo-B may be used as predictors of ischaemic stroke components.

The Pattern of Serum Calcium, Phosphate and Parathyroid Hormone Levels in Pre-Diagnosed Chronic Kidney Disease Patients

Chronic kidney disease (CKD) is an international health problem affecting 5-10% of the world population. Patients with chronic kidney disease were known to have higher prevalence of changes in serum calcium, phosphate and parathyroid hormone in Western countries, but data on the impact of CKD on serum calcium, phosphate and parathyroid hormone in our country are scarce. This cross-sectional type of descriptive study was conducted in the Department of Medicine, Mymensingh Medical College Hospital, Mymensingh, Bangladesh from March 2016 to September 2016. The aim of this study is to estimate serum calcium, phosphate and parathyroid hormone levels in chronic kidney disease (CKD) patients for early recognition of abnormalities, understanding of their patho-physiological consequences & planning management strategies to prevent their progression, thus reducing the morbidity & mortality. This study shows Hypocalcemia, hyperphosphataemia and elevated serum PTH levels are noted in later CKD stages & worsen with disease progression.

Pattern and Extent of Tricuspid Valve Involvement in Chronic Rheumatic Heart Disease

Rheumatic heart disease causes a significant number of morbidity and mortality in Bangladesh. Although the mitral and the aortic valve are the two most involved valves in rheumatic heart disease, the tricuspid valve disease is not uncommon secondary to, or in association with, mitral or aortic valve disease, but receives less attention as compared to the primary left-sided valve disease. Appropriate treatment of the tricuspid valve disease may improve long-term functional outcome. But the pattern and extent of the tricuspid valve involvement was not studied recently. This study was carried out to observe the pattern and extent of tricuspid valve involvement in Rheumatic Heart Disease patients. This observational analytical study was undertaken in the department of Cardiology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh from December 2010 to September 2011. Considering all ethical issues, data were collected from 173 subjects who underwent Echocardiography for their Chronic Rheumatic heart disease. Pattern of tricuspid valve involvement was observed by using Transthoracic Echocardiography by 2D, M mode and Doppler assessment. One hundred seventy three (173) patients with Rheumatic Heart disease was studied, out of these, 36 patients had evidence of tricuspid valve involvement based on echocardiographic findings. Fifteen (15) patients had Tricuspid stenosis and 36 patients had Tricuspid Regurgitation in the patients with TV involvement. All the patients with TV involvement had thickened leaflets. Doming, restriction of motion and calcification were present in different proportions. From this study, it can be concluded that organic tricuspid valve involvement in RHD is not uncommon in our country.

Prevalence of GERD in Type II Diabetes Mellitus Patients Admitted in A Tertiary Care Hospital of Bangladesh

Gastroesophageal reflux disease (GERD) is defined as symptoms or complications associated with regurgitation from the stomach and/or the duodenum to the esophagus. Patients with type II diabetes mellitus (DM) were known to have higher prevalence of GERD in the Western countries, but data on the impact of GERD on DM patients in our country are scarce. The aim of this cross-sectional study was to evaluate the presence of GERD in type II DM patients admitted at the Department of Medicine, Mymensingh Medical College Hospital, Mymensingh, Bangladesh from April 2015 to September 2015. A total of 137 type II DM cases were purposively collected. Reflux Disease Questionnaire (RDQ) was used to check the presence of GERD. Patient's characteristics, laboratory data, face-to-face interview data were analyzed. Out of 137 type 2 DM patients 108 were suffering from GERD giving a prevalence rate of 78.8% which is quite high. Pathophysiological factors like age, sex, duration of DM, weight, waist circumference (WC) had no significant difference between GERD-DM and non-GERD-type II DM patients. Only hypertension and frequent eating fatty food were found to have significant differences between the two groups. From the study findings it could be said that the higher rate of GERD in patients with type II DM may be associated with lifestyle factor and some pathophysiological factors like hypertension. Psychiatric factors may also play role in contributing GERD. Further in-depth and large scale studies are necessary in our country in this regard.

Investigating potential roles of extruded flaxseed and α-tocopherol acetate supplementation for production of healthier broiler meat

The present study was conducted to evaluate the role of extruded flaxseed (EFS) and α-tocopherol acetate (ATA) for the enhancement of polyunsaturated fatty acids ratio (PUFA) over saturated fatty acids (SFA) in broiler meat as a source of healthier meat. A total of 96 one-d-old Cobb 550 broilers were randomly divided into 8 treatments with three replicates having 4 birds in each. EFS (extruded at 155°C) at 100, 150 and 200 g/kg alone and in combination with ATA at 200 mg/kg were supplemented through normal feed from the third week onward. During the 6-week growth period, body weight gain (BWG), feed intake (FI), feed conversion ratio (FCR) and mortality were recorded. At slaughter, weight of liver, heart and kidney and fat content in breast and leg meat were measured. Fatty acid profiles in breast and leg meat were developed to estimate the PUFA to SFA ratio. The results revealed that FI and FCR changed significantly in all groups and BWG increased in all the supplemented groups. The weight of liver, kidney and heart increased more in the supplemented group containing the maximum level of EFS with ATA compared with single supplementation of EFS. The fat content in breast and leg meat decreased as the inclusion level of EFS increased. The level was low in leg meat compared with breast meat. Mortality decreased in all supplemented groups. The PUFA to SFA ratio was significantly higher in leg meat (3.23) compared with breast meat (1.81) and the study therefore indicates that ATA and EFS supplementation could be used to improve the PUFA to SFA ratio in broiler meat.

Formulation of PEG-ylated L-asparaginase loaded poly (lactide-co-glycolide) nanoparticles: influence of Pegylation on enzyme loading, activity and in vitro release

The present paper describes the advantage of PEG-ylation of L-asparaginase before encapsulation over its incorporation in the native form. During encapsulation a considerable amount of native protein undergoes denaturation and forms insoluble aggregates. In an effort to overcome this problem, L-asparaginase was PEG-ylated before subjecting it to the harsh conditions as encountered during double emulsion solvent evaporation technique. L-asparaginase was conjugated with succinimidyl succinate derivative of polyethylene glycol (SS-PEG, MW 5000) followed by characterization of the formed conjugate using size exclusion-HPLC and SDS PAGE. The PEG-ylated L-asparaginase consisted of different isomers from mono to multi PEG-ylated depending upon the number of Lysine residues (14 in case of L-asparaginase) with about 5% as native protein. The specific activity as retained after PEG-ylation was 62.84 +/- 8.2% and further about 82.7% of activity was recovered from the particles. Imitated studies with the native protein confirmed the enhanced stability of the conjugated protein when exposed to the organic solvent and sonication and showed comparatively less encapsulation efficiency due to increased hydrophilicity. Release profiles for native as well as conjugated proteins consisted of sustained release of about 66.66% and 44.45% in 28 days, respectively. The decrease in the release can be attributed to the increase in the molecular weight of the conjugated protein. The study finally proved that PEG-ylation protected the enzyme and prevented it from denaturation during encapsulation.

A New Approach for Modelling Gene Regulatory Networks Using Fuzzy Petri Nets

Gene Regulatory Networks are models of genes and gene interactions at the expression level. The advent of microarray technology has challenged computer scientists to develop better algorithms for modeling the underlying regulatory relationship in between the genes. Fuzzy system has an ability to search microarray datasets for activator/repressor regulatory relationship. In this paper, we present a fuzzy reasoning model based on the Fuzzy Petri Net. The model considers the regulatory triplets by means of predicting changes in expression level of the target based on input expression level. This method eliminates possible false predictions from the classical fuzzy model thereby allowing a wider search space for inferring regulatory relationship. Through formalization of fuzzy reasoning, we propose an approach to construct a rule-based reasoning system. The experimental results show the proposed approach is feasible and acceptable to predict changes in expression level of the target gene.

Kikuchi-Fujimoto disease

A 14 year-old Bangladeshi girl presented with high fever, painful swellings in the neck, anorexia, weight loss and night sweating. On examination she had multiple enlarged and tender cervical lymph nodes. Other systems were normal. Laboratory investigations for sepsis and autoimmune diseases were negative. Initial fine needle aspiration and cytology of affected lymph node was suggestive of tubercular lymphdenitis. But she did not respond to anti-tubercular treatment. Kikuchi-Fujimoto disease was diagnosed from the histopathological appearance of excised lymph node. She completely recovered with symptomatic treatment. Kikuchi-Fujimoto disease, also called Kikuchi's disease or histiocytic necrotizing lymphadenitis is a rare, benign but enigmatic disease of unknown aetiology. The disease is self-limited and has an excellent prognosis. Its recognition is crucial because it can be mistaken for systemic lupus erythematosus, malignant lymphoma, tubercular lymphadenitis or even, for metastatic adenocarcinoma. Clinicians' and pathologists' awareness of this disease may help prevent misdiagnosis and inappropriate treatment.

The technique of detecting systolic and diastolic pressure from the transducer output of a PC-based blood pressure monitoring system

A pressure to voltage transducer is used along with a cuff, in a PC-based blood pressure and pulse rate monitoring system for human body. During the blood pressure measurement cycle, the output voltage of the pressure to voltage transducer is recorded digitally using a data acquisition system. The recorded data are then analyzed using software routines to determine the blood pressure and pulse rate of the person under test. However, it is difficult to identify the points of systole and diastole correctly from the recorded data. This paper presents the technique that may be used to determine the systolic and diastolic pressure from the collected data.

Arsenicosis in Bangladesh: prevalence and socio-economic correlates

The potential effects of arsenic-contaminated drinking water on health are of concern, but our understanding of the risk factors of arsenicosis remains limited. This study assessed the prevalence of and socio-economic differentials in arsenic-associated skin lesions in a rural community in Bangladesh. Data were collected from a village where the Bangladesh Rural Advancement Committee has operated a health surveillance system and a community-based arsenic mitigation project since 1999. In total, 1654 residents in the study village were examined in May 2000 for arsenic-associated lesions on their skin. Socio-economic information was extracted from the surveillance system database covering the village. Nearly 2.9% of the study population had clinical manifestations of arsenic poisoning. The prevalence of arsenicosis was associated with age, sex, education and the economic status of the household. Multivariate analysis identified age and economic status as significant predictors of arsenicosis controlling for education and gender. In conclusion, a clear understanding of the socio-economic distribution of arsenicosis in different demographic and socio-economic groups will be useful in identifying the high-risk groups from arsenic-affected communities. More studies are needed to design effective interventions to mitigate the effects of arsenic in Bangladesh.

Updating of hereditary haemoglobin disorders

Hereditary haemoglobin disorders (E-beta Thalassaemia & Thalassaemia) are inherited as recessive disorders so that the heterozygote subjects are generally healthy. They commonly present with progressive pallor, thalassaemic facies, splenohepatomegaly & growth retardation. Diagnosis of carriers & patients are usually confirmed by haemoglobin electrophoresis. Transfusion-chelation therapy is usually employed for their treatment. Allogenic bone marrow transplantation is the only definite cure. Gene therapy remains to be the major challenging goal of future curative therapy. During the last 10 years wit medical advances, the number of pregnancies in thalassaemia is increasing. Normal pregnancy can be maintained with regular packed blood cells transfusion given carefully. In Bangladesh, HHD can be prevented by I. carrier identification and marriage counseling, II. passing and enforcing laws against marriage between two carriers, III. introducing thalassaemia in school curriculum and IV. creating public awareness.

Late onset lattice corneal dystrophy with systemic familial amyloidosis, amyloidosis V, in an English family

AIMS

To establish a clinical and molecular diagnosis in a family with late onset lattice corneal dystrophy.

METHODS

Linkage analysis, single strand conformation polymorphism (SSCP) analysis, and direct sequencing of genomic DNA were performed. A review of the patients' clinical symptoms and signs was undertaken.

RESULTS

Linkage to chromosome 9q34 was established and a mutation in the gelsolin gene was found in affected individuals. Numerous symptoms experienced by the patients were attributable to this mutation.

CONCLUSION

A diagnosis of amyloidosis type V (familial amyloidosis, Finnish type, FAF/Meretoja syndrome/gelsolin related amyloidosis) was made. This is the first case of amyloidosis type V described in the UK. This emphasises the importance of recognition of the extraocular manifestations of eye disease both in the diagnosis and management of the patient. In addition, these findings can help molecular geneticists in their search for disease-causing mutations.

Heterogeneity in granular corneal dystrophy: identification of three causative mutations in the TGFBI (BIGH3) gene-lessons for corneal amyloidogenesis

Six autosomal dominant corneal dystrophies are caused by mutations in the TGFBI (BIGH3) gene on chromosome 5q31: three types of lattice corneal dystrophy (LCD), including type I and type IIIA, granular, Avellino (ACD), and Reis-Bucklers. Initially an exact genotype-phenotype correlation was reported. We report three families, with differing clinical features, all presenting with "granular" corneal dystrophy. We analysed the TGFBI gene by SSCP analysis and direct sequencing in order to further assess the genotype-phenotype correlation. We describe three separate mutations in TGFBI: one novel, one initially described as causing ACD, and one previously described. The novel mutation, R124S, is at the identical position to the mutation causing LCD type I (CDL1). We review the clinical and histological phenotypes of the corneal dystrophies and hypothesize that the ability of a mutation to cause amyloid deposition depends on the location and nature of the mutation. In addition, we suggest that the classification of the granular corneal dystrophies be revised according to mutation type and that ACD should not be classified as a distinct morphological entity.

Primary structure of rabbit lens alpha-crystallins

The primary structure and posttranslational modifications of rabbit lens alpha-crystallins were examined using electrospray ionization mass spectrometry to determine the molecular weights of the intact proteins and fast atom bombardment mass spectrometry to analyze proteolytic digests of the alpha A- and alpha B-crystallins. The previously determined primary structure of alpha A-crystallin was confirmed. Posttranslational modifications detected included one phosphorylation site and the presence of a truncated form minus the five C-terminal residues. The previously undetermined amino acid sequence of rabbit alpha B-crystallin was determined to be the same as the bovine alpha B-crystallin sequence except at three residues: Thr 40, Thr 132, and Pro 153. Rabbit alpha B-crystallin showed evidence of phosphorylation at the same three sites as bovine alpha B-crystallin. The molecular weights of the intact proteins indicated that any one molecule had a maximum of two phosphorylations. Also, there was a truncated form which did not include the five C-terminal residues.

The effect of gluconeogenesis on phospholipid turnover in isolated chick proximal tubule cells

Previous work from this laboratory has shown that isolated chick renal proximal tubule cells possess an Na+-dependent Pi transport system and that Pi uptake is stimulated under gluconeogenic conditions. It is shown in the present paper that gluconeogenesis is associated with a rapid incorporation of Pi into membrane phospholipids, particularly phosphatidylinositol, and some evidence has been obtained for a change in the relative amounts of phosphatidylinositol polyphosphates under gluconeogenic conditions. There is no increase in the total phospholipid phosphate content however, suggesting that pyruvate-induced incorporation of Pi into phospholipids represents accelerated turnover rather than a net increase in synthesis. It is suggested that the stimulation of Na+-dependent Pi uptake by pyruvate is related to the increased rate of phospholipid turnover. Thus Pi transport may be a further example of a physiological system that is influenced by phosphatidylinositol metabolism. The role of phosphatidylinositol phosphates could be to stimulate transfer of transporter molecules from internal stores to the brush-border membrane of the cell.

The interaction between gluconeogenic metabolism and accumulation of phosphate by chick kidney tubule cells

Pyruvate promotes both phosphate uptake and glucose synthesis by isolated chick kidney proximal tubule cells. 3-Mercaptopicolinate inhibits both glucose synthesis and the promoted phosphate accumulation to the same extent. Glycerol also stimulates glucose synthesis, but does not affect phosphate accumulation. Oxygen utilization by the tissue is slightly stimulated by glycerol and pyruvate, but the enhancement of uptake by pyruvate is unlikely to result from raised cellular oxidative phosphorylation. The action of pyruvate is not a direct effect on the phosphate transporter, or on the transport of phosphate across the basolateral membrane, but entails an obligatory flux to triose phosphate.

Lack of a direct role for cyclic AMP in parathyrin action on phosphate reabsorption by the kidney

Isolated chick kidney proximal tubule cells have been used in a study of the mechanism by which PTH inhibits Na+-dependent Pi transport in the kidney. Treatment with PTH inhibits Pi uptake by the cells by 13% and stimulates cyclic AMP production by 77%. Forskolin, a potent activator of adenyl cyclase, brought about an 11-fold stimulation of cyclic AMP production by the cells, but in contrast to PTH, the drug had no effect on Na+-dependent Pi uptake. These results provide evidence that PTH action on phosphate transport is not mediated by cyclic AMP.

Detection of Uropathogens by Using Chromogenic Media (Hicrome UTI agar), CLED agar and other Conventional Media

This study was undertaken to find media better than routinely used media in isolation of uropathogens.Three hundred urine samples having pus cells >_ 5/ HPF were enrolled for the study. Comparison of isolation and identification of uropathogens among HiCrome UTI Agar media, 5% Sheep Blood agar & MacConkey agar and CLED agar media were done. Among them 95(31.67%) samples showed single growth, 6 (2%) showed mixed growth and 199 (66.67%) showed no growth. Rate of presumptive identification of organisms in primary culture plate were high in HiCrome UTI agar media. For Escherichia coli, it was 94.20% whereas in CLED agar it was 79.71% and by Blood agar and MacConkey agar media in combination it was 82.61%. All the Enterococcus spp. were identified in HiCrome UTI agar media, 33.33% in CLED agar media but none in Blood agar and MacConkey agar media. Among the mixed growth, 100% organisms were identified on HiCrome UTI Agar media due to distinct colour produced by the different organisms, whereas in one (16.67%) sample (mixed Esch.coli and Pseudomonas spp.) organisms were identified on other three media. Key words: UTI; Uropathogen; HiCrome UTI Agar media DOI: 10.3329/fmcj.v6i1.7411 Faridpur Med. Coll. J. 2011;6(1): 46-50