Aquincola agrisoli sp. nov., isolated from rhizospheric soil of eggplant and in silico genome mining for the prediction of biosynthetic gene clusters

A Gram-stain negative, aerobic, rod-shaped, motile and flagellated novel bacterial strain, designated MAHUQ-54T, was isolated from the rhizospheric soil of eggplant. The colonies were observed to be light pink coloured, smooth, spherical and 0.2-0.6 mm in diameter when grown on R2A agar medium for 2 days. MAHUQ-54T was able to grow at 15-40 °C, at pH 5.5-9.0 and in the presence of 0-0.5 % NaCl (w/v). The strain gave positive results for both catalase and oxidase tests. The strain was positive for hydrolysis of l-tyrosine, urea, Tween 20 and Tween 80. On the basis of the results of 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Aquincola and is closely related to Aquincola tertiaricarbonis L10T (98.8 % sequence similarity) and Leptothrix mobilis Feox-1T (98.2 %). MAHUQ-54T has a draft genome size of 5 994 516 bp (60 contigs), annotated with 5348 protein-coding genes, 45 tRNA and 5 rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) values between MAHUQ-54T and its closest phylogenetic neighbours were 75.8-83.3 and 20.8-25.3 %, respectively. In silico genome mining revealed that MAHUQ-54T has a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 70.4 %. The predominant isoprenoid quinone was ubiquinone-8. The major fatty acids were identified as C16  :  0, summed feature 3 (comprising C16  :  1ω7c and/or C16  :  1ω6c) and summed feature 8 (comprising C18  :  1ω7c and/or C18  :  1ω6c). On the basis of dDDH, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAHUQ-54T represents a novel species within the genus Aquincola, for which the name Aquincola agrisoli sp. nov. is proposed, with MAHUQ-54T (=KACC 22001T = CGMCC 1.18515T) as the type strain.

Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses

Plant protein phosphatase 2C (PP2C) plays vital roles in responding to various stresses, stimulating growth factors, phytohormones, and metabolic activities in many important plant species. However, the PP2C gene family has not been investigated in the economically valuable plant species sunflower (Helianthus annuus L.). This study used comprehensive bioinformatics tools to identify and characterize the PP2C gene family members in the sunflower genome (H. annuus r1.2). Additionally, we analyzed the expression profiles of these genes using RNA-seq data under four different stress conditions in both leaf and root tissues. A total of 121 PP2C genes were identified in the sunflower genome distributed unevenly across the 17 chromosomes, all containing the Type-2C phosphatase domain. HanPP2C genes are divided into 15 subgroups (A-L) based on phylogenetic tree analysis. Analyses of conserved domains, gene structures, and motifs revealed higher structural and functional similarities within various subgroups. Gene duplication and collinearity analysis showed that among the 53 HanPP2C gene pairs, 48 demonstrated segmental duplications under strong purifying selection pressure, with only five gene pairs showing tandem duplications. The abundant segmental duplication was observed compared to tandem duplication, which was the major factor underlying the dispersion of the PP2C gene family in sunflowers. Most HanPP2C proteins were localized in the nucleus, cytoplasm, and chloroplast. Among the 121 HanPP2C genes, we identified 71 miRNAs targeting 86 HanPP2C genes involved in plant developmental processes and response to abiotic stresses. By analyzing cis-elements, we identified 63 cis-regulatory elements in the promoter regions of HanPP2C genes associated with light responsiveness, tissue-specificity, phytohormone, and stress responses. Based on RNA-seq data from two sunflower tissues (leaf and root), 47 HanPP2C genes exhibited varying expression levels in leaf tissue, while 49 HanPP2C genes showed differential expression patterns in root tissue across all stress conditions. Transcriptome profiling revealed that nine HanPP2C genes (HanPP2C12, HanPP2C36, HanPP2C38, HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73) exhibited higher expression in leaf tissue, and five HanPP2C genes (HanPP2C13, HanPP2C47, HanPP2C48, HanPP2C54, and HanPP2C95) showed enhanced expression in root tissue in response to the four stress treatments, compared to the control conditions. These results suggest that these HanPP2C genes may be potential candidates for conferring tolerance to multiple stresses and further detailed characterization to elucidate their functions. From these candidates, 3D structures were predicted for six HanPP2C proteins (HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73), which provided satisfactory models. Our findings provide valuable insights into the PP2C gene family in the sunflower genome, which could play a crucial role in responding to various stresses. This information can be exploited in sunflower breeding programs to develop improved cultivars with increased abiotic stress tolerance.

Leveraging immunoinformatics for developing a multi-epitope subunit vaccine against Helicobacter pylori and Fusobacterium nucleatum

Gastric ulcers caused by Helicobacter pylori and Fusobacterium nucleatum remain a significant global health concern without an established vaccine. In this study, we utilized immunoinformatics methods to design a multi-epitope vaccine targeting these pathogens. Outer membrane proteins from H. pylori and F. nucleatum were scrutinized to identify high antigenic T-cell and B-cell epitopes. The resulting vaccine comprised carefully analyzed and evaluated epitopes, including cytotoxic T-lymphocytes, helper T-lymphocytes, and linear B-lymphocytes epitopes. This vaccine exhibited notable antigenicity, suitable immunogenicity, and demonstrated non-allergenicity and non-toxicity. It displayed favorable physiochemical characteristics and high solubility. In interaction studies, the vaccine exhibited robust binding to toll-like receptor 4 (TLR4). Molecular dynamic simulations revealed cohesive structural integrity and stable attachment. Codon adaptation utilizing Escherichia coli K12 host yielded a vaccine with elevated Codon Adaptation Index (CAI) and optimal GC content. In silico cloning into the pET28+(a) vector demonstrated efficient expression. Immune simulations indicated the vaccine's ability to initiate immune responses in humans, mirroring real-life scenarios. Based on these comprehensive findings, we propose that our developed vaccine has the potential to confer robust immunity against H. pylori and F. nucleatum infections.Communicated by Ramaswamy H. Sarma.

Bioactive ZnO Nanoparticles: Biosynthesis, Characterization and Potential Antimicrobial Applications

In recent years, biosynthesized zinc oxide nanoparticles (ZnONPs) have gained tremendous attention because of their safe and non-toxic nature and distinctive biomedical applications. A diverse range of microbes (bacteria, fungi and yeast) and various parts (leaf, root, fruit, flower, peel, stem, etc.) of plants have been exploited for the facile, rapid, cost-effective and non-toxic synthesis of ZnONPs. Plant extracts, microbial biomass or culture supernatant contain various biomolecules including enzymes, amino acids, proteins, vitamins, alkaloids, flavonoids, etc., which serve as reducing, capping and stabilizing agents during the biosynthesis of ZnONPs. The biosynthesized ZnONPs are generally characterized using UV-VIS spectroscopy, TEM, SEM, EDX, XRD, FTIR, etc. Antibiotic resistance is a serious problem for global public health. Due to mutation, shifting environmental circumstances and excessive drug use, the number of multidrug-resistant pathogenic microbes is continuously rising. To solve this issue, novel, safe and effective antimicrobial agents are needed urgently. Biosynthesized ZnONPs could be novel and effective antimicrobial agents because of their safe and non-toxic nature and powerful antimicrobial characteristics. It is proven that biosynthesized ZnONPs have strong antimicrobial activity against various pathogenic microorganisms including multidrug-resistant bacteria. The possible antimicrobial mechanisms of ZnONPs are the generation of reactive oxygen species, physical interactions, disruption of the cell walls and cell membranes, damage to DNA, enzyme inactivation, protein denaturation, ribosomal destabilization and mitochondrial dysfunction. In this review, the biosynthesis of ZnONPs using microbes and plants and their characterization have been reviewed comprehensively. Also, the antimicrobial applications and mechanisms of biosynthesized ZnONPs against various pathogenic microorganisms have been highlighted.

Identification of genetic biomarkers, drug targets and agents for respiratory diseases utilising integrated bioinformatics approaches

Respiratory diseases (RD) are significant public health burdens and malignant diseases worldwide. However, the RD-related biological information and interconnection still need to be better understood. Thus, this study aims to detect common differential genes and potential hub genes (HubGs), emphasizing their actions, signaling pathways, regulatory biomarkers for diagnosing RD and candidate drugs for treating RD. In this paper we used integrated bioinformatics approaches (such as, gene ontology (GO) and KEGG pathway enrichment analysis, molecular docking, molecular dynamic simulation and network-based molecular interaction analysis). We discovered 73 common DEGs (CDEGs) and ten HubGs (ATAD2B, PPP1CB, FOXO1, AKT3, BCR, PDE4D, ITGB1, PCBP2, CD44 and SMARCA2). Several significant functions and signaling pathways were strongly related to RD. We recognized six transcription factor (TF) proteins (FOXC1, GATA2, FOXL1, YY1, POU2F2 and HINFP) and five microRNAs (hsa-mir-218-5p, hsa-mir-335-5p, hsa-mir-16-5p, hsa-mir-106b-5p and hsa-mir-15b-5p) as the important transcription and post-transcription regulators of RD. Ten HubGs and six major TF proteins were considered drug-specific receptors. Their binding energy analysis study was carried out with the 63 drug agents detected from network analysis. Finally, the five complexes (the PDE4D-benzo[a]pyrene, SMARCA2-benzo[a]pyrene, HINFP-benzo[a]pyrene, CD44-ketotifen and ATAD2B-ponatinib) were selected for RD based on their strong binding affinity scores and stable performance as the most probable repurposable protein-drug complexes. We believe our findings will give readers, wet-lab scientists, and pharmaceuticals a thorough grasp of the biology behind RD.

Isolation and characterization of Pinibacter soli sp. nov., and in silico genome mining of Pinibacter for biosynthetic gene cluster prediction

A Gram-stain-negative, aerobic, rod-shaped, non-motile and non-flagellated novel bacterial strain, designated MAH-24T, was isolated from the rhizospheric soil of a pine garden. The colonies were observed to be orange-coloured, smooth, spherical and 0.4-0.8 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAH-24T was found to be able to grow at 10-35 °C, at pH 6.0-9.0 and in the presence of 0-1.0 % NaCl (w/v). The strain was found to be positive for the catalase and oxidase tests. The strain was positive for hydrolysis of aesculin and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pinibacter and to be closely related to Pinibacter aurantiacus MAH-26T (99.2 % sequence similarity). The novel strain MAH-24T has a draft genome size of 5 918 133 bp (13 contigs), annotated with 4613 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-24T and the closest type strain P. aurantiacus MAH-26T were in the range of 85.3 and 29.9 %, respectively. In silico genome mining revealed that both novel strain MAH-24T and P. aurantiacus MAH-26T have a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 41.0 mol%. The predominant isoprenoid quinone was menaquinone-7. The major fatty acids were identified as C15:0 iso, C15:1 iso G and C17:0 iso 3OH. On the basis of dDDH, ANI, genotypic, chemotaxonomic and physiological data, strain MAH-24T represents a novel species within the genus Pinibacter, for which the name Pinibacter soli sp. nov. is proposed, with MAH-24T (=KACC 19747T=CGMCC 1.13659T) as the type strain.

Sphingobium agri sp. nov., isolated from rhizospheric soil of eggplant

A Gram-stain-negative, aerobic, short rod-shaped and motile bacterial strain, designated MAH-33T, was isolated from rhizospheric soil of eggplant. The colonies were observed to be yellow-coloured, smooth, spherical and 0.1-0.3 mm in diameter when grown on TSA agar medium for 2 days. Strain MAH-33T was found to be able to grow at 10-40 °C, at pH 5.0-10.0 and at 0-3.0 % NaCl (w/v). The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of tyrosine and aesculin. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingobium and to be closely related to Sphingobium quisquiliarum P25T (98.4 % similarity), Sphingobium mellinum WI4T (97.8 %), Sphingobium fuliginis TKPT (97.3 %) and Sphingobium herbicidovorans NBRC 16415T (96.9 %). The novel strain MAH-33T has a draft genome size of 3 908 768 bp (28 contigs), annotated with 3689 protein-coding genes, 45 tRNA and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-33T and closely related type strains were in the range of 79.8-81.6 % and 23.2-24.5 %, respectively. The genomic DNA G+C content was determined to be 62.2 %. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as C16 : 0 and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipids identified in strain MAH-33T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine; one unknown phospholipid and one unknown lipid. On the basis of digital DNA-DNA hybridization, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAH-33T represents a novel species within the genus Sphingobium, for which the name Sphingobium agri sp. nov. is proposed, with MAH-33T (=KACC 19973T = CGMCC 1.16609T) as the type strain.

Bacterial mediated green synthesis of silver nanoparticles and their antibacterial and antifungal activities against drug-resistant pathogens

In the healthcare sector, the production of bioactive silver nanoparticles (AgNPs) with antimicrobial properties is of great importance. In this study, a novel bacterial strain, Paenibacillus sp. MAHUQ-63, was identified as a potential candidate for facile and rapid biosynthesis of AgNPs. The synthesized AgNPs were used to control the growth of human pathogens, Salmonella Enteritidis and Candida albicans. The bacterial culture supernatant was used to synthesize the nanoparticles (NPs). Field emission transmission electron microscope examination showed spherical-shaped NPs with 15-55 nm in size. Fourier transform-infrared analysis identified various functional groups. The synthesized AgNPs demonstrated remarkable activity against S. Enteritidis and C. albicans. The zones of inhibition for 100 µl (0.5 mg ml-1) of AgNPs against S. Enteritidis and C. albicans were 18.0 ± 1.0 and 19.5 ± 1.3 mm, respectively. The minimum inhibitory concentrations were 25.0 and 12.5 µg ml-1 against S. Enteritidis and C. albicans, respectively. Additionally, the minimum bactericidal concentrations were 25.0 µg ml-1 against both pathogenic microbes. The field emission scanning electron microscopy analysis showed that the treatment of AgNPs caused morphological and structural damage to both S. Enteritidis and C. albicans. Therefore, these AgNPs can be used as a new and effective antimicrobial agent.

Sphingomonas oryzagri sp. nov., isolated from a rice field

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-71T, was isolated from the soil of a rice field. The colonies were observed to be milky yellow-coloured, smooth, spherical and 0.1-0.4 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-71T was found to be able to grow at 15-37 °C, pH 5.0-10.0 and with 0-3.0 % NaCl (w/v). The strain was found to be positive for the catalase test, but negative for the oxidase test. The strain was positive for hydrolysis of aesculin and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and to be closely related to Sphingomonas chungangi MAH-6T (98.5 % sequence similarity), Sphingomonas polyaromaticivorans B2-7T (98.4 %) and Sphingomonas oligoaromativorans SY-6T (96.6 %). Strain MAHUQ-71T has a draft genome size of 4 255 278 bp (10 contigs), annotated with 4098 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-71T and the closest type strain S. chungangi MAH-6T were in the range of 85.6 and 30.6 %, respectively. The genomic DNA G+C content was determined to be 66.7 mol%. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C14 : 0 2OH. The main polar lipids were phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and sphingoglycolipid. On the basis of dDDH and ANI values, as well as the results of genotypic, chemotaxonomic and physiological analyses, strain MAHUQ-71T represents a novel species within the genus Sphingomonas, for which the name Sphingomonas oryzagri sp. nov. is proposed, with MAHUQ-71T (=KACC 22252T=CGMCC 1.19065T) as the type strain.

Transcatheter Aortic Valve Replacement in Bicuspid Aortic Valve: A Case Report

Among other valvular heart disease Aortic stenosis (AS) is the most common in the developed world. Transcatheter Aortic Valve Replacement (TAVR) is most acceptable treatment option for patient with severely calcified aortic stenosis with high and intermediate risk group. Among several challenges, one of the main challenges is to deal with bicuspid aortic valve (BAV). Non-circular annulus, bulky leaflets leading to perivalvular leaks and risk for rupture and often very severe calcification may contribute to periprocedural strokes leading to poor clinical outcome. This case, a 68-year-old woman with a history of type 2 diabetes mellitus (DM), hypothyroidism, bicuspid aortic valve and severe aortic stenosis, bronchial asthma, who had repeatedly refused any suggestion for open heart surgery, was our volunteer candidate for TAVR. After successful TAVR the peak pressure gradient decreased from 100mmHg to 17mmHg. So, TAVR could be a viable option for highly selected patients with severe aortic stenosis and bicuspid aortic valve who have favourable anatomy.

Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg12O12 and Zn12O12 nanoclusters: an in silico strategy for COVID-19 treatment

Pandemic new severe acute respiratory syndrome coronavirus (SARS-CoV-2) virus has increased throughout the world. There is no effective treatment against this virus until now. Since its appearance in Wuhan, China in December 2019, SARS-CoV-2 becomes the largest challenge the world is opposite today, including the discovery of an antiviral drug for this virus. Several viral proteins have been prioritized as SARS-CoV-2 antiviral drug targets, among them the papain-like protease (PLpro) and the main protease (Mpro). Inhibition of these proteases would target viral replication, viral maturation and suppression of host innate immune responses. Potential candidates have been identified to show inhibitory effects against Mpro, both in biochemical assays and viral replication in cells. There are different molecules such as lopinavir and favipiravir considerably inhibit the activity of Mpro in vitro. Different studies have shown that structurally improved favipiravir and other similar compounds can inhibit SARS-CoV-2 main protease. In this work, we study the interactions between favipiravir with Mg12O12 and Zn12O12 nanoclusters by density functional theory (DFT) and quantum mechanics atoms in molecules (QMAIM) methods to summarize the ability to load favipiravir onto Mg12O12 and Zn12O12 nanoclusters. Favipiravir-Mg12O12 and favipiravir-Zn12O12 lowest structures complexes were chosen to dock inside the SARS-CoV-2 main protease by molecular docking study. The molecular docking analysis revealed that the binding affinity of Mg12O12 and Zn12O12 nanoclusters inside the Mpro receptor is larger than that of favipiravir. Also, the loading of favipiravir on the surface of Mg12O12 and Zn12O12 nanoclusters increased the binding affinity against the Mpro receptor. Subsequently, 100 ns molecular dynamics simulation of the favipiravir-Mg12O12, and favipiravir-Zn12O12 docked inside the Mpro complexes established that favipiravir-Mg12O12, forms the most stable complex with the Mpro. Further molecular mechanics Poisson Boltzmann surface area (MMPBSA) analyses using the MD trajectories also demonstrated the higher binding affinity of favipiravir-Mg12O12 inside the Mpro. In summary, this study demonstrates a new way to characterize leads for novel anti-viral drugs against SARS-CoV-2, by improving the drug ability of favipiravir via loading it on Mg12O12 and Zn12O12 nanoclusters.Communicated by Ramaswamy H. Sarma.

A subunit vaccine against pneumonia: targeting Streptococcus pneumoniae and Klebsiella pneumoniae

Community-acquired pneumonia is primarily caused by Streptococcus pneumoniae and Klebsiella pneumoniae, two pathogens that have high morbidity and mortality rates. This is largely due to bacterial resistance development against current antibiotics and the lack of effective vaccines. The objective of this work was to develop an immunogenic multi-epitope subunit vaccine capable of eliciting a robust immune response against S. pneumoniae and K. pneumoniae. The targeted proteins were the pneumococcal surface proteins (PspA and PspC) and choline-binding protein (CbpA) of S. pneumoniae and the outer membrane proteins (OmpA and OmpW) of K. pneumoniae. Different computational approaches and various immune filters were employed for designing a vaccine. The immunogenicity and safety of the vaccine were evaluated by utilizing many physicochemical and antigenic profiles. To improve structural stability, disulfide engineering was applied to a portion of the vaccine structure with high mobility. Molecular docking was performed to examine the binding affinities and biological interactions at the atomic level between the vaccine and Toll-like receptors (TLR2 and 4). Further, the dynamic stabilities of the vaccine and TLRs complexes were investigated by molecular dynamics simulations. While the immune response induction capability of the vaccine was assessed by the immune simulation study. Vaccine translation and expression efficiency was determined through an in silico cloning experiment utilizing the pET28a(+) plasmid vector. The obtained results revealed that the designed vaccine is structurally stable and able to generate an effective immune response to combat pneumococcal infection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13721-023-00416-3.

Relationship of Conduction Defects and In-Hospital Outcome after Acute ST Segment Elevation Myocardial Infarction

The presence of conduction defects complicating acute myocardial infarction (MI) is relatively frequent and is associated with increased short and long term mortality. Thrombolytic therapy has been established to reduce the mortality in acute MI, however its role in reducing the incidence of conduction defects is less clearly defined. Morbidity and mortality associated with conduction defects also remain unchanged. This study was aimed to assess the correlation between conduction defects and adverse in-hospital outcome of patients with acute ST segment elevation MI. This cross sectional descriptive type of observational study was conducted among 100 purposively selected patients with acute ST segment elevation MI in the coronary care unit (CCU) of Mymensingh Medical College Hospital, Bangladesh from June 2012 to March 2013. The patients were divided into two groups depending on the presence or absence of conduction defects namely Group A- 40 patients with conduction defects and Group B- 60 patients without conduction defects. Highest number of the patients (36.0%) was in the age group of 45-55 years. In case of inferior MI, age groups 45-55 years and 55-65 years had equal number of patients (30.4%). Only 2.0% patients were in age group of 75-85 years and this group had only inferior MI. Total number of female patients were 16(16.0%). Female patients had more inferior MI (17.4%) than anterior MI (15.9%). Number of MI patients was slightly more in inferior MI (46.0%) than anterior MI (44.0%). Group B had equal number of patients in both anterior and inferior MI. Conduction defects were more common in inferior MI (43.5%) than anterior MI (40.9%). Atrio-ventricular conduction defects were more common in inferior MI whereas intra-ventricular conduction defects were more common in anterior MI. Complete heart block (CHB) was more prevalent in inferior MI. Complications were more common in Group A (65.0%) than Group B (18.3%). In terms of complications the difference between two groups were significant (p<0.001). Group A showed higher rate of mortality (20.0%) than Group B (3.3%). In cases of anterior MI difference in mortality between Group A and Group B was highly significant (p<0.001). Conduction defects in the setting of acute MI are a common finding. Atrio-ventricular conduction defects occur more frequently in inferior MI whereas intra-ventricular conduction defects were more frequently encountered in anterior MI. Patients with conduction defects had more complications than those without conduction defects. Presence of conduction defects significantly increases the mortality of patients with anterior MI.

Immune epitopes identification and designing of a multi-epitope vaccine against bovine leukemia virus: a molecular dynamics and immune simulation approaches

Background

Bovine leukemia virus (BLV) is an oncogenic delta-retrovirus causing bovine leucosis. Studies on BLV have shown the association with human breast cancer. However, the exact molecular mechanism is neither known nor their appropriate preventative measure to halt the disease initiation and progression. In this study, we designed a multi-epitope vaccine against BLV using a computational analyses.

Methods

Following a rigorous assessment, the vaccine was constructed using the T-cell epitopes from each BLV-derived protein with suitable adjuvant and linkers. Both physicochemistry and immunogenic potency as well as the safeness of the vaccine candidate were assessed. Population coverage was done to evaluate the vaccine probable efficiency in eliciting the immune response worldwide. After homology modeling, the three-dimensional structure was refined and validated to determine the quality of the designed vaccine. The vaccine protein was then subjected to molecular docking with Toll-like receptor 3 (TLR3) to evaluate the binding efficiency followed by dynamic simulation for stable interaction.

Results

Our vaccine construct has the potential immune response and good physicochemical properties. The vaccine is antigenic and immunogenic, and has no allergenic or toxic effect on the human body. This novel vaccine contains a significant interactions and binding affinity with the TLR3 receptor.

Conclusions

The proposed vaccine candidate would be structurally stable and capable of generating an effective immune response to combat BLV infections. However, experimental evaluations are essential to validate the exact safety and immunogenic profiling of this vaccine.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00262-022-03181-w.

Comparison between Lichtenstein And Laparoscopic Totally Extraperitonial (TEP) Tension Free Mesh Repair of Inguinal Hernia

To compare the outcome of the laparoscopic totally extra peritoneal (Lap TEP) and open Lichtenstein tension free mesh repair (OLMR) of inguinal hernia. This study was conducted as a prospective comparative (Quasi experimental) study from January 2010 to December 2010 at Combined Military Hospital (CMH), Dhaka, Bangladesh. A total of 100 male patients aged 24 to 70 years who underwent laparoscopic totally extra-peritoneal (Lap TEP) and open Lichtenstein tension free mesh repair (OLMR) of inguinal hernia were included in this study. Data of operating time, intraoperative and short-term postoperative complications, postoperative pain, postoperative hospital stay and return to normal activity were recorded and analyzed with SPSS program. Mean age of the patients was 51.39±15.099 years in OLMR group (Group A) and 47.10±9.338 years in Lap TEP group (Group B). Mean operating time was longer in Laparoscopic TEP group (Group B, 57.67±6.915 minutes) then open Lichtenstein mesh repair group (Group A, 50.56±6.292 minutes). Patient in the Lap TEP group (Group B) experienced less post operative pain, less post operative complications, shorter hospital stay and early return to normal activity then OLMR group (Group A). One patient (3.33%) in group B needed conversion to open Lichtenstein method. Two (6.66%) patients developed pneumoperitoneum in Group B (Lap TEP repair). Superficial wound infection developed in five (7.14%) patients in OLMR group (Group A) and two (6.66%) patients in Lap TEP group (Group B). In Laparoscopic TEP group (Group B) and Lichtenstein group (Group A), patients return to normal activity within on an average 07 and 11 days respectively. Laparoscopic totally extra peritoneal (TEP) mesh repair technique was associated with less post operative pain, less post operative complications, shorter hospital stay, faster recovery with early return to normal activity compared with Lichtenstein tension free mesh repair of inguinal hernia.

Human health implications of trace metal contamination in topsoils and brinjal fruits harvested from a famous brinjal-producing area in Bangladesh

A study was undertaken to determine the contents of trace metals in 60 topsoils and 80 brinjal fruits samples from a famous brinjal-producing area of Bangladesh using atomic absorption spectrophotometer. The study also looked at soil pollution levels, dietary intake of nutritionally important trace elements, and human health risks from toxic metals induced by dermal soil exposure and consumption of brinjal. The content of Pb, Ni, Cd, Cu, Fe, Mn, and Zn in brinjal fruits harvested from farmer′s fields ranged from 0.204–0.729, 0.031–0.212, < 0.010–0.061, 1.819–2.668, 3.267–5.910, < 0.010–0.866 and 2.160–3.846 µg g^-1, respectively, while the amount of Cr was negligible. The calculated enrichment factors showed that 70, 50, and 25% of soil sampling sites had values in the 2.00–5.00 range for Pb, Zn, and Cd, respectively, while 30% of sites had values > 5.00 for Cd, indicating moderate to significant enrichment of these metals in the soil. The study also revealed that brinjal consumption provides a tiny amount of nutritionally important trace elements required for an adult human. Regarding the computed incremental lifetime cancer risks (ILCR), the study revealed that the values for Pb and Ni in all samples and Cd in 40% of samples were several hundred times higher for males and females than the USEPA threshold level due to oral ingestion of brinjal fruits. In contrast, dermal exposures to soil trace elements were within an acceptable range. The PCA results revealed that the contents of Cd, Pb, Ni, and Cu in soils showed strong positive correlations with those elements present in brinjal. The current study suggests future traceability research, focusing on pinpointing potential entry routes for toxic elements into the vegetable food chain.

Estimation of Serum Lipid Profile among Patients Admitted with Myocardial Infarction in a Tertiary Level Hospital of Bangladesh

Different studies worldwide showed that dyslipidaemia is involved in the pathogenesis of ischemic heart diseases (IHD). This cross sectional descriptive type of observational study was carried out at Mymensingh Medical College Hospital during the period of six months from January 2021 to September 2021 to estimate the lipid profile among patients admitted in the coronary care unit (CCU) with myocardial infarction (MI). Data were collected from purposively selected 343 patients with MI by face to face interview and laboratory investigations using a case record form. Informed written consent of participants was taken prior to interview. Data were analyzed by using SPSS version 21.0. The study results revealed that mean age of the patients with myocardial infarction was 53.16 years with a standard deviation of 11.68 years. Majority of them (284, 82.8%) were male and the remaining (59, 17.2%) were female. Proportion of risk factors for ischaemic heart disease (IHD) were estimated and found that 244(71.1%) patients were smoker; 150(43.7%) had hypertension and 110(32.2%) had family history of IHD. Ninety nine (28.9%) patents were obese with BMI ≥25kg/m². Eighty three (24.2%) patients had diabetes mellitus; 66(19.2%) lead sedentary life and 61(17.8%) patients with myocardial infarction had dyslipidaemia. Mean LDL of patients with myocardial infarction was 103.65±39.73mg/dl; mean total cholesterol (TC) was 189.44±45.41mg/dl; mean TG was 243.11±205.19mg/dl and mean HDL was 39.29±8.98mg/dl. LDL was increased in 10(2.9%) patients; total cholesterol was raised in 121 (35.3%) patients and TG was raised in 195(56.9%) patients. HDL was raised in 26(7.6%) patients and it was lowered in 57(16.6%) patients. Mean LDL, TC, TG and HDL of younger (≤45 years) and older (>45 years) patients were compared and t-test showed no significant difference (p>0.05). Similarly mean LDL, TC, TG and HDL of male and female were compared and again t-test showed no significant difference (p>0.05). Though the pattern of lipid profile was found similar in younger and older patients and in males and females, a significant number of patients (61, 17.8%) with MI had dyslipidaemia which should be address by dietary and lifestyle modification.

Psychological Assessment of Health-Care Workers Working during COVID-19 Pandemic Condition in Bangladesh

The study was aimed to assess the psychological aspects and relevant factors of the health-care workers (HCWs) working in COVID 19 pandemic condition in Bangladesh. This online cross-sectional survey was conducted from different tertiary, secondary and primary hospitals in Bangladesh. Eligible 638 HCWs who were directly involved in the caring of confirmed or suspected COVID-19 patients were recruited in this study. The mental health was assessed by the Patient Health Questionnare-9 (PHQ-9), Generalized Anxiety Disorder-7 (GAD-7) and Athens Insomnia Scale (AIS). High frequency of depression 536(84.0%), anxiety 386(60.5%) and insomnia 302(47.3%) was found among the HCWs, which were significantly higher in physicians (p<0.001) than nurses. Moderate to severe depression was significantly higher in female, whereas minimal to mild depression was significant in male HCWs (p=0.014). Symptoms of depression (p<0.001), anxiety (p<0.001) and insomnia (p=0.004) were significantly higher among the HCWs of primary and secondary compared to the tertiary level. The HCWs developed psychological trauma due to family health (45.3%) and contagious disease property (66.6%). After adjusting confounders, multivariable logistic regression analysis showed that physicians and HCWs of secondary hospital had significant symptoms of severe depression (OR=2.95, 95% CI=0.50-17.24; p<0.001), anxiety (OR=2.64, 95% CI=0.80-8.72; p<0.001) and insomnia (OR=2.67, 95% CI=1.23-5.84; p=0.018); whereas female HCWs had more risk of developing symptoms of severe insomnia (OR= 1.84; 95% CI=1.23-2.75; p=0.003). High rate of depression, anxiety and insomnia was found among HCWs working in the COVID-19 pandemic condition in this survey.

Finding gaps in routine TB surveillance activities in Bangladesh

BACKGROUND :

TB was the leading cause of death from a single infectious pathogen globally between 2014 and 2019. Fine-scale estimates of TB prevalence and case notifications can be combined to guide priority-setting for strengthening routine surveillance activities in high-burden countries. We produce policy-relevant estimates of the TB epidemic at the second administrative unit in Bangladesh.

METHODS :

We used a Bayesian spatial framework and the cross-sectional National TB Prevalence Survey from 2015–2016 in Bangladesh to estimate prevalence by district. We used case notifications to calculate prevalence-to-notification ratio, a key metric of under-diagnosis and under-reporting.

RESULTS :

TB prevalence rates were highest in the north-eastern districts and ranged from 160 cases per 100,000 (95% uncertainty interval [UI] 80–310) in Jashore to 840 (UI 690–1020) in Sunamganj. Despite moderate prevalence rates, the Rajshahi and Dhaka Divisions presented the highest prevalence-to-notification ratios due to low case notifications. Resolving subnational disparities in case detection could lead to 26,500 additional TB cases (UI 8,500–79,400) notified every year.

CONCLUSION :

This study is the first to produce and map subnational estimates of TB prevalence and prevalence-to-notification ratios, which are essential to target prevention and treatment efforts in high-burden settings. Reaching TB cases currently missing from care will be key to ending the TB epidemic.

Association of Body Mass Index with Angiographic Severity of Coronary Artery disease in patients with Acute Coronary Syndrome

Coronary artery disease (CAD) is the leading cause of death in developed and developing countries. Associated co-morbidities like diabetes, hypertension and obesity are making the situation worse. WHO enlisted obesity as an epidemic which also affects a great number of young population. Some recent studies showed the presence of an apparent paradoxical relationship between obesity and cardiovascular prognosis in certain subsets of patents. As BMI is an established marker of obesity; an attempt has been made to assess relationship between BMI and angiographic severity of coronary artery disease in Acute Coronary Syndrome (ACS) patients of Bangladeshi origin. To assess the association between body mass index and angiographic severity of coronary artery disease in patients with acute coronary syndrome; this cross sectional analytical study was conducted in the Department of Cardiology, Mymensingh Medical College Hospital (MMCH) and Bangabandhu Sheikh Mujib Medical University (BSMMU) from December 2016 to February 2018 among purposively selected 65 patients. Relevant ethical issues were taken into consideration. Coronary angiogram was done in the same index hospitalization period. After coronary angiogram performed patients were grouped into two groups according to their BMI. Patients with BMI <25kg/m² as Group I and those ≥25kg/m² as Group II. Angiographic severity of coronary artery disease was assessed by vessel score and Syntax score. Mean age of Group I was 54.45±10.42 years, while in Group II it was 50.76±8.89 years reflecting the early presentation of higher BMI patients. Male to female ratio was 12:1. Mean BMI of Group I and Group II was 22.56±1.59 and 28.67±2.64 respectively. In Group I, 10(25.0%) had single vessel lesion, 15(37.5%) had double vessel lesion and 14(35.0%) had triple vessel lesion, while in Group II, 6(24.0%) had single vessel lesion, 12(48.0%) had double vessel lesion and 5(20.0%) had triple vessel lesion. Mean Syntax score of Group I and Group II was 13.18±8.45 and 10.42±7.14 respectively. Patients in the increasing BMI class had a higher prevalence of diabetes, hypertension and dyslipidaemia. A negative correlation was observed between BMI and angiographic severity (Vessel score, Syntax score and HRCA e.g. LM disease) of CAD indicating that patients with higher BMI had a lower coronary artery disease (CAD) severity than their normal BMI counterparts. Patients with high BMI have a lower CAD severity than usually expected. After adjustment for co-morbidities, BMI was not found as an independent predictor of severity of coronary artery disease.

Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods

A novel infectious agent, SARS-CoV-2, is responsible for causing the severe respiratory disease COVID-19 and death in humans. Spike glycoprotein plays a key role in viral particles entering host cells, mediating receptor recognition and membrane fusion, and are considered useful targets for antiviral vaccine candidates. Therefore, computational techniques can be used to design a safe, antigenic, immunogenic, and stable vaccine against this pathogen. Drawing upon the structure of the S glycoprotein, we are trying to develop a potent multi-epitope subunit vaccine against SARS-CoV-2. The vaccine was designed based on cytotoxic T-lymphocyte and helper T-lymphocyte epitopes with an N-terminal adjuvant via conducting immune filters and an extensive immunoinformatic investigation. The safety and immunogenicity of the designed vaccine were further evaluated via using various physicochemical, allergenic, and antigenic characteristics. Vaccine-target (toll-like receptors: TLR2 and TLR4) interactions, binding affinities, and dynamical stabilities were inspected through molecular docking and molecular dynamic (MD) simulation methods. Moreover, MD simulations for dimeric TLRs/vaccine in the membrane-aqueous environment were performed to understand the differential domain organization of TLRs/vaccine. Further, dynamical behaviors of vaccine/TLR systems were inspected via identifying the key residues (named HUB nodes) that control interaction stability and provide a clear molecular mechanism. The obtained results from molecular docking and MD simulation revealed a strong and stable interaction between vaccine and TLRs. The vaccine's ability to stimulate the immune response was assessed by using computational immune simulation. This predicted a significant level of cytotoxic T cell and helper T cell activation, as well as IgG, interleukin 2, and interferon-gamma production. This study shows that the designed vaccine is structurally and dynamically stable and can trigger an effective immune response against viral infections.

Combining ability analysis in bitter gourd (Momordica charantia L.) for potential quality improvement

Combining ability analysis provides useful information for the selection of parents, also information regarding the nature and magnitude of involved gene actions. Crops improvement involves strategies for enhancing yield potentiality and quality components. Targeting the improvement of respective characters in bitter gourd, combining ability and genetic parameters for 19 characters were estimated from a 6×6 full diallel analysis technique. The results revealed that the variances due to general combining ability (GCA) and specific combining ability (SCA) were highly significant for most of the important characters. It indicated the importance of both additive and non-additive gene actions. GCA variances were higher in magnitude than SCA variances for all the characters studied indicating the predominance of the additive gene effects in their inheritance. The parent P2 (BG 009) appeared as the best general combiner for earliness; P1 (BG 006) for number of fruits, average single fruit weight and fruit yield; P4 (BG 027) for node number of first female flower and days to seed fruit maturity; P3 (BG 011) for fruit length and thickness of the fruit flesh; P5 (BG 033) for 100-seed weight; and P6 for number of nodes per main vine. The SCA effect as well as reciprocal effect was also significant for most of the important characters in different crosses.

A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.

Spike protein recognizer receptor ACE2 targeted identification of potential natural antiviral drug candidates against SARS-CoV-2

Angiotensin-converting enzyme 2 (ACE2), also known as peptidyl-dipeptidase A, belongs to the dipeptidyl carboxydipeptidases family has emerged as a potential antiviral drug target against SARS-CoV-2. Most of the ACE2 inhibitors discovered till now are chemical synthesis; suffer from many limitations related to stability and adverse side effects. However, natural, and selective ACE2 inhibitors that possess strong stability and low side effects can be replaced instead of those chemicals' inhibitors. To envisage structurally diverse natural entities as an ACE2 inhibitor with better efficacy, a 3D structure-based-pharmacophore model (SBPM) has been developed and validated by 20 known selective inhibitors with their correspondence 1166 decoy compounds. The validated SBPM has excellent goodness of hit score and good predictive ability, which has been appointed as a query model for further screening of 11,295 natural compounds. The resultant 23 hits compounds with pharmacophore fit score 75.31 to 78.81 were optimized using in-silico ADMET and molecular docking analysis. Four potential natural inhibitory molecules namely D-DOPA (Amb17613565), L-Saccharopine (Amb6600091), D-Phenylalanine (Amb3940754), and L-Mimosine (Amb21855906) have been selected based on their binding affinity (−7.5, −7.1, −7.1, and −7.0 kcal/mol), respectively. Moreover, 250 ns molecular dynamics (MD) simulations confirmed the structural stability of the ligands within the protein. Additionally, MM/GBSA approach also used to support the stability of molecules to the binding site of the protein that also confirm the stability of the selected four natural compounds. The virtual screening strategy used in this study demonstrated four natural compounds that can be utilized for designing a future class of potential natural ACE2 inhibitor that will block the spike (S) protein dependent entry of SARS-CoV-2 into the host cell.

Role of High Neutrophil Lymphocyte Ratio as an Independent Predictor of Adverse In-Hospital Outcomes in Patients with First Attack of ST-Elevation Myocardial Infarction Thrombolysed with Streptokinase

Atherosclerosis is the pathognomic sign of ischaemic heart disease. Inflammation of the coronary artery contributes to the development of atherosclerosis. Neutrophil-to-lymphocyte ratio (NLR) has been reported to predict the risk of CAD and associated events in patients with ST-Segment elevation myocardial infarction (STEMI). This study was done to investigate the role of neutrophil-to-lymphocyte ratio (NLR) in predicting in-hospital adverse cardiac events in patients with STEMI thrombolysed with streptokinase (STK). This cross sectional descriptive type of study was conducted in the Department of Cardiology, Mymensingh Medical College Hospital, Mymensingh, Bangladesh from August, 2017 to October, 2018. The STEMI patients, thrombolysed with STK had blood samples at admission, analyzed for complete blood counts and NLR calculated. They were grouped into two, low and high NLR, taking 4.50 as cut-off value. Chi square test was used to compare rate of adverse events and death in hospital stay. Logistic regression analysis was used to estimate predictive ability of NLR for in-hospital cardiac events. A total of 87 (39.90%) patients had complications. Patients in high NLR group had higher rate of complications (48.3% vs. 22.5%, p<0.001) in hospital than those in low NLR group. Arrhythmias (21.1% vs. 9.9%, p<0.041), heart failure (27.9% vs. 14.1%, p=0.024), cardiogenic shock (16.3% vs. 4.2%, p<0.011), death (6.8% vs. 2.8%, p=0.227), re-infarction /post MI angina (4.1% vs. 0.0% p=0.084) occurred more in high NLR group. Mean NLR was significantly different between Group I and Group II (3.11±0.84 vs. 10.20±6.08, p<0.0001). Multivariate regression analysis showed NLR an independent predictor of in-hospital adverse cardiac events (p<0.0001). High on admission NLR is an independent predictor for in-hospital adverse cardiac events in patients with STEMI thrombolysed with streptokinase.

Accuracy of Magnetic Resonance Cholangiopancreatography in Case of Biliary Obstruction Comparing Post-operative Findings: A Study of 50 Cases

Complete assessment of obstructive jaundice requires the use of various imaging modalities that are required to detect the cause and level of obstruction thus helping in treatment planning. Magnetic Resonance Cholangio Pancreatography (MRCP) is a current available technology which is a non-invasive technique that visualizes the gallbladder, biliary tree and pancreatic duct and also provides information about surrounding structures. This study was done to correlate the MRCP findings with post-operative result and thereby demonstrate the specificity, sensitivity and efficacy of MRCP as an accurate investigatory tool for biliary obstruction. Total of fifty (50) patients of clinically diagnosed obstructive jaundice were studied from March 2017 to August 2017 in the Department of Radiology and Imaging, Combined Military Hospital, Dhaka, Bangladesh. In all these cases, USG was the initial screening investigation followed by MRCP. Cause and level of obstruction were evaluated using MRCP findings. MRCP results were correlated with surgical findings and few cases also with direct ERCP findings. Statistical analysis was done to see the sensitivity, specificity, accuracy, positive and negative predictive values of MRCP in diagnosis of biliary obstruction. In this study, USG detected level of obstruction in 56% (28 out of 50) cases. USG could detect causes of obstruction in 100% (02 out of 02) cases of choledocal cyst and 66.67% (02 out of 03) benign stricture, 60% (03 out of 05) cases of periampullary carcinoma, 57.70% (06 out of 14) cases of choledocholithiasis, and 42.86% (15 out of 26) cases of cholangiocarcinoma. On the other hand, MRCP detected level of obstruction in 98% (49 out of 50) cases. MRCP could detect causes of obstruction in 100% cases of cholangiocarcinoma, choledocholithiasis, benign stricture and choledocal cyst and 80% (04 out of 05) cases of periampullary carcinoma. In this study, ERCP could detect causes of obstruction in 32 cases of choledocholithiasis and benign stricture, but in case of cholangiocarcinoma ERCP was failed in 3 cases. In this study, for detection of cause of obstruction, ERCP had the highest sensitivity (97.79%); followed by MRCP (96.65%) and USG (60.25%). The overall diagnostic accuracy for detection of cause of obstruction was the highest for ERCP (95.50%); followed by MRCP (94.50%) and USG (64.50%). MRCP can be done in a short duration and is a noninvasive diagnostic modality compared to ERCP. MRCP needs to be advocated as a viable and non-invasive alternative with compararable sensitivity and specificity to ERCP.

Salinity Influences Plant-Pest-Predator Tritrophic Interactions

Climate change-induced salinity intrusion into agricultural soils is known to negatively impact crop production and food security. However, the effects of salinity increase on plant-herbivore-natural enemy systems and repercussions for pest suppression services are largely unknown. Here, we examine the effects of increased salinity on communities of rice (Oryza sativa), brown planthopper (BPH), Nilaparvata lugens, and green mirid bug (GMB), Cyrtorhinus lividipennis, under greenhouse conditions. We found that elevated salinity significantly suppressed the growth of two rice cultivars. Meanwhile, BPH population size also generally decreased due to poor host plant quality induced by elevated salinity. The highest BPH density occurred at 2.0 dS/m salinity and declined thereafter with increasing salinity, irrespective of rice cultivar. The highest population density of GMB also occurred under control conditions and decreased significantly with increasing salinity. Higher salinity directly affected the rice crop by reducing plant quality measured with reference to biomass production and plant height, whereas inducing population developmental asynchrony between BPH and GMB observed at 2 dS/m salinity and potentially uncoupling prey-predator dynamics. Our results suggest that increased salinity has harmful effects on plants, herbivores, natural enemies, as well as plant-pest-predator interactions. The effects measured here suggest that the bottom-up effects of predatory insects on rice pests will likely decline in rice produced in coastal areas where salinity intrusion is common. Our findings indicate that elevated salinity influences tritrophic interactions in rice production landscapes, and further research should address resilient rice insect pest management combining multipests and predators in a changing environment.

Alternative Medicine as a Treatment Option for COVID-19

:

COVID-19, a viral disease caused by SARS-CoV-2, is the reason for a global pandemic since the starting of the year 2020. The characteristics of the disease vary from mild common coldlike symptoms to acute respiratory distress syndrome and multi-organ failure leading to death. The world has already observed 213,453 deaths from this disease while 3,095,839 have been infected in 210 countries in total, till 28 April 2020. This disease has had a devastating impact on the health care system because of its high infectivity, easy mode of transmission, lack of proper medicine and vaccine, and deficiency of effectively supportive healthcare arrangement. On the verge of this situation, scientists are searching for treatment options. However, nature has provided us with a large number of herbs, which have disease preventive, as well as have medicinal properties. In this article, we have reviewed several of these plants (ginger, clove, tea, black seed, tulsi, neem), some vitamins (vitamin C and vitamin D) and zinc, which have antiviral, anti-inflammatory, antioxidant, and anti-asthmatic properties with scientific evidence. The intake of these products regularly to keep the immune system active and to experience its positive aspects, might be supportive to prevent infection with the new coronavirus or to treat COVID-19.

Rehabilitation Approach of a Patient with Myositis Ossificans: Non-surgical Management, Hazard of being Unguided Over Exercised

Myositis ossificans (MO) is a condition where calcification occurs in the soft tissue as well as around the bone following fracture, vigorous exercise or trauma. Although it is a radiological diagnosis, it often leads physician to an incorrect or missed diagnosis as recurrent fracture. Frequently, it follows haemorrhage into the muscle in the tissue space. We report a 45 years old house-wife presented with the complaints of weakness of right side of body and pain with restricted range of motion (ROM) in right lower limb. She was a diagnosed case of recurrent stroke with rheumatic valvular heart disease. After discharge, vigorous physical exercise was done at home by local physiotherapist without appropriate guidance from physiatrist. Gradually pain was so severe that she didn't allow moving her right lower limb. Over the course of time, she became incapacite and bed bound. She denied any positive family history. With the hip and lower limb problems she consulted with orthopedic surgeon and was referred to Physical Medicine and Rehabilitation department of Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh for further management & rehabilitation. This case is presented to focus on hazard of being unguided, over-exercised and non-surgical management approach of this rare condition.

Prevalence and Pattern of Dyslipidemia in Diabetes Mellitus Patients Admitted in the Department of Cardiology, Mymensingh Medical College Hospital, Mymensingh, Bangladesh

Patients with Diabetes Mellitus are at high risk of cardiovascular events because of abnormal lipid metabolism. Dyslipidemia is common in patients with Diabetes Mellitus (DM). However; in Bangladesh this issue is not yet properly addressed. The aim of this study is to determine the prevalence and patterns of dyslipidaemia in patients with DM in a divisional city Mymensingh. This cross-sectional study was conducted in randomly selected eligible patients from the indoor registry of the Department of Cardiology, Mymensingh Medical College Hospital (MMCH), Bangladesh from April 2012 to March 2013. A well structured questionnaire and blood investigation for lipid profile and blood sugar were the tools of data collection from 120 randomly selected DM patients registered in the department of cardiology, MMCH. Out of 120 enrolled participants the prevalence of dyslipidemia in DM patients was 86.0%, prevalence of dyslipidemia in males was 88.0% while in females was 85.0% but the difference was not significant (p=0.42). Regarding age group, BMI and duration of DM, there is no significant association exists with dyslipidemia. About half of the studied DM patients have high serum total cholesterol level (50.83%), while 22.5% had low serum HDL-C levels and 35.0% had high serum LDC-C level, most of patients had serum triglyceride levels above normal range (67.5%) and so the common patterns of dyslipidemia in this study were serum triglyceride level followed by total cholesterol. High prevalence of dyslipidemia among diabetes mellitus in Mymensingh city were observed and so the common patterns of dyslipidemia is triglyceride followed by total cholesterol. This study emphasizes the importance of screening of lipid profile as these abnormalities may lead to development of cardiovascular diseases.

Computer-based identification of potential compounds from Salviae miltiorrhizae against Neirisaral adhesion A regulatory protein

In silico studies are attracting considerable interest due to their ability to understand protein-ligand interactions at the atomic level. The main principal tools of this in silico analyses are molecular docking and molecular dynamic (MD) simulation. This paper examines how can natural compounds that are derived from Salviae miltiorrhizae to block Neisseria adhesion A Regulatory protein (NadR). In molecular docking analysis, only four compounds were found in higher binding affinity with NadR among 10 candidates (tanshinol B, tanshinol A, lithospermic acid and tournefolal were -7.61, -7.56, -8.22 and -7.81 kcal/mol, respectively, compared to -7.23 kcal/mol of native ligand). Absorption, distribution, metabolism, excretion (ADME) and toxicity properties, medicinal chemistry profile, and physicochemical features were displayed that tournefolal contains good properties to work as a safe and good anti-adhesive drug. Therefore, the complexes of these four ligands with NadR protein were subjected to 100 ns of MD simulation. RMSD, RMSF, RG and hydrogen bonding exhibited that tournefolal showed stable binding affinity and molecular interaction with NadR protein. In light of these results, there is now a need to conduct much more in vitro and in vivo studies about the efficacy of tournefolal.Communicated by Ramaswamy H. Sarma.

Combination of QSAR, molecular docking, molecular dynamic simulation and MM-PBSA: analogues of lopinavir and favipiravir as potential drug candidates against COVID-19

Pandemic COVID-19 infections have spread throughout the world. There is no effective treatment against this disease. Viral RNA-dependent RNA polymerase (RdRp) catalyzes the replication of RNA from RNA and the main protease (M^pro) has a role in the processing of polyproteins that are translated from the RNA of SARS-CoV-2, and thus these two enzymes are strong candidates for targeting by anti-viral drugs. Small molecules such as lopinavir and favipiravir significantly inhibit the activity of M^pro and RdRp in vitro. Studies have shown that structurally modified lopinavir, favipiravir, and other similar compounds can inhibit COVID-19 main protease (M^pro) and RNA-dependent RNA polymerase (RdRp). In this study, lopinavir and its structurally similar compounds were chosen to bind the main protease, and favipiravir was chosen to target RNA-dependent RNA polymerase. Molecular docking and the quantitative structure-activity relationships (QSAR) study revealed that the selected candidates have favorable binding affinity but less druggable properties. To improve the druggability, four structural analogues of lopinavir and one structural analogue of favipiravir was designed by structural modification. Molecular interaction analyses have displayed that lopinavir and favipiravir analogues interact with the active site residues of M^pro and RdRp, respectively. Absorption, distribution, metabolism, excretion and toxicity (ADMET) properties, medicinal chemistry profile, and physicochemical features were shown that all structurally modified analogues are less toxic and contain high druggable properties than the selected candidates. Subsequently, 50 ns molecular dynamics simulation of the top four docked complexes demonstrated that CID44271905, a lopinavir analogue, forms the most stable complex with the M^pro. Further MMPBSA analyses using the MD trajectories also confirmed the higher binding affinity of CID44271905 towards M^pro. In summary, this study demonstrates a new way to identify leads for novel anti-viral drugs against COVID-19.

Communicated by Ramaswamy H. Sarma

Molecular Detection of Human Brucellosis among Patients with Pyrexia of Unknown Origin

This study describes the molecular detection of human brucellosis among patients with pyrexia of unknown origin. It was a cross-sectional descriptive study and was carried out in the Department of Microbiology, Mymensingh Medical College, Mymensingh, Bangladesh. Non-probability purposive type of sampling technique was used. Blood samples were collected from 400 pyretic patients from September 2018 to August 2019. BCSP31 Brucella genus-specific TaqMan real-time PCR and SYBR Green real-time PCR were undertaken for molecular detection. Out of 400 samples, 22 (5.5%) samples found BCSP31 Brucella genus-specific real-time PCR positive. The study revealed that a considerable number of brucellosis is present in rural areas among risk as well as non-risk group study population having definite male predominancy, most prone to develop among >40-80 years age group. Brucella genus and species-specific real-time PCR might be performed for confirmation and also to avoid unjustified costs, drug toxicity, and un-masking of other potentially dangerous diseases.

Relationship of Plasma Vitamin-D Level with Left Ventricular Ejection Fraction in Patients with First Attack of Acute Myocardial Infarction

It has been widely reported that vitamin D deficiency is associated with Coronary heart disease (CHD), especially acute Myocardial infarction (MI). Many factors are responsible for reduced Left ventricular ejection fraction (LVEF) and acute Left ventricular fraction (LVF) after acute MI. This cross sectional descriptive type of study was conducted in the Cardiology department of Mymensingh Medical College Hospital from October 2017 to March 2019 to investigate the relationship of plasma vitamin D with LVEF in patients with first attack of acute MI. Total 185 patients of first attack of acute MI were included considering inclusion and exclusion criteria. Fasting blood samples were analyzed for plasma vitamin D level. Sample population were grouped at first into two, normal and low vitamin D level, taking 30ng/ml as cut-off value, low vitamin D level is further subdivided into insufficiency (21-29ng/ml), deficiency (10-20ng/ml) and severe deficiency (<10ng/ml). LVEF among the patients was observed. LVEF was found 49.88±8.58% patients having normal vitamin D level (>30ng/ml), 47.60±8.24% of patients having vitamin D insufficiency (21-29ng/ml), 44.38±8.12% of patients having vitamin D deficiency (10-20ng/ml) and 40.61±8.64% patients having severe vitamin D deficiency (<10ng/ml), which was statistically significant (p<0.05). So, low plasma vitamin D level is associated with reduced LVEF in patients hospitalized with first attack of acute MI.

Ramlibacter pinisoli sp. nov., a novel bacterial species isolated from pine garden soil

A Gram-stain-negative, aerobic, non-motile and rod- or coccoid-shaped novel bacterial strain, designated MAH-25^T, was isolated from soil sampled in a pine garden. The colonies were observed to be light pink-coloured, smooth, spherical and 1-2 mm in diameter when grown on nutrient agar for 2 days. Strain MAH-25^T was found to be able to grow at 15-35 °C, at pH 5.0-8.0 and at 0-2.0 % NaCl. Cell growth occurred on Reasoner's 2A agar and nutrient agar. The strain was found to be positive in both oxidase and catalase tests. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Ramlibacter and closely related to Ramlibacter solisilvae 5-10^T (98.0 % similarity), Ramlibacter henchirensis TMB834^T (97.7 %), Ramlibacter tataouinensis TTB310^T (97.6 %) and Ramlibacter rhizophilus YS3.2.7^T (97.3 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-25^T and the four closely related type strains were in the range of 78.8-81.3 % and 22.3-24.1 %, respectively. The novel strain MAH-25^T has a draft genome size of 5 505 957 bp (11 contigs), annotated with 5210 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content was determined to be 70.3 mol%. The predominant isoprenoid quinone was ubiquinone 8 (Q-8). The major fatty acids were identified as C_16 : 0, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. On the basis of DNA-DNA hybridization, genotypic analysis, chemotaxonomic and physiological data, strain MAH-25^T represents a novel species within the genus Ramlibacter, for which the name Ramlibacter pinisoli sp. nov. is proposed, with MAH-25^T (=KACC 19839^T=CGMCC1.13660^T) as the type strain.

Homology Modeling and Probable Active Site Cavity Prediction of Uncharacterized Arsenate Reductase in Bacterial spp

The arsC gene-encoded arsenate reductase is a vital catalytic enzyme for remediation of environmental arsenic (As). Microorganisms containing the arsC gene can convert pentavalent arsenate (As[V]) to trivalent arsenite (As[III]) to be either retained in the bacterial cell or released into the air. The molecular mechanism governing this process is unknown. Here we present an in silico model of the enzyme to describe their probable active site cavities using SCFBio servers. We retrieved the amino acid sequence of bacterial arsenate reductase enzymes in FASTA format from the NCBI database. Enzyme structure was predicted using the I-TASSER server and visualized using PyMOL tools. The ProSA and the PROCHECK servers were used to evaluate the overall significance of the predicted model. Accordingly, arsenate reductase from Streptococcus pyogenes, Oligotropha carboxidovorans OM5, Rhodopirellula baltica SH 1, and Serratia ureilytica had the highest quality scores with statistical significance. The plausible cavities of the active site were identified in our examined arsenate reductase enzymes which were abundant in glutamate and lysine residues with 6 to 16 amino acids. This in silico experiment may contribute greatly to the remediation of arsenic pollution through the utilization of microbial species.

Bifidobacterium longum DS0956 and Lactobacillus rhamnosus DS0508 culture-supernatant ameliorate obesity by inducing thermogenesis in obese-mice

Excessive body fat and the related dysmetabolic diseases affect both developed and developing countries. The aim of this study was to investigate the beneficial role of a bacterial culture supernatant (hereafter: BS) of Lactobacillus and Bifidobacterium and their potential mechanisms of action on white-fat browning and lipolysis. For selection of four candidates among 55 Lactic acid producing bacteria (LAB) from human infant faeces, we evaluated by Oil Red O staining and Ucp1 mRNA quantitation in 3T3-L1 preadipocytes. The expression of browning and lipolysis markers was examined along with in vitro assays. The possible mechanism was revealed by molecular and biological experiments including inhibitor and small interfering RNA (siRNA) assays. In a mouse model, physiological, histological, and biochemical parameters and expression of some thermogenesis-related genes were compared among six experimental groups fed a high-fat diet and one normal-diet control group. The results allow us to speculate that BS treatment promotes browning and lipolysis both in vitro and in vivo. Moreover, the BS may activate thermogenic programs via a mechanism involving PKA-CREB signaling in 3T3-L1 cells. According to our data, we can propose that two LAB strains, Bifidobacterium longum DS0956 and Lactobacillus rhamnosus DS0508, may be good candidates for a dietary supplement against obesity and metabolic diseases; however, further research is required for the development as dietary supplements or drugs.

Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach

Ongoing COVID-19 outbreak has raised a drastic challenge to global public health security. Most of the patients with COVID-19 suffer from mild flu-like illnesses such as cold and fever; however, few percentages of the patients progress from severe illness to death, mostly in an immunocompromised individual. The causative agent of COVID-19 is an RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite these debilitating conditions, no medication to stop the disease progression or vaccination is available till now. Therefore, we aimed to formulate a multi-epitope vaccine against SARS-CoV-2 by utilizing an immunoinformatics approach. For this purpose, we used the SARS-CoV-2 spike glycoprotein to determine the immunodominant T- and B-cell epitopes. After rigorous assessment, we designed a vaccine construct using four potential epitopes from each of the three epitope classes such as cytotoxic T-lymphocytes, helper T-lymphocyte, and linear B-lymphocyte epitopes. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. More importantly, the predicted vaccine structure was similar to the native protein. Further investigations indicated a strong and stable binding interaction between the vaccine and the toll-like receptor (TLR4). Strong binding stability and structural compactness were also evident in molecular dynamics simulation. Furthermore, the computer-generated immune simulation showed that the vaccine could trigger real-life-like immune responses upon administration into humans. Finally, codon optimization based on Escherichia coli K12 resulted in optimal GC content and higher CAI value followed by incorporating it into the cloning vector pET28+(a). Overall, these results suggest that the designed peptide vaccine can serve as an excellent prophylactic candidate against SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

Correlation of Mean Platelet Volume with ST Segment Resolution after Thrombolytic Therapy in Patients with ST Elevation Myocardial Infarction

Acute occlusive thrombosis of the coronary artery is the principal cause of myocardial infarction where platelets play an important role. Large size platelets, easily measured by mean platelets volume (MPV) are thrombogenic and commonly seen after ST-segment elevation myocardial infarction (STEMI). ST segment resolution has been shown as a simple non-invasive marker that reflects both epicardial and myocardial reperfusion following thrombolysis. The present study intended to investigate whether MPV on admission correlated with ST segment resolution following thrombolysis in STEMI patient. This cross-sectional analytical study was conducted in the department of cardiology, Mymensingh Medical College and Hospital (MMCH), Mymensingh, Bangladesh from December, 2016 to June, 2018. Total 284 patients with first attack of STEMI were included after considering inclusion and exclusion criteria. Sample population was divided into two groups, Group I - Patients with successful ST segment resolution (≥50%). Group II - Patients with impaired ST segment resolution (<50%). MPV on admission was estimated during estimation of Complete Blood Count (CBC) by Automated Haematology Analyzer & compared between two groups. Successful ST segment resolution (≥50%) was seen in 67% of patients after thrombolysis. Admission MPV was higher in patients with impaired ST segment resolution (<50%) group than patients with ≥50% ST-segment resolution group (12.42±0.89fl vs.10.35±0.77fl respectively, p=0.001). Statistically significant strong negative correlation between MPV and ST segment resolution percentage (r = -0.742, p=0.001) suggesting that the higher the level of MPV, the lower the ST segment resolution percentage in first attack of STEMI patients. Multivariate regression analysis found MPV level on admission as an independent predictor of ST segment resolution. The study concluded that high MPV on admission correlate with impaired ST segment resolution following thrombolysis in STEMI patients.

Association of Stress Hyper-Glycaemia on Outcomes of Hospitalized Non Diabetic Patients with First Attack of Acute ST Elevated Myocardial Infarction Underwent Thrombolysis

Coronary heart disease (CHD) is the most common cause of heart disease and serious cause of early death in developed countries around the world. Stress hyper-glycaemia has a bad prognostic implication in hospital outcomes in acute ST elevated myocardial infarction patients. It serves as a marker of myocardial damage, provides information about complications of acute MI and bad prognosis. The aim of this cross-sectional descriptive study was to find out prognostic implications of Stress hyper-glycaemia in non diabetic patients with first attack of acute ST elevated myocardial infarction underwent thrombolysis and conducted in the department of Cardiology in Mymensingh Medical College Hospital, Mymensingh, Bangladesh from June 2017 to May 2018. Total 249 first attack of Acute STEMI patients were included considering inclusion and exclusion criteria. The sample population was divided into two groups: Group I: Patients with first attack of acute STEMI underwent thrombolysis with non diabetic stress hyper-glycaemia (Blood sugar >7.8mmol/L and HbA1c <6.5), Group II: Patients with first attack of acute STEMI underwent thrombolysis with non diabetic normo-glycaemia (Blood sugar <7.8mmol/L and HbA1c <6.5). In this study, in non diabetic Stress hyperglycemic patients' death was 5.7% and in non diabetic normo-glycemic patients death was 0.6%. It was statistically significant (p<0.05). In non diabetic stress hyperglycemic patients, heart failure was 78.31% patients and in non diabetic normo-glycemic patients, it was 21.6%. It was statistically significant (p<0.01). Echocardiography showed that patients with non diabetic Stress hyper-glycaemia had mean ejection fraction (LVEF) was 44.01±4.93 and patients with non diabetic normo-glycaemia had mean ejection fraction (LVEF) was 47.70±5.71. It was statistically significant (p<0.01). In this study, in non diabetic Stress hyperglycaemic patients, cardiogenic shock was 16.1% and in non diabetic normo-glycemic patients, it was 3.7%. It was statistically significant (p<0.05). Mean duration of hospital stay, in non diabetic Stress hyperglycaemic patients was 5.07±0.566 and in non diabetic normo-glycemic patients, it was 3.52±0.850. It was statistically significant (p<0.001). In conclusion, the incidence of death, heart failure, cardiogenic shock and hospital stay were higher in non diabetic Stress hyperglycaemic patients than non diabetic normo-glycemic patients who admitted with first attack of acute ST elevated myocardial infarction.

PROM1 and PROM2 expression differentially modulates clinical prognosis of cancer: a multiomics analysis

Prominin 1 (PROM1) is considered a biomarker for cancer stem cells, although its biological role is unclear. Prominin 2 (PROM2) has also been associated with certain cancers. However, the prognostic value of PROM1 and PROM2 in cancer is controversial. Here, we performed a systematic data analysis to examine whether prominins can function as prognostic markers in human cancers. The expression of prominins was assessed and their prognostic value in human cancers was determined using univariate and multivariate survival analyses, via various online platforms. We selected a group of prominent functional protein partners of prominins by protein-protein interaction analysis. Subsequently, we investigated the relationship between mutations and copy number alterations in prominin genes and various types of cancers. Furthermore, we identified genes that correlated with PROM1 and PROM2 in certain cancers, based on their levels of expression. Gene ontology and pathway analyses were performed to assess the effect of these correlated genes on various cancers. We observed that PROM1 was frequently overexpressed in esophageal, liver, and ovarian cancers and its expression was negatively associated with prognosis, whereas PROM2 overexpression was associated with poor overall survival in lung and ovarian cancers. Based on the varying characteristics of prominins, we conclude that PROM1 and PROM2 expression differentially modulates the clinical outcomes of cancers.

Combined effect of salt stress and Xanthomonas axonopodis pv citri on citrus (Citrus aurantifolia)

Xanthomonas axonopodis pv citri (Xac) and salt stress are two crucial hindrances to citrus production. The effect of continuous salt application and Xac infection in citrus has been investigated. Citrus plants were exposed to salt stress by irrigating with 50 mM, 100 mM, 150 mM, and 200 mM NaCl solution on weekly basis and challenged by Xac. Salt stress affected the defense response of Citrus plants to Xac and therefore lesion diameter and disease severity were gradually increased at higher salt concentration. Meanwhile, accumulation of Na+ and Cl- in the leaves were also increased with the increase of salt concentration. Besides, physiological performance (PP) of plants was estimated based on the parameters such as net assimilation rate, chlorophyll content, stomatal conductance, transpiration rate and intercellular CO2 concentration. The PP of sole Xac treated plants was gradually increased and maintained up to end of the experiment, whereas plants treated with Xac+50 mM and Xac+100 mM NaCl showed the highest PP up to 30 days after inoculation and then decreased. However, the PP of Xac+150 mM and Xac+200 mM NaCl treated plants gradually decreased till the end of experiment. Similarly, the PP of 200 mM NaCl treated plants declined continuously. Interestingly, the PP in 50 mM and 100 mM NaCl treated plants was higher initially and then decreased at 30 DAI to 40 DAI. This study revealed that citrus canker disease development was enhanced by salt stress. In addition, the physiological performance of the plants was enhanced by Xac and Xac + moderate salt stress but then demolished under severe salt stress.

Redefinition of site percolation in light of entropy and the second law of thermodynamics

In this article, we revisit random site and bond percolation in a square lattice, focusing primarily on the behavior of entropy and the order parameter. In the case of traditional site percolation, we find that both the quantities are zero at p=0, revealing that the system is in the perfectly ordered and in the disordered state at the same time. Moreover, we find that entropy with 1-p, which is the equivalent counterpart of temperature, first increases and then decreases again, but we know that entropy with temperature cannot decrease. However, bond percolation does not suffer from either of these two problems. To overcome this, we propose an alternative definition for site percolation where we occupy sites to connect bonds and we measure cluster size by the number of bonds connected by occupied sites. This resolves all the problems without affecting any of the existing known results.

Study of Diameter of Lymphoid Follicle of Vermiform Appendix in Bangladeshi People of Different Age and Sex

A cross sectional descriptive study was performed on 40 postmortem vermiform appendix (male 24 and female 16) to find out the diameter of lymphoid follicle of vermiform appendix of Bangladeshi people. The specimens were collected from autopsy laboratory of the Department of Forensic Medicine, Mymensingh Medical College, Mymensingh, Bangladesh by purposive sampling technique and were divided into four age groups. They were Group A (upto 20 years), Group B (21 to 40 years), Group C (41 to 60 years) and Group D (above 60 years). For this purpose, about 3mm long of whole thickness transverse section was taken from the middle of the vermiform appendix and thus the permanent slides were made for microscopic examination. To measure the diameter of the lymphoid follicle two measurements were taken. One was taken at the maximum diameter and another was perpendicular to it by ocular micrometer. Diameter of one largest and one smallest lymphoid follicles were measured and find out the mean diameter of lymphoid follicle between them. Diameter of lymphoid follicle = (Maximum transverse diameter + perpendicular diameter) /2. All data were recorded in the predesigned data sheet, analyzed by SPSS program (version 21, 2012) and compared with the findings of other national and international studies and standard text books. It was observed that diameter of lymphoid follicle of vermiform appendix gradually decreased as age advanced. The mean±SD diameter of lymphoid follicle was 580.31±37.07, 545.58±38.37, 485.68±40.20 and 428.12±68.41μm in Group A, B, C and D respectively. Statistical analysis shows that the mean differences of diameter of lymphoid follicle between A&B, C&D were statistically non significant at p= or >0.05 level, difference between Group B&C was statistically moderately significant at p<0.01 level and differences between Group A&C, B&D, A&D were statistically highly significant at p<0.001 level. Mean diameter of lymphoid follicle of vermiform appendix in male was higher (584.30±12.65μm in Group A, 549.42±38.36μm in Group B, 487.38±39.91μm in Group C, 430.68±70.30μm in Group D) than in female (576.31±53.77μm in Group A, 536.61±45.14μm in Group B, 483.14±46.68μm in Group C, 424.28±75.95μm in Group D) but mean difference between sexes in the different groups was statistically non significant at p=or >0.05 level. The present study will help to increase the information pool on the diameter of lymphoid follicle of vermiform appendix of Bangladeshi people.

Antibacterial activities of green tea crude extracts and synergistic effects of epigallocatechingallate (EGCG) with gentamicin against MDR pathogens

Plant extracts and their purified compounds were examined for synergistic antimicrobial activity using selected multi-drug resistant (MDR) pathogens. The study aims to investigate the antibacterial activity of green tea (Camellia sinensis) and its purified compound epigallocatechingallate (EGCG). The synergistic relation of the compound with antibiotic was detected against selected potential Gram positive and Gram negative pathogens. Staphylococcus aureus and Escherichia coli were used as test pathogens which were resistant to different groups of antibiotics. After collection of fresh green tea leaves, samples were washed and air dried. EGCG is one of the bioactive compounds and was separated from tea plant. Antibacterial activity of EGCG and crude extracts of green tea were done by microdilution method (minimum inhibitory concentration and minimum bactericidal concentration). The synergistic effect of EGCG and gentamicin was determined. MIC value of green tea extract was found at 125 μg/mL in case of MDR E. coli, MDR S. aureus and their reference strains and MBC at 500 μg/mL against S. aureus. No MBC value was found against E. coli. EGCG showed better activity on Gram positive pathogen compared to that of Gram negative. MBC value of this compound was 1250 μg/mL for E. coli where 625 μg/mL for S. aureus. Strong synergistic relation (FICI 0.325) was found against pathogens in the combination of EGCG with gentamycin. The purified EGCG compound of green tea has great synergistic effect against MDR pathogens. More investigation is needed to know the inhibitory effect of these plant extracts and their components.

Prevalence and Predictors of Depression among Patients with Type 2 Diabetes: A Multicenter Cross-sectional Study from Bangladesh

Depression is a common comorbidity of type 2 diabetes mellitus (T2DM) which adversely affects diabetes management and outcome. Identifying and treating comorbid depression may improve diabetes care. This cross-sectional study was conducted in several tertiary hospitals throughout Bangladesh from July 2017 to April 2018. Nine hundred (900) adult patients with T2DM aging ≥25 years having diabetes for at least 6 months and equal numbers of non-diabetic otherwise healthy controls were recruited from the outpatient departments of these centers. Depression was assessed in all consenting patients and controls by administering the Bangla (local language) version of the PRIME-MD Patient Health Questionnaire (PHQ-9); participants obtaining a score of 5 or more were labeled to have depression. Depression was present in 60.3% of T2DM patients and in 29.4% of controls. Statistically significant difference was found in age, marital status, occupation, body mass index (BMI), waist circumference, systolic blood pressure (BP), diastolic BP and PHQ-9 score between diabetic and non-diabetic subjects (<0.001). T2DM subjects had 4.71-fold higher odds of depression in comparison to the controls (95% CI: 3.76-5.90; p<0.001). Age ≥50 years, unmarried status, years of schooling ≤10 years, underweight, abdominal obesity, and hypertension appeared to be the significant predictors of depression in the study subjects. In T2DM subjects, diabetes in the family members, the presence of other comorbidities, diabetic complications, diabetes duration >5 years, insulin use, using insulin syringe for injection, albuminuria and CKD were the important predictors of depression. Our study found higher prevalence and risk of depression in T2DM patients than their non-diabetic counterparts. T2DM patients should be screened for depression in order to achieve and maintain the treatment goals.

Outcome of Transcanalicular Endolaser and External Dacryocystorhinostomy in Chronic Dacryocystitis

Nasolacrimal duct obstruction due to chronic dacryocystitis is the most common cause of epiphora. Dacryocystorhinostomy (DCR) is the treatment of choice for chronic dacryocystitis. This can be carried out by external, endoscopic and endolaser surgical approach. Though external DCR is still a gold standard and most popular method, the latest procedure of less traumatic DCR is transcanalicular approach. The study was done to evaluate the outcome of Transcanalicular Endolaser DCR regarding epiphora and surgery related complications by measuring anatomical success rate (patency assessed by irrigation), functional success rate (symptom free) and complication rate and to compare with External DCR (Ext-DCR). This prospective interventional study was conducted from October 2011 to September 2012 in Ophthalmology department of Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh. Total 62 patients included in the study as per inclusion and exclusion criteria of them 31 for TCEL-DCR and 31 for Ext-DCR. But during follow-up one patient was dropped from each group and finally outcome of 30 patients analyzed in each group. Mean age of the patients TCEL-DCR was 38.3±11.54 and of Ext-DCR was 38.4±14.01. In both groups females were the most sufferer (female: male = 1.5: 1). Functional and anatomical success rate of TCEL-DCR showed 93.3% and 83.3% after 3 months; 83.3% and 76.7% after 6 months respectively. Statistically non-significant difference was observed about success rate in comparison between groups. Per-operative complications were pain excessive bleeding. In TCEL-DCR pain complained 13.3% and excessive bleeding occurred in 3.3%. Where as in Ext-DCR pain complained 16.7% and excessive bleeding occurred in 20%; difference was statistically significant (p=0.001). Post-operative complications were bleeding and scar formation. Bleeding occurred in TCEL-DCR 6.67% and in Ext-DCR 10%. So, TCEL-DCR could be an alternative option for the treatment of chronic dacryocystitis especially for those patients who are conscious about scar formation and afraid about Ext-DCR technique.

Prevalence of clinical and subclinical caprine mastitis of northern region in Bangladesh

Mastitis is a multifactorial and infectious disease of the udder of dairy animals. Infected animals suffer from pain and fever and causing damage in udder and changes in milk. The aim of this work was to determine the prevalence of clinical and sub-clinical caprine mastitis associated with bacterial pathogens during the period from January to June, 2017. A total of 120 lactating goats were randomly selected from different villages of Dinajpur district and 240 milk samples from each udder half were aseptically collected. The udders were examined and screened for the evidence of clinical and subclinical mastitis by clinical examination of udders and examining milk samples. Subclinical mastitis was detected by California Mastitis Test (CMT). Milk samples of all clinical and subclinical mastitis goats were cultured in/on bacteriological media for isolation and characterization of responsible bacterial pathogens. The overall prevalence of clinical and subclinical mastitis in goats was found to be 11.67% and 38.75%, respectively. Bacteriological examination of mastitic milk samples of caprine revealed Staphylococcus spp. (32.5%) as the major pathogen followed by Escherichia coli (22.5%), Pseudomonas spp. (12.5%), Klebsiella spp. (12.5%) and Bacillus spp. (5%). Results of this study indicated that about 50% of caprine udder were infected with mastitis (38.75%), which may render lowering milk production and mortality of goats and kids. It needs to screen milk sample of lactating goats by CMT, identify mastitic goats with infected bacteria, evaluate antibiotic sensitivity and design control strategy accordingly.Progressive Agriculture 29 (2): 127-138, 2018

Clinicopathological Study of Enterocutaneous Fistula in Mymensingh Medical College Hospital

Enterocutaneous fistulae are a major catastrophe to the patients and surgeons and it still has high incidence of morbidity and mortality and their management remains a big challenge. Enterocutaneous fistula presents the surgeon with challenges of metabolic disorders and extensive sepsis. Total management of an intestinal fistula requires skill in nutritional support, stoma therapy, elimination of sepsis, well timed and well carried out surgery. Postoperative enterocutaneous fistulae account for approximately 80% of enterocutaneous fistulae. The majority of the intestinal fistula (75-85%) is iatrogenic occurring in the postoperative period following anastomotic dehiscence. They arise following emergency abdominal surgery for intestinal obstruction, inflammatory bowel disease or cancers. Protein calorie malnutrition alters the patients immune response, inflammatory reactions and tissue regenerations, all of which are essential for wound repair. The present study is an effort to highlight the incidence of enterocutaneous fistula after emergency and elective resection and anastomosis of gut with discussion over recent trends and developments in its management and compare with other studies. Objectives of the study are to determine the various clinicopathological features and management protocol of enterocutaneous fistula. There are recent advances in nutritional support. This descriptive type of cross-sectional study was carried out in the Department of Surgery, Mymensingh Medical College and Hospital, Mymensingh, Bangladesh from October 2010 to September 2011. Total 42 cases of enterocutaneous fistulae were selected purposively. Enterocutaneous fistulae are more common in patients of low economic condition. Enterocutaneous fistulae are more common after emergency abdominal surgery. Spontaneous closure occurred in 17(40.48%) cases and surgery needed in 25(59.52%) cases. Of them 20(80.00%) were healed and 5(20.00%) were expired. In spite of improvement in the management protocol of enterocutaneous fistula, there is still high unacceptable morbidity and mortality rate. Total parenteral nutrition (TPN) is not available and very costly, and health care facilities are also limited in our country. Patients with enterocutaneous fistula require fluid, electrolytes and nutritional support. Anaemia, dehydration, electrolytes imbalance should be corrected prior to abdominal surgery if possible. Surgical treatment for enterocutaneous fistula should be performed only after failure of conservative treatment of more than 12 weeks.

Healthcare-associated (HA) and community-associated (CA) methicillin resistant Staphylococcus aureus (MRSA) in Bangladesh - Source, diagnosis and treatment

Methicillin-resistant Staphylococcus aureus (MRSA) has long been a common pathogen in healthcare facilities, but now, it has emerged as a problematic pathogen in the community setting as well. This study reported source, diagnosis and treatment of HA-MRSA and CA-MRSA.

A total of sixty-five clinical samples (urine, pus, wound swab) were collected from clinical origin of Dhaka city, Bangladesh. All the isolates were tested phenotypically by conventional methods and genotypically by PCR targeting nuc, pvl and mecA genes. Finally sequencing was carried out for pvl gene to know the mutagenic variation or any amino acid changes in pvl gene. Chi square test was employed for statistical analysis. Patients of age group 51–60 years are more susceptible (46.15%) to MRSA, CA-MRSA or HA-MRSA infection. Female are (32.30%) more susceptible to MRSA infection. Among 65 isolates 53 isolates identified phenotypically as S. aureus. These were positive for amplification of nuc (270 bp) gene of S. aureus. Moreover, among 53 isolates 33 phenotypically considered as MRSA and 38 (72%) showed positive amplification for mecA (162 bp) gene. Among 38 MRSA isolates 22 (57.89%) confirmed as CA-MRSA and 16 (42.10%) as HA-MRSA. Finally, sequence analysis for lukS/F-PV genes from 4 representative isolates detected a new single nucleotide polymorphism in comparison with the control sequence. However, no amino acid changes were found. Statistical analysis showed HA-MRSA isolates were more commonly found in urine sample and CA-MRSA in pus and wound swab. CA-MRSA isolates were more resistant to tested antibiotics than HA-MRSA.