Molecular Cloning, In Silico Analysis, and Characterization of a Novel Cellulose Microfibril Swelling Gene Isolated from Bacillus sp. Strain AY8.

A novel cellulose microfibril swelling (Cms) gene of Bacillus sp. AY8 was successfully cloned and sequenced using a set of primers designed based on the conserved region of the gene from the genomic database. The molecular cloning of the Cms gene revealed that the gene consisted of 679 bp sequences encoding 225 amino acids. Further in silico analysis unveiled that the Cms gene contained the NlpC/P60 conserved region that exhibited a homology of 98% with the NlpC/P60 family proteins found in both the strains, Burkholderialata sp. and Burkholderia vietnamiensis. The recombinant Cms enzyme had a significant impact on the reduction of crystallinity indices (CrI) of various substrates including a 3%, a 3.97%, a 4.66%, and a substantial 14.07% for filter paper, defatted cotton fiber, avicel, and alpha cellulose, respectively. Additionally, notable changes in the spectral features were observed among the substrates treated with recombinant Cms enzymes compared to the untreated control. Specifically, there was a decrease in band intensities within the spectral regions of 3000-3450 cm-1, 2900 cm-1, 1429 cm-1, and 1371 cm-1 for the treated filter paper, cotton fiber, avicel, and alpha cellulose, respectively. Furthermore, the recombinant Cms enzyme exhibited a maximum cellulose swelling activity at a pH of 7.0 along with a temperature of 40 °C. The molecular docking data revealed that ligand molecules, such as cellobiose, dextrin, maltose 1-phosphate, and feruloyated xyloglucan, effectively bonded to the active site of the Cms enzyme. The molecular dynamics simulations of the Cms enzyme displayed stable interactions with cellobiose and dextrin molecules up to 100 ns. It is noteworthy to mention that the conserved region of the Cms enzyme did not match with those of the bioadditives like expansins and swollenin proteins. This study is the initial report of a bacterial cellulose microfibril swellase enzyme, which could potentially serve as an additive to enhance biofuel production by releasing fermentable sugars from cellulose.

In silico analysis of a novel hypothetical protein (YP_498675.1) from Staphylococcus aureus unravels the protein of tryptophan synthase beta superfamily (Try-synth-beta_ II).

BACKGROUND: Staphylococcus aureus is a gram-positive spherical bacteria and the most common cause of nosocomial infections in the world. Given its clinical significance, the genome sequence of S. aureus has been elucidated to enhance our comprehension of its lifestyle and pathogenicity. The research aimed to summarize a potential hypothetical protein that may play an important role in S. aureus virulence and pathogenicity, covering its anticipated structure, probable biological functions, and importance in this context. RESULTS: A hypothetical protein, YP_498675.1 with 281 amino acid residues of S. aureus, was chosen for analysis and modeling by several bioinformatics tools and databases in this work. According to primary and secondary structure analyses, YP_498675.1 is a stable hydrophilic protein with a significant proportion of α-helices. Subcellular localization predictions by CELLO, PSORTb, and SOSUI server indicate that it is a cytoplasmic protein. NCBI-CDD, Pfam, and InterProScan functional genomics research revealed that the hypothetical protein may include the pyridoxal phosphate (PLP)-dependent 2, 3-diaminopropionate biosynthesis protein SbnA domain. In the homology modeling method, the HHpred server was employed to create its 3D structure using the template structure of a Staphyloferrin B precursor biosynthetic enzyme SbnA bound to PLP (PDB ID: 5D84_A), an X-ray diffraction model having 100% sequence identity with the hypothetical protein. After energy minimization, several quality assessments and validation factors determined that the generated protein model was reliable and of reasonable quality. CONCLUSION: The present study has characterized and functionally annotated the hypothetical protein YP_498675.1 of S. aureus. Further experimental validation would aid in determining the actual function of YP_498675.1 as well as confirm the protein's value as a therapeutic target.

Association of CAPN10 gene (rs3842570) polymorphism with the type 2 diabetes mellitus among the population of Noakhali region in Bangladesh: a case-control study.

Type 2 diabetes mellitus (T2DM) is a multifactorial, polygenic, and metabolically complicated disease. A large number of genes are responsible for the biogenesis of T2DM and calpain10 (CAPN10) is one of them. The association of numerous CAPN10 genetic polymorphisms in the development of T2DM has been widely studied in different populations and noticed inconclusive results. The present study is an attempt to evaluate the plausible association of CAPN10 polymorphism SNP-19 (rs3842570) with T2DM and T2DM-related anthropometric and metabolic traits in the Noakhali region of Bangladesh. This case-control study included 202 T2DM patients and 75 healthy individuals from different places in Noakhali. A significant association (p < 0.05) of SNP-19 with T2DM in co-dominant 2R/3R vs. 3R/3R (odds ratio [OR], 2.7; p=0.0014) and dominant (2R/3R) + (2R/2R) vs. 3R/3R (OR, 2.47; p=0.0011) genetic models was observed. High-risk allele 2R also showed a significant association with T2DM in the allelic model (OR, 1.67; p=0.0109). The genotypic frequency of SNP-19 variants showed consistency with Hardy-Weinberg equilibrium (p > 0.05). Additionally, SNP-19 genetic variants showed potential associations with the anthropometric and metabolic traits of T2DM patients in terms of body mass index, systolic blood pressure, diastolic blood pressure, total cholesterol, and triglycerides. Our approach identifies the 2R/3R genotype of SNP-19 as a significant risk factor for biogenesis of T2DM in the Noakhali population. Furthermore, a large-scale study could be instrumental to correlate this finding in overall Bangladeshi population.

The prevalence of general obesity, abdominal obesity, and hypertension and its related risk factors among young adult students in Bangladesh.

Hypertension is a major cause of cardiovascular disease and related mortality worldwide. The presence of general and abdominal obesity in hypertensive individuals increases the risk of cardiovascular mortality. However, evidence on the burden of obesity and hypertension and associated factors are lacking or limited among young adult students in Bangladesh. This study measured the prevalence and factors associated with general and abdominal obesity and hypertension among university students in Bangladesh. In this study, a total of 1011 students (647 males and 364 females) were enrolled on nine public universities in eight divisional regions of Bangladesh. Data were collected on socio-demographic, anthropometric, and lifestyle in a questionnaire form. Unadjusted and adjusted logistic regression analyses were performed to evaluate the association of general obesity, abdominal obesity and hypertension with different factors. The prevalence of general obesity, abdominal obesity and hypertension was 8.3%, 20.7%, and 10.2%, respectively. The females had a higher prevalence of general obesity (8.8%) and abdominal obesity (26.3%) compared to the males (8.0% and 17.7%, respectively). However, a higher prevalence of hypertension was observed in males (12.2%) than in the female (6.1%) patients. In regression analysis, age showed a significant association with general obesity, whereas, age and female sex were significantly associated with abdominal obesity. The analysis also identified the male sex and high BMI as the increased risk factors for hypertension. Our study suggests a comprehensive screening program and campaigns to increase awareness about obesity and hypertension and its risk factors among young adults in Bangladesh.

Cogon grass (Imperata cylindrica), a potential biomass candidate for bioethanol: cell wall structural changes enhancing hydrolysis in a mild alkali pretreatment regime.

BACKGROUND: Imperata cylindrica is being considered as a biomass candidate for bioethanol. This work aimed to evaluate a mild alkali pretreatment effect on the Imperata recalcitrant structure. Therefore, varied concentrations of NaOH (0, 7.5, 15, 20, and 25 g L(-1) ) were applied as treatments to Imperata at 105 °C for 10 min. RESULTS: Scanning electron microscopy, atomic force microscopy, and Fourier transform infrared spectroscopy studies revealed that 20 to 25 g L(-1) NaOH-treated Imperata exposed amorphous cellulose on surface granules composed of lignin, waxes, and partly hemicelluloses were abolished due to the comprehensive disruption of the linkages between lignin and carbohydrates. The cellulose crystalline index was increased with 7.5 to 20 g L(-1) NaOH treatments and reduced with a 25 g L(-1) NaOH treatment. In fact, the cellulose content in solids increased with the increasing NaOH concentration and was estimated to be 720 and 740 g kg(-1) for the 20 and 25 g L(-1) NaOH treatments, respectively. The yield of the reducing sugar was obtained 805 and 813 mg g(-1) from 20 and 25 g L(-1) NaOH-treated Imperata, respectively. CONCLUSION: Considering the cost of pretreatment, the 20 g L(-1) NaOH treatment is judged to be effective for disrupting Imperata recalcitrance in this pretreatment regime.

Stress defense mechanisms of NADPH-dependent thioredoxin reductases (NTRs) in plants.

Plants establish highly and systemically organized stress defense mechanisms against unfavorable living conditions. To interpret these environmental stimuli, plants possess communication tools, referred as secondary messengers, such as Ca(2+) signature and reactive oxygen species (ROS) wave. Maintenance of ROS is an important event for whole lifespan of plants, however, in special cases, toxic ROS molecules are largely accumulated under excess stresses and diverse enzymes played as ROS scavengers. Arabidopsis and rice contain 3 NADPH-dependent thioredoxin reductases (NTRs) which transfer reducing power to Thioredoxin/Peroxiredoxin (Trx/Prx) system for scavenging ROS. However, due to functional redundancy between cytosolic and mitochondrial NTRs (NTRA and NTRB, respectively), their functional involvements under stress conditions have not been well characterized. Recently, we reported that cytosolic NTRA confers the stress tolerance against oxidative and drought stresses via regulation of ROS amounts using NTRA-overexpressing plants. With these findings, mitochondrial NTRB needs to be further elucidated.

Cloning and expression of ophB gene encoding organophosphorus hydrolase from endophytic Pseudomonas sp. BF1-3 degrades organophosphorus pesticide chlorpyrifos.

Chlorpyrifos is an organophosphate pesticide that has adverse effect on animals and plants. We isolated endophytic bacterial strain, Pseudomonas sp. BF1-3, from balloon flower root which can hydrolyze chlorpyrifos. A gene (ophB) encoding a protein involved in chlorpyrifos degradation from this strain was cloned into Escherichia coli DH5α for confirming enzyme activity. After sequencing, total 1024bp nucleotide sequences were found in the open reading frame of ophB. The chlorpyrifos degradation patterns by E. coli DH5α (ophB) were observed. During incubation in minimal salt (M9) medium supplemented with chlorpyrifos (100mgL(-1)), the E. coli DH5α harboring ophB degraded about 97% initial chlorpyrifos (100mgL(-1)) and accumulated 86mgL(-1) 3,5,6-trichloro-2-pyridinol (TCP) within 9 days. In addition, optical density (OD) of E. coli DH5α (ophB) culture at 600nm was increased from 0.172 to 1.118 within 2 days of inoculation in the chlorpyrifos supplemented M9 medium. The estimated molecular weight of purified OphB protein was determined to be 31.4kDa by SDS-PAGE. The OphB enzyme was most active at pH 8 and an optimal temperature around 35°C. These results indicate that endophytic bacteria are supposed to be useful for biological control of environments contaminated with pesticides.

Alkali pretreatment of wheat straw (Triticum aestivum) at boiling temperature for producing a bioethanol precursor.

We evaluated the effect of dilute sodium hydroxide (NaOH) on wheat straw at boiling temperature for removing lignin and increasing the yield of reducing sugar. Various concentrations of NaOH (0.5% to 2%) were used for pretreating wheat straw at 105 °C for 10 min. Scanning electron microscopy, atomic force microscopy, and Fourier transform infrared spectroscopy studies revealed that the 2% NaOH-pretreated sample exposed more cellulose fiber. The maximum respective removal of lignin and hemicellulose was 70.3% and 68.2% from the 2% NaOH-pretreated liquor. The reducing sugar yield was 84.6% using an enzyme dose containing 20 FPU of cellulase, 40 IU of ß-glucosidase and 4 FXU of xylanase/g of substrate. However, 2% NaOH-treated wheat straw had the lowest crystalline index of 52.5%, due to destructured cellulose fibers. The results indicate the effectiveness of producing the bioethanol precursor from wheat straw by using 2% NaOH at boiling temperature.