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1.
Microbiol Resour Announc ; 13(3): e0103223, 2024 Mar 12.
Article in English | MEDLINE | ID: mdl-38329357

ABSTRACT

We present the complete genome of Opitutales bacterium ASA1, isolated from soil. The genome is 5,821,695 bp with 4,638 protein-coding sequences. The genome data suggest that this strain belongs to the class Opitutae of the phylum Verrucomicrobiota, and its genome has six unique biosynthetic gene clusters associated with secondary metabolites.

2.
Medicine (Baltimore) ; 102(40): e35402, 2023 Oct 06.
Article in English | MEDLINE | ID: mdl-37800843

ABSTRACT

Semitendinosus and Gracilis autografts are commonly used for anterior cruciate ligament (ACL) reconstruction. However, its main drawback is individual variation in the tendon diameter. This study aimed to evaluate the usefulness of the anthropometric measurements for the prediction of Semitendinosus and Gracilis combined (quadrupled) strands graft diameter in arthroscopic ACL reconstruction among the Bengali population. Sixty consecutive patients who underwent ACL reconstruction between July 2019 to June 2020 were observed in this cross-sectional study. In all cases, the doubled (2 strands) Gracilis and Semitendinosus tendons were combined to get the final quadrupled (combined 4 strands) graft for use. Anthropometries such as body mass index (BMI), body weight, and height were recorded preoperatively and quadrupled combined tendon diameter was measured at the operating theater. The relationship between these parameters was statistically determined using the Pearson correlation coefficient, and scatter diagrams were plotted. Among the study subjects, most (54) were male, and the mean age of all subjects was 24 ±â€…6.92 years. The average graft diameter was 7.20 ±â€…0.76 mm. Correlations between the mean graft diameter with BMI (r = 0.018, and P = .891), body height (r = 0.011 and P = .933), and weight (r = 0.028 and P = .832) were not significant. Scatter diagrams also showed that the variables were not correlated. Anthropometries like BMI, body weight, or body height cannot be used in predicting Semitendinosus and Gracilis tendon graft diameter for arthroscopic ACL reconstruction among the Bengali population.


Subject(s)
Anterior Cruciate Ligament Injuries , Hamstring Muscles , Hamstring Tendons , Humans , Male , Adolescent , Young Adult , Adult , Female , Anterior Cruciate Ligament/surgery , Cross-Sectional Studies , Anthropometry , Hamstring Tendons/transplantation , Body Weight , Anterior Cruciate Ligament Injuries/surgery
3.
Int J Mol Sci ; 24(13)2023 Jun 25.
Article in English | MEDLINE | ID: mdl-37445776

ABSTRACT

Antimicrobial peptides (AMPs) are naturally occurring molecules found in various organisms that can help to defend against invading microorganisms and reduce the likelihood of drug resistance development. This study focused on the isolation of new AMPs from the genome library of a Gram-positive bacterium called Arthrobacter sp. H5. To achieve this, we used the Bacillus subtilis expression system and employed bioinformatics techniques to optimize and modify the peptides, resulting in the development of a new synthetic antimicrobial peptide (SAMP). Ap920 is expected to be a new antimicrobial peptide with a high positive charge (+12.5). Through optimization, a new synthetic antimicrobial peptide, Ap920-WI, containing only 15 amino acids, was created. Thereafter, the antimicrobial and antifungal activities of Ap920-WI were determined using minimum inhibitory concentration (MIC) and the concentration for 50% of maximal effect (EC50). The Ap920-WI peptide was observed to target the outer membrane of fungal hyphae, leading to inhibition of growth in Rhizoctonia Solani, Sclerotinia sclerotiorum, and Botrytis cinerea. In plants, Ap920-WI showed significant antifungal activity and inhibited the infestation of S. sclerotiorum on rape leaves. Importantly, Ap920-WI was found to be safe for mammalian cells since it did not show any hemolytic activity against sheep red blood cells. Overall, the study found that the new synthetic antimicrobial peptide Ap920-WI exhibits broad-spectrum activity against microorganisms and may offer a new solution for controlling plant diseases, as well as hold potential for drug development.


Subject(s)
Anti-Infective Agents , Arthrobacter , Animals , Sheep , Antimicrobial Cationic Peptides/pharmacology , Antimicrobial Peptides , Antifungal Agents/pharmacology , Anti-Infective Agents/pharmacology , Bacillus subtilis , Plant Diseases/microbiology , Microbial Sensitivity Tests , Anti-Bacterial Agents , Mammals
4.
Medicine (Baltimore) ; 102(9): e32943, 2023 Mar 03.
Article in English | MEDLINE | ID: mdl-36862908

ABSTRACT

Anterior cruciate ligament (ACL) tears are frequent ligamentous injuries that necessitate reconstruction in many cases. The patellar tendon and the hamstring tendon are the most frequently utilized autografts for reconstruction. However, both have certain disadvantages. We hypothesized that the peroneus longus tendon would be an acceptable graft for arthroscopic ACL reconstruction. The aim of this study is to determine whether a peroneus Longus tendon transplant is a functionally viable option for arthroscopic ACL reconstruction without compromising donor ankle activity. In this prospective study 439 individuals aged between 18 to 45 years, who underwent ACL reconstruction using ipsilateral Peroneus longus tendon autograft were observed. The injury to the ACL was initially assessed by physical examinations and further confirmed by magnetic resonance imaging (MRI). The outcome was assessed at 6, 12, and 24 months after the surgery using Modified Cincinnati, International Knee Documentation Committee (IKDC), and Tegner-Lysholm scores. The donor ankle stability was evaluated using foot and ankle disability index (FADI) and AOFAS scores, as well as hop tests. Significant (P < .001) improvement in the result of the IKDC score, Modified Cincinnati, and Tegner-Lysholm score was observed at the final follow-up. The Lachman test was mildly (1+) positive only in 7.70% of cases, the anterior drawer became negative in all cases, and the pivot shift test was negative in 97.43% of cases at 24 months after the surgery. FADI and AOFAS scores for donor's ankle functional assessment were impressive, as were single hop test, triple hop test, and cross over hop test results at 2 years. None of the patients had any neurovascular deficit. However, 6 cases of superficial wound infection were observed, 4 at the port site and 2 at the donor site. All resolved after appropriate oral antibiotic therapy. The peroneus longus tendon can be considered a safe, effective, and promising graft of choice for arthroscopic primary single-bundle ACL reconstruction because it has a good functional outcome and impressive donor ankle function after surgery.


Subject(s)
Anterior Cruciate Ligament Injuries , Hamstring Tendons , Humans , Adolescent , Young Adult , Adult , Middle Aged , Prospective Studies , Foot , Lower Extremity , Tendons , Anterior Cruciate Ligament Injuries/surgery
5.
PLoS One ; 17(10): e0276602, 2022.
Article in English | MEDLINE | ID: mdl-36279291

ABSTRACT

Flag leaf is an important organ for photosynthesis of wheat plants, and a key factor affecting wheat yield. In this study, quantitative trait loci (QTL) for flag leaf morphological traits in wheat reported since 2010 were collected to investigate the genetic mechanism of these traits. Integration of 304 QTLs from various mapping populations into a high-density consensus map composed of various types of molecular markers as well as QTL meta-analysis discovered 55 meta-QTLs (MQTL) controlling morphological traits of flag leaves, of which 10 MQTLs were confirmed by GWAS. Four high-confidence MQTLs (MQTL-1, MQTL-11, MQTL-13, and MQTL-52) were screened out from 55 MQTLs, with an average confidence interval of 0.82 cM and a physical distance of 9.4 Mb, according to the definition of hcMQTL. Ten wheat orthologs from rice (7) and Arabidopsis (3) that regulated leaf angle, development and morphogenesis traits were identified in the hcMQTL region using comparative genomics, and were speculated to be potential candidate genes regulating flag leaf morphological traits in wheat. The results from this study provides valuable information for fine mapping and molecular markers assisted selection to improve morphological characters in wheat flag leaf.


Subject(s)
Quantitative Trait Loci , Triticum , Triticum/genetics , Bread , Chromosome Mapping/methods , Phenotype , Plant Leaves/genetics , Plant Leaves/anatomy & histology
6.
Medicine (Baltimore) ; 101(34): e30216, 2022 Aug 26.
Article in English | MEDLINE | ID: mdl-36042621

ABSTRACT

Post-endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis (PEP) is a dreaded complication. But the frequency of this complication varies widely (1%-40%) among the literature and across geographical regions. With uncertainty in the estimation of occurrence and having no accepted, safe, effective method to prevent it, identification of its frequency and predictable risk factors is very crucial in a local or regional setting. The aim of this study was to identify the frequency of PEP and its risk factors from 4 tertiary care referral centers from a country in the South East Asia Region. This cross-sectional study was done on 1042 consecutive ERCP in adult patients (age >18 years) with baseline serum amylase levels less than 3 times the upper level of standard value. On the basis of clinical features and the amylase level at 24 hours (the next morning), the procedure was evaluated to confirm PEP. The frequency of PEP was calculated and procedure, patient, or operator-related independent risk factors for occurring PEP were analyzed using univariate and multivariate analyses. The study found 204 (19.6%) cases of PEP. In multivariate regression analysis, young age, suspected Sphincter of Oddi Dysfunction, recurrent pancreatitis, needle papillotomy, and pancreatic sphincterotomy were significant risk factors. The univariate analysis also found difficult cannulation and pancreatic duct injection with contrast as significant risk factors. Both patient-related and procedure-related risk factors acted independently for the development of PEP, which occurred in 19.6% of cases. This multicenter assessment of the frequency and risk factors for PEP in our patients would be extremely beneficial for future prevention of this complication.


Subject(s)
Cholangiopancreatography, Endoscopic Retrograde , Pancreatitis , Adult , Amylases , Cholangiopancreatography, Endoscopic Retrograde/adverse effects , Cross-Sectional Studies , Asia, Eastern , Hospitals , Humans , Pancreatitis/epidemiology , Pancreatitis/etiology , Pancreatitis/prevention & control , Risk Assessment , Risk Factors , Tertiary Healthcare
7.
IJID Reg ; 2: 55-59, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35721430

ABSTRACT

Introduction: The second wave of COVID-19 arrived in Bangladesh in March 2021. This pilot research from a tertiary care COVID-dedicated hospital observed the clinicodemographic profile, intensive care unit (ICU) utilization, and mortality rate among COVID-19 patients admitted during the second wave. Methods: Reverse transcription-polymerase chain reaction or chest high-resolution computed tomography confirmed 972 COVID-19 cases included in this cross-sectional study from 24 March to 23 June 2021, recruited using convenience sampling. Data regarding clinicodemographic profile, ICU utilization and mortality rate were analyzed. Results: The mean study cohort age was 54.47±12.73 years, with most patients (48.3%) aged 41-60; 64.1% were men. Fever (77.9%) and cough (75.9%) were the most common symptoms, and hypertension (43.6%) and diabetes (42.15%) the most common comorbidities. Nearly half of patients had total lung involvement of 26%-50%, and 23.8% required ICU. Overall mortality was 16.5%, whereas the mortality rate among ICU admitted patients was 56.1%. The most important predictors of mortality were older age, chronic renal illness, the proportion of lung involvement and ICU requirement. Conclusions: We found higher mortality and ICU utilization rate and greater total lung involvement during the second wave. The mortality rate among the elderly and ICU patients was also higher than earlier.

8.
Int J Mol Sci ; 23(9)2022 Apr 21.
Article in English | MEDLINE | ID: mdl-35563004

ABSTRACT

Antimicrobial peptides (AMPs) have natural antibacterial activities that pathogens find difficult to overcome. As a result of this occurrence, AMPs can act as an important substitute against the microbial resistance. In this study, we used plate confrontation tests to screen out 20 potential endophytes from potato tubers. Among them, endophyte F5 was found to significantly inhibit the growth of five different pathogenic fungi. Following that, phylogenetic analysis revealed that the internal transcribed spacer (ITS) sequences were 99% identical to Chaetomium globosum corresponding sequences. Thereafter, the Bacillus subtilis expression system was used to create a C. globosum cDNA library in order to isolate the resistance genes. Using this approach, the resistance gene screening technology in the indicator bacteria built-in library was used to identify two antimicrobial peptides, CgR2150 and CgR3101, with broad-spectrum antibacterial activities. Furthermore, the results showed that CgR2150 and CgR3101 have excellent UV, thermal, and enzyme stabilities. Also, these two peptides can significantly inhibit the growth of various bacteria (Xanthomonas oryzae pv. oryzae, Xanthomonas oryzae pv. oryzicola, Clavibacter michiganensis, and Clavibacter fangii) and fungi (Fusarium graminearum, Rhizoctonia solani, and Botrytis cinerea). Scanning electron microscopy (SEM) observations revealed that CgR2150 and CgR3101 peptides act against bacteria by disrupting bacterial cell membranes. Moreover, hemolytic activity assay showed that neither of the two peptides exhibited significant hemolytic activity. To conclude, the antimicrobial peptides CgR2150 and CgR3101 are promising in the development of a new antibacterial agent and for application in plant production.


Subject(s)
Anti-Infective Agents , Chaetomium , Solanum tuberosum , Anti-Bacterial Agents/pharmacology , Anti-Infective Agents/pharmacology , Bacillus subtilis/genetics , Chaetomium/genetics , Endophytes/genetics , Peptides/genetics , Phylogeny , Xanthomonas
9.
PLoS One ; 17(4): e0266124, 2022.
Article in English | MEDLINE | ID: mdl-35390032

ABSTRACT

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is one of the most severe global pandemic due to its high pathogenicity and death rate starting from the end of 2019. Though there are some vaccines available against SAER-CoV-2 infections, we are worried about their effectiveness, due to its unstable sequence patterns. Therefore, beside vaccines, globally effective supporting drugs are also required for the treatment against SARS-CoV-2 infection. To explore commonly effective repurposable drugs for the treatment against different variants of coronavirus infections, in this article, an attempt was made to explore host genomic biomarkers guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches. At first, we identified 138 differentially expressed genes (DEGs) between SARS-CoV-1 infected and control samples by analyzing high throughput gene-expression profiles to select drug target key receptors. Then we identified top-ranked 11 key DEGs (SMAD4, GSK3B, SIRT1, ATM, RIPK1, PRKACB, MED17, CCT2, BIRC3, ETS1 and TXN) as hub genes (HubGs) by protein-protein interaction (PPI) network analysis of DEGs highlighting their functions, pathways, regulators and linkage with other disease risks that may influence SARS-CoV-1 infections. The DEGs-set enrichment analysis significantly detected some crucial biological processes (immune response, regulation of angiogenesis, apoptotic process, cytokine production and programmed cell death, response to hypoxia and oxidative stress), molecular functions (transcription factor binding and oxidoreductase activity) and pathways (transcriptional mis-regulation in cancer, pathways in cancer, chemokine signaling pathway) that are associated with SARS-CoV-1 infections as well as SARS-CoV-2 infections by involving HubGs. The gene regulatory network (GRN) analysis detected some transcription factors (FOXC1, GATA2, YY1, FOXL1, TP53 and SRF) and micro-RNAs (hsa-mir-92a-3p, hsa-mir-155-5p, hsa-mir-106b-5p, hsa-mir-34a-5p and hsa-mir-19b-3p) as the key transcriptional and post- transcriptional regulators of HubGs, respectively. We also detected some chemicals (Valproic Acid, Cyclosporine, Copper Sulfate and arsenic trioxide) that may regulates HubGs. The disease-HubGs interaction analysis showed that our predicted HubGs are also associated with several other diseases including different types of lung diseases. Then we considered 11 HubGs mediated proteins and their regulatory 6 key TFs proteins as the drug target proteins (receptors) and performed their docking analysis with the SARS-CoV-2 3CL protease-guided top listed 90 anti-viral drugs out of 3410. We found Rapamycin, Tacrolimus, Torin-2, Radotinib, Danoprevir, Ivermectin and Daclatasvir as the top-ranked 7 candidate-drugs with respect to our proposed target proteins for the treatment against SARS-CoV-1 infections. Then, we validated these 7 candidate-drugs against the already published top-ranked 11 target proteins associated with SARS-CoV-2 infections by molecular docking simulation and found their significant binding affinity scores with our proposed candidate-drugs. Finally, we validated all of our findings by the literature review. Therefore, the proposed candidate-drugs might play a vital role for the treatment against different variants of SARS-CoV-2 infections with comorbidities, since the proposed HubGs are also associated with several comorbidities.


Subject(s)
Antiviral Agents , COVID-19 Drug Treatment , Computational Biology , Drug Repositioning , Severe Acute Respiratory Syndrome , Antiviral Agents/pharmacology , Humans , MicroRNAs/genetics , Molecular Docking Simulation , Severe acute respiratory syndrome-related coronavirus , SARS-CoV-2/genetics , Severe Acute Respiratory Syndrome/drug therapy , Transcription Factors/genetics , Transcriptome
10.
Infect Prev Pract ; 4(1): 100205, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35243317

ABSTRACT

BACKGROUND: Tibia fractures represent the most prevalent open long-bone injuries. Indiscriminate, extensive, and unnecessary use of antibiotics has led to the emergence of infections caused by multidrug resistant organisms that increase morbidity and mortality. This study evaluated the spectrum of current organisms infecting the open tibia fractures and their antibiotic susceptibility pattern. This research did not alter the exiting practice of the institute to evaluate the current status. METHODS: This was a cross-sectional study on 628 patients presenting with open fractures of the tibia from July 2018 to July 2020. Sampling for three successive culture (and sensitivity) tests were carried out, 1st on specimens taken in the emergency room (upon patient presentation), 2nd in the emergency theatre after initial debridement, and 3rd in the ward between 12 to 14 days post operatively. RESULTS: The average age of the patients was 36.2± 15.4 years, with motor vehicle accidents being the predominant aetiology (72.2%). Results of specimen culture demonstrated that debridement could reduce microbial contamination significantly (P<.05) from 38.5 % to 26.4%. But from the ward sample, the infection rate was 45.1%, while contamination at entering the ward was only 26.4%. The bacteriological study found predominant multidrug-resistant Gram-negative organisms, namely Pseudomonas spp., Escherichia coli, Klebsiella spp., Acinetobacter spp., Enterobacter spp. and Proteus spp. Though Gram-positive Staphylococcus aureus was found significantly in the initial culture, they contributed minimally (1.4%) to infect the fracture site. CONCLUSION: The current study found a predominant shift in the trend toward multidrug-resistant Gram-negative organisms in orthopaedic infection, which was accompanied by a worrying pattern of hospital-acquired infection. These results will help to inform future research and policies within our institution.

11.
Int J Appl Basic Med Res ; 11(4): 238-242, 2021.
Article in English | MEDLINE | ID: mdl-34912687

ABSTRACT

INTRODUCTION: Serum amylase level can rise asymptomatically after endoscopic retrograde cholangiopancreatography (ERCP). Thus, its assay can lead to overprediction of post-ERCP pancreatitis (PEP). Lipase assay is used to diagnose other forms of pancreatitis but usually not for PEP. OBJECTIVES: The aim of this study was to predict whether lipase may be of better use for the early prediction of PEP. METHODS: One hundred and twenty-five consecutive ERCPs performed over a period of 1 year and 9 months were observed. On admission (baseline) and after ERCP at 4 and 24 h, serum amylase and lipase were measured. Based on sensitivity and specificity from the receiver operator characteristic (ROC) curve, optimal cutoff levels for the enzyme, serum lipase, and amylase levels were employed to predict PEP. RESULTS: Out of 125 patients, 26 (20.8%) developed PEP. In multivariate analysis, young age, suspected sphincter of Oddi dysfunction, recurrent pancreatitis, and needle papillotomy were significant risk factors. Considering the optimum cutoff level (single value with the best sensitivity and specificity), both the enzyme amylase and lipase evaluated at 4 h were significant (Chi-square test: P =0.0001 for both the enzymes). However, multivariate regression analysis and levels of enzymes at different cutoff values in the ROC found that 4-h lipase levels were more (about 4 times) increased of the upper limit of normal range than amylase levels (1.19 times). CONCLUSION: The enzyme, serum amylase, and lipase evaluated at 4 h after ERCP were satisfactory predictors for PEP. However, when compared, serum lipase was more reliable than amylase.

13.
Medicine (Baltimore) ; 100(37): e27281, 2021 Sep 17.
Article in English | MEDLINE | ID: mdl-34664887

ABSTRACT

ABSTRACT: In December 2019, with pneumonia-like clinical manifestations, a new severe acute respiratory syndrome coronavirus 2 emerged and quickly escalated into a pandemic. Since the first case detected in early March of last year, 8668 have died with an infection mortality rate of 1.52%, as of March 20, 2021. Bangladesh has been struck by the 2nd wave from mid-march 2021. As data on the second wave are sparse, the present study observed the demographic profile, symptoms, and outcomes of Coronavirus Disease 2019 (COVID-19) patients during this wave.The study was conducted at Sheikh Russel National Gastroliver Institute on 486 admitted cases during the 2nd wave of COVID-19 in Bangladesh (March 24-April 24, 2021) using a cross-sectional study design and a convenient sampling technique.Out of 486 cases, 306 (62.9%) were male, and 180 were female, with a mean age of 53.47 ±â€Š13.86. The majority of patients (32.5%) were between the ages of 51 and 60. While fever and cough being the predominant symptoms (>70% cases), the most common co-morbidities were hypertension (41.4) and diabetes mellitus (39.4). Intensive care unit utilization rate was 25%, and a half of the patients had 51% to 70% tomographic lung involvement with an overall mortality rate of 19.3%. Older age, chronic renal disease, percentage of lung involvement, and intensive care unit necessity were important mortality determinants.The present study gives an insight into the demographic profiles and outcomes of admitted patients with COVID-19 during the second wave at a covid dedicated hospital in Bangladesh.


Subject(s)
COVID-19/complications , Demography/statistics & numerical data , Outcome Assessment, Health Care/statistics & numerical data , Adult , Aged , Bangladesh/epidemiology , COVID-19/epidemiology , COVID-19/mortality , Cross-Sectional Studies , Female , Hospitalization/statistics & numerical data , Humans , Male , Middle Aged , Outcome Assessment, Health Care/methods , Retrospective Studies
14.
Heliyon ; 7(8): e07815, 2021 Aug.
Article in English | MEDLINE | ID: mdl-34466701

ABSTRACT

Genetic polymorphism of the SLC6A4 gene is associated with several behavioral disorders, including depression. Since studying the total nonsynonymous single nucleotide polymorphisms (nsSNPs) of the SLC6A4 gene at the population level is a difficult task, we aim to utilize in silico approach to detect the most deleterious nsSNPs of the SLC6A4 gene. In our study, 7 computational tools were used in the initial stage, including SIFT, Polyphen-2, PROVEAN, SNAP2, PhD-SNP, PANTHER, and SNPs&GO to find out the most damaging nsSNPs. In the second phase, we performed structural, functional, and stability analysis of SLC6A4 protein by popular computation tools, including I-Mutant 2.0 and MutPred2. Also, the ConSurf server was utilized to find the conserved region of the SLC6A4 protein to determine the relationship between these conserved regions with high-risk nsSNPs. Based on these analyses, 5 high-risk mutations of the SLC6A4 protein were selected. Then, we carried out comparative modeling by using the Robetta server and aligned the mutant protein model with the native protein structure. Later, we performed the post-translational modification and functional domain analysis of the SLC6A4 protein. This study concludes that Arginine → Tryptophan at position 79 and Arginine → Cysteine at position 104 are the two significant mutations in SLC6A4 protein which might play an essential role in causing diseases. Future studies should take these high-risk nsSNPs (rs1221448303, rs200953188) into consideration while exploring diseases related to the SLC6A4 gene. Besides, our research is the first-ever comprehensive in silico investigation of the SLC6A4 gene. Thus, the findings of this study could be beneficial for developing precision medicines against diseases caused by SLC6A4 malfunction. Furthermore, extensive wet-lab research and experiments on various model organisms might be helpful to investigate the precise role of these damaging nsSNPs of the SLC6A4 gene.

15.
Int J Mol Sci ; 22(16)2021 Aug 13.
Article in English | MEDLINE | ID: mdl-34445412

ABSTRACT

Even in a natural ecosystem, plants are continuously threatened by various microbial diseases. To save themselves from these diverse infections, plants build a robust, multilayered immune system through their natural chemical compounds. Among the several crucial bioactive compounds possessed by plants' immune systems, antimicrobial peptides (AMPs) rank in the first tier. These AMPs are environmentally friendly, anti-pathogenic, and do not bring harm to humans. Antimicrobial peptides can be isolated in several ways, but recombinant protein production has become increasingly popular in recent years, with the Escherichia coli expression system being the most widely used. However, the efficacy of this expression system is compromised due to the difficulty of removing endotoxin from its system. Therefore, this review suggests a high-throughput cDNA library-based plant-derived AMP isolation technique using the Bacillus subtilis expression system. This method can be performed for large-scale screening of plant sources to classify unique or homologous AMPs for the agronomic and applied field of plant studies. Furthermore, this review also focuses on the efficacy of plant AMPs, which are dependent on their numerous modes of action and exceptional structural stability to function against a wide range of invaders. To conclude, the findings from this study will be useful in investigating how novel AMPs are distributed among plants and provide detailed guidelines for an effective screening strategy of AMPs.


Subject(s)
Plants/metabolism , Pore Forming Cytotoxic Proteins/isolation & purification , Protein Engineering/methods , Bacillus subtilis/genetics , Bacillus subtilis/growth & development , Gene Library , Humans , Plant Proteins/genetics , Plant Proteins/isolation & purification , Plants/genetics , Pore Forming Cytotoxic Proteins/genetics , Pore Forming Cytotoxic Proteins/pharmacology
16.
Brief Bioinform ; 22(2): 1402-1414, 2021 03 22.
Article in English | MEDLINE | ID: mdl-33517367

ABSTRACT

The new coronavirus (SARS-CoV-2) halts the world economy and caused unbearable medical emergency due to high transmission rate and also no effective vaccine and drugs has been developed which brought the world pandemic situations. The main protease (Mpro) of SARS-CoV-2 may act as an effective target for drug development due to the conservation level. Herein, we have employed a rigorous literature review pipeline to enlist 3063 compounds from more than 200 plants from the Asian region. Therefore, the virtual screening procedure helps us to shortlist the total compounds into 19 based on their better binding energy. Moreover, the Prime MM-GBSA procedure screened the compound dataset further where curcumin, gartanin and robinetin had a score of (-59.439, -52.421 and - 47.544) kcal/mol, respectively. The top three ligands based on binding energy and MM-GBSA scores have most of the binding in the catalytic groove Cys145, His41, Met165, required for the target protein inhibition. The molecular dynamics simulation study confirms the docked complex rigidity and stability by exploring root mean square deviations, root mean square fluctuations, solvent accessible surface area, radius of gyration and hydrogen bond analysis from simulation trajectories. The post-molecular dynamics analysis also confirms the interactions of the curcumin, gartanin and robinetin in the similar binding pockets. Our computational drug designing approach may contribute to the development of drugs against SARS-CoV-2.


Subject(s)
COVID-19/virology , Plants/chemistry , Protease Inhibitors/metabolism , SARS-CoV-2/enzymology , Humans , Molecular Dynamics Simulation
17.
Sci Rep ; 10(1): 13346, 2020 08 07.
Article in English | MEDLINE | ID: mdl-32770019

ABSTRACT

Antimicrobial genes play an important role as a primary defense mechanism in all multicellular organisms. We chose Bacillus subtilis as a target pathogen indicator and transferred the Aegilops tauschii Cosson cDNA library into B. subtilis cells. Expression of the candidate antimicrobial gene can inhibit B. subtilis cell growth. Using this strategy, we screened six genes that have an internal effect on the indicator bacteria. Then, the secreted proteins were extracted and tested; two genes, AtR100 and AtR472, were found to have strong external antimicrobial activities with broad-spectrum resistance against Xanthomonas oryzae pv. oryzicola, Clavibacter fangii, and Botrytis cinerea. Additionally, thermal stability tests indicated that the antimicrobial activities of both proteins were thermostable. Furthermore, these two proteins exhibited no significant hemolytic activities. To test the feasibility of application at the industrial level, liquid fermentation and spray drying of these two proteins were conducted. Powder dilutions were shown to have significant inhibitory effects on B. cinerea. Fluorescence microscopy and flow cytometry results showed that the purified protein impaired and targeted the cell membranes. This study revealed that these two antimicrobial peptides could potentially be used for replacing antibiotics, which would provide the chance to reduce the emergence of drug resistance.


Subject(s)
Aegilops/chemistry , Anti-Infective Agents/pharmacology , Bacillus subtilis/drug effects , Botrytis/drug effects , Cell Membrane/drug effects , Xanthomonas/drug effects
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