Journal, genetic engineering & biotechnology最新文献

The relationship between nutrition and genes has long been hinted at and sometimes plainly associated with certain diseases. Now, after many years of research and coincidental findings, it is believed that this relationship, termed "Nutrigenomics," is certainly a factor of major importance in various conditions. In this review article, we discuss nutrigenomics, starting with basics definitions and enzymatic functions and ending with its palpable association with cancer. Now, diet is basically what we eat on a daily basis. Everything that enters through our alimentary tract ends up broken down to minute molecules and amino acids. These molecules interact with our microbiome and genome in discreet ways. For instance, we demonstrate how proper intake of probiotics enhances beneficial bacteria and may alleviate IBS and prevent colorectal cancer on the long term. We also show how a diet rich in folic acid is essential for methylenetetrahydrofolate reductase (MTHFR) function, which lowers risk of colorectal cancer. Also, we discuss how certain diets were associated with development of certain cancers. For example, red and processed meat are highly associated with colorectal and prostate cancer, salty diets with stomach cancer, and obesity with breast cancer. The modification of these diets significantly lowered the risk and improved prognosis of these cancers among many others. We also examined how micronutrients had a role in cancer prevention, as vitamin A and C exert anti-carcinogenic effects through their function as antioxidants. In addition, we show how folic acid prevent DNA mutations by enhancing protein methylation processes. Finally, after a systematic review of myriad articles on the etiology and prevention of cancer, we think that diet should be a crucial feature in cancer prevention and treatment programs. In the future, healthy diets and micronutrients may even be able to successively alter the liability to genetic mutations that result in cancer. It also will play a role in boosting treatment and improving prognosis of diagnosed cancers.

This study identified an extracellular bacterial polysaccharide produced by Bacillus velezensis strain 40B that contains more than 90% of the monosaccharide glucose as alpha-glucan. A prominent peak at 1074 cm^-1, a characteristic of glycoside couplings, was visible in the FTIR spectrum. There were traces of xylose, sucrose, and lactose, according to the HPLC study. The ability of this bacterial glucan to operate as a biosorbent of the heavy metals cobalt, chromium, copper, and lead from aqueous solutions was investigated in conjunction with Ca-alginate beads. It proved that glucan 40B has a low affinity for chromium ions and is selective for lead. Initial concentration measurements showed an inverse relationship between concentration and the amount of metal ions eliminated. Lead and chromium removal increased as the glucan dose was increased. It was shown that as the pH of the starting solution is elevated, there is an increase in the sorption of metal ions onto the glucan. It was clear that when the temperature increased, the fraction of metal ion sorption slightly increased. Glucan has a wide range of industrial applications, from food and medicine to health and nutrition. As a result, the investigation's scope was expanded to include heavy metal removal.

Background: Certain Bacillus species play a vital role in polyhydroxyalkanoate (PHA) production. However, most of these isolates did not properly identify to species level when scientifically had been reported.

Results: From NGS analysis, 5719 genes were predicted in the de novo genome assembly. Based on genome annotation using RAST server, 5,527,513 bp sequences were predicted with 5679 bp number of protein-coding sequence. Its genome sequence contains 35.1% and 156 GC content and contigs, respectively. In RAST server analysis, subsystem (43%) and non-subsystem coverage (57%) were generated. Ortho Venn comparative genome analysis indicated that Bacillus sp. BNPI-92 shared 2930 gene cluster (core gene) with B. cereus ATCC 14579 ^T (AE016877), B. paranthracis Mn5T (MACE01000012), B. thuringiensis ATCC 10792 T (ACNF01000156), and B. antrics Amen T (AE016879) strains. For our strain, the maximum gene cluster (190) was shared with B. cereus ATCC 14579 ^T (AE016877). For Ortho Venn pair wise analysis, the maximum overlapping gene clusters thresholds have been detected between Bacillus s p.BNPI-92 and Ba. cereus ATCC 14579 ^T (5414). Average nucleotide identity (ANI) such as OriginalANI and OrthoANI, in silicon digital DND-DNA hybridization (isDDH), Type (Strain) Genome Server (TYGS), and Genome-Genome Distance Calculator (GGDC) were more essentially related Bacillus sp. BNPI-92 with B. cereus ATCC 14579 ^T strain. Therefore, based on the combination of RAST annotation, OrthoVenn server, ANI and isDDH result Bacillus sp.BNPI-92 strain was strongly confirmed to be a B. cereus type strain. It was designated as B. cereus BNPI-92 strain. In B. cereus BNPI-92 strain whole genome sequence, PHA biosynthesis encoding genes such as phaP, phaQ, phaR (PHA synthesis repressor phaR gene sequence), phaB/phbB, and phaC were predicted on the same operon. These gene clusters were designated as phaPQRBC. However, phaA was located on other operons.

Conclusions: This newly obtained isolate was found to be new a strain based on comparative genomic analysis and it was also observed as a potential candidate for PHA biosynthesis.

Background: Immunoinformatics is an emerging interdisciplinary field which integrates immunology, bioinformatics, and computational biology to study the immune system. In this study, we apply immunoinformatics approaches to explore the dengue proteome in order to design a multi-epitope vaccine construct.

Methods: We used existing databases and algorithms to predict potential epitopes on dengue proteins and used a bioinformatics approach to identify the most promising epitopes. We then used molecular modelling to develop a multi-epitope construct which could be used as a potential vaccine. The results of this study demonstrate that immunoinformatics is a powerful tool for exploring and designing potential vaccines for infectious diseases like dengue.

Results: Here, we found four CD4+ epitopes NLKYSVIVTVHTGDQ, ANPIVTDKEKPVNIE, LDPVVYDAKFEKQL, and VGAIALDFKPGTSGS that were used to design vaccine construct. The vaccine construct docked with TLR5. RMSD values suggest that docked complex of TLR5 and vaccine construct have putative stable interaction to induce immunogenic effects on host.

Conclusions: Furthermore, our study provides a proof of concept for the use of immunoinformatics approaches in DENV vaccine design. This vaccine can be effective in treating patients infected with DENV virus.

Background: DNA polymerase is an essential component in PCR assay for DNA synthesis. Improving DNA polymerase with characteristics indispensable for a powerful assay is crucial because it can be used in wide-range applications. Derived from Pyrococcus furiosus, Pfu DNA polymerase (Pfu pol) is one of the excellent polymerases due to its high fidelity. Therefore, we aimed to develop Pfu pol from a synthetic gene with codon optimization to increase its protein yield in Escherichia coli.

Results: Recombinant Pfu pol was successfully expressed and purified with a two-step purification process using nickel affinity chromatography, followed by anion exchange chromatography. Subsequently, the purified Pfu pol was confirmed by Western blot analysis, resulting in a molecular weight of approximately 90 kDa. In the final purification process, we successfully obtained a large amount of purified enzyme (26.8 mg/L). Furthermore, the purified Pfu pol showed its functionality and efficiency when tested for DNA amplification using the standard PCR.

Conclusions: Overall, a high-level expression of recombinant Pfu pol was achieved by employing our approach in the present study. In the future, our findings will be useful for studies on synthesizing recombinant DNA polymerase in E. coli expression system.

Objectives: At the present time, there is a persistent need to get rid of environmental contaminants by eco-friendly, sustainable, and economical technologies. Uncontrolled disposal practices of domestic and industrial solid and liquid wastes led to water pollution which has negative impacts on public health, environment, and socio-economic development. Several water-borne diseases are spreading man to man by microorganisms such as pathogenic bacteria. For the protection of water bodies, all wastewater from various sources should be managed and remediated properly. Myco-remediation is a form of bioremediation in which fungi are used to get rid of contaminants. Fungi are attractive agents for the biosynthesis of nanoparticles especially silver nanoparticles (AgNPs) which are considered one of the most widely utilized nanoparticles because of their unique characteristics such as antibacterial, antiviral, antifungal, and anti-inflammatory properties.

Methods: This study uses silver nitrate and supernatants of four marine fungi; Penicillium simplicissimum, Aspergillus terreus, Aspergillus japonicus, and Aspergillus oryzae for extracellular biosynthesis of silver nanoparticles and to evaluate its activity against different pathogenic microorganisms. These nanoparticles may subsequently be applied for the treatment or nano-bioremediation of microbial contaminants in water bodies and improve water quality.

Results: Silver nanoparticles were synthesized and the results revealed that spherical and well-dispersed nanoparticles of different sizes were formed with sizes ranging between 3.8 and 23 nm. Characterization results approved the existence of stable nanocrystalline elemental silver. Antibacterial activity results revealed that AgNPs can be used as a powerful antimicrobial agent for several pathogenic bacteria, yeast, and fungi. Among the biosynthesized NPs mediated by the four marine fungi, AgNPs mediated by A. japonicus (5 mM) had the highest antibacterial activity, while AgNPs mediated by Penicillium simplicissmum (8 mM) had the highest antifungal activity.

Conclusion: Marine fungi can biosynthesize stable AgNPs that exhibit potent antimicrobial activity against a variety of pathogens.

Background: Breast cancer is the most significant threat to women worldwide. Most chemotherapeutic drugs cause cancer cell death and apoptosis by inducing oxidative stress and producing reactive oxygen species (ROS). Cancer cells have a higher rate of metabolic activity than normal cells and thus produce more ROS. Glutathione and its related enzymes are the most significant antioxidant defense mechanisms that protect cells from oxidative and chemotherapeutic impacts. The anticancer actions of phenolic compounds were greatly confirmed. Using phenolic compounds as drugs in combination with chemotherapy may improve health, improve treatment outcomes, and reduce dose and damage. The goal of the study was to treat breast cancer cell lines (MCF-7) with Tamarindus indica extract individually and in combination with the anticancer drug tamoxifen (TAM) to improve therapeutic efficacy.

Results: After 48 h of incubation at IC₂₅ concentrations of T. indica extract (47.3 g/mL), tamoxifen (0.8 g/mL), and their co-treatments, the biochemical and genotoxic effects on MCF-7 cell lines were investigated. In MCF7 cell lines, T. indica extract increased reduced glutathione levels as well as glutathione transferase, glutathione peroxidase, and glutathione reductase activities. The same was true for oxidative state indicators, where higher levels of catalase and lactate dehydrogenase activity were associated with higher levels of malondialdehyde. T. indica has almost no effect on the DNA damage parameters. All of these variations can produce alterations in cancer cell genotoxicity and apoptotic pathways, explaining the restoration of DNA moment to normal levels and enhanced survival.

Conclusion: Cytotoxic and genotoxic effect of treatment with T. indica extract could be attributed to the dynamic interaction of glutathione cycle and antioxidant enzymes to combat oxidative stress, which can be considered as a positive therapeutic effect. On the other hand, the negative response of tamoxifen efficacy when co-treated with T. indica reversed tamoxifen's genotoxicity and enhanced survival.

Background: Antimicrobial peptides (AMPs), innate immune response molecules in organisms, are also known for their dual functionality, exemplified by hepcidin-an immunomodulator and iron regulator. Identifying and studying various AMPs from fish species can provide valuable insights into the immune profiles of aquaculturally significant fish, which can be made use of in its culture.

Results: Hepcidin, a dual-function antimicrobial peptide, was isolated from the gill tissue of Genetically Improved Farmed Tilapia (GIFT-Hep). GIFT-Hep consists of a 90 amino acid pre-propeptide with a 24-mer signal, a 40-mer propeptide, and a 26-mer mature peptide region. The mature peptide had a molecular weight of 3015.61 Da, a theoretical pI of 8.78, a net charge of +4.25, and a protein-binding potential of 2.06 kcal/mol. Four disulfide bonds were formed by eight cysteine residues in the mature region. The presence of positively charged arginine residues renders the peptide 50% hydrophobic. Molecular analysis of GIFT-Hep revealed the presence of a furin propeptide convertase motif, RX(K/R)R, which facilitates trimming of the peptide to yield the mature GIFT-Hep. The hypothetical iron regulatory sequence, QSHLSL, was also identified in the mature peptide. In silico predictions about the characteristics of GIFT-Hep, such as charge, hydrophobicity, high surface accessibility, transmembrane helical regions, hydrophobic faces, hot spots, and cell-penetrating properties, suggest that the peptide functions as an iron regulatory antimicrobial agent.

Conclusions: This study reports a hepcidin antimicrobial peptide with both HAMP1 and HAMP2 properties isolated from genetically improved farmed tilapia, and further evaluation of the properties will prove the feasibility of GIFT-Hep being used as a therapeutant in aquaculture.

Background: Cervical cancer caused by the human papillomavirus (HPV) is one of the most frequent malignances globally. HPV 52 is a high-risk cancer-causing genotype that has been identified as the most prevalent type in Indonesia. Virus-like particles (VLP)-based vaccinations against HPV infection could benefit from self-assembled VLP of L1 capsid protein.

Result: The recombinant HPV 52 L1 was expressed in Pichia pastoris on a shake-flask scale with 0.5% methanol induction in this study. The copy number was used to compare the expression level and stability. The colony that survived on a solid medium containing 2000 μg/ml of Zeocin was selected and cultured to express HPV 52 L1. DNA was extracted from the chosen colony, and the copy was determined using qPCR. HPV 52 L1 protein was then purified through fast performance liquid chromatography. Transmission electron microscopy (TEM) evaluation confirmed the VLP self-assembly. The genomic DNA remained intact after 100 generations of serial cultivation under no selective pressure medium conditions, and the protein produced was relatively stable. However, the band intensity was slightly lower than in the parental colony. In terms of copy number, a low copy transformant resulted in low expression but produced a highly stable recombinant clone. Eventually, the L1 protein expressed in Pichia pastoris can self-assemble into VLP. Therefore, recombinant HPV possesses a stable clone and the ability to self-assemble into VLP.

Conclusion: The recombinant L1 HPV 52 protein is successfully expressed in P. pastoris within a size range of approximately 55 kDa and demonstrated favorable stability. The L1 protein expressed in Pichia pastoris successful self-assembled of HPV VLPs, thereby establishing their potential efficacy as a prophylactic vaccine.

Background: Salmonella Typhi stands as the etiological agent responsible for the onset of human typhoid fever. The pressing demand for innovative therapeutic targets against S. Typhi is underscored by the escalating prevalence of this pathogen and the severe nature of its infections. Consequently, this study employs pangenome analysis to scrutinize 119 S. Typhi-resistant strains, aiming to identify the most promising therapeutic targets originating from its core genome.

Results: Subtractive genomics was employed to systematically eliminate non-homologous (n=1147), essential (n=551), drug-like (n=80), and pathogenicity-related (n=18) proteins from the initial pool of 3351 core genome proteins. Consequently, lipopolysaccharide 1,2-glucosyltransferase RfaJ was designated as the optimal pharmacological target due to its potential versatility. Furthermore, a compendium of 9000 FDA-approved compounds was repurposed for evaluation against the RfaJ drug target, with the specific intent of prioritizing novel, high-potency therapeutic candidates for combating S. Typhi. Ultimately, four compounds, namely DB00549 (Zafirlukast), DB15637 (Fluzoparib), DB15688 (Zavegepant), and DB12411 (Bemcentinib), were singled out as potential inhibitors based on the ligand-protein binding affinity (indicated by the lowest anticipated binding energy) and the overall stability of these compounds. Notably, molecular dynamics simulations, conducted over a 50 nanosecond interval, convincingly demonstrated the stability of these compounds in the context of the RfaJ protein.

Conclusion: In summary, the present findings hold significant promise as an initial stride in the broader drug discovery endeavor against S. Typhi infections. However, the experimental validation of the identified drug target and drug candidate is further required to increase the effectiveness of the applied methodology.