Molecular Biology Research Communications最新文献

The present study aims to identify the differentially expressed genes in HIGK treated with Fusobacterium nucleatum (Fn) and their possible role in establishing head and neck squamous cell carcinoma. The study design follows a computational approach wherein multiple databases and tools are used to derive the possible association between Fn exposure and the development of HNSCC. The GEOmnibus dataset GSE6927 provided data on the differentially expressed genes in the HIGK treated with Fn. The GEO2R analysis revealed 22 differentially expressed genes in HIGK cells treated with Fn. The expression profile of these genes was then analyzed in the HNSCC (TCGA, Firehose Legacy) dataset employing the UALCAN database. The present study revealed 5 genes viz., GSDMD, NUP214, ZNF426, FUT2, and SERPINB2 exhibiting similar expression patterns in Fn-treated HIGK and HNSCC datasets. The GSDMD and NUP214 were found to be upregulated, and the genes ZNF426, FUT2, and SERPINB2 were downregulated. Among the five genes, the ZNF426 demonstrated a significant association with the survival of HNSCC patients. The low expression of ZNF426 presented a poor prognosis compared to the high expression. The study's results identified ZNF426 as a candidate gene involved in Fusobacterium nucleatum infection and HNSCC. Validating this result is necessary to gain insights into the role of the ZNF426 gene in developing HNSCC. Furthermore, probing the epigenetic factors targeting ZNF426 can be a potential therapeutic lead.

Genetic polymorphisms in interleukin-13 (IL13) gene have been associated with asthma susceptibility in different ethnicities. We investigated the association of two polymorphisms in the IL13 gene [rs1800925 (c.-93+487C>T), and rs20541 (p.Gln144Arg)] with asthma susceptibility among Sudanese patients. A case-control study was conducted at Al-Shaab Teaching Hospital between April and October 2022. Involving fifty asthmatic patients and fifty controls. The genotypes were determined using an allele-specific polymerase chain reaction. For rs1800925, a significant association with asthma in multivariate analysis (aOR=3.15, 95% CI: 1.13-8.76; p=0.028). The T allele was the most frequent in cases and showed a significant association with asthma (aOR=1.99, 95% CI: 1.13-3.5; p=0.016). The rs20541 did not show any association with asthma. The rs1800925 is associated with an increased risk of asthma in Sudanese patients.

Pseudomonas syringae is a gram-negative bacterium that causes a diversity of diseases in numerous plants. Strategies to inhibit P. syringae growth include protective procedures; however, controlling the disease is complicated due to its rapid spread. Several antimicrobial agents can prevent this disease, such as chemical compounds, biological agents, secondary metabolites, nanoparticles, bacteriophages, and antimicrobial peptides (AMPs). The most effective way to control the disease is through chemical control. Using copper compounds and antibiotics is a conventional practice to decrease canker disease symptoms. However, due to environmental pollution caused by chemicals and bactericides and the resistance of different pathovars of P. syringae, other methods for bacterial pathogens control are needed. Biological control, using antagonistic bacteria has shown promising results against P. syringae under in vitro conditions. New studies focus on using secondary metabolites from plants to control plant diseases. Studies have shown that essential oils when preserved from degradation and evaporation by nanoparticles like mesoporous silica, can increase their antibacterial activities. Using nanoparticles, especially silver, is a suitable strategy for controlling P. syringae. However, high concentrations of silver nanoparticles are toxic. Bacteriophages and AMPs are recommended as alternatives to control bacterial infections in agriculture, including P. syringae. Combined treatments of phages and secondary metabolites have shown higher efficacy, potentially overcoming resistance. However, bacteriophages and AMPs are expensive and limited. In the end, using secondary metabolites and nanoparticles at low concentrations presents economic benefits and antibacterial activities without phytotoxic properties.

Chinese Hamster Ovary (CHO) cells are essential in biopharmaceutical manufacturing. Scientists use CRISPR to enhance productivity. mRNAs contain UTRs that regulate gene expression, affecting protein abundance. Targeting these regions creates desirable knockout cells. The Caspase 8 Associated Protein 2 (CASP8AP2) gene is a promising target for improving host cell viability. This study used the CRISPR-Homology-Independent Targeted Integration (HITI) strategy to modify the 3'UTR region of the CASP8AP2 gene in CHO cells. The aim was to evaluate the effects of CASP8AP2 silencing on cell proliferation, viability, apoptosis, and the cell cycle. CASP8AP2 silencing was assessed post-modification by extracting genomic DNA from modified and unmodified CHO cells, followed by PCR and sequencing to confirm deletions. Cell proliferation and viability were measured using MTT assays, and cell cycle analysis was performed via flow cytometry. Apoptosis was evaluated through Annexin V/PE staining and flow cytometry, with apoptosis resistance assessed by determining the IC₅₀ of sodium butyrate. Results showed CASP8AP2 deletion did not affect cell proliferation or the cell cycle but improved CHO cell viability and increased resistance to apoptosis. The IC₅₀ for sodium butyrate was higher in CASP8AP2 knockout cells (7.84 mM) compared to native cells (3.43 mM), indicating enhanced apoptosis resistance. This study highlights CASP8AP2's role in apoptosis regulation without impacting cell proliferation or the cell cycle. CASP8AP2 deletion enhances viability and resistance to apoptosis, suggesting it as a target for improving recombinant protein production. Further research is needed to elucidate the molecular mechanisms and develop therapeutic strategies based on this approach.

The bioremediation method is considered an economical and environmentally friendly strategy for the remediation of oil-contaminated soils. However, some oil field areas have extreme environmental conditions that make it difficult to establish microbes for bioreme-diation. In this study, bacteria were isolated from oil-contaminated soils of the Dehloran oil fields, which have very harsh soil and weather conditions. Soil samples were collected from two highly contaminated mud pits. The petroleum content and physicochemical characteristics of the soil were investigated. Soil samples pollution were about 8%, sandy and alkaline, and their EC reached up to 125.6 ds/m in some samples. The isolated bacteria were screened according to their ability to grow on the M9 mineral medium containing crude oil as the sole carbon source. Moreover, their physiological characteristics in diesel degradation were investigated. The phenotypic, biochemical, and molecular characteristics of selected isolates and their stability under extreme conditions such as drought, salinity and high temperatures were investigated. Two isolates NC39 and NB391 showed the highest ability in diesel degradation. The results of 16SrRNA sequencing showed that NC39 isolate had 98% similarity to Pseudomonas sp. and isolate NB391 belonged to Pantoea agglomerans with 99% similarity. These two isolates showed a high ability to tolerate high salinity (10%), temperature (50°C), and drought (-0.73 MPa) stress. Exploiting these extremophile strains is a promising tool in the bioremediation of oil-contaminated soils in extreme environments.

Testis specific gene antigen 10 (TSGA10) is a protein which has roles in spermatogenesis and cancers so that deletion or mutation in the TSGA10 gene resulted in non-obstructive infertility and aberrant expression of this protein, was detected in solid tumors and leukemia. Despite the crucial roles of TSGA10 in tumorigenesis and infertility, yet it is not obvious how various nsSNPs of its gene impress the structure and function of the TSGA10. Therefore, it is worthwhile to investigate the potential highly deleterious nsSNPs by several in-silico tools before launching costly experimental approaches. In the current study, we employed several different machine learning algorithms in a two-step screening procedure to analyze single nucleotide substitutions of TSGA10 gene. Prediction tools were included SIFT, PROVEAN, PolyPhen-2, SNAP2, SNPs & GO, PhD-SNP for the first step and the second step included predictive tools such as I-mutant 3.0, MUpro, SNPeffect 4.0 (LIMBO, WALTZ, TANGO, FoldX), MutationTaster and CADD. Also, the 3D models of significantly damaging variants were built by Phyre2. The results elucidated 15 amino acid alterations as the most deleterious ones. Among these S563P, E578K, Q580P, R638L, R638C, R638G, R638S, L648R, R649C, R649H were located in a domain which is approved to has interaction with the HIF1-A protein and D62Y, R105G, D106V and D111Y were located on phosphodiesterase domain. In sum, these predicted mutations significantly influence the function of TSGA10 and they could be used for precise study of this protein in infertility and cancer experimental investigations.

The Type V secretion system, or "autotransporter", is a secretion system that enables bacteria to directly export proteins from the cell interior to the extracellular membrane. mCherry is a second-generation monomeric red fluorescent protein that has an improvement in photostability compared to the first generation of RFP. In this research, we conducted the fusion of the mRFP into the C-terminal domain of EhaA - the translocation domain of the autotransporter protein transport system - to investigate the expression of mRFP on the surface of Escherichia coli , a model organism commonly utilized in recombinant protein research. The induction of the mRFP-EhaA C-terminal domain complex expression was achieved using isopropyl β-D-1-thiogalactopyranoside (IPTG) and confirmed through SDS-PAGE stained with Coomassie Brilliant Blue and Western blotting using anti-6X His tag antibodies. The surface expression of the mRFP-EhaA C-terminal complex protein was validated through the fluorescent properties of mRFP and further confirmed using fluorescent microscopy. This study laid the groundwork for surface expression on cost-effective Gram-negative bacteria, E. coli.

Long non-coding RNAs (lncRNAs) have recently emerged as critical regulators of oncogenic or tumor-suppressive pathways in human cancers. LINC01133 is a lncRNA that has exhibited dichotomous roles in various malignancies but to the best of our knowledge, the role of LINC01133 in laryngeal squamous cell carcinoma (LSCC) has not been previously investigated. This study aimed to investigate the expression, clinical significance, and potential functions of the LINC01133 in LSCC. Integrative bioinformatics analysis of sequencing data obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets revealed LINC01133 as a differentially expressed lncRNA in head and neck/laryngeal cancers. Experimental validation via quantitative real-time PCR in 41 pairs of stage III and IV LSCC tissues and normal tissues adjacent to the tumor (NAT) demonstrated significant downregulation of LINC01133 in tumors (p<0.0001). Decreased LINC01133 expression associated with advanced tumor stage (p=0.0206) and lymph node metastasis (p=0.0203). The receiver operating characteristic analysis indicated potential diagnostic utility (AUC=0.7115, p=0.001). Bioinformatic predictions and literature mining suggested two potential competing endogenous RNA (ceRNA) mechanisms whereby LINC01133 may act as a tumor suppressor by sponging miR-205-5p to derepress the leucine-rich repeat kinase 2 (LRRK2) and androgen receptor, leading to dysregulation of cancer-related signaling cascades. This study provides initial evidence that loss of lncRNA LINC01133 expression may promote LSCC tumorigenesis, possibly by dysregulating microRNA interactions. Further verification of its regulatory mechanisms and diagnostic value is warranted.

The recent pernicious COVID-19 pandemic is caused by SARS-CoV-2. While most therapeutic strategies have focused on the viral spike protein, Open Reading Frame 8 (ORF8) plays a critical role in causing the severity of the disease. Nonetheless, there still needs to be more information on the ORF8 binding epitopes and their appropriate safe inhibitors. Herein, the protein binding sites were detected through comprehensive structural analyses. The validation of the binding sites was investigated through protein conservation analysis and blind docking. The potential natural product (NP) inhibitors were selected based on a structure-function approach. The solo and combined inhibition functions of these NPs were examined through molecular docking studies. Two binding epitopes were identified, one between the ORF8 monomers (DGBM) and the other on the surface (Gal1-Like). E92 was predicted to be pivotal for DGBM, and R101 for Gal1-like, which was then confirmed through molecular dockings. The inhibitory effects of selected phytochemical (Artemisinin), bacterial (Ivermectin), and native-liken (DEG-168) NPs were compared with the Remdesivir. Selected NPs showed solo- and co-functionality against Remdesivir to inhibit functional regions of the ORF8 structure. The DGBM is highly engaged in capturing the NPs. Additionally, the co-functionality study of NPs showed that the Ivermectin-DEG168 combination has the strongest mechanism for inhibiting all the predicted binding sites. Ivermectin can interfere with ORF8-MHC-I interaction through inhibition of A51 and F120. Two new binding sites on this non-infusion protein structure were introduced using a combination of approaches. Additionally, three safe and effective were found to inhibit these binding sites.

Heterocephalus glaber, known as the Naked mole-rat, has an extraordinary immunity to Alzheimer's disease. The pathological hallmark of Alzheimer's disease is cerebral accumulations of plaques, consisting of self-aggregated amyloid beta peptides. Homo sapiens and H. glaber amyloid beta peptides are different in only one amino acid. Herein, computational structural analyses were carried out to determine whether plaque development in H. glaber is prevented by the replacement of His13 with Arg13 in the amyloid beta peptide. AlphaFold2 was used to predict the structure of the H. glaber amyloid beta peptide. HADDOCK and Hex were used to self-dock the peptides and dock ions on peptides, respectively. Illustrations were made by PyMol and ChimeraX. Using VMD, we calculated the radius of gyration. The phylogenetic analysis was conducted by Mega. The results showed an accurate structure with two alpha helices separated by a short coil for H. glaber. Self-docking of the two amyloid beta peptides demonstrated a globular conformation in the H. glaber dimer, implying the unlikeliness of amyloid beta peptides' self-aggregation to form fibrillar structures. This conformational state resulted in lower electrostatic energy compared to H. sapiens, contributing to H. glaber's lower tendency for fibril and, ultimately, plaque formation. Phylogenetic analysis confirmed that amyloid precursor protein is highly conserved in each taxon of rodentia and primata. This study provides insight into the connection between the structure of H. glaber amyloid beta and its plaque formation properties, showing that the Arg13 in H. glaber leads to fibril instability, and might prevent senile plaque accumulation.