WGS-based screening of the co-chaperone protein DjlA-induced curved DNA binding protein A (CbpA) from a new multidrug-resistant zoonotic mastitis-causing Klebsiella pneumoniae strain: a novel molecular target of selective flavonoids.

The research aimed to establish a multidrug-resistant Klebsiella pneumoniae-induced genetic model for mastitis considering the alternative mechanisms of the DjlA-mediated CbpA protein regulation. The Whole Genome Sequencing of the newly isolated K. pneumoniae strain was conducted to annotate the frequently occurring antibiotic resistance and virulence factors following PCR and MALDI-TOF mass-spectrophotometry. Co-chaperon DjlA was identified and extracted via restriction digestion on PAGE. Based on the molecular string property analysis of different DnaJ and DnaK type genes, CbpA was identified to be regulated most by the DjlA protein during mastitis. Based on the quantum tunnel-cluster profiles, CbpA was modeled as a novel target for diversified biosynthetic, and chemosynthetic compounds. Pharmacokinetic and pharmacodynamic analyses were conducted to determine the maximal point-specificity of selective flavonoids in complexing with the CbpA macromolecule at molecular docking. The molecular dynamic simulation (100 ns) of each of the flavonoid-protein complexes was studied regarding the parameters RMSD, RMSF, Rg, SASA, MMGBSA, and intramolecular hydrogen bonds; where all of them resulted significantly. To ratify all the molecular dynamic simulation outputs, the potential stability of the flavonoids in complexing with CbpA can be remarked as Quercetin > Biochanin A > Kaempherol > Myricetin, which were all significant in comparison to the control Galangin. Finally, a comprehensive drug-gene interaction pathway for each of the flavonoids was developed to determine the simultaneous and quantitative-synergistic effects of different operons belonging to the DnaJ-type proteins on the metabolism of the tested pharmacophores in CbpA. Considering all the in vitro and in silico parameters, DjlA-mediated CbpA can be a novel target for the tested flavonoids as the potential therapeutics of mastitis as futuristic drugs.

Parallel evolution of methyltransferases leads to vobasine biosynthesis in Tabernaemontana elegans and Catharanthus roseus.

Monoterpenoid indole alkaloids (MIA) are one of the largest and most complex alkaloid class in nature, boasting many clinically significant drugs such as anticancer vinblastine and antiarrhythmic ajmaline. Many MIAs undergo nitrogen N-methylation, altering their reactivity and affinity to the biological targets through a straightforward reaction. Remarkably, all known MIA N-methyltransferases (NMT) originate from the neofunctionalization of ancestral γ-tocopherol C-methyltransferases (γTMTs), a phenomenon seemingly unique to the Apocynaceae family. In this study, we unveil and characterize a new γTMT-like enzyme from the plant Tabernaemontana elegans (toad tree): perivine Nß-methyltransferase (TePeNMT). TePeNMT and other homologs form a distinct clade in our phylogenetic study, setting them apart from other γTMTs and γTMT-like NMTs discovered to date. Enzyme kinetic experiments and enzyme homology modeling studies reveal the significant differences in enzyme active sites between TePeNMT and CrPeNMT, a previously characterized perivine Nß-methyltransferase from Catharanthus roseus (Madagascar periwinkle). Collectively, our findings suggest that parallel evolution of ancestral γTMTs may be responsible for the occurrence of perivine N-methylation in T. elegans and C. roseus.

COVID-19 in Bangladesh: Wave-centric assessments and mitigation measures for future pandemics.

The ongoing pandemic COVID-19 caused by Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) has wreaked havoc globally by affecting millions of lives. Although different countries found the implementation of emergency measures useful to combat the viral pandemic, many countries are still experiencing the resurgence of COVID-19 cases with new variants even after following strict containment guidelines. Country-specific lessons learned from the ongoing COVID-19 pandemic can be utilized in commencing a successful battle against the potential future outbreaks. In this article, we analyzed the overall scenario of the COVID-19 pandemic in Bangladesh from Alpha to Omicron variant and discussed the demographic, political, economic, social, and environmental influences on the mitigation strategies employed by the country to combat the pandemic. We also tried to explore the preparedness and precautionary measures taken by the responsible authorities, the choice of strategies implemented, and the effectiveness of the response initiated by the government and relevant agencies. Finally, we discussed the possible strategies that might help Bangladesh to combat future COVID-19 waves and other possible pandemics based on the experiences gathered from the ongoing COVID-19 pandemic.

Spike protein mutations and structural insights of pangolin lineage B.1.1.25 with implications for viral pathogenicity and ACE2 binding affinity.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID -19, is constantly evolving, requiring continuous genomic surveillance. In this study, we used whole-genome sequencing to investigate the genetic epidemiology of SARS-CoV-2 in Bangladesh, with particular emphasis on identifying dominant variants and associated mutations. We used high-throughput next-generation sequencing (NGS) to obtain DNA sequences from COVID-19 patient samples and compared these sequences to the Wuhan SARS-CoV-2 reference genome using the Global Initiative for Sharing All Influenza Data (GISAID). Our phylogenetic and mutational analyzes revealed that the majority (88%) of the samples belonged to the pangolin lineage B.1.1.25, whereas the remaining 11% were assigned to the parental lineage B.1.1. Two main mutations, D614G and P681R, were identified in the spike protein sequences of the samples. The D614G mutation, which is the most common, decreases S1 domain flexibility, whereas the P681R mutation may increase the severity of viral infections by increasing the binding affinity between the spike protein and the ACE2 receptor. We employed molecular modeling techniques, including protein modeling, molecular docking, and quantum mechanics/molecular mechanics (QM/MM) geometry optimization, to build and validate three-dimensional models of the S_D614G-ACE2 and S_P681R-ACE2 complexes from the predominant strains. The description of the binding mode and intermolecular contacts of the referenced systems suggests that the P681R mutation may be associated with increased viral pathogenicity in Bangladeshi patients due to enhanced electrostatic interactions between the mutant spike protein and the human ACE2 receptor, underscoring the importance of continuous genomic surveillance in the fight against COVID -19. Finally, the binding profile of the S_D614G-ACE2 and S_P681R-ACE2 complexes offer valuable insights to deeply understand the binding site characteristics that could help to develop antiviral therapeutics that inhibit protein-protein interactions between SARS-CoV-2 spike protein and human ACE2 receptor.

Studying Iridoid Transport in Catharanthus roseus by Grafting.

The plant Catharanthus roseus is well known for its spatial separation of iridoid and monoterpenoid indole alkaloid (MIA) biosynthesis at both intracellular and intercellular levels, collectively suggested by RNA in situ hybridization, enzymatic and transcriptomic studies using leaf epidermis, and fluorescent protein tagging studies. Although documented in other plant species, the long-distance transport of iridoid glycosides, such as secologanin, has not been known in C. roseus until a recent study suggested that secologanin is transported from root to shoot, by grafting low iridoid/MIA mutant scions onto wild-type stock plants. This chapter describes the in vitro cultivation of C. roseus plants and grafting techniques to enable studies concerning iridoid/MIA transport between organs. The iridoid and MIA analysis methods are also provided.

Generating an EMS Mutant Population and Rapid Mutant Screening by Thin-Layer Chromatography Enables the Studies of Monoterpenoid Indole Alkaloids Biosynthesis in Catharanthus Roseus.

Decades of research on the medicinal plant Catharanthus roseus have led to the complete elucidation of the 29-step pathway for the biosynthesis of the anticancer drug vinblastine from geraniol and tryptophan precursors. Several approaches have been used to identify the enzymes involved in this iconic and remarkably complex pathway. This chapter describes the use of the classic ethyl methanesulfonate (EMS) mutagenesis to create a selfed M2 mutant population, which can be rapidly screened to select mutants with altered monoterpenoid indole alkaloid (MIA) biosynthesis with a simple, high-throughput thin-layer chromatography (TLC)-based screening strategy. This TLC-based MIA screening has led to the discovery and characterization of three enzymes responsible for vinblastine biosynthesis.

Identification of the prognostic and therapeutic values of cyclin E1 (CCNE1) gene expression in Lung Adenocarcinoma and Lung Squamous Cell Carcinoma: A database mining approach.

Cyclin E1 (CCNE1) is a protein-coding gene that belongs to the Cyclin family of genes which controls the G1/S phase transition of the cell cycle. Previously, its abnormal expression pattern has been examined and found to be correlated with ovarian and breast cancer progression. Herein, we exploited a bioinformatics and database mining strategy to unveil the therapeutic and prognostic significance of CCNE1 gene expression in Lung Adenocarcinoma (LUAD) and Lung Squamous Cell Carcinoma (LUSC). CCNE1 gene was reported to be highly expressed in LUAD and LUSC tissues. Its promoter and coding sequences were reported to be aberrantly methylated in LUAD and LUSC tissues than in normal tissues. Moreover, around 12 somatic mutations (frequency: 0.7%) were recorded in the CCNE1 coding region from different studies involving LUAD and LUSC patients' whole genome sequences. The CCNE1 gene expression was also correlated with LUAD and LUSC patients' overall and disease-specific survival. Immune infiltration analysis revealed the association between CCNE1 gene expression and the abundance of numerous immune cells (i.e., T cells and B Cells) infiltration in LUAD and LUSC patients. Two previously known genes involved in oncogenic processes i.e., CDC45 and PDCD5 were identified as the most highly co-expressed genes of CCNE1 in LUAD and LUSC tissues. Altogether, the CCNE1 gene and its transcriptional and translational products may serve as a prognostic or therapeutic target in the diagnosis and treatment of LUAD and LUSC patients. The scientific findings of this study should assist in translating CCNE1 into clinical practice for lung cancer diagnosis and treatment.

Functional food: complementary to fight against COVID-19.

Background: The novel coronavirus has embarked on a global pandemic and severe mortality with limited access for its treatments and medications. For the lack of time, research, and enough efficacy, most vaccines are underdeveloped or unreachable to society. However, many recent studies suggest various alternative, complementary remedies for COVID-19, which are functional foods. This review provides an overview of how functional foods can play a great role through modulating the host immune system, generating antiviral activities, and synthesizing biologically active agents effective against the coronavirus. Main body: This review article summarizes the natural defense mechanisms in tackling SARS-CoV-2 alongside conventional therapeutic options and their corresponding harmful side effects. By analyzing bioactive components of functional foods, we have outlined its different contributions to human health and its potential immunomodulatory and antiviral properties that can enhance resistivity to viral infection. Moreover, we have provided a myriad of accessible and cost-effective functional foods that could be further investigated to target specific key symptoms of COVID-19 infections. Finally, we have found various functional foods with potent bioactive compounds that can inhibit or prevent COVID-19 infections and disease progression. Short conclusion: Numerous functional foods can help the body fight COVID-19 through several mechanisms such as the reduced release of pro-inflammatory cytokines, reduced expression of ACE2 receptors in cells, and inhibiting essential enzymes in SARS-CoV-2.

Klebsiella pneumoniae pathogenicity in silk moth larvae infection model.

The emergence of antibiotic resistant bacteria is a major health concern worldwide in recent years. The objective of this study is to establish the larvae of the silk moth (commonly known as silkworm), Bombyx mori as an infection model to study antibacterial effect of antibiotics against Klebsiella pneumoniae. In this study, the pathogenicity of a K. pneumoniae strain isolated from food to silkworm larvae was examined. Within 72 h of bacterial injection, all silkworm larvae were killed in a dose-dependent manner with their body color turning into black due to increased melanization. Bacterial numbers in the larval hemolymph (blood) significantly increased after 9 h of infection with a decrease in viable circulatory hemocytes in hemolymph. When presented with bacteria laden leaves, larvae did not eat but injection of bacteria directly into the midgut killed larvae within 12 h with a higher load required in comparison to that required for the killing by hemolymph injection. Administration of four different antibiotics into larval hemolymph showed therapeutic effect at different doses with varying efficacies against hemolymph-injected K. pneumoniae. These results indicate that the silkworm larvae can be used as an infection model not only to study the pathogenicity of K. pneumoniae but also to perform rapid screening for the identification of antibiotics effective against multidrug-resistant strains of K. pneumoniae.

Investigating the Anticancer Potential of Salvicine as a Modulator of Topoisomerase II and ROS Signaling Cascade.

Salvicine is a new diterpenoid quinone substance from a natural source, specifically in a Chinese herb. It has powerful growth-controlling abilities against a broad range of human cancer cells in both in vitro and in vivo environments. A significant inhibitory effect of salvicine on multidrug-resistant (MDR) cells has also been discovered. Several research studies have examined the activities of salvicine on topoisomerase II (Topo II) by inducing reactive oxygen species (ROS) signaling. As opposed to the well-known Topo II toxin etoposide, salvicine mostly decreases the catalytic activity with a negligible DNA breakage effect, as revealed by several enzymatic experiments. Interestingly, salvicine dramatically reduces lung metastatic formation in the MDA-MB-435 orthotopic lung cancer cell line. Recent investigations have established that salvicine is a new non-intercalative Topo II toxin by interacting with the ATPase domains, increasing DNA-Topo II interaction, and suppressing DNA relegation and ATP hydrolysis. In addition, investigations have revealed that salvicine-induced ROS play a critical role in the anticancer-mediated signaling pathway, involving Topo II suppression, DNA damage, overcoming multidrug resistance, and tumor cell adhesion suppression, among other things. In the current study, we demonstrate the role of salvicine in regulating the ROS signaling pathway and the DNA damage response (DDR) in suppressing the progression of cancer cells. We depict the mechanism of action of salvicine in suppressing the DNA-Topo II complex through ROS induction along with a brief discussion of the anticancer perspective of salvicine.

Comparison study of classification methods of intramuscular electromyography data for non-human primate model of traumatic spinal cord injury.

Traumatic spinal cord injury is a serious neurological disorder. Patients experience a plethora of symptoms that can be attributed to the nerve fiber tracts that are compromised. This includes limb weakness, sensory impairment, and truncal instability, as well as a variety of autonomic abnormalities. This article will discuss how machine learning classification can be used to characterize the initial impairment and subsequent recovery of electromyography signals in an non-human primate model of traumatic spinal cord injury. The ultimate objective is to identify potential treatments for traumatic spinal cord injury. This work focuses specifically on finding a suitable classifier that differentiates between two distinct experimental stages (pre-and post-lesion) using electromyography signals. Eight time-domain features were extracted from the collected electromyography data. To overcome the imbalanced dataset issue, synthetic minority oversampling technique was applied. Different ML classification techniques were applied including multilayer perceptron, support vector machine, K-nearest neighbors, and radial basis function network; then their performances were compared. A confusion matrix and five other statistical metrics (sensitivity, specificity, precision, accuracy, and F-measure) were used to evaluate the performance of the generated classifiers. The results showed that the best classifier for the left- and right-side data is the multilayer perceptron with a total F-measure of 79.5% and 86.0% for the left and right sides, respectively. This work will help to build a reliable classifier that can differentiate between these two phases by utilizing some extracted time-domain electromyography features.