RNA sequencing of olfactory bulb in Parkinson's disease reveals gene alterations associated with olfactory dysfunction.

The olfactory bulb is involved early in the pathophysiology of Parkinson's disease (PD), which is consistent with the early onset of olfactory dysfunction. Identifying the molecular mechanisms through which PD affects the olfactory bulb could lead to a better understanding of the pathophysiology and etiology of olfactory dysfunction in PD. We specifically aimed to assess gene expression changes, affected pathways and co-expression network by whole transcriptomic profiling of the olfactory bulb in subjects with clinicopathologically defined PD. Bulk RNA sequencing was performed on frozen human olfactory bulbs of 20 PD and 20 controls without dementia or any other neurodegenerative disorder, from the Arizona Study of Aging and Neurodegenerative disorders and the Brain and Body Donation Program. Differential expression analysis (19 PD vs 19 controls) revealed 2164 significantly differentially expressed genes (1090 upregulated and 1074 downregulated) in PD. Pathways enriched in downregulated genes included oxidative phosphorylation, olfactory transduction, metabolic pathways, and neurotransmitters synapses while immune and inflammatory responses as well as cellular death related pathways were enriched within upregulated genes. An overrepresentation of microglial and astrocyte-related genes was observed amongst upregulated genes, and excitatory neuron-related genes were overrepresented amongst downregulated genes. Co-expression network analysis revealed significant modules highly correlated with PD and olfactory dysfunction that were found to be involved in the MAPK signaling pathway, cytokine-cytokine receptor interaction, cholinergic synapse, and metabolic pathways. LAIR1 (leukocyte associated immunoglobulin like receptor 1) and PPARA (peroxisome proliferator activated receptor alpha) were identified as hub genes with a high discriminative power between PD and controls reinforcing an important role of neuroinflammation in the olfactory bulb of PD subjects. Olfactory identification test score positively correlated with expression of genes coding for G-coupled protein, glutamatergic, GABAergic, and cholinergic receptor proteins and negatively correlated with genes for proteins expressed in glial olfactory ensheathing cells. In conclusion, this study reveals gene alterations associated with neuroinflammation, neurotransmitter dysfunction, and disruptions of factors involved in the initiation of olfactory transduction signaling that may be involved in PD-related olfactory dysfunction.

The facile synthesis of and light-driven water splitting on a hetero-metallic bismuth oxide catalyst.

The process of water photo-electrolysis possesses the capability to generate sustainable and renewable hydrogen fuels, consequently addressing the challenge of the irregularity of solar energy. Thus, developing highly-efficient and low-cost electrocatalysts for the use in contemporary renewable energy devices is critical. Herein, we report the fabrication of a novel BaCeFex-yBixO6 nanocrystalline material through a one-step solvothermal route using a post-annealing process at 500 °C. The synthesized material was investigated for its light-induced electrochemical HER and OER activities in alkaline media and the results revealed that the as-prepared BaCeFex-yBixO6-500 °C exhibited an excellent OER activity with an overpotential of 100 mV to achieve a current density of 10 mA cm-2, thus outperforming the IrO2 electrocatalyst. Besides its excellent water oxidation performance, the catalyst also demonstrated an admirable HER activity comparable to that of the Pt/C catalyst, indicating that the higher temperature treatment plays a significant role in achieving the maximum performance of the developed electrocatalyst. This work provides insights into the enhancement of light-induced OER and HER activities of bismuth oxides for a wide range of catalytic applications.

Cydonia oblonga-Seed-Mucilage-Based pH-Sensitive Graft Copolymer for Controlled Drug Delivery-In Vitro and In Vivo Evaluation.

The primary objective of this study was to assess the potential utility of quince seed mucilage as an excipient within a graft copolymer for the development of an oral-controlled drug delivery system. The Cydonia oblonga-mucilage-based graft copolymer was synthesized via a free radical polymerization method, employing potassium per sulfate (KPS) as the initiator and N, N-methylene bisacrylamide (MBA) as the crosslinker. Various concentrations of monomers, namely acrylic acid (AA) and methacrylic acid (MAA), were used in the graft copolymerization process. Metoprolol tartarate was then incorporated into this graft copolymer matrix, and the resultant drug delivery system was subjected to comprehensive characterization using techniques such as Fourier-transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The swelling behavior of the drug delivery system was evaluated under different pH conditions, and in vitro drug release studies were conducted. Furthermore, pharmacokinetic parameters including the area under the curve (AUC), maximum plasma concentration (Cmax), time to reach Cmax (Tmax), and half-life (t1/2) were determined for metoprolol-loaded hydrogel formulations in rabbit plasma, and these results were compared with those obtained from a commercially available product. The key findings from the study include observations that higher concentrations of acrylic acid (AA) and Cydonia oblonga mucilage (CM) in the graft copolymer enhanced swelling, while the opposite trend was noted at elevated concentrations of methacrylic acid (MAA) and N, N-methylene bisacrylamide (MBA). FTIR analysis confirmed the formation of the graft copolymer and established the compatibility between the drug and the polymer. SEM imaging revealed a porous structure in the prepared formulations. Additionally, the swelling behavior and drug release profiles indicated a pH-sensitive pattern. The pharmacokinetic assessment revealed sustained release patterns of metoprolol from the hydrogel network system. Notably, the drug-loaded formulation exhibited a higher Cmax (156.48 ng/mL) compared to the marketed metoprolol product (96 ng/mL), and the AUC of the hydrogel-loaded metoprolol was 2.3 times greater than that of the marketed formulation. In conclusion, this study underscores the potential of quince seed mucilage as an intelligent material for graft-copolymer-based oral-controlled release drug delivery systems.

Measuring Up: A Comparison of TapeStation 4200 and Bioanalyzer 2100 as Measurement Tools for RNA Quality in Postmortem Human Brain Samples.

The determination of RNA integrity is a critical quality assessment tool for gene expression studies where the experiment's success is highly dependent on the sample quality. Since its introduction in 1999, the gold standard in the scientific community has been the Agilent 2100 Bioanalyzer's RNA integrity number (RIN), which uses a 1-10 value system, from 1 being the most degraded, to 10 being the most intact. In 2015, Agilent launched 4200 TapeStation's RIN equivalent, and reported a strong correlation of r2 of 0.936 and a median error < ±0.4 RIN units. To evaluate this claim, we compared the Agilent 4200 TapeStation's RIN equivalent (RINe) and DV200 to the Agilent 2100 Bioanalyzer's RIN for 183 parallel RNA samples. In our study, using RNA from a total of 183 human postmortem brain samples, we found that the RIN and RINe values only weakly correlate, with an r2 of 0.393 and an average difference of 3.2 RIN units. DV200 also only weakly correlated with RIN (r2 of 0.182) and RINe (r2 of 0.347). Finally, when applying a cut-off value of 6.5 for both metrics, we found that 95.6% of samples passed with RIN, while only 23.5% passed with RINe. Our results suggest that even though RIN (Bioanalyzer) and RINe (TapeStation) use the same 1-10 value system, they should not be used interchangeably, and cut-off values should be calculated independently.

Measuring up: A Comparison of Tapestation 4200 and Bioanalyzer 2100 as Measurement Tools for RNA Quality in Postmortem Human Brain Samples.

Determining RNA integrity is a critical quality assessment tool for gene expression studies where the experiment's success is highly dependent on sample quality. Since its introduction in 1999, the gold standard in the scientific community has been the Agilent 2100 Bioanalyzer's RNA Integrity Number (RIN) which uses a 1-10 value system with 1 being the most degraded to 10 being the most intact. In 2015, Agilent launched the 4200 Tapestation's RIN equivalent and reported a strong correlation of r 2 of 0.936 and median error < ± 0.4 RIN units. To evaluate this claim, we compared the Agilent 4200 Tapestation's RIN equivalent (RINe) and DV200 to the Agilent 2100 Bioanalyzer's RIN for 183 parallel RNA samples. In our study, using RNA from a total of 183 human postmortem brain samples, we found that the RIN and RINe values only weakly correlate with an r 2 of 0.393 and an average difference of 3.2 RIN units. DV200 also only weakly correlated with RIN (r 2 of 0.182) and RINe (r 2 of 0.347). Finally, when applying a cut-off value of 6.5 for both metrics, we found that 95.6% of samples passed with RIN, while only 23.5% passed with RINe. Our results suggest that even though RIN (Bioanalyzer) and RINe (Tapestation) use the same 1-10 value system, they should not be used interchangeably, and cut-off values should be calculated independently.

Insulinoma Mimicking Psychiatric Illness: A Covert Endocrine Tumor.

Insulinomas are rare neuroendocrine tumors with an annual incidence of four cases per million people in the general population. They have varied presentations making their diagnosis a challenging task necessitating a thorough patient assessment to ascertain early detection of this clinical entity by treating physicians. Insulinomas are characterized by the presence of Whipple's triad comprising of hypoglycemic symptoms, biochemical demonstration of hypoglycemia, and improvement of those symptoms after glucose administration. Biochemical detection of insulinoma by supervised 72-hour fasting test with plasma glucose, insulin, C-peptide, and proinsulin level measurements remains the gold standard of diagnosis. In this report, we present an interesting case of delayed diagnosis of pancreatic insulinoma. He was treated for more than six years as a psychiatric illness before receiving the correct diagnosis and treatment. Herein, a middle-aged man with a history of recurrent episodes of altered talk and confusion that resolved after eating something sweet. Biochemical investigations were suggestive of endogenous hyperinsulinemia. Pancreatic insulinoma was localized by a computed tomography scan. The patient underwent surgical resection of the tumor with complete resolution of his symptoms.

Bombax ceiba flower extract mediated synthesis of Se nanoparticles for antibacterial activity and urea detection.

Plant mediated synthesis of metallic nanomaterials has emerged as a non-toxic and economical approach to their applications in diverse fields especially in biomedical sciences. Herein, this study first time reporting the use of Bombax ceiba flower extract for synthesis of selenium nanoparticles (SeNPs). Initially, SeNPs were confirmed by turning the color of reaction mixtures from light yellow to brick-red. Scanning electron microscope (SEM) and Transmission electron microscopy (TEM) images showed spherical shaped nanoparticles with smooth surface, size ranges between 30 and 150 nm. Dynamic light scattering (DLS) showed 100-150 nm for the distribution of particle size. X-ray diffraction (XRD) analysis revealed SeNPs crystallinity and confirmed by matching with selenium JCPD card No. 06-362. Energy-dispersive X-ray (EDX) spectra showed presence of pure Se peaks that corroborate the conversion of selenium ions into its elemental form by bio-reduction. Fourier-transform infrared spectroscopy (FTIR) spectra demonstrated that involvement of -OH, C-H, C=C, and C=O functional groups for SeNPs formation. Raman Spectra peaks at 250 cm-1 represent asymmetric trigonal selenium (t-Se). Ultraviolet-visible spectrophotometer (UV-Vis) peaks at 296 and 306 nm which is an indication of surface plasmon resonance (SPR). Moreover, maximum antibacterial activity of SeNPs were observed against Staphylococcus aureus- a gram positive bacteria that possess zone of inhibition (ZOI) 20 mm and Klebsiella pneumonia and Pseudomonas aeruginosa-gram negative bacteria with ZOI 28 mm, respectively, at concentration 100 µg/ml. In addition, the surface functionalities induced through extract components adhere over Se binds with urea and give its detection up to 1mM in milk sample. Conclusively, synthesized SeNPs may function as a potential antibacterial pharmaceutical candidate.

Integrated Pangenome Analysis and Pharmacophore Modeling Revealed Potential Novel Inhibitors against Enterobacter xiangfangensis.

Enterobacter xiangfangensis is a novel, multidrug-resistant pathogen belonging to the Enterobacter genus and has the ability to acquire resistance to multiple antibiotic classes. However, there is currently no registered E. xiangfangensis drug on the market that has been shown to be effective. Hence, there is an urgent need to identify novel therapeutic targets and effective treatments for E. xiangfangensis. In the current study, a bacterial pan genome analysis and subtractive proteomics approach was employed to the core proteomes of six strains of E. xiangfangensis using several bioinformatic tools, software, and servers. However, 2611 nonredundant proteins were predicted from the 21,720 core proteins of core proteome. Out of 2611 nonredundant proteins, 372 were obtained from Geptop2.0 as essential proteins. After the subtractive proteomics and subcellular localization analysis, only 133 proteins were found in cytoplasm. All cytoplasmic proteins were examined using BLASTp against the virulence factor database, which classifies 20 therapeutic targets as virulent. Out of these 20, 3 cytoplasmic proteins: ferric iron uptake transcriptional regulator (FUR), UDP-2,3diacylglucosamine diphosphatase (UDP), and lipid-A-disaccharide synthase (lpxB) were chosen as potential drug targets. These drug targets are important for bacterial survival, virulence, and growth and could be used as therapeutic targets. More than 2500 plant chemicals were used to molecularly dock these proteins. Furthermore, the lowest-binding energetic docked compounds were found. The top five hit compounds, Adenine, Mollugin, Xanthohumol C, Sakuranetin, and Toosendanin demonstrated optimum binding against all three target proteins. Furthermore, molecular dynamics simulations and MM/GBSA analyses validated the stability of ligand-protein complexes and revealed that these compounds could serve as potential E. xiangfangensis replication inhibitors. Consequently, this study marks a significant step forward in the creation of new and powerful drugs against E. xiangfangensis. Future studies should validate these targets experimentally to prove their function in E. xiangfangensis survival and virulence.

Association of Candida Species with Novel SARS-CoV-2 and Biomarkers for Fungal Premalignant Oral Lesions.

Oral fungal infections can be caused by certain species of fungi among which candida albicans is the most implicated. Oral candidiasis is correlated with multiple conditions, such as coronavirus disease-2019, oral leukoplakia and oral erythroplakia. Tenascin is a glycoprotein and is present at the site of tissue injury and chronic inflammation, and tends to be over-expressed in cases of malignancy. Matrix metalloproteinase-9 belongs to a family of zinc-dependent endopeptidases and is involved in the degradation of extracellular matrix, leading to tissue invasion and metastasis. The current narrative review was planned to shed light on the fungal co-infections of coronavirus disease-2019 and molecular mechanisms of matrix metalloproteinase-9 and tenascin involved in the pathogenesis of fungus-associated oral leukoplakia and oral erythroplakia.

Screening of drug candidates against Endothelin-1 to treat hypertension using computational based approaches: Molecular docking and dynamics simulation.

Hypertension (HTN) is a major risk factor for cardiovascular and renal diseases, cerebrovascular accidents (CVA) and a prime underlying cause of worldwide morbidity and mortality. Hypertension is a complex condition and a strong interplay of multiple genetic, epigenetic and environmental factors is involved in its etiology. Previous studies showed an association of overexpression of genes with hypertension. Satisfactory control of Blood Pressure (BP) levels is not achieved in a major portion of hypertensive patients who take antihypertensive drugs. Since existing antihypertensive drugs have many severe or irreversible side effects and give rise to further complications like frequent micturition and headaches, dizziness, dry irritating cough, hypoglycemia, GI hemorrhage, impaired left ventricular function, hyperkalemia, Anemia, angioedema and azotemia. There is a need to identify new antihypertensive agents that can inhibit the expression of these overexpressed genes contributing to hypertension. The study was designed to identify drug-able targets against overexpressed genes involved in hypertension to intervene the disease. The structure of the protein encoded by an overexpressed gene Endothelin-1 was retrieved from Protein Database (PDB). A library of five thousand phytochemicals was docked against Endothelin-1. The top four hits against Endothelin-1 protein were selected based on S score and Root Mean Square Deviation (RMSD). S score is a molecular docking score which is used to determine the preferred orientation, binding mode, site of the ligand and binding affinity. RMSD refines value for drug target identification. Absorption, distribution, metabolism, excretion, and toxicity profiling (ADMET) was done. The study provides novel insights into HTN etiology and improves our understanding of BP pathophysiology. These findings help to understand the impact of gene expression on BP regulation. This study might be helpful to develop an antihypertensive drug with a better therapeutic profile and least side effects.

Network Pharmacology and Bioinformatics Approach Reveals the Multi-Target Pharmacological Mechanism of Fumaria indica in the Treatment of Liver Cancer.

Liver cancer (LC), a frequently occurring cancer, has become the fourth leading cause of cancer mortality. The small number of reported data and diverse spectra of pathophysiological mechanisms of liver cancer make it a challenging task and a serious economic burden in health care management. Fumaria indica is a herbaceous annual plant used in various regions of Asia to treat a variety of ailments, including liver cancer. Several in vitro investigations have revealed the effectiveness of F. indica in the treatment of liver cancer; however, the exact molecular mechanism is still unrevealed. In this study, the network pharmacology technique was utilized to characterize the mechanism of F. indica on liver cancer. Furthermore, we analyzed the active ingredient-target-pathway network and uncovered that Fumaridine, Lastourvilline, N-feruloyl tyramine, and Cryptopine conclusively contributed to the development of liver cancer by affecting the MTOR, MAPK3, PIK3R1, and EGFR gene. Afterward, molecular docking was used to verify the effective activity of the active ingredients against the prospective targets. The results of molecular docking predicted that several key targets of liver cancer (along with MTOR, EGFR, MAPK3, and PIK3R1) bind stably with the corresponding active ingredient of F. indica. We concluded through network pharmacology methods that multiple biological processes and signaling pathways involved in F. indica exerted a preventing effect in the treatment of liver cancer. The molecular docking results also provide us with sound direction for further experiments. In the framework of this study, network pharmacology integrated with docking analysis revealed that F. indica exerted a promising preventive effect on liver cancer by acting on liver cancer-associated signaling pathways. This enables us to understand the biological mechanism of the anti liver cancer activity of F. indica.

Comprehensive computational analysis reveals H5N1 influenza virus-encoded miRNAs and host-specific targets associated with antiviral immune responses and protein binding.

H5N1 virus (H5N1V) is highly contagious among birds and it was first detected in humans in 1997 during a poultry outbreak in Hong Kong. As the mechanism of its pathogenesis inside the host is still lacking, in this in-silico study we hypothesized that H5N1V might create miRNAs, which could target the genes associated with host cellular regulatory pathways, thus provide persistent refuge to the virus. Using bioinformatics approaches, several H5N1V produced putative miRNAs as well as the host genes targeted by these miRNAs were found. Functional enrichment analysis of targeted genes revealed their involvement in many biological pathways that facilitate their host pathogenesis. Eventually, the microarray dataset (GSE28166) was analyzed to validate the altered expression level of target genes and found the genes involved in protein binding and adaptive immune responses. This study presents novel miRNAs and their targeted genes, which upon experimental validation could facilitate in developing new therapeutics against H5N1V infection.

Integrating Network Pharmacology and Molecular Docking Approaches to Decipher the Multi-Target Pharmacological Mechanism of Abrus precatorius L. Acting on Diabetes.

Type 2 diabetes mellitus (T2DM) is a notable health care load that imposes a serious impact on the quality of life of patients. The small amount of reported data and multiple spectra of pathophysiological mechanisms of T2DM make it a challenging task and serious economic burden in health care management. Abrus precatorius L. is a slender, perennial, deciduous, and woody twining plant used in various regions of Asia to treat a variety of ailments, including diabetes mellitus. Various in vitro studies revealed the therapeutic significance of A. precatorius against diabetes. However, the exact molecular mechanism remains unclarified. In the present study, a network pharmacology technique was employed to uncover the active ingredients, their potential targets, and signaling pathways in A. precatorius for the treatment of T2DM. In the framework of this study, we explored the active ingredient-target-pathway network and figured out that abrectorin, abrusin, abrisapogenol J, sophoradiol, cholanoic acid, precatorine, and cycloartenol decisively contributed to the development of T2DM by affecting AKT1, MAPK3, TNFalpha, and MAPK1 genes. Later, molecular docking was employed to validate the successful activity of the active compounds against potential targets. Lastly, we conclude that four highly active constituents, namely, abrusin, abrisapogenol J, precatorine, and cycloartenol, help in improving the body's sensitivity to insulin and regulate the expression of AKT1, MAPK3, TNFalpha, and MAPK1, which may act as potential therapeutic targets of T2DM. Integrated network pharmacology and docking analysis revealed that A. precatorius exerted a promising preventive effect on T2DM by acting on diabetes-associated signaling pathways. This provides a basis to understand the mechanism of the anti-diabetes activity of A. precatorius.

Designing a multi-epitope vaccine against Chlamydia pneumoniae by integrating the core proteomics, subtractive proteomics and reverse vaccinology-based immunoinformatics approaches.

Chlamydia pneumoniae, a pneumonia causing specie belonging to chlamydia bacterium. C. pneumonia is considered as a leading cause of pneumonia. Apart from that, C. pneumoniae infection can also cause a variety of inflammatory disorders. There is an urgent need to tackle the major concerns arises due to infections causing by C. pneumoniae as no licensed vaccine available against this bacterial infection. In the framework of this study, a core proteome was generated C. pneumoniae strains was generated which revealed a total of 4754 core proteins. Later, 4 target proteins were obtained from 4754 core proteins by applying subtractive proteomics pipeline. Finally, MEV construct was designed by applying reverse vaccinology-based immunoinformatics approach on four target proteins. Molecular docking analysis were conducted to better understand thermodynamic stability, binding affinities, and interaction of vaccine. The binding interactions of MEV construct against TLR4, MHCII and MHCII showed that these candidate vaccines perfectly fit into the binding domains of the receptors. In addition, MEV construct has a better binding energy of 103.7 ± 15.4, 72.1 ± 9.1, and 70.4 ± 16.0 kcal/mol against TLR4, MHCII and MHCI. MD simulation was run at 200ns on docked complexes which further strengthened the current findings. Respective codon of vaccine construct was optimized and then in silico cloned into an E. coli expression host to ensure maximum vaccine protein expression. Despite the fact that the in-silico analysis used in this research produced reliable results, more studies are needed to validate the effectiveness and performance of proposed vaccine candidate.

Proteome based mapping and reverse vaccinology techniques to contrive multi-epitope based subunit vaccine (MEBSV) against Streptococcus pyogenes.

Streptococcus pyogenes is a root cause of human infection like pharyngitis, tonsillitis, scarlet fever, impetigo, and respiratory tract infections. About 11 million individuals in the US suffer from pharyngitis every year. Unfortunately, no vaccine against S. pyogenes is available yet. The purpose of this study is to create a multiepitope-based subunit vaccine (MEBSV) targeting S. pyogenes top four highly antigenic proteins by using a combination of immunological techniques and molecular docking to tackle term group A streptococcal (GAS) infections. T-cell (HTL & CTL), B-cell, and IFN-γ of target proteins were forecasted and epitopes having high antigenic properties being selected for subsequent research. For designing of final vaccine, 5LBL, 9CTL, and 4HTL epitopes were joined by the KK, AAY, and GPGPG linkers. To enhance the immune response, the N-end of the vaccine was linked by adjuvant (Cholera enterotoxin subunit B) with a linker named EAAAK. With the addition of adjuvants and linkers, the construct size was 421 amino acids. IFN-γ and B-cell epitopes illustrate that the modeled construct is optimized for cell-mediated immune or humoral responses. The developed MEBSV structure was assessed to be highly antigenic, non-toxic, and non-allergenic. Moreover, disulphide engineering further enhanced the stability of the final vaccine protein. Molecular docking of the MEBSV with toll-like receptor 4 (TLR4) was conducted to check the vaccine's compatibility with the receptor. Besides, in-silico cloning has been carried out for credibility validation and proper expression of vaccine construct. These findings suggested that the multi-epitope vaccine produced might be a potential immunogenic against Group A streptococcus infections but further experimental testing is required to validate this study.

The Screening of Phytochemicals Against NS5 Polymerase to Treat Zika Virus Infection: Integrated Computational Based Approach.

BACKGROUND: The recent Zika Virus (ZIKV) outbreak provides a spur for new, efficient, and safe anti-Zika Virus agents. RNA-dependent RNA polymerase (RdRp) is critical amongst the seven non-structural proteins for viral replication and considered an attractive drug target. METHODS: In this study, molecular docking approach was used to rationally screen the library of 5000 phytochemicals to find inhibitors against NS5 RdRp. LigX tool was used to analyze the 2D plots of receptor-ligand interactions. The top-ranked compounds were then subjected to in-silico pharmacokinetic study. RESULTS: The compounds namely Polydatin, Dihydrogenistin, Liquiritin, Rhapontin and Cichoriin were successfully bound inside the pocket of NS5 RdRp. Polydatin was the leading phytochemical that showed high docking score -18.71 (kcal/mol) and bonding interaction at the active-site of NS5 RdRp. They were subjected to analyze drug-like properties that further reinforced their validation and showed that they have more capability to attach with the receptor as compared to SOFOSBUVIR control drug. MD simulation of the top two complexes was performed and the simulated complexes showed stability and ligands were kept within the bonding pocket. CONCLUSION: The study might facilitate the development of a natural and cost-effective drug against ZIKV. Further validation, however, is necessary to confirm its effectiveness and its biocompatibility.

Pattern of rifampicin resistance and gene xpert based molecular typing of tuberculosis patients in tertiary care hospitals.

Mycobacterium tuberculosis associated morbidity, mortality and drug resistance is a global health issue. The Gene Xpert is used for early diagnosis of TB and simultaneous detection of Rifampicin (RIF) resistance. We aimed to determine situation analysis of clinical TB in tertiary care hospitals of Faisalabad and to find out frequency of TB and drug resistance pattern by Gene Xpert. A total of 220 samples from suspected patients of TB were included in this study and 214 samples were detected as positive by Gene Xpert. Samples were classified on the basis of gender, age group (<30, 30-50 and >50 years), type of sample (sputum and pleural) and number of M. tuberculosis by ct value (cycle threshold). The results of present study showed high positive frequency of TB in male patients and in 30-50 years of age groups by Gene Xpert. High number of M. tuberculosis was found in low and medium category in TB patients. Out of 214 positive TB patients, rifampicin resistance was detected in 16 patients. In conclusion, our study identified that Gene Xpert is an effective approach for diagnosing TB by detection of M. tuberculosis and rifampicin resistance in <2 hours for rapid diagnosis and management of TB.

In Silico Core Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pyogenes.

Streptococcus pyogenes is a significant pathogen that causes skin and upper respiratory tract infections and non-suppurative complications, such as acute rheumatic fever and post-strep glomerulonephritis. Multidrug resistance has emerged in S. pyogenes strains, making them more dangerous and pathogenic. Hence, it is necessary to identify and develop therapeutic methods that would present novel approaches to S. pyogenes infections. In the current study, a subtractive proteomics approach was employed to core proteomes of four strains of S. pyogenes using several bioinformatic software tools and servers. The core proteome consists of 1324 proteins, and 302 essential proteins were predicted from them. These essential proteins were analyzed using BLASTp against human proteome, and the number of potential targets was reduced to 145. Based on subcellular localization prediction, 46 proteins with cytoplasmic localization were chosen for metabolic pathway analysis. Only two cytoplasmic proteins, i.e., chromosomal replication initiator protein DnaA and two-component response regulator (TCR), were discovered to have the potential to be novel drug target candidates. Three-dimensional (3D) structure prediction of target proteins was carried out via the Swiss Model server. Molecular docking approach was employed to screen the library of 1000 phytochemicals against the interacting residues of the target proteins through the MOE software. Further, the docking studies were validated by running molecular dynamics simulation and highly popular binding free energy approaches of MM-GBSA and MM-PBSA. The findings revealed a promising candidate as a novel target against S. pyogenes infections.

Correction: Integrative bioinformatics approaches to map key biological markers and therapeutic drugs in Extramammary Paget's disease of the scrotum.

[This corrects the article DOI: 10.1371/journal.pone.0254678.].

Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches.

Chlamydia trachomatis, a Gram-negative bacterium that infects the rectum, urethra, congenital sites, and columnar epithelium of the cervix. It is a major cause of preventable blindness, ectopic pregnancy, and bacterial sexually transmitted infections worldwide. There is currently no licensed multi-epitope vaccination available for this pathogen. This study used core proteomics, immuno-informatics, and subtractive proteomics approaches to identify the best antigenic candidates for the development of a multi-epitope-based vaccine (MEBV). These approaches resulted in six vaccine candidates: Type III secretion system translocon subunit CopD2, SctW family type III secretion system gatekeeper subunit CopN, SycD/LcrH family type III secretion system chaperone Scc2, CT847 family type III secretion system effector, hypothetical protein CTDEC_0668, and CHLPN 76kDa-like protein. A variety of immuno-informatics tools were used to predict B and T cell epitopes from vaccine candidate proteins. An in silico vaccine was developed using carefully selected epitopes (11 CTL, 2 HTL & 10 LBL) and then docked with the MHC molecules (MHC I & MHC II) and human TLR4. The vaccine was coupled with Cholera toxin subunit B (CTB) adjuvant to boost the immune response. Molecular dynamics (MD) simulations, molecular docking, and MMGBSA analysis were carried out to analyze the molecular interactions and binding affinity of MEBV with TLR4 and MHC molecules. To achieve the highest level of vaccine protein expression, the MEBV was cloned and reverse-translated in Escherichia coli. The highest level of expression was achieved, and a CAI score of 0.97 was reported. Further experimental validation of the MEBV is required to prove its efficacy. The vaccine developed will be useful in preventing infections caused by C. trachomatis.