In this study, surface-enhanced Raman spectroscopy (SERS) technique, along with principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA), is used as a simple, quick, and cost-effective analysis method for identifying biochemical changes occurring due to induced mutations in the Aspergillus niger fungus strain. The goal of this study is to identify the biochemical changes in the mutated fungal cells (cell mass) as compared to the control/nonmutated cells. Furthermore, multivariate data analysis tools, including PCA and PLS-DA, are used to further confirm the differentiating SERS spectral features among fungal samples. The mutations are caused in A. niger by the clustered regularly interspaced palindromic repeat CRISPR-Cas9 genomic editing method to improve their biotechnological potential for the production of cellulase enzyme. SERS was employed to detect the changes in the cells of mutated A. niger fungal strains, including one mutant producing low levels of an enzyme and another mutant producing high levels of the enzyme as a result of mutation as compared with an unmutated fungal strain as a control sample. The distinctive features of SERS corresponding to nucleic acids and proteins appear at 546, 622, 655, 738, 802, 835, 959, 1025, 1157, 1245, 1331, 1398, and 1469 cm-1. Furthermore, PLS-DA is used to confirm the 89% accuracy, 87.7% precision, 87% sensitivity, and 88.9% specificity of this method, and the value of the area under the curve (AUROC) is 0.67. It has been shown that surface-enhanced Raman spectroscopy is an effective method for identifying and differentiating biochemical changes in genome-modified fungal samples.
In the current study, surface-enhanced Raman scattering (SERS) was performed to evaluate the antibacterial activity of lab-synthesized drug (1-isopentyl-3-pentyl-1H-imidazole-3-ium bromide salt) and commercial drug tinidazole againstBacillus subtilis. The changes in SERS spectral features were studied for unexposed bacillus and exposed one with various dosages of drug synthesized in the lab (1-isopentyl-3-pentyl-1H-imidazole-3-ium bromide salt), and SERS bands were assigned associated with the drug-induced biochemical alterations in bacteria. Multivariate data analysis tools including principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) have been utilized to analyze the antibacterial activity of the imidazole derivative (lab drug). PCA was employed in differentiating all the SERS spectral data sets associated with the various doses of the lab-synthesized drug. There is clear discrimination among the spectral data sets of a bacterial strain treated with different concentrations of the drug, which are analyzed by PLS-DA with 86% area under the curve in receiver operating curve (ROC), 99% sensitivity, 100% accuracy, and 98% specificity. Various dominant spectral features are observed with a gradual increase in the different concentrations of the applied drug including 715, 850, 1002, 1132, 1237, 1396, 1416, and 1453 cm-1, which indicate the possible biochemical changes caused in bacteria during the antibacterial activity of the lab-synthesized drug. Overall, the findings show that imidazole and imidazolium compounds generated from tinidazole with various alkyl lengths in the amide substitution can be effective antibacterial agents with low cytotoxicity in humans, and these results indicate the efficiency of SERS in pharmaceuticals and biomedical applications.
Marburg virus (MV) is a highly etiological agent of haemorrhagic fever in humans and has spread across the world. Its outbreaks caused a 23-90% human death rate. However, there are currently no authorized preventive or curative measures yet. VP40 is the MV matrix protein, which builds protein shell underneath the viral envelope and confers hallmark filamentous. VP40 alone is able to induce assembly and budding of filamentous virus-like particles (VLPs), which resemble authentic virions. As a result, this research is credited with clarifying the function of VP40 and leading to the discovery of new therapeutic targets effective in combating MV disease (MVD). Virtual screening, molecular docking and molecular dynamics (MD) simulation were used to find the putative active chemicals based on a 3D pharmacophore model of the protein's active site cavity. Initially, andrographidine-C, a potent inhibitor was selected for the development of the pharmacophore model. Later, a library of 30,000 compounds along with the andrographidine-C was docked against VP40 protein. Three best hits including avanafil, diuvaretin and macrourone were subjected to further MD simulation analysis, as these compounds had better binding affinities as compared to andrographidine-C. Furthermore, throughout the 100 ns simulations, the back bone of VP40 protein in presence of avanafil, diuvaretin and macrourone remained stable which was further validated by MM-PBSA analysis. Additionally, all of these compounds depict maximum drug-like properties. The predicted drugs based on the ligand, avanafil, diuvaretin and macrourone could be exploited and developed as an alternative or complementary therapy for the treatment of MVD.Communicated by Ramaswamy H. Sarma.
In the present research work, a selenium N-heterocyclic carbene (Se-NHC) complex/adduct was synthesized and characterized by using different analytical methods including FT-IR, 1HNMR, and 13CNMR. The antifungal activity of the Se-NHC complex against Aspergillus flavus (A. flavus) fungus was investigated with disc diffusion assay. Moreover, the biochemical changes occurring in this fungus due to exposure of different concentrations of the in-house synthesized compound are characterized by surface-enhanced Raman spectroscopy (SERS) and are illustrated in the form of SERS spectral peaks. SERS analysis yields valuable information about the probable mechanisms responsible for the antifungal effects of the Se-NHC complex. As demonstrated by the SERS spectra, this Se-NHC complex caused denaturation and conformational changes in the proteins as well as decomposition of the fungal cell membrane. The SERS spectra were analyzed using two chemometric tools such as principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA). The fungal samples' SERS spectra were differentiated using PCA, while various groups of spectra were discriminated with ultrahigh sensitivity (98%), high specificity (99.7%), accuracy (100%), and area under the receiver operating characteristic curve (87%) using PLS-DA.
The Two-component system (TCS) consists of Histidine kinases (HKs), Phosphotransfers (HPs), and response regulator (RR) proteins. It has an important role in signal transduction to respond to a wide variety of abiotic stresses and hence in plant development. Brassica oleracea (cabbage) is a leafy vegetable, which is used for food and medicinal purposes. Although this system was identified in several plants, it had not been identified in Brassica oleracea yet. This genome-wide study identified 80 BoTCS genes consisting of 21 HKs, 8 HPs, 39 RRs, and 12 PRRs. This classification was done based on conserved domains and motif structure. Phylogenetic relationships of BoTCS genes with Arabidopsis thaliana, Oryza sativa, Glycine max, and Cicer arietinum showed conservation in TCS genes. Gene structure analysis revealed that each subfamily had conserved introns and exons. Both tandem and segmental duplication led to the expansion of this gene family. Almost all of the HPs and RRs were expanded through segmental duplication. Chromosomal analysis showed that BoTCS genes were dispersed across all nine chromosomes. The promoter regions of these genes were found to contain a variety of cis-regulatory elements. The 3D structure prediction of proteins also confirmed the conservation of structure within subfamilies. MicroRNAs (miRNAs) involved in the regulation of BoTCSs were also predicted and their regulatory roles were also evaluated. Moreover, BoTCSs were docked with abscisic acid to evaluate their binding. RNA-seq-based expression analysis and validation by qRT-PCR showed significant variation of expression for BoPHYs, BoERS1.1, BoERS2.1, BoERS2.2, BoRR10.2, and BoRR7.1 suggesting their importance in stress response. These genes showing unique expression can be further used in manipulating the plant's genome to make the plant more resistant the environmental stresses which will ultimately help in the increase of plant's yield. More specifically, these genes have altered expression in shade stress which clearly indicates their importance in biological functions. These findings are important for future functional characterization of TCS genes in generating stress-responsive cultivars.
BACKGROUND: Surface-enhanced Raman spectroscopy (SERS) is an efficient technique which has been used for the analysis of filtrate portions of serum samples of Hepatitis B (HBV) and Hepatitis C (HCV) virus. OBJECTIVES: The main reason for this study is to differentiate and compare HBV and HCV serum samples for disease diagnosis through SERS. Hepatitis B and hepatitis C disease biomarkers are more predictable in their centrifuged form as compared in their uncentrifuged form. For differentiation of SERS spectral data sets of hepatitis B, hepatitis C and healthy person principal component analysis (PCA) proved to be a helpful. Centrifugally filtered serum samples of hepatitis B and hepatitis C are clearly differentiated from centrifugally filtered serum samples of healthy individuals by using partial least square discriminant analysis (PLS-DA). METHODOLOGY: Serum sample of HBV, HCV and healthy patients were centrifugally filtered to separate filtrate portion for studying biochemical changes in serum sample. The SERS of these samples is performed using silver nanoparticles as substrates to identify specific spectral features of both viral diseases which can be used for the diagnosis and differentiation of these diseases. The purpose of centrifugal filtration of the serum samples of HBV and HCV positive and control samples by using filter membranes of 50 KDa size is to eliminate the proteins bigger than 50 KDa so that their contribution in the SERS spectrum is removed and disease related smaller proteins may be observed. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are statistical tools which were used for the further validation of SERS. RESULTS: HBV and HCV centrifugally filtered serum sample were compared and biomarkers including (uracil, phenylalanine, methionine, adenine, phosphodiester, proline, tyrosine, tryptophan, amino acid, thymine, fatty acid, nucleic acid, triglyceride, guanine and hydroxyproline) were identified through PCA and PLS-DA. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) were used as a multivariate data analysis tool for the diagnosis of the characteristic SERS spectral features associated with both types of viral diseases. For the classification and differentiation of centrifugally filtered HBV, HCV, and control serum samples, Principal component analysis is found helpful. Moreover, PLS-DA can classify these two distinct sets of SERS spectral data with 0.90 percent specificity, 0.85 percent precision, and 0.83 percent accuracy. CONCLUSIONS: Surface enhanced Raman spectroscopy along with chemometric analysis like PCA and PLS-DA have been successfully differentiated HBV and HCV and healthy individuals' serum samples.
Hepatitis B , Hepatitis C , Metal Nanoparticles , Photochemotherapy , Humans , Metal Nanoparticles/chemistry , Silver/chemistry , Photochemotherapy/methods , Photosensitizing Agents , Discriminant Analysis , Hepatitis C/diagnosis , Spectrum Analysis, Raman/methods , Hepatitis B/diagnosis , Principal Component Analysis
BACKGROUND: Bacterial resistance against antibiotics remains a challenge and Raman Spectroscopy (SERS) may provide critical information concerning this. OBJECTIVES: In the current study, surface enhances Raman spectroscopy (SERS) has been used to determine the biochemical changes induced during the antibacterial activity of the in house synthesized imidazole derivative (1-benzyl-3-(secbutyl)-1H-imidazole-3-ium bromide) in comparison to commercially available drugs (fasygien) against both gram-positive and gram-negative bacteria. METHODS: For this purpose, the antibacterial activity of this compound was assessed on Bacillus subtilis and Escherichia coli. The SERS spectral changes are detected which can be associated with the biochemical changes in the bacterial cells as a result of the application of both drugs, including fasygien and the imidazole derivative drug demonstrating the technique's potential for analyzing the antibacterial activities of drug candidates. RESULTS: The chemometric techniques such as Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were performed for the differentiation of SERS spectral data sets of unexposed, exposed with imidazole derivative and commercially available antibacterial drugs for two different bacteria including E. coli and Bacillus. CONCLUSIONS: PCA was found helpful for the qualitative differentiation of all drug-treated E. coli and Bacillus in the form of separate clusters of spectral data sets and PLS-DA discriminated the unexposed and the exposed bacteria with imidazole derivative and commercially available drug with 93% sensitivity and 96% specificity for Bacillus and with 90% sensitivity and 89% specificity for E. coli.
Bacillus subtilis , Photochemotherapy , Escherichia coli , Anti-Bacterial Agents/pharmacology , Spectrum Analysis, Raman/methods , Bromides , Gram-Negative Bacteria , Photosensitizing Agents , Photochemotherapy/methods , Imidazoles/pharmacology
BACKGROUND: Surface Enhanced Raman Spectroscopy (SERS) is a very promising and fast technique for studying drugs and for detecting chemical nature of a molecule and DNA interaction. In the current study, SERS is employed to check the interaction of different concentrations of n-propyl imidazole derivative ligand with salmon sperm DNA using silver nanoparticles as SERS substrates. OBJECTIVES: Multivariate data analysis technique like principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) are employed for the detailed analysis of the SERS spectral features associated with the mode of action of the imidazole derivative ligand with DNA. METHODOLOGY: Silver nanoparticles were used as a SERS substrate in DNA-drug interaction. Five different concentrations of ligands were interacted with DNA and mix with Ag-NPs as substrate. The SERS spectra of were acquired for all seven samples and processed using MATLAB. Additionally, PCA and PLS-DA were used to assessed the ability SERS to differentiate interaction of DNA-drug. RESULTS: Differentiating SERS features having changes in their peak position and intensities are observed including 629, 655, 791, 807, 859, 1337, 1377 and 1456 cm-1. These SERS features reveal that binding of ligand with DNA is electrostatic in nature, and have specificity to major groove where it forms GC-CG interstrand cross-linking with the DNA double helix. CONCLUSIONS: SERS give significant information regarding to Drug-DNA interaction mechanism, SERS spectra inferred the mode of action of anticancer compound that are imidazole in nature.
Metal Nanoparticles , Photochemotherapy , Animals , Male , Spectrum Analysis, Raman/methods , Metal Nanoparticles/chemistry , Silver/chemistry , Salmon , Ligands , Semen , Photochemotherapy/methods , Photosensitizing Agents , Imidazoles
Surface-enhanced Raman spectroscopy (SERS) is used to identify the biochemical changes associated with the antifungal activities of selenium and zinc organometallic complexes against Aspergillus niger fungus. These biochemical changes identified in the form of SERS peaks can help to understand the mechanism of action of these antifungal agents which is important for development of new antifungal drugs. The SERS spectral changes indicate the denaturation and conformational changes of proteins and fungal cell wall decomposition in complex exposed fungal samples. The SERS spectra of these organometallic complexes exposed fungi are analyzed by using statistical tools like principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). PCA is employed to differentiate the SERS spectra of fungal samples exposed to ligands and complexes. The PLS-DA discriminated different groups of spectra with 99.8% sensitivity, 100% specificity, 98% accuracy and 86 % area under receiver operating characteristic (AUROC) curve.
Organometallic Compounds , Selenium , Antifungal Agents/pharmacology , Selenium/pharmacology , Zinc/pharmacology , Spectrum Analysis, Raman/methods , Discriminant Analysis , Principal Component Analysis
Lactic acid bacteria produce a variety of antibacterial and larvicidal metabolites, which could be used to cure diseases caused by pathogenic bacteria and to efficiently overcome issues regarding insecticide resistance. In the current study, the antibacterial and larvicidal potential of Bis-(2-ethylhexyl) phthalate isolated from Lactiplantibacillus plantarum BCH-1 has been evaluated. Bioactive compounds were extracted by ethyl acetate and were fractionated by gradient column chromatography from crude extract. Based on FT-IR analysis followed by GC-MS and ESI-MS/MS, the active compound was identified to be Bis-(2-ethylhexyl) phthalate. Antibacterial potential was evaluated by disk diffusion against E. coli (12.33 ± 0.56 mm inhibition zone) and S. aureus (5.66 ± 1.00 mm inhibition zone). Larvicidal potency was performed against Culex quinquefasciatus Say larvae, where Bis-(2-ethylhexyl) phthalate showed 100% mortality at 250 ppm after 72 h with LC50 of 67.03 ppm. Furthermore, after 72 h the acetylcholinesterase inhibition was observed as 29.00, 40.33, 53.00, 64.00, and 75.33 (%) at 50, 100, 150, 200, and 250 ppm, respectively. In comet assay, mean comet tail length (14.18 ± 0.28 µm), tail DNA percent damage (18.23 ± 0.06%), tail movement (14.68 ± 0.56 µm), comet length (20.62 ± 0.64 µm), head length (23.75 ± 0.27 µm), and head DNA percentage (39.19 ± 0.92%) were observed at 250 ppm as compared to the control. The current study for the first time describes the promising antibacterial and larvicidal potential of Bis-(2-ethylhexyl) phthalate from Lactiplantibacillus plantarum that would have potential pharmaceutical applications.
Aedes , Anopheles , Culex , Insecticides , Animals , Insecticides/chemistry , Acetylcholinesterase/pharmacology , Spectroscopy, Fourier Transform Infrared , Staphylococcus aureus , Tandem Mass Spectrometry , Escherichia coli , Plant Extracts/chemistry , Larva , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/analysis , Plant Leaves/chemistry
BACKGROUND: Surface-enhanced Raman spectroscopy (SERS) is explored to design a rapid screening method for the characterization and diagnosis of typhoid fever by employing filtrate fractions of blood serum samples obtained by centrifugal filtration with 50 KDa filters. OBJECTIVES: The purpose of this study, to separate the filtrate portions of blood serum samples in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire the SERS spectral features of smaller proteins more effectively which are probably associated with typhoid disease. Disease caused by Salmonella typhi diagnose more effectively by using surface-enhanced Raman spectroscopy (SERS) and multivariate data analysis tools. METHODS: SERS was used as a diagnostic tool for typhoid fever by comparison between healthy and diseased samples. For this purpose, all the samples were analyzed by comparing their SERS spectral features. Over the spectral range of 400-1800cm-1, multivariate data analysis techniques such as Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) are applied to diagnose and differentiate different filtrate fractions of blood serum samples of patients of typhoid fever and healthy ones. RESULTS: By comparing SERS spectra of healthy filtrate with that of filtrate of typhoid sample, the SERS spectral features associated with disease development are identified including PCA is found to be efficient for the qualitative differentiation of all of the samples analyzed. Moreover, PLS-DA successfully identified and classified healthy and typhoid positive blood serum samples with 97 % accuracy, 99 % specificity, 91 % sensitivity and 0.78 area under the receiver operating characteristic (AUROC) curve. CONCLUSIONS: Surface enhanced Raman spectroscopy using silver nanoparticles SERS substrate, is found to be useful technique for the quick identification and evaluation of filtrate fractions of the blood serum samples of healthy and typhoid samples for disease diagnosis.
Metal Nanoparticles , Photochemotherapy , Typhoid Fever , Humans , Spectrum Analysis, Raman/methods , Metal Nanoparticles/chemistry , Silver/chemistry , Typhoid Fever/diagnosis , Serum , Photochemotherapy/methods , Principal Component Analysis
Epstein-Barr Virus (EBV) is a human pathogen that has a morbidity rate of 90% in adults worldwide. Infectious mononucleosis is caused by EBV replication in B cells and epithelial cells of the host. EBV has also been related to autoimmune illnesses, including multiple sclerosis and cancers like nasopharyngeal carcinomas and Burkitt's lymphoma. Currently, no effective medications or vaccinations are available to treat or prevent EBV infection. Thus, the current study focuses on a bioinformatics approach to design an mRNA-based multi-epitope (MEV) vaccine to prevent EBV infections. For this purpose, we selected six antigenic proteins from the EBV proteome based on their role in pathogenicity to predict, extract, and analyze T and B cell epitopes using immunoinformatics tools. The epitopes were directed through filtering parameters including allergenicity, toxicity, antigenicity, solubility, and immunogenicity assessment, and finally, the most potent epitopes able to induce T and B cell immune response were selected. In silico molecular docking of prioritized T cell peptides with respective Human Leukocytes Antigens molecules, were carried out to evaluate the individual peptide's binding affinity. Six CTL, four HTL, and ten linear B cell epitopes fulfilled the set parameters and were selected for MEV-based mRNA vaccine. The prioritized epitopes were joined using suitable linkers to improve epitope presentation. The immune simulation results affirmed the designed vaccine's capacity to elicit a proper immune response. The MEV-based mRNA vaccine constructed in this study offers a promising choice for a potent vaccine against EBV.
Epstein-Barr Virus Infections , Herpesvirus 4, Human , Humans , Herpesvirus 4, Human/genetics , Epitopes, B-Lymphocyte/chemistry , Epitopes, B-Lymphocyte/genetics , Epstein-Barr Virus Infections/prevention & control , Molecular Docking Simulation , Epitopes, T-Lymphocyte/genetics , Epitopes, T-Lymphocyte/chemistry , RNA, Messenger/genetics , Proteome , Immunity , Peptides , Computational Biology/methods , mRNA Vaccines
Fungal infection causes deterioration, discoloration, and loss of nutritional values of food products. The use of lactic acid bacteria has diverse applications in agriculture to combat pathogens and to improve the nutritional values of cereal grains. The current research evaluated the potential of Loigolactobacillus coryniformis BCH-4 against aflatoxins producing toxigenic Aspergillus flavus strain. The cell free supernatant (CFS) of Loig. coryniformis was used for the protection of Zea mays L. treated with A. flavus. No fungal growth was observed even after seven days. The FT-IR spectrum of untreated (T1: without any treatment) and treated maize grains (T2: MRS broth + A. flavus; T3: CFS + A. flavus) showed variations in peak intensities of functional group regions of lipids, proteins, and carbohydrates. Total phenolics, flavonoid contents, and antioxidant activity of T3 were significantly improved in comparison with T1 and T2. Aflatoxins were not found in T3 while observed in T2 (AFB1 and AFB2 = 487 and 16 ng/g each). HPLC analysis of CFS showed the presence of chlorogenic acid, p-coumaric acid, 4-hydroxybenzoic acid, caffeic acid, sinapic acid, salicylic acid, and benzoic acid. The presence of these acids in the CFS of Loig. coryniformis cumulatively increased the antioxidant contents and activity of T3 treated maize grains. Besides, CFS of Loig. coryniformis was passed through various treatments (heat, neutral pH, proteolytic enzymes and catalase), to observe its stability. It suggested that the inhibitory potential of CFS against A. flavus was due to the presence of organic acids, proteinaceous compounds and hydrogen peroxide. Conclusively, Loig. coryniformis BCH-4 could be used as a good bioprotecting agent for Zea mays L. by improving its nutritional and antioxidant contents.
Aflatoxins , Aflatoxins/analysis , Antioxidants/metabolism , Antioxidants/pharmacology , Aspergillus flavus/metabolism , Lactobacillus , Spectroscopy, Fourier Transform Infrared , Zea mays/metabolism
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.
BACKGROUND: Raman spectroscopy is able to analyze non-invasively, disease related to body fluids. OBJECTIVES: For the qualitative and quantitative analysis of HCV serum samples surface-enhanced Raman spectroscopy (SERS) based method is developed. METHOD: Surface-enhanced Raman spectroscopy (SERS) technique is employed for analysis of filtrate portions of blood serum samples of hepatitis C virus (HCV) infected patients and healthy ones by using 50 kDa centrifugal filter device. The filtrate portions of the serum obtained in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire SERS spectral features of smaller proteins more effectively which are probably associated with Hepatitis C infection. Moreover, SERS spectral features of the filtrates of different level of viral load including low, medium and high viral loads are compared with SERS spectral features of the filtrate portions of healthy/control serum samples. SERS spectral data sets of different samples are further analyzed by using multivariate data analysis techniques such as principal component analysis (PCA) and partial least square regression (PLSR). Some SERS spectral features are solely observed in the filtrate portions of the serum samples of hepatitis C and their intensities are increased as the level of viral load increases and might be used for HCV diagnosis. RESULTS: PCA was found helpful for differentiation of SERS spectral data sets of filtrate portions of the serum samples of hepatitis C and healthy persons. The PLSR model helped for the quantification of viral loads in the unknown serum samples with 99% accuracy.
Hepatitis C , Photochemotherapy , Hepacivirus , Hepatitis C/diagnosis , Humans , Photochemotherapy/methods , Principal Component Analysis , Serum , Spectrum Analysis, Raman/methods
Microalgae have the highest capability to fix the atmospheric carbon and wastewater-derived nutrients to produce high-value bioproducts including lipids and carotenoids. However, their lower titers and single-product-oriented biomass processing have made the overall process expensive. Hence, increased metabolite titer and processing of the biomass for more than one product are required to ensure the commercial robustness of the algal biorefinery. In this study, a newly isolated algal strain was identified as Bracteacoccus pseudominor BERC09 through phylogenetic analysis based on the 18S rRNA gene sequence. Basic characterization of the strain revealed its promising potential to produce carotenoids and lipids. The lipids and carotenoid biosynthesis pathways of BERC09 were further triggered by manipulating the abiotic factors including nitrogen sources (NaNO3, KNO3, NH4Cl, Urea), nitrogen concentrations (0.06-0.36 gL-1), light intensity (150 µmolm-2s-1 to 300 µmolm-2s-1), and light quality (white and blue). Resultantly, 300 µmolm-2s-1 of blue light yielded 0.768 gL-1 of biomass, 8.4 mgg-1 of carotenoids, and 390 mgg-1 of lipids, and supplementation of 0.36 gL-1 of KNO3 further improved metabolism and yielded 0.814 gL-1 of biomass, 11.86 mgg-1 of carotenoids, and 424 mgg-1 of lipids. Overall, the optimal combination of light and nitrogen concurrently improved biomass, carotenoids, and lipids by 3.5-fold, 6-fold, and 4-fold than control, respectively. Besides, the excellent glycoproteins-based self-flocculation ability of the strain rendered an easier harvesting via gravity sedimentation. Hence, this biomass can be processed in a cascading fashion to use this strain as a candidate for a multiproduct biorefinery to achieve commercial robustness and environmental sustainability.
Chlorophyceae , Microalgae , Biomass , Carotenoids/metabolism , Chlorophyceae/metabolism , Lipids , Microalgae/metabolism , Nitrogen/metabolism , Phylogeny
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.
Influenza A Virus, H5N1 Subtype , Influenza, Human , MicroRNAs , Antiviral Agents , Humans , Immunity , Influenza A Virus, H5N1 Subtype/genetics , Influenza, Human/epidemiology , MicroRNAs/genetics , Protein Binding
Fungal spoilage led to a considerable economic loss of foodstuff which ultimately affects public health due to mycotoxins production. Moreover, the consumption of commercial antifungal drugs creates side effects and develops antifungal resistance. To overcome these challenges, the current work was aimed to investigate novel antifungal cyclic dipeptide (CDP) from Lactobacillus coryniformis (Loigolactobacillus coryniformis) BCH-4. CDPs have flexible, cyclic, and stable conformation. The proline-based CDPs provide additional structural compatibility and bio-functional values. Keeping in view, high-performance liquid chromatography (HPLC) was performed to explore cyclo(L-Leu-L-Pro) from L. coryniformis BCH-4. The HPLC detected concentration (135 ± 7.07 mg/mL) exhibited in vitro antifungal activity of 5.66 ± 0.57 mm (inhibitory zone) against Aspergillus flavus. Based on these results, cyclo(L-Leu-L-Pro) was used as a bioprotectant for selected food samples (grapes, lemon, cashew nuts, and almonds). A significant impact of cyclo(L-Leu-L-Pro) was observed in contrast with MRS broth (control) and cell-free supernatant. In silico molecular docking analysis of this CDP was carried out against FAD glucose dehydrogenase, dihydrofolate reductase, and urate oxidase of A. flavus as target proteins. Among these proteins, FAD glucose dehydrogenase exerted strong interactions with cyclo(L-Leu-L-Pro) having S-score of - 8.21. The results evaluated that the detected CDP has strong interactions with selected proteins, causing excellent growth inhibition of A. flavus. Therefore, cyclo(L-Leu-L-Pro) could be used as a potent bioprotectant against food-borne pathogenic fungi.
Antifungal Agents , Aspergillus flavus , Antifungal Agents/chemistry , Cell Proliferation , Flavin-Adenine Dinucleotide , Lactobacillus , Microbial Sensitivity Tests , Molecular Docking Simulation
Green synthesis of nanoparticles (NPs) has emerged as an eco-friendly alternative to produce nanomaterials with diverse physical, chemical, and biological characteristics. Previously used, physical and chemical methods involve the production of toxic byproducts, costly instrumentation, and energy-intensive experimental processes thereby, limiting their applicability. Biogenic synthesis of nanoparticles has come forward as a potential alternative, providing an eco-friendly, cost-effective, and energy-efficient approach for the synthesis of a diverse range of NPs. Several biological entities are employed in the biosynthesis of NPs including bacteria, fungi, and algae. However, the distinguishing characteristics of microalgae and cyanobacteria make them promising candidates for NPs synthesis because of their higher growth rate, substantially higher rate of sequestering CO2, hyperaccumulation of heavy metals, absence of toxic byproducts, minimum energy input, and employment of biomolecules (pigments and enzymes) as reducing and capping agents. Algal extract, being a natural reducing and capping agent, serves as a living cell factory for the efficient green synthesis of nanoparticles. Physiological and biological methods allow algal cells to uptake heavy metals and utilize them as nutrient source to generate biomass by regulating their metabolic processes. Despite their enormous potential, studies on the microalgae-based synthesis of nanoparticles for the removal of toxic pollutants from wastewater remained an unexplored research area in the literature. This review was aimed to summarize the recent advancements and prospects in the algae-based synthesis of nanoparticles for environmental applications particularly treating the wastewater.
Metal Nanoparticles , Nanostructures , Green Chemistry Technology , Metal Nanoparticles/chemistry , Plant Extracts , Plants , Wastewater
