78 research outputs found
Karanjin, A Promising Bioactive Compound Possessing Anti-cancer Activity against Experimental Model of Non-small Cell Lung Cancer Cells
No full textAims: The aim of this study is to isolate the Millettia pinnata (Karanj) leaf extract for pure compound with anticancer properties and to study the molecular target of the isolates in non-small cell lung cancer cell lines. Background: In our earlier research Millettia pinnata leaf extract has demonstrated potential anticancer activities. Thus, in pursuit of the bioactive compounds, the most potential active extract from our previous study was purified. Furthermore, the anticancer properties of the isolated compound karanjin was studied and aimed for apopto-sis and restraining growth. Methods: A novel method was developed through column chromatography for isolation and purification of the compound karanjin from leaf chloroform extract. The purified component was then characterised using FTIR, mass spectrometry, and NMR. An MTT-based cytotoxicity assay was used to analyse cell cytotoxicity, whereas fluorescence staining was used for apoptosis and reactive oxygen species inhibition quantification. Furthermore, the real-time PCR assay was used to determine the molecular mechanism of action in cells causing cytotoxicity induced by karanjin dosing. Results: The anticancer activity of karanjin in A549 cell line exhibited prominent activity revealing IC50 value of 4.85 μM. Conferring the predicted molecular pathway study, karanjin restrains the proliferation of cancer cells through apoptosis, which is controlled by extrinsic pathway proteins FAS/FADD/Caspases 8/3/9. Down-regulation of KRAS and dependent gene expression also stopped cell proliferation. Conclusion: Karanjin has been identified as a compound with potential effect in non-small cell lung cancer cells. Molecular mechanism for apoptosis and inhibition of reactive oxygen species induced through H2O2 were observed, concluding karanjin have medicinal and antioxidant properties
In silico structural and functional characterization of Antheraea mylitta cocoonase
No full textBACKGROUND: Cocoonase is a serine protease present in sericigenous insects and majorly involved in dissolving of sericin protein allowing moth to escape. Cocoon structure is made up of sericin protein which holds fibroin filaments together. Cocoonase enzyme hydrolyzes sericin protein without harming the fibroin. However, until date, no detailed characterization of cocoonase enzyme and its presence in wild silk moth Antheraea mylitta has been carried out. Therefore, current study aimed for detailed characterization of amplified cocoonase enzyme, secondary and tertiary structure prediction, sequence and structural alignment, phylogenetic analysis, and computational validation. Several computational tools such as ProtParam, Iterative Threading Assembly Refinement (I-TASSER), PROCHECK, SAVES v6.0, TM-align, Molecular Evolutionary Genetics Analysis (MEGA) X, and Figtree were employed for characterization of cocoonase protein. RESULTS: The present study elucidates about the isolation of RNA, cDNA preparation, PCR amplification, and in silico characterization of cocoonase from Antheraea mylitta. Here, total RNA was isolated from head region of A. mylitta, and gene-specific primers were designed using Primer3 followed by PCR-based amplification and sequencing. The newly constructed 377-bp length sequence of cocoonase was subjected to in silico characterization. In silico study of A. mylitta cocoonase showed 26% similarity to A. pernyi strain Qing-6 cocoonase using Blastp and belongs to member of chymotrypsin-like serine protease superfamily. From phylogenetic study, it was found that A. mylitta cocoonase sequence is closely related to A. pernyi cocoonase sequence. CONCLUSIONS: The present study revealed about the detailed in silico characterization of cocoonase gene and encoded protein obtained from A. mylitta head region. The results obtained infer the presence of cocoonase enzyme in the wild silkworm A. mylitta and can be used for cocoon degumming which will be a valuable and cost-effective strategy in silk industry. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s43141-022-00367-8
Status of Fish Culture in Joypurhat District, Northern Bangladesh
No full textThe study was carried out for a period of seven months (January 2006 to July 2006) from 50 farm owners and 50 local people near the farms of different Upazilla (Joypurhyat sadar, Panchbibi, Akkelpur, Khetlal and Kalai) in Joypurhat district. The study indicated that most of the farms (46%) were established within last ten years. Fifteen different fish species were cultured. Three types of farm were observed, such as own (48%), leased (38%) and both (14%). Fish farming (58%) was the major income source for farm owners. Most of the (72%) farms depend on underground water. Various types of chemicals and toxic substances like rotenone (16% farm), phostoxin (10% farm), bleaching powder (6% farm), disel/kerosin (22% farm) and sumithion (4% farm) were used. Among all the farms 32%, 56% and 34% were affected by tail and fin rot, oxygen deficiency and disease, respectively. Lime (76% farm), salt (34%) and sumithion (18%) were widely used as antibiotics for disinfection, prevention and control of fish disease. Total fish productions have gradually been increased in all the farms. The benefits of fish farm owners were increased in income (92% farm owners), social status (74% farm owners), employment opportunity (58% farm owners), ingestion of fish (42% farm owners) and poverty alleviation (70% farm owners)
Molecular marker survey and expression analyses of the rice submergence-tolerance gene SUB1A
No full textThe major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.Namrata Singh, Trang T. M. Dang, Georgina V. Vergara, Dev Mani Pandey, Darlene Sanchez, C. N. Neeraja, Endang M. Septiningsih, Merlyn Mendioro, Evelyn Mae Tecson-Mendoza, Abdelbagi M. Ismail, David J. Mackill, Sigrid Heue
MOLECULAR BEACON PROBE BASED PROMOTER MOTIFS VALIDATION IN ANOXIA RESPONSIVE DIFFERENTIALLY EXPRESSED GENES AND THEIR IN SILICO INTERACTION STUDIES WITH AP2/EREBP TF IN RICE (ORYZA SATIVA L.)
No full textObjective: Progressive evolution in molecular biology revealed the differential expression of genes and their regulatory mechanism in rice under anoxia. In addition to that the consensus promoter motifs (GCC and TCC box) were identified in differentially expressed genes (DEGs) from microarray analysis through in silico study. These promoter motifs need to be validated and their interaction study with the transcription factors (TFs) are essential.Methods: To unravel the regulatory mechanism in rice during anoxia, we identified and validated the promoter motifs through Molecular Beacon Probes (MBP) based Real Time PCR. In silico protein-DNA interaction was studied between highly up-regulated APETALA2/Ethylene-responsive element binding proteins (AP2/ERBP) TF under anoxia and validated promoter motifs through the HADDOCK and SiteMap module.Results: It was identified that consensus promoter motif GCC and TCC box were present in highly up-regulated methyl-transferase domain containing protein gene (MT) and down-regulated RhoGAP domain containing protein gene (RG), respectively.Conclusion: These promoter motifs were validated through MBP and further their interaction with AP2/ERBP shows the significant binding affinity towards GCC and TCC box present on MT and RG, respectively.Â
Additional file 1 of In silico structural and functional characterization of Antheraea mylitta cocoonase
No full textAdditional file 1: Figure S1. NCBI blast result of cocoonase sequence against Antheraea mylitta—GCA_014332785.1 (AM_v1.0). The blast result show that sequences are matched with A. mylitta isolate AMDABA2020 scaffold18_size7685921, whole genome shotgun sequence. Figure S2. NCBI blast result of cocoonase sequence against Antheraea mylitta—GCA_014332785.1 (AM_v1.0). The blast result indicated the 2 matches only with A. mylitta isolate AMDABA2020 scaffold18_size7685921, whole genome shotgun sequence. Figure S3. Secondary structure prediction of Antheraea mylitta cocoonase (AmCoc) from PSPIRED server: (a) Predicted helix, strand and coil of the protein (b) Secondary structure map of cocoonase. Figure S4. MEME tool based result of Antheraea mylitta cocoonase (AmCoc) of KM388539.1 showing two strong motifs in the sequence highlighted in red (MFCAGPPEGGKDSCQGDSGGP) at position 84–104 and in lime green (INKVPYQAYLLLQKBNEYFQC) at position 56- 76. Figure S5. Enzyme Commission numbers and active sites for Antheraea mylitta predicted cocoonase based on the template of PDB ID: 3cskA having C-score of 0.065. The predicted active-site residues are 9, 12, 25, 38, 42 and 77 is highlighted with magenta color code
Study on cocoonase, sericin, and degumming of silk cocoon: computational and experimental
No full textAbstract Background Cocoonase is a proteolytic enzyme that helps in dissolving the silk cocoon shell and exit of silk moth. Chemicals like anhydrous Na2CO3, Marseille soap, soda, ethylene diamine and tartaric acid-based degumming of silk cocoon shell have been in practice. During this process, solubility of sericin protein increased resulting in the release of sericin from the fibroin protein of the silk. However, this process diminishes natural color and softness of the silk. Cocoonase enzyme digests the sericin protein of silk at the anterior portion of the cocoon without disturbing the silk fibroin. However, no thorough characterization of cocoonase and sericin protein as well as imaging analysis of chemical- and enzyme-treated silk sheets has been carried out so far. Therefore, present study aimed for detailed characterization of cocoonase and sericin proteins, phylogenetic analysis, secondary and tertiary structure prediction, and computational validation as well as their interaction with other proteins. Further, identification of tasar silkworm (Antheraea mylitta) pupa stage for cocoonase collection, its purification and effect on silk sheet degumming, scanning electron microscope (SEM)-based comparison of chemical- and enzyme-treated cocoon sheets, and its optical coherence tomography (OCT)-based imaging analysis have been investigated. Various computational tools like Molecular Evolutionary Genetics Analysis (MEGA) X and Figtree, Iterative Threading Assembly Refinement (I-TASSER), self-optimized predicted method with alignment (SOPMA), PROCHECK, University of California, San Francisco (UCSF) Chimera, and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) were used for characterization of cocoonase and sericin proteins. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), protein purification using Sephadex G 25-column, degumming of cocoon sheet using cocoonase enzyme and chemical Na2CO3, and SEM and OCT analysis of degummed cocoon sheet were performed. Results Predicted normalized B-factors of cocoonase and sericin with respect to α and β regions showed that these regions are structurally more stable in cocoonase while less stable in sericin. Conserved domain analysis revealed that B. mori cocoonase contains a trypsin-like serine protease with active site range 45 to 180 query sequences while substrate binding site from 175 to 200 query sequences. SDS-PAGE analysis of cocoonase indicated its molecular weight of 25–26 kDa. Na2CO3 treatment showed more degumming effect (i.e., cocoon sheet weight loss) as compared to degumming with cocoonase. However, cocoonase-treated silk cocoon sheet holds the natural color of tasar silk, smoothness, and luster compared with the cocoon sheet treated with Na2CO3. SEM-based analysis showed the noticeable variation on the surface of silk fiber treated with cocoonase and Na2CO3. OCT analysis also exemplified the variations in the cross-sectional view of the cocoonase and Na2CO3-treated silk sheets. Conclusions Present study enlightens on the detailed characteristics of cocoonase and sericin proteins, comparative degumming activity, and image analysis of cocoonase enzyme and Na2CO3 chemical-treated silk sheets. Obtained findings illustrated about use of cocoonase enzyme in the degumming of silk cocoon at larger scale that will be a boon to the silk industry
Lie perfect, Lie central extension and generalization of nilpotency in multiplicative Lie algebras
No full textsummary:This paper aims to introduce and explore the concept of Lie perfect multiplicative Lie algebras, with a particular focus on their connections to the central extension theory of multiplicative Lie algebras. The primary objective is to establish and provide proof for a range of results derived from Lie perfect multiplicative Lie algebras. Furthermore, the study extends the notion of Lie nilpotency by introducing and examining the concept of local nilpotency within multiplicative Lie algebras. The paper presents an innovative adaptation of the Hirsch-Plotkin theorem specifically tailored for multiplicative Lie algebras.\looseness -
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