In silico Gene Characterization and biological annotation of Aspergillus niger CBS 513.88

Genome annotation is the process of estimation of biological features from genomic data. The target of a genome annotation is to identify the key features of the genome sequence particularly, the genes and gene products. The characteristics of a gene, its products, and gene prediction programs of Aspergillus niger are discussed. Although the number of genomes in genomic databases are increasing day by day, genome-wide analyses are affected by the quality of the genome annotations. This study illustrates the importance of integrative approaches for automatic annotations of genomes of Aspergillus niger by computational methods. However, the annotation process is more complicated in Eukaryotes; we used a comparative study for gene prediction using the FgenesH algorithm by various software providers. The final annotation of Aspergillus niger CBS 513.88. has been created as a GB file in Artemis, A sequence viewer and annotation tool was developed in the anger Institute

Anti-Inflammatory and Antioxidative Stress Effects of Oryzanol in Glaucomatous Rabbits

Purpose. γ-Oryzanol works by anti-inflammatory and radical scavenging activity as a neuroprotective, anticancer, antiulcer, and immunosuppressive agent. The present study was conducted to investigate effect of oryzanol in acute and chronic experimental glaucoma in rabbits. Methods. Effect of oryzanol was evaluated in 5% dextrose induced acute model of ocular hypertension in rabbit eye. Chronic model of glaucoma was induced with subconjunctival injection of 5% of 0.3 ml phenol. Treatment with oryzanol was given for next two weeks after induction of glaucoma. From anterior chamber of rabbit eye aqueous humor was collected to assess various oxidative stress parameters like malondialdehyde, superoxide dismutase, glutathione peroxidase, catalase, nitric oxide, and inflammatory parameters like TNF-α and IL-6. Structural damage in eye was examined by histopathological studies. Results. In acute model of ocular hypertension oryzanol did not alter raised intraocular pressure. In chronic model of glaucoma oryzanol exhibited significant reduction in oxidative stress followed by reduction in intraocular pressure. Oryzanol treatment reduced level of TNF-α and IL-6. Histopathological studies revealed decreased structural damage of trabecular meshwork, lamina cribrosa, and retina with oryzanol treatment. Conclusions. Oryzanol showed protective effect against glaucoma by its antioxidative stress and anti-inflammatory property. Treatment with oryzanol can reduce optic nerve damage

Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts

Patient-derived xenografts (PDXs) are resected human tumors engrafted into mice for preclinical studies and therapeutic testing. It has been proposed that the mouse host affects tumor evolution during PDX engraftment and propagation, affecting the accuracy of PDX modeling of human cancer. Here, we exhaustively analyze copy number alterations (CNAs) in 1,451 PDX and matched patient tumor (PT) samples from 509 PDX models. CNA inferences based on DNA sequencing and microarray data displayed substantially higher resolution and dynamic range than gene expression-based inferences, and they also showed strong CNA conservation from PTs through late-passage PDXs. CNA recurrence analysis of 130 colorectal and breast PT/PDX-early/PDX-late trios confirmed high-resolution CNA retention. We observed no significant enrichment of cancer-related genes in PDX-specific CNAs across models. Moreover, CNA differences between patient and PDX tumors were comparable to variations in multiregion samples within patients. Our study demonstrates the lack of systematic copy number evolution driven by the PDX mouse host.</p

Author Correction:Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts (Nature Genetics, (2021), 53, 1, (86-99), 10.1038/s41588-020-00750-6)

This paper was originally published without open access. As of the date of this correction, the paper is available online as an open-access paper under a Creative Commons Attribution 4.0 International License. *Lists of authors and their affiliations appear online

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment.

Development of candidate cancer treatments is a resource-intensive process, with the research community continuing to investigate options beyond static genomic characterization. Toward this goal, we have established the genomic landscapes of 536 patient-derived xenograft (PDX) models across 25 cancer types, together with mutation, copy number, fusion, transcriptomic profiles, and NCI-MATCH arms. Compared with human tumors, PDXs typically have higher purity and fit to investigate dynamic driver events and molecular properties via multiple time points from same case PDXs. Here, we report on dynamic genomic landscapes and pharmacogenomic associations, including associations between activating oncogenic events and drugs, correlations between whole-genome duplications and subclone events, and the potential PDX models for NCI-MATCH trials. Lastly, we provide a web portal having comprehensive pan-cancer PDX genomic profiles and source code to facilitate identification of more druggable events and further insights into PDXs\u27 recapitulation of human tumors

Application of non-fluorescent carbon particles as scavengers for heavy metal ions: A waste utilisation approach

<p>In the preparation of fluorescent carbon nanoparticles, formation of non-fluorescent carbon particles (CPs) as waste matter is indispensible. This work is introducing CPs as adsorbents for some toxic metal ions in aqueous medium. CPs were characterised and their particle size, surface area, porosity, morphology etc. were compared with their parent material (charcoal). The effects of the initial metal ion concentration, contact time and pH on adsorption were undertaken. Adsorption data were evaluated for Langmuir and Freundlich isotherm models. The adsorption capacities (mg/g) of Ni²⁺, Pb²⁺, Zn²⁺, Co^2+, Cd²⁺ and Cu²⁺ were 85, 76, 75, 67, 58 and 46, respectively.</p

Comparative clinical evaluation of a local drug delivery of cranberry and garcinia fruit gel with tetracycline fibers for amelioration of periodontitis: A split mouth study

Background: The present study formulates and evaluates a polyberry gel comprising extracts of cranberry (Vaccinium macrocarpon) and brindle berry (Garcinia cambogia) in patients suffering from chronic periodontitis. Materials and Methods: The polyberry gel was evaluated for various physicochemical parameters, in vitro permeability and stability, and the active phytoconstituents were quantified by High-performance thin layer chromatography (HPTLC). Total phenolic content, total antioxidants, and ascorbic acid were estimated in the two extracts by in vitro assays. Patients suffering from chronic periodontitis with probing pocket depth (PPD) up to 5 mm were divided into 3 groups of 21 patients each and treated with scaling and root planing (SRP) or SRP followed by subgingival placement of polyberry gel or tetracycline fibers (standard). Plaque Index (PI), Gingival Index (GI), PPD, Clinical Attachment Level (CAL), and the salivary aspartate aminotransferase (AST) and C-reactive protein (CRP) levels were recorded at baseline and after 1 month. Results: A significant (P < 0.01) reduction in the periodontic disease parameters was observed in the standard and gel-treated groups between their baseline and 1-month time-interval readings. The polyberry gel treatment significantly (P < 0.05 for AST and P < 0.01 for the rest) attenuated the periodontitis-elevated PI, GI PPD, CAL, AST and CRP levels when compared with SRP at the end of the study and was comparable with tetracycline. Conclusion: The amelioration of periodontitis and gingival inflammation may be attributed to the potent antioxidant activity of the polyphenolic phytoconstituents of the gel. The polyberry gel may thus be used as a safe adjunct to SRP/tetracycline in chronic periodontitis

An adsorption study of Sr²⁺ from saline sources by coconut shell charcoal

<p>The adsorption potential of charcoal for the removal of heavy metal ions is well documented in the literature. However, its exploration for uptake of technologically valuable metal ions such as Sr²⁺ is poorly known. In this work, the batch adsorption study of Sr²⁺ ion from aqueous solution as well as from saline matrix (>3% of NaCl) onto charcoal has been carried out. The experiments were conducted with two charcoals, i.e., our prepared charcoal (coconut shell charcoal) and commercial charcoal. Strontium adsorption has been investigated as a function of its initial concentration, contact time, and varied mass of adsorbent. Equilibrium adsorption data were evaluated for Langmuir and Freundlich isotherm models. The adsorption capacities (mg/g) of Sr²⁺ present in the salt matrix onto coconut shell charcoal and commercial charcoal was found to be 18.4 and 22.2, respectively. Uptake of Sr²⁺ from subsoil brine onto coconut shell charcoal has been successfully demonstrated in this work.</p