Glycopeptide analysis by mass spectrometry may provide an important opportunity in discovery of biomarkers to aid in early detection of Alzheimer's Disease (AD). In this work, we have used a NanoLC-Stepped-HCD-DDA-MS/MS platform and a NanoLC-Stepped-HCD-PRM-MS platform for large-scale screening and quantification of novel N-glycopeptide biomarkers for early detection of AD in patient serum. N-glycopeptides were retrieved from 10 μL of serum in patients with mild cognitive impairment (MCI, a prodromal phase of AD) and normal controls, respectively, after trypsin digestion, glycopeptide enrichment, fractionation, and NanoLC-Stepped-HCD-DDA-MS/MS or NanoLC-Stepped-HCD-PRM-MS analysis. Using a combination of Byonic, Byologic and Skyline softwares, we were able to accomplish both identification and label-free quantitation of site-specific N-glycopeptides between MCI and normal controls. Differential quantitation analysis by Byologic showed that 29 N-glycopeptides derived from 16 glycoproteins were significantly changed in MCI compared to normal controls. Further, HCD-PRM-MS quantitative analysis of the selected N-glycopeptide candidates confirmed that EHEGAIYPDN138TTDFQR_HexNAc(4)Hex(5)-Fuc(2)NeuAc(1) from CERU, and VCQDCPLLAPLN156DTR_HexNAc(4)Hex(5)NeuAc(2) from AHSG can significantly discriminate MCI from normal controls. These two glycopeptides had the area under the receiver operating characteristic curve (AUC) of 0.850 (95% CI, 0.66-1.0) and 0.867 (95% CI, 0.68-1.0), respectively (p<0.05). The result demonstrates that changes in the expression level of the N-glycopeptides provide potential serum biomarkers for detection of AD at a very early stage.
In the latest years spray drying has been adopted from other disciplines as a process to convert liquid proteins/ peptides into more stable dry powder drug substances and products. By removing water, the molecular motion is reduced, which hence can improve storage stability and furthermore remove stringent and costly requirements for the storage temperature. Spray drying offers certain advantages above other drying methods with a more proven track record, amongst others time, cost, scale flexibility, continuous process and particle engineering. There is though still an on going hesitation for the full utilisation of spray drying for manufacturing of dry powder macromolecules in the industry due to the utilisation of heat in the process. For solvent evaporation, input energy is in the form of a hot drying gas around 100-200°C, which in the ears of a peptide/protein specialist may not sound like a recipe for success for such heat labile molecules. This presentation will however go through some common misconceptions about the spray drying process and discuss why spray drying holds a future in securing stable protein/peptide formulations. Furthermore we will present some concrete examples showing that we shouldn’t fear the high temperature used in the process and even in some cases embrace it in order to produce high quality, stable dry powder proteins and peptides.
Salt stress as one of the major abiotic stresses limits the world crop production. Sugar beet monosomic addition line M14 is a unique germplasm with salt stress tolerance, and root is directly exposed to salt stress in the soil. Here we report changes in root membrane proteome of the M14 plants in response to 0, 200 mM and 400 mM NaCl treatment using iTRAQ LC-MS/MS quantitative proteomics. A total of 115 differentially expressed membrane proteins (96 increased and 19 decreased) were identified with a significant fold change of >2.0. The proteins were mainly involved in the processes of transport, signaling, stress and defense, energy, protein degradation, and transcription. Transcriptional changes of 10 genes encoding the differential membrane proteins were analyzed using real-time PCR, and seven genes showed a positive correlation between transcriptional and protein levels. These results have revealed interesting mechanisms underlying the M14 root response to the salt stress, which may have potential applications toward improving crop salt tolerance through genetic engineering and molecular breeding.
This study was conducted to determine the fungal contaminants of garri in Dutsinma metropolis. A total of 150 samples were bought at random, 75 each of white and red garri from three different markets including Wednesday market, Abuja road market and Old market respectively. The fungi isolated using standard microbiological techniques were Alternaria spp. (3.7%), Aspergillus spp. (14.8%), Cladosporium spp. (27.8%), Fusarium spp. (9.3%), Mucor spp. (12.9%), Penicillium spp. (16.7%) and Rhizopus spp. (14.8%) in white garri. For yellow garri: Alternaria spp. (2.9%), Aspergillus spp. (8.8%), Cladosporium spp. (29.4%), Fusarium spp. (8.8%), Mucor spp. (11.8%), Penicillium spp. (20.6%) and Rhizopus spp. (17.6%) with Cladosporium and Rhizopus recording the highest occurrence in both white and yellow garri. Higher fungi species were isolated from white garri (54) compared to yellow (34) samples. Moisture content recorded showed higher content in white garri than in the yellow garri. Identification of the isolated fungi based on their morphological and cultural characteristics was carried out. The results show that consumers are exposed to the risk of aflatoxin poisoning. Efforts should therefore be made to improve the quality of Cassava farina by addressing its handling and processing practices.
Diabetic mellitus and cataracts are common mitochondrial diseases in Indonesia, occurring as a result of a lack of ATP, which is produced in mitochondria via oxidative phosphorylation (OXPHOS). The OXPHOS chain is composed of five complex proteins encoded by genes from nuclear DNA and mitochondrial DNA. One such gene is the CYB gene, with its locus in mitochondrial DNA. The CYB gene encodes part of the complex III subunit, cytochrome b, an electron transfer agent. A novel mutation has been identified at T15458C in type 2 diabetes mellitus patients and T15663C in cataract patients, both of which are in the CYB gene, leading to amino acid alterations S238P and I306T. This study investigated the relationship between T15458C and T15663C mutations in the CYB gene of mitochondrial DNA to the OXPHOS process via an in silico method. Wild type and mutant CYB were modelled via homology modelling using Modeller 9.19 with a 5XTE template, then evaluated using the Ramachandran plot, packaging quality score, and the DOPE profile. The results of the S238P mutant structure analysis showed that proline acts as a helix-breaker due to the loss of a hydrogen bond, while I306T causes a hydrophobic interaction as the helix stabiliser is lost in the mutant. It is assumed the threonine was phosphorylation mutations also destabilises the complex, as proven by the ΔΔG < 0. In conclusion, S238P and I306T mutations affect the function of complex III as an electron transfer agent in the respiratory process.
Molecular Biology is the field of biology that studies the composition, structure and interactions of cellular molecules
Cancer is a class of disease, culpable for abnormal growth of cells. Colon cancer is a chronic intestinal cancer that accounts for 10% of cancer-related fatalities in all around the world. Recently it is established that MSH6 protein target contribute to elevated glioma and colon cancer sensitivity. The toxicological impact of various therapies remains a subtle question whether to recommend a drug/compound for invitro and clinical assessment or not. Majority of anticancer therapies approved by higher governing authorities elicit strong adverse and toxic responses upon administration, hence hinder their exploitation in these types of cancer types. Therefore, an elaborate toxicological approach was adopted to screen anticancer equipped with immunomodulatory properties drugs library to procure low toxic drug candidates which were further docked against MSH6 receptor using PatchDock. Thirty compounds having anticancer nature and immune stimulating activities were selected, only nine anticancer compounds qualified based on minimal toxic response and further utilized as a potential ligand for docking studies. Upon interaction, the results were classified based on Hydrogen bonding, and minimal binding free energy. Capacitabine and luvocrine had an effective anticancer activity as Capacitabine two hydrogen bonds with MSH6 residues (GLN-132 and PHE-133) with the binding free energy of -27.26 kJ/mol and Luvocrine formed three hydrogen bonds with (CYS-88, LYS-145 and LEU-448) amino acid residues having -44.06 kJ/mol. Based on their interaction, these drugs could be proposed as a strong anticancer compound for invivo potency for future examination. The significance of the present study is clearly reflected by the identification of best inhibitor against colorectal cancer respectively.
Protein mass spectrometry demands that proteins in solution or solid form be ionised in the gas phase before being injected and accelerated in an electric or magnetic field for analysis. Electrospray Ionisation (ESI) and matrix-assisted laser desorption/ionization are the two most used techniques for ionising proteins. Electrospray allows delicate molecules to be ionised whole, sometimes retaining non-covalent connections, since the ions are generated from proteins in solution. In MALDI, proteins are placed in a matrix that is typically solid, and ions are generated by laser light pulses. Electrospray generates more multiply-charged ions than MALDI, allowing for higher mass protein measurement and better fragmentation for identification, whereas MALDI is faster and less susceptible to contamination, buffers, and additives.
The structural and molecular characterization of long non-coding DNA molecules has created tremendous scope for gaining insights into the molecular genetics of different types of malignancies. Studies have clearly indicated that these long-non coding DNAs are excellent candidates as far as cancer interventions are concerned and recent developments in different bioinformatics tools and paradigms have completely changed our cancer therapeutic and diagnostic outlook. The inherent objective of this review article in to present an overview on the molecular characteristics of lncRNAs and their role in cancer progression and discuss the far reaching implications for cancer diagnostics and therapeutics through bioinformatics analysis of lncRNAs. This review elaborates on the bioinformatics analysis of RNA-seq data from expression profiling of lncRNAs and also emphasizes on the significance of different lncRNA databases.
Covid 19 is a viral disease that emerged in China in December 2019 and has already spread throughout the world, with a high mortality and a high proliferation rates. It currently consists of a major focus of study, and among recent studies, one presented a set of 94 genes expressed in the human body with influence on Covid 19. The aim of this study is to understand the interaction of these 94 genes with other genes expressed in the human body, characterizing their properties by means of a gene expression network containing thousands of genes expressed in the human body. This characterization may concern a diverse set of properties. This study enabled the discovery of a limited set of genes with a regulatory role and a high influence on the human genes. The analysis also showed that although the 94 genes linked to Covid 19 may integrate several distinct metabolic pathways, they present great participation in only two main groups. Thus, this study has deepened the understanding on the genetic functioning of Covid 19 and may support explanations on the phenomena related to the disease, such as its high proliferation or the various phenotypic side effects caused by it. The author would also like to thank Capes, Fapemig and UFMG for the funding.
Objective: Today, Human Papilloma Viruses (HPV) is considered as second most frequent carcinogens. It has been distinguished that structural proteins of HPVs are involved in their carcinogenicity. The aim of this work was analysis of the HPV proteins and classifying them into two categories, low and high-risk, based on their physiochemical properties and Chou’s Pseudo Amino Acid concept. Materials and Methods: Initially, sequences of 69 proteins belonging to high-risk viruses and 107 proteins belonging to low-risk viruses were collected from NCBI database and Uniprot. Then the PseAAC server was used to analyze these sequences. In the next step, the information obtained from this server was analyzed software. The KNN algorithm was used to classify the datasets. Furthermore, 10 and 6 fold-cross validation test was applied on the classifier to evaluate our prediction method. Results: Specificity, sensitivity, and accuracy of our proposed method were achieved 87.64%, 87.22% and 87.39% in the treated dataset and 91.11%, 82.60% and 86.66% in the tested dataset, respectively. Conclusion: In this study, we developed a sequence-based method for predicting the carcinogenicity potent of HPV proteins and dividing them into high risk and low-risk categories.
Bacopa monnieri plant extract has been used as a nerve tonic in ancient Indian folklore since ages and bacosides are the main key component behind neuro-potential of the herb. Accumulated β-amyloid protein causes the hyperphosphorylation of tau protein which in turn is the cause of tangled nerve projections in Alzheimer’s brain. However, the interaction of bacosides with amyloid protein has not been studied so far. Computational approach including docking analysis showed hydrogen bonding of bacoside molecule with important amino acid residues present in amyloid protein which proved the potential of bacoside A3 in targeting Alzheimer’s. In addition to this, in vitro culture conditions have demonstrated their critical influence on secondary plant metabolism. Kinetic studies conducted in our experiment showed that cell suspension cultures of bacopa placed under shaking light conditions produce more bacoside content as compared to other conditions. Besides these properties, bacopa plants have also been known to improve the chemical characteristics of saline and clayey soils thus, enhancing the growth of agriculturally important crops. In this work, we attempted the docking of the bacoside A3 molecule to find the binding mechanism with the suitable target which will be helpful in understanding the molecular mechanism involved in the development of Alzheimer’s disease. Up-scaling of memory enhancer bacoside molecule has also been attempted under in vitro conditions that should deliver maximum benefits with minimal tissue loss during harvestation.
Actinobacteria is a large and diverse phylum of bacteria that contains medically and ecologically relevant organisms. Many members are valuable sources of bioactive natural products and chemical precursors that are exploited in the clinic and made using the enzyme pathways encoded in their complex genomes. Whilst the number of sequenced genomes has increased rapidly in the last 20 years, the large size, complexity and high G+C content of many actinobacterial genomes means that the sequences remain incomplete and consist of large numbers of contigs with poor annotation, which hinders large- scale comparative genomic and evolutionary studies. To enable greater understanding and exploitation of actinobacterial genomes, specialized genomic databases must be linked to highquality genome sequences. Here, we provide a curated database of 612 highquality actinobacterial genomes from 80 genera, chosen to represent a broad phylogenetic group with equivalent genome reannotation. Utilizing this database will provide researchers with a framework for evolutionary and metabolic studies, to enable a foundation for genome and metabolic engineering, to facilitate discovery of novel bioactive therapeutics and studies on gene family evolution. This article contains data hosted by Microreact.
Glioblastoma multiforme (GBM) is a malignant tumor affecting the brain or spine, is a fast growing and aggressive brain tumor. There is a need to identify novel targets in GBM to improve our understanding of disease biology and that can be used for developing new therapeutics. Hence, the aim of our study was to explore key genes which are associated with GBM using computational methods. In the present study, we have constructed an interaction network of 159 genes in GBM. 13 out of 159 genes were selected as hub genes using topological analysis methods i.e. CYTOHUBBA and MCODE. Functional enrichment analysis for these 13 genes were performed using DAVID and found that the genes were enriched in various functions and pathways among which regulation of apoptotic process, cell proliferation were the most associated with it. Gene ontology analysis reveals that 14, 111 and 17 terms were found in the cellular process, biological process and molecular function respectively. The survival analysis for these 13 genes was performed using the Kaplan Meier plot. This revealed that 9 out of 13 hub genes were related to overall survival of GBM patients. VEGFA, TP53, STAT3, EGFR, NOTCH2, MMP9, MYC, HRAS, PTEN may serve as potential key genes which are associated with GBM for diagnosis, prognosis and treatment of GBM.
