Methodology of predicting novel key regulators in ovarian cancer network: a network theoretical approach.

BACKGROUND: Identification of key regulator/s in ovarian cancer (OC) network is important for potential drug target and prevention from this cancer. This study proposes a method to identify the key regulators of this network and their importance. METHODS: The protein-protein interaction (PPI) network of ovarian cancer (OC) is constructed from curated 6 hundred genes from standard six important ovarian cancer databases (some of the genes are experimentally verified). We proposed a method to identify key regulators (KRs) from the complex ovarian cancer network based on the tracing of backbone hubs, which participate at all levels of organization, characterized by Newmann-Grivan community finding method. Knockout experiment, constant Potts model and survival analysis are done to characterize the importance of the key regulators in regulating the network. RESULTS: The PPI network of ovarian cancer is found to obey hierarchical scale free features organized by topology of heterogeneous modules coordinated by diverse leading hubs. The network and modular structures are devised by fractal rules with the absence of centrality-lethality rule, to enhance the efficiency of signal processing in the network and constituting loosely connected modules. Within the framework of network theory, we device a method to identify few key regulators (KRs) from a huge number of leading hubs, that are deeply rooted in the network, serve as backbones of it and key regulators from grassroots level to complete network structure. Using this method we could able to identify five key regulators, namely, AKT1, KRAS, EPCAM, CD44 and MCAM, out of which AKT1 plays central role in two ways, first it serves as main regulator of ovarian cancer network and second serves as key cross-talk agent of other key regulators, but exhibits disassortive property. The regulating capability of AKT1 is found to be highest and that of MCAM is lowest. CONCLUSIONS: The popularities of these key hubs change in an unpredictable way at different levels of organization and absence of these hubs cause massive amount of wiring energy/rewiring energy that propagate over all the network. The network compactness is found to increase as one goes from top level to bottom level of the network organization.

Genetic diversity and population structure of the threatened chocolate mahseer (Neolissochilus hexagonolepis McClelland 1839) based on SSR markers: implications for conservation management in Northeast India.

Neolissochilus hexagonolepis (MacClend 1839), commonly known as chocolate mahseer, is an ecologically threatened fish species. The species is reported from Southeast Asia and in India, it is distributed across the Northeast region. The present study was carried out to develop species-specific novel microsatellite markers using next-generation sequencing and to assess the genetic diversity of wild chocolate mahseer populations distributed through Northeastern India. A total of 25 polymorphic loci (mean PIC = 0.933) were amplified in 194 individuals belonging to seven different populations. We observed high genetic diversity across the loci with mean observed (Ho) and expected heterozygosity (He) of 0.557 and 0.939 respectively. The studied loci didn't show significant deviation from Hardy-Weinberg equilibrium. Genetic analyses indicate substantial pairwise Nei's genetic distance and moderate to high levels of genetic differentiation among populations (mean FST = 0.23). The structure, factor and cluster analysis identified five major clusters that can be considered as different conservation units while formulating any management measures. Furthermore, the migration analysis inferred that there is no active migration among the studied populations. Results suggested that two populations i.e. Dikrong river (Arunanchal Pradesh) and Umiam river have high genetic diversity. These populations can be utilized for the breeding programme to achieve substantial genetic variations in the descendant populations. The Nongbareh populations showed very less genetic vigor and need an immediate attention for conservation. The SSR markers developed in the present study will provide a valuable resource for future population genetic assessment and implementation of effective conservation strategies for wild chocolate mahseer.

From ZikV genome to vaccine: in silico approach for the epitope-based peptide vaccine against Zika virus envelope glycoprotein.

Zika virus (ZikV) has emerged as a potential threat to human health worldwide. A member of the Flaviviridae, ZikV is transmitted to humans by mosquitoes. It is related to other pathogenic vector-borne flaviviruses including dengue, West Nile and Japanese encephalitis viruses, but produces a comparatively mild disease in humans. As a result of its epidemic outbreak and the lack of potential medication, there is a need for improved vaccine/drugs. Computational techniques will provide further information about this virus. Comparative analysis of ZikV genomes should lead to the identification of the core characteristics that define a virus family, as well as its unique properties, while phylogenetic analysis will show the evolutionary relationships and provide clues about the protein's ancestry. Envelope glycoprotein of ZikV was obtained from a protein database and the most immunogenic epitope for T cells and B cells involved in cell-mediated immunity, whereas B cells are primarily responsible for humoral immunity. We mainly focused on MHC class I potential peptides. YRIMLSVHG, VLIFLSTAV and MMLELDPPF, GLDFSDLYY are the most potent peptides predicted as epitopes for CD4+ and CD8+ T cells, respectively, whereas MMLELDPPF and GLDFSDLYY had the highest pMHC-I immunogenicity score and these are further tested for interaction against the HLA molecules, using in silico docking techniques to verify the binding cleft epitope. However, this is an introductory approach to design an epitope-based peptide vaccine against ZikV; we hope that this model will be helpful in designing and predicting novel vaccine candidates.

Phylogenetic relationship and molecular identification of five Indian Mahseer species using COIsequence.

This study examined the phylogenetic relationship and identification of five Mahseer species (Tor putitoro, Tor tor, Tor khudree, Tor chelynoides and Neolissochilus hexogonolopis) using partial sequencing of a Cytochrome Oxidase I (COl) DNA barcodes. The sequence analysis data showed that 134 (21.61%) sites out of 628 sites were variable without insertion or deletion. Rate of transition (70.5%) were higher than transversion (29.41%). There was a high inter-species divergence (range 4.1% to 12.2%) in Mahseer species as compared to intra-specific sequence divergence (1.7% for T. putitora, 1.2% for T tor, 1.4% for T. khudree, 3.0% for T chelynoides, 0.26 % for N. hexagonolopis). The phylogenetic tree, constructed by maximum parsimony, maximum likelihood and unweighted pair group average methods revealed similar results suggesting that T. putitoro, T. tor and T. khudree had a close relationship to each other while maximum divergence was observed in T. chelynoides, which was also confirmed by the genetic distance data. The results indicate that COl sequencing or bar-coding is useful in unravelling phylogenetic relationship and identification of Mahseer species.

Single-cell RNA sequencing of human epidermis identifies Lunatic fringe as a novel regulator of the stem cell compartment.

Single-cell RNA sequencing (scRNA-seq) of human skin provides a tool for validating observations from in vitro experimental models. By analyzing a published dataset of healthy adult epidermis, we confirm that the basal epidermal layer is heterogeneous, and three subpopulations of non-dividing cells can be distinguished. We show that Delta-like ligand 1 (DLL1) is expressed in a subset of basal cells previously identified as stem cells in cultured human keratinocytes and map the distribution of other Notch ligands and receptors to specific epidermal cell compartments. Although DLL1 is expressed at low levels, it is expressed in the same cell state as the Notch regulator, Lunatic -fringe (LFNG, O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase). Overexpression of LFNG amplifies the effects of DLL1 in cultured keratinocytes, increasing proliferation and colony-forming ability. We conclude that using scRNA-seq resources from healthy human skin not only validates previous experimental data but allows formulation of testable new hypotheses.

Myc-dependent dedifferentiation of Gata6+ epidermal cells resembles reversal of terminal differentiation.

Dedifferentiation is the process by which terminally differentiated cells acquire the properties of stem cells. During mouse skin wound healing, the differentiated Gata6-lineage positive cells of the sebaceous duct are able to dedifferentiate. Here we have integrated lineage tracing and single-cell mRNA sequencing to uncover the underlying mechanism. Gata6-lineage positive and negative epidermal stem cells in wounds are transcriptionally indistinguishable. Furthermore, in contrast to reprogramming of induced pluripotent stem cells, the same genes are expressed in the epidermal dedifferentiation and differentiation trajectories, indicating that dedifferentiation does not involve adoption of a new cell state. We demonstrate that dedifferentiation is not only induced by wounding, but also by retinoic acid treatment or mechanical expansion of the epidermis. In all three cases, dedifferentiation is dependent on the master transcription factor c-Myc. Mechanotransduction and actin-cytoskeleton remodelling are key features of dedifferentiation. Our study elucidates the molecular basis of epidermal dedifferentiation, which may be generally applicable to adult tissues.

Molecular cloning and expression profile of snow trout GPDH gene in response to abiotic stress.

Glycerol-3-phosphate dehydrogenase (GPDH) gene possibly plays a key role for cold acclimation process in snow trout during winter months when water temperature goes down to 4-5 °C. In this study, 1,012 bp nucleotide fragment of GPDH gene was obtained from two snow trout species (Schizothorax richardsonii and S. niger; family: Cyprinidae), distributed in several Himalayan rivers. The gene encoded a protein of 334 amino acids. The encoded protein sequence was very similar to GPDH of Danio rerio (94.36 %) using BLASTx searches. In S. richardsonii the qRT-PCR showed highest expression in muscle tissue followed by liver and also revealed 19 fold gene expression in liver tissue under cold (5 °C) in comparison with warm (15 °C) condition. The elevated expression levels of GPDH cDNA on cold treatment furthermore suggest that GPDH plays a role in stress related responses in S. richardsonii. The phylogenetic analysis showed that the two snow trout species GPDH share the same clade with characterized GPDHs from other teleost fishes suggesting a common evolutionary origin and a similar catalytic function. In addition, the Ka/Ks ratios of these sequences suggested that they are under purifying selection. Moreover, the expression profile of GPDH gene among co generic species of genus Schizothorax showed that GPDH cDNA expression was highest in S. richardsonii and lowest in S. esocinus which gives an indication of species specific adaptation in relation to different geographical areas.

Intercellular synchronization of coupled smooth muscle cells via Ca2+ propagation.

The propagation of Ca2+ wave through gap junction in smooth muscle cell is studied as a function of electrical coupling parameter (g) modulated by Ca2+ level in the cell. The range of activation time of Ca2+ propagation with amplitude is found to increase as increase in electrical coupling parameter g, which is identified by increase in critical time of activation, T(F) as a function of g. Then identical Ca2+ oscillators are allowed to interact via electrical and diffusive coupling of Ca2+ ions diffused through gap junctions, and rate of intercellular synchronization among them is studied. The phase diagrams in (T(F) - g) and (T(F) - epsilon) parameter spaces separate oscillation death and damped oscillations regimes which correspond to deactivated and activated regimes of Ca2+ level. The effect of on T(F) is significantly very slow, however it enhances the rate of synchronization among the coupled oscillators. The increase in g comparatively slows down the rate of synchronization of the coupled oscillators as shown in the phase diagram in (epsilon - g) parameter space which separates desynchronized and synchronized regimes.

Deciphering key genes in cardio-renal syndrome using network analysis.

Cardio-renal syndrome (CRS) is a rapidly recognized clinical entity which refers to the inextricably connection between heart and renal impairment, whereby abnormality to one organ directly promotes deterioration of the other one. Biological markers help to gain insight into the pathological processes for early diagnosis with higher accuracy of CRS using known clinical findings. Therefore, it is of interest to identify target genes in associated pathways implicated linked to CRS. Hence, 119 CRS genes were extracted from the literature to construct the PPIN network. We used the MCODE tool to generate modules from network so as to select the top 10 modules from 23 available modules. The modules were further analyzed to identify 12 essential genes in the network. These biomarkers are potential emerging tools for understanding the pathophysiologic mechanisms for the early diagnosis of CRS. Ontological analysis shows that they are rich in MF protease binding and endo-peptidase inhibitor activity. Thus, this data help increase our knowledge on CRS to improve clinical management of the disease.

In Silico Integrative Approach Revealed Key MicroRNAs and Associated Target Genes in Cardiorenal Syndrome.

Cardiorenal syndromes constellate primary dysfunction of either heart or kidney whereby one organ dysfunction leads to the dysfunction of another. The role of several microRNAs (miRNAs) has been implicated in number of diseases, including hypertension, heart failure, and kidney diseases. Wide range of miRNAs has been identified as ideal candidate biomarkers due to their stable expression. Current study was aimed to identify crucial miRNAs and their target genes associated with cardiorenal syndrome and to explore their interaction analysis. Three differentially expressed microRNAs (DEMs), namely, hsa-miR-4476, hsa-miR-345-3p, and hsa-miR-371a-5p, were obtained from GSE89699 and GSE87885 microRNA data sets, using R/GEO2R tools. Furthermore, literature mining resulted in the retrieval of 15 miRNAs from scientific research and review articles. The miRNAs-gene networks were constructed using miRNet (a Web platform of miRNA-centric network visual analytics). CytoHubba (Cytoscape plugin) was adopted to identify the modules and the top-ranked nodes in the network based on Degree centrality, Closeness centrality, Betweenness centrality, and Stress centrality. The overlapped miRNAs were further used in pathway enrichment analysis. We found that hsa-miR-21-5p was common in 8 pathways out of the top 10. Based on the degree, 5 miRNAs, namely, hsa-mir-122-5p, hsa-mir-222-3p, hsa-mir-21-5p, hsa-mir-146a-5p, and hsa-mir-29b-3p, are considered as key influencing nodes in a network. We suggest that the identified miRNAs and their target genes may have pathological relevance in cardiorenal syndrome (CRS) and may emerge as potential diagnostic biomarkers.

Network-Based Approach and IVI Methodologies, a Combined Data Investigation Identified Probable Key Genes in Cardiovascular Disease and Chronic Kidney Disease.

In fact, the risk of dying from CVD is significant when compared to the risk of developing end-stage renal disease (ESRD). Moreover, patients with severe CKD are often excluded from randomized controlled trials, making evidence-based therapy of comorbidities like CVD complicated. Thus, the goal of this study was to use an integrated bioinformatics approach to not only uncover Differentially Expressed Genes (DEGs), their associated functions, and pathways but also give a glimpse of how these two conditions are related at the molecular level. We started with GEO2R/R program (version 3.6.3, 64 bit) to get DEGs by comparing gene expression microarray data from CVD and CKD. Thereafter, the online STRING version 11.1 program was used to look for any correlations between all these common and/or overlapping DEGs, and the results were visualized using Cytoscape (version 3.8.0). Further, we used MCODE, a cytoscape plugin, and identified a total of 15 modules/clusters of the primary network. Interestingly, 10 of these modules contained our genes of interest (key genes). Out of these 10 modules that consist of 19 key genes (11 downregulated and 8 up-regulated), Module 1 (RPL13, RPLP0, RPS24, and RPS2) and module 5 (MYC, COX7B, and SOCS3) had the highest number of these genes. Then we used ClueGO to add a layer of GO terms with pathways to get a functionally ordered network. Finally, to identify the most influential nodes, we employed a novel technique called Integrated Value of Influence (IVI) by combining the network's most critical topological attributes. This method suggests that the nodes with many connections (calculated by hubness score) and high spreading potential (the spreader nodes are intended to have the most impact on the information flow in the network) are the most influential or essential nodes in a network. Thus, based on IVI values, hubness score, and spreading score, top 20 nodes were extracted, in which RPS27A non-seed gene and RPS2, a seed gene, came out to be the important node in the network.

Anaesthetic management of two patients with beta-thalassaemia intermedia.

There is paucity of literature regarding the anaesthetic management of patients with thalassaemia intermedia. In this case study, the anaesthetic management and concerns in two children with thalassaemia intermedia aged eleven and nine years undergoing herniotomy and splenectomy respectively is reported. Both children had unanticipated difficulty in airway management and high intraoperative blood pressure trends. These cases are representative of the range of problems seen in children with thalassaemia intermedia.

The complete mitochondrial genome of the medicinal fish, Cyprinion semiplotum: Insight into its structural features and phylogenetic implications.

Assamese kingfish (Cyprinion semiplotum) belonging to the subfamily Barbinae is an important food as well as aquarium fish having identified pharmacological benefits. The species has a complex taxonomic history and its phylogenetic position remains uncertain. Molecular data employed in earlier phylogenetic studies was inadequate for its phylogenetic placement. Therefore, we characterized 16,671 bp long complete mitogenome of C. semiplotum using next-generation sequencing. The mitogenome encodes the typical set of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. Its gene organization, distribution pattern, nucleotide composition, tRNA secondary structure and codon usage was similar to other Cyprinid mitogenomes. However, a distinctive 90 bp insertion was found in 3' periphery of the AT-rich control region. This can be a tool for identification of the species at the population level. Further, we reconstructed the most comprehensive phylogenetic trees of Cyprinidae based on complete mitogenome. In the resulting phylogenetic trees, C. semiplotum clustered tightly with other Barbinae species and exhibited a sister relationship with the species of the genera Aulopye, Barbus, Luciobarbus and Capoeta. The results presented herein will support future investigations on molecular taxonomy, population genetics, evolution and molecular phylogeny of C. semiplotum and its relatives.

Data on solute carrier transporter genes of a threatened Himalayan fish species - Schizothorax richardsonii.

The Snowtrout, Schizothorax richardsonii, is a vulnerable fish species found in different rivers and rivulets of the Himalayan region. The species is also a suitable poikilotherm to study the low-temperature tolerance as it dwells well at a temperature range of 5-20 °C. The solute carrier (SLC) group of membrane transport proteins play an integral role in cellular acclimation response. The present RNA sequencing was done to identify solute carrier transporter which are the major gene cascades responsible for transport of sugars, amino acids, oligonucleotides, ions, drugs, etc. to and from the cell organelles. A reference transcriptome database was created from liver tissue of Schizothorax richardsonii through RNA sequencing on Illumina HiSeq 2000 platform. The sequences were annotated and characterized under various solute carrier families in the species. So far, 113 transcripts were identified as solute carrier transporter genes categorized under 13 different families. This data will be useful for many researchers working on gene cloning and differential expression of solute carriers.

Molecular identification and genetic diversity analysis of Chocolate mahseer (Neolissochilus hexagonolepis) populations of Northeast India, using mitochondrial DNA markers.

The population genetic structure and genetic diversity of Neolissochilus hexagonolepis were studied using three mitochondrial genes (CoxI, Cytb, ATPase 6/8). A total of 120 individuals representing nine populations from different drainages of Northeast India were used for the study. Thirty-three distinct haplotypes were identified from concatenated gene analysis. The total haplotype and nucleotide diversities are 0.8880 and 0.0280, respectively. The analysis of molecular variance (AMOVA) reveals that the main variation (89.33%) was among populations. Most of the populations showed high polymorphisms, parsimony and haplotype diversity which indicate genetically healthy stocks in the wild. The genetic differentiation patterns were consistent with geographical distributions. Pairwise FST comparison of populations showed significant genetic differentiation (0.9088, p < .05). The pattern of haplotype network and phylogenetic tree revealed six major groups. Results suggested that chocolate mahseer populations in Northeast India having high haplotype diversity and genetic differentiation can be utilized in breeding programs to maintain genetic diversity in the descendant populations. The present study would be beneficial for sustainable management, stock-specific strategies for breeding and conservation of the wild population of N. hexagonolepis in future.

Structure-Guided Approach to Identify Potential Inhibitors of Large Envelope Protein to Prevent Hepatitis B Virus Infection.

Hepatitis B virus (HBV) infection is one of the major causes of liver diseases, which can lead to hepatocellular carcinoma. The role of HBV envelope proteins is crucial in viral morphogenesis, infection, and propagation. Thus, blocking the pleiotropic functions of these proteins especially the PreS1 and PreS2 domains of the large surface protein (LHBs) is a promising strategy for designing efficient antivirals against HBV infection. Unfortunately, the structure of the LHBs protein has not been elucidated yet, and it seems that any structure-based drug discovery is critically dependent on this. To find effective inhibitors of LHBs, we have modeled and validated its three-dimensional structure and subsequently performed a virtual high-throughput screening against the ZINC database using RASPD and ParDOCK tools. We have identified four compounds, ZINC11882026, ZINC19741044, ZINC00653293, and ZINC15000762, showing appreciable binding affinity with the LHBs protein. The drug likeness was further validated using ADME screening and toxicity analysis. Interestingly, three of the four compounds showed the formation of hydrogen bonds with amino acid residues lying in the capsid binding region of the PreS1 domain of LHBs, suggesting the possibility of inhibiting the viral assembly and maturation process. The identification of potential lead molecules will help to discover more potent inhibitors with significant antiviral activities.

Assessment of the key regulatory genes and their Interologs for Turner Syndrome employing network approach.

Turner Syndrome (TS) is a condition where several genes are affected but the molecular mechanism remains unknown. Identifying the genes that regulate the TS network is one of the main challenges in understanding its aetiology. Here, we studied the regulatory network from manually curated genes reported in the literature and identified essential proteins involved in TS. The power-law distribution analysis showed that TS network carries scale-free hierarchical fractal attributes. This organization of the network maintained the self-ruled constitution of nodes at various levels without having centrality-lethality control systems. Out of twenty-seven genes culminating into leading hubs in the network, we identified two key regulators (KRs) i.e. KDM6A and BDNF. These KRs serve as the backbone for all the network activities. Removal of KRs does not cause its breakdown, rather a change in the topological properties was observed. Since essential proteins are evolutionarily conserved, the orthologs of selected interacting proteins in C. elegans, cat and macaque monkey (lower to higher level organisms) were identified. We deciphered three important interologs i.e. KDM6A-WDR5, KDM6A-ASH2L and WDR5-ASH2L that form a triangular motif. In conclusion, these KRs and identified interologs are expected to regulate the TS network signifying their biological importance.

Exploring novel key regulators in breast cancer network.

The breast cancer network constructed from 70 experimentally verified genes is found to follow hierarchical scale free nature with heterogeneous modular organization and diverge leading hubs. The topological parameters (degree distributions, clustering co-efficient, connectivity and centralities) of this network obey fractal rules indicating absence of centrality lethality rule, and efficient communication among the components. From the network theoretical approach, we identified few key regulators out of large number of leading hubs, which are deeply rooted from top to down of the network, serve as backbone of the network, and possible target genes. However, p53, which is one of these key regulators, is found to be in low rank and keep itself at low profile but directly cross-talks with important genes BRCA2 and BRCA3. The popularity of these hubs gets changed in unpredictable way at various levels of organization thus showing disassortive nature. The local community paradigm approach in this network shows strong correlation of nodes in majority of modules/sub-modules (fast communication among nodes) and weak correlation of nodes only in few modules/sub-modules (slow communication among nodes) at various levels of network organization.

Recent trends in ZikV research: A step away from cure.

Zika virus (ZikV) is a member of the Flaviviridae virus family, genus Flavivirus has emerged as a potential threat to human health worldwide. Consequences of vertical infections includes microcephaly with brain and eye anomalies, and adult infections includes Guillain-Barrésyndrome (GBS), brain ischemia, myelitis and meningoencephalitis. To develop a better treatment, many efforts are being made, like drug-repurposing concept for FDA-approved drugs for antiviral activity are screened against ZikV infection and emerging as a promising alternative to expedite drug development and various vaccines like DNA, ZPIV, LAIV, mRNA and AGS-v vaccines have been designed and in under clinical trial phases. Moreover, few pharmacological agents like Mycophenolicacid, Niclosamide, PHA-690509, Emricasan and Bortezomib are most potent anti-ZikV candidates and highly effective single or combining treatment with these drugs. This article reviews the ZikV illness, transmission patterns, pathophysiology of disease, global efforts, challenges and the prospects for the development of vaccines and antiviral agents.

Dynamical states, possibilities and propagation of stress signal.

The stress driven dynamics of Notch-Wnt-p53 cross-talk is subjected to a few possible dynamical states governed by simple fractal rules, and allowed to decide its own fate by choosing one of these states which are contributed from long range correlation with varied fluctuations due to active molecular interaction. The topological properties of the networks corresponding to these dynamical states have hierarchical features with assortive structure. The stress signal driven by nutlin and modulated by mediator GSK3 acts as anti-apoptotic signal in this system, whereas, the stress signal driven by Axin and modulated by GSK3 behaves as anti-apoptotic for a certain range of Axin and GSK3 interaction, and beyond which the signal acts as favor-apoptotic signal. However, this stress system prefers to stay in an active dynamical state whose counterpart complex network is closest to hierarchical topology with exhibited roles of few interacting hubs. During the propagation of stress signal, the system allows the propagator pathway to inherit all possible properties of the state to the receiver pathway/pathways with slight modifications, indicating efficient information processing and democratic sharing of responsibilities in the system via cross-talk. The increase in the number of cross-talk pathways in the system favors to establish self-organization.