Arboviruses are some of the important causative agents of mosquito-mediated viral diseases. These viruses are transmitted between vector and host during the blood meal. Upon viral entry, host replication machinery is hijacked, supporting new virus particle production and thereby allowing viral survival in the host. In this process, host proteins interact with viral proteins to either facilitate viral replication, or they may provide antiviral defense mechanisms. In this study, we analyzed the impact of chikungunya virus (CHIKV) infection on the global proteome of Dicer active Aedes albopictus cells during the early and late time points of infection. We utilized a bottom-up approach of global proteomics analysis, and we used label-free quantitative mass spectrometry to identify the global protein signatures of Ae. albopictus at two different time points upon CHIKV infection. The mass spectrometry data analysis of the early time point revealed that proteins belonging to pathways such as translation, RNA processing, and cellular metabolic processes were less in abundance, whereas those belonging to pathways such as cellular catabolic process and organic substance transport were significantly abundant. At later time points, proteins belonging to pathways such as cellular metabolic processes, primary metabolic process, organonitrogen compound metabolic process, and organic substance metabolic process were found to be decreased in their presence, whereas those belonging to pathways such as RNA processing, gene expression, macromolecule metabolic processing, and nitrogen compound metabolic processing were found to be abundant during CHIKV infection, indicating that modulation in gene expression favoring cell survival occurs at a later time point, suggesting a survival strategy of Aedes cells to counter prolonged CHIKV infection.

Chikungunya virus (CHIKV), a mosquito-borne alphavirus, has re-emerged, causing widespread outbreaks and a significant clinical burden. Despite advances in virology, the molecular mechanisms governing CHIKV’s interaction with host cells remain poorly understood. In this study, we aimed to identify novel host protein interactors of the CHIKV nonstructural protein 3 (nsP3), a critical component of the viral replication complex, using mass spectrometry-based proteomic profiling in liver-derived Huh7 cells. Co-immunoprecipitation followed by LC-MS/MS identified a wide array of host proteins associated with nsP3, revealing 52 proteins classified as high-confidence (FDR of 1%, and unique peptides > 2) CHIKV-specific interactors. A bioinformatic analysis using STRING and Cytoscape uncovered interaction networks enriched in metabolic processes, RNA processing, translation regulation, cellular detoxification, stress responses, and immune signaling pathways. A subcellular localization analysis showed that many interactors reside in the cytosol, while others localize to the nucleus, nucleolus, and mitochondria. Selected novel host protein interactions were validated through co-immunoprecipitation and immunofluorescence assays. Our findings provide new insights into the host cellular pathways hijacked by CHIKV and highlight potential targets for therapeutic intervention. This is the first report mapping direct nsP3–host protein interactions in Huh7 cells during CHIKV infection.

Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting.

Background: DNA barcoding is an imperative implementation of chloroplast rbcL and matK regions exploited as standard molecular barcodes for species identification. MatK is highly conserved in plants and has been used extensively as a phylogenetic marker for classification of plants. In this study matK sequences of Leguminosae were retrieved for variant analysis and phylogentics. From online resources, maturase sequences were retrieved; redundant sequences and partials along with poor quality reads were filtered to compile 3639 complete non-redundant matK sequences and constructed into a database for ready reference. The database FabElm_BarcodeDb made available at app.bioelm.com was constructed using available sequence resources. Results: The chloroplast genome of plants contains matK gene of 1500 bp, positioned between intron of trnK associated in-group II intron splicing. Mitochondrial matR and genomic matN sequences were compared with chloroplast matK . These maturase sequences share regions of homology with chloroplast and mitochondrial regions and are expected to be regulated by miRNA in producing splice variants contributing to speciation. Conclusion: Base substitution rates of nuclear maturase were comparable with mitochondrial maturase and are different from matK sequences. Hence, few identified species in this investigation were clustered with other tribes when analysed using matK. MatK is effective in resolving the species level variations as splicing contributes to speciation; but utilization of matK alone as a barcode marker for legumes is dubious, as it could not resolve some species identity. Abbreviations: InDels Insertions and deletions ITS Internal transcribed spacer matK Maturase K rbcL Ribulose-bisphosphate carboxylase gene

Handful of theories explained modes of gene fixation and drift by contradicting one after the other hypothesis. Detailed analyses of these hypothetical or established theories illustrate that, all these theories holds good at one or the other circumstances existing in a living cell and whole organism as well, at a functional balance of gene expression. This theory explains that, the earlier reported neutral theories based on selection acquiesce as it tries to conquer an expression balance of genes. The meagre existence of a deleterious gene is being even- handed by suppression of negative gene expression into a functional protein. At an exacting time there is a planned balance attained by the individual cell to survive; otherwise abscission, apoptosis or necrosis occurs, leading to death of a cell or organ or the organism. This balance could be of ions or cytosolic pH or the impact of total proteins imparting cellular quiescence. Mutations at active domains impede cellular processes by blocking a network of genes and finally protein pool of any functional cell. Balancing pH of any cell at a time is a final outcome of its acidic or alkaline components being regulated by gene expression at a particular time. Whether to make the cell survive or to initiate cell death is decided by pH flux, either to protect the adjacent cells from spreading pathogen invasion or any other physiological stress. Variations in such traits are obtained through evolutionary phenomenon which is an underlying, powerful, fundamental and important concept of life. Speculations in genomics and proteomics ponder upon network of functional proteins encoding genes in manifesting phenotype of an intact organism through proteome. Though it is counterintuitive, many tried a direct way of creating a mutant that has acquired changes or deletions in theirnucleotidesequences or knockouts to find its missing functions during its absence. To establish the fact that alterations in a single gene cannot be stable and it needs to balance another set of genes the present investigation was carried out.

Background: Carbonic anhydrase regulates various cellular processes. Intracellular pH flux impacted by carbonic anhydrase alters the enzyme’s allosteric active site which effects several downstream cellular processes. Earlier, we reported that, the catalytic activity of carbonic anhydrase is independent, but direction of catalysis is affected by cellular pH level. On the other hand carbonic anhydrase alters the cytosolic pH level to facilitate allosteric phosphorylation of proteins which further leads to cellular differentiation through a process being regulated by ncRNAs. Results: This study illustrates various ways of cell differentiation/ organ development regulation via carbonic anhydrase interacting network of proteins involved in various cellular processes. It is involved in protein degradation process of other proteins like RPT, 26S proteasome, AT3G15120 and its variant producing ncRNA, etc. Carbonic anhydrase indirectly involved in signaling process along with MAPK in providing innate resistance against biotic and abiotic stresses. It is also indirectly linked to cell membrane transporters like H ⁺ -ATPase and V-ATPase B. Conclusions: Though carbonic anhydrase is not directly linked with EMS1 as revealed by network analyses and protein-protein interaction there could be a suitable condition generated by the carbonic anhydrase for EMS1 to be active. Hence, we report that carbonic anhydrase, along with other pH regulating gene complexes plays a major role for making EMS1 functional.