R Shyama Prasad Rao

NITTE University, India

SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 5.0 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2, posing a serious challenge to the global vaccination effort and COVID-19 management. The evolutiona...

Background: Helicobacter pylori, a member of campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains uncl...

The recent widespread emergence of monkeypox (mpox), a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R0 ≈ 0.58) and fatality rate (0–3%) are low, as it causes prolonged morbidity, the World Health Organization has declared monkeypox as a public health emergency of international conce...

Despite a million infections every year and an estimated one billion people at risk, scrub typhus is regarded as a neglected tropical disease. The causative bacterium Orientia tsutsugamushi, a member of rickettsiae, seems to be intrinsically resistant to several classes of antibiotics. The emergence of antibiotic-resistant scrub typhus is likely to...

α-Synuclein (α-Syn) is an intrinsically disordered protein which self-assembles into highly organized β-sheet structures that accumulate in plaques in brains of Parkinson's disease patients. Oxidative stress influences α-Syn structure and self-assembly; however, the basis for this remains unclear. Here we characterize the chemical and physical effe...

Members of the calcium-dependent protein kinase (CDPK/CPK) and SNF-related protein kinase (SnRK) superfamilies are commonly found in plants and some protists. Our knowledge of client specificity of the members of this superfamily is fragmentary. As this family is represented by over 30 members in Arabidopsis thaliana, the identification of kinase-s...

Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclea...

Hemoglobinopathies are a group of disorders in which the hemoglobin molecule has abnormal production or structure. The hemoglobin molecules in red blood cells (RBC) are impacted by the blood disease known as sickle cell disease (SCD), and Thalassemia is one of the major monogenic disorders that reduces hemoglobin production( Kohne et al ., 2011). T...

The mpox virus (MPXV), a member of the Poxviridae family, which recently appeared outside of the African continent has emerged as a global threat to public health. Given the scarcity of antiviral treatments for mpox disease, there is a pressing need to identify and develop new therapeutics. We investigated 5715 phytochemicals from 266 species avail...

Background: Azole-resistant Candida infections are on the rise. Resistant substitutions at Y132 in sterol 14α-demethylase, the key target of azole drugs, are frequent. However, it is unclear why only some Y132 substitutions are favoured or how they exert differential effects on different azoles. Materials and Methods: Reported instances of Y132 sub...

The pathogen Streptococcus agalactiae, or Group B Streptococcus (GBS) infection is the leading cause of neonatal sepsis and meningitis in neonates. In this study, we aimed to investigate the occurrence and diversity of the CRISPR-Cas system in S. agalactiae genomes using computational biology approaches. A total of 51 out of 52 complete genomes (98...

Stenotrophomonas maltophilia, an emerging multidrug-resistant opportunistic bacterium in humans is of major concern for immunocompromised individuals for causing pneumonia and bloodborne infections. This bacterial pathogen is associated with a considerable fatality/case ratio, with up to 100%, when presented as hemorrhagic fever. It is resistant to...

Hemoglobinopathies are a group of disorders in which the hemoglobin molecule has abnormal production or structure. The hemoglobin molecules in red blood cells (RBC) are impacted by the blood disease known as sickle cell disease (SCD), and Thalassemia is one of the major monogenic disorders that reduces hemoglobin production. This disorder results i...

Over the last 34 months, at least 10 severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) distinct variants have evolved. Among these, some were more infectious while others were not. These variants may serve as candidates for identification of the signature sequences linked to infectivity and viral transgressions. Based on our previous hij...

Blood serum is arguably the most analyzed biofluid for disease prediction and diagnosis. Herein, we benchmarked five different serum abundant protein depletion (SAPD) kits with regard to the identification of disease-specific biomarkers in human serum using bottom-up proteomics. As expected, the IgG removal efficiency among the SAPD kits is highly...

Stenotrophomonas maltophilia , an emerging multidrug-resistant opportunistic bacterium in humans is of major concern for immunocompromised individuals for causing pneumonia and bloodborne infections. This bacterial pathogen is associated with a considerable fatality/case ratio, with up to 100%, when presented as hemorrhagic fever. It is resistant t...

The protein-protein interaction (PPI) network analysis of specific genes identified for biofilm production and virulence/secretion system mediated by quorum sensing. The PPI depicted 13 hub proteins (namely rhlR, lasR, pscU, vfr, exsA, lasI, gacA, toxA, pilJ, pscC, fleQ, algR, and chpA) out of 160 nodes involving 627 edges. The PPI network analysis...

Hypoxia afflicts the microenvironment of solid tumors fueling malignancy. We investigated the impact of long hypoxia exposure on transcriptional remodeling, tumor mutational burden (TMB), and genomic instability of cancer cells that were grouped based on their inherent sensitivity or resistance to hypoxia. A hypoxia score was used as a metric to di...

Long-term socioeconomic progress requires a healthy environment/ecosystem, but anthropogenic activities cause environmental degradation and biodiversity loss. Constant ecological monitoring is, therefore, necessary to assess the state of biodiversity and ecological health. However, baseline data are lacking even for ecologically sensitive regions s...

Despite a million infections every year and an estimated one billion people at risk, scrub typhus is regarded as a neglected tropical disease. The causative bacterium Orientia tsutsugamushi, a member of rickettsiae, seems to be intrinsically resistant to several classes of antibiotics. The emergence of antibiotic-resistant scrub typhus is likely to...

The recent widespread emergence of monkeypox, a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R0 ≈ 0.58) and fatality rate (0-3%) are low, as it causes prolonged morbidity, monkeypox is leading to considerable public health anxiety. Thus, effective containment and disease management...

Hypoxia afflicts the microenvironment of solid tumors fueling tumor malignancy. Using an 8-gene in vitro hypoxia signature, we have recently shown that pancreatic cancer patients with highly hypoxic tumors experience worse survival and exhibit markers of an immunosuppressed microenvironment. Simultaneously, we obtained evidence of increased mutatio...

Mycobacterium tuberculosis is a leading cause of human mortality worldwide and the emergence of drug-resistantstrains, demands the discovery of new classes of antimycobacterials that can be employed in the therapeutic pipeline. Previously, a secondary metabolite Chrysomycin A, isolated from Streptomyces sp. OA161 was shown to have potent bactericid...

Long-term socioeconomic progress requires a healthy environment/ecosystem, but anthropogenic activities cause environmental degradation and biodiversity loss. Constant ecological monitoring is therefore necessary to assess the state of biodiversity and ecological health. However, baseline data is lacking even for ecologically sensitive regions such...

As the pace of socioeconomic developments continues to accelerate, the environmental degradation and biodiversity loss become the norm. While it is crucial to constantly monitor and assess ecological impacts, baseline data are scanty for ecologically sensitive regions and biodiversity hotspots such as the Western Ghats. With their great public appe...

Structural complexity of ecological networks facilitate the functional robustness of natural ecosystems. Threatened by the human actions such as habitat destruction and climate change, species may be more or less prone to ecological perturbations depending on the nature of their interactions. We examined the host network of tropical butterflies fro...

Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete absence of nuclear-encoded complex I genes in the transcriptome of Viscum album. Compared to Arab...

SARS-CoV-2, responsible for the current COVID-19 pandemic that claimed over 4.2 million lives, belongs to a class of enveloped viruses that undergo quick evolutionary adjustments under selection pressure. Numerous variants have emerged in SARS-CoV-2 that are currently posing a serious challenge to the global vaccination effort and COVID-19 manageme...

Intratumoral hypoxia is a widely established element of the pancreatic tumor microenvironment (TME) promoting immune escape, tumor invasion, and progression, while contributing to treatment resistance and poor survival. Despite this critical role, hypoxia is underrepresented in molecular signatures of pancreatic ductal adenocarcinoma (PDA) and conc...

While protein-protein interaction is the first step of the SARS-CoV-2 infection, recent comparative proteomic profiling enabled the identification of over eleven thousand protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and ration...

While protein‐protein interaction is the first step of the SARS‐CoV‐2 infection, recent comparative proteomic profiling enabled the identification of over eleven thousand protein dynamics, thus providing a comprehensive reflection of the molecular mechanisms underlying the cellular system in response to viral infection. Here we summarize and ration...

[This corrects the article DOI: 10.1371/journal.pone.0234570.].

To function as a metabolic hub, plant mitochondria have to exchange a wide variety of metabolic intermediates as well as inorganic ions with the cytosol. As identified by proteomic profiling or as predicted by MU-LOC, a newly developed bioinformatics tool, Arabidopsis thaliana mitochondria contain 128 or 143 different transporters, respectively. Th...

Background The National Family Health Surveys (NFHS) in India apply adult cutoffs of nutritional status for the estimation of undernutrition/overweight in the 15–19 age group. The prevalence of thinness in boys and girls thus estimated is 58.1% and 46.8% in NFHS-3, and 45% and 42% in NFHS-4 respectively. But the WHO recommends using age and sex-spe...

O-Phosphorylation (phosphorylation of the hydroxyl-group of S, T, and Y residues) is among the first described and most thoroughly studied posttranslational modification (PTM). Y-Phosphorylation, catalyzed by Y-kinases, is a key step in both signal transduction and regulation of enzymatic activity in mammalian systems. Canonical Y-kinase sequences...

HIV-1 exists in a latent form in all infected patients. When antiretroviral therapy is stopped, viral replication resumes. The HIV-1 Tat protein is a potent activator of viral transcription. Our previous work has demonstrated that exosomal formulations of Tat can reverse HIV-1 latency in primary CD4+ T lymphocytes isolated from long term antiretrov...

Here, we present the proteome profiling of low-molecular weight (< 50 kDa) proteins of seven different lentil cultivars developed by Bangladesh Agricultural Research Institute. A total of 2873 peptides corresponding to 180 unique proteins were identified wherein > 24% of them were described lentil allergens. Comparative relative quantitation showed...

Epithelial Ovarian Cancer (EOC) is associated with dismal survival rates due to the fact that patients are frequently diagnosed at an advanced stage and eventually become resistant to traditional chemotherapeutics. Hence, there is a crucial need for new and innovative therapies. Septin-2, a member of the septin family of GTP binding proteins, has b...

So far, the chemical quality of different grades of white tea has largely remained unexplored. The objective of this study was to establish a model for quality evaluation of different grades of Bai Mudan white tea. We applied non-targeted ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry in combination with multiva...

Targeting and translocation of proteins to the appropriate subcellular compartments are crucial for cell organization and function. Newly synthesized proteins are transported to mitochondria with the assistance of complex targeting sequences containing either an N-terminal pre-sequence or a multitude of internal signals. Compared with experimental...

Fig. S3. Densitometric analysis of the expression of MEK1, MEK2 and phospho‐MEK1/2 in K562‐STI‐R cells (untreated) and K562‐STI‐R cells cultured in the presence of 25 μm IM, 25 μm U0126, 25 μm PS‐1145, 100 nm dasatinib and combinations of 100 nm dasatinib and 25 μm PS‐1145, 25 μm U0126 and 25 μm PS‐1145, 100 nm dasatinib and 25 μm U0126 and 100 nm...

Fig. S1. (A) Detailed map of the bicistronic pENTR‐CMV‐HBG‐3xHA‐IRES‐hrGFP vector. This vector allows the CMV promoter‐driven co‐expression of an open‐reading frame cloned between unique BamHI and XhoI sites and a humanized Renilla reniformis GFP via an IRES. The upstream human beta globin intron serves to increase transcription. (B) Histograms sho...

Fig. S2. Densitometric analysis of the expression of MEK1, MEK2 and phospho‐MEK1/2, (B) ERK1, ERK2 and phospho‐ERK1/2 and (C) NF‐κB and phospho‐NF‐κB in K562 and K562‐STI‐R cells. The intensities of bands are expressed as the relative intensity fold‐change, with the intensity of each band normalized to control (K562) cells. Whole cell lysates of K5...

Table S1. Comparison of abundances of phosphopeptides identified in K562 vs. K562‐STI‐R cells by quantitative phosphoproteomics.

Fig. S5. Densitometric analysis of the expression of Src and phospho‐Src in K562‐STI‐R cells (untreated) and K562‐STI‐R cells cultured in the presence of 25 μm IM, 25 μm U0126, 25 μm PS‐1145, 100 nm dasatinib, the combination of 100 nm dasatinib and 25 μm PS‐1145, the combination of 25 μm U0126 and 25 μm PS‐1145, the combination of 100 nm dasatinib...

Fig. S4. Densitometric analysis of the expression of ERK1/2 and phospho‐ERK1/2 in K562‐STI‐R cells (untreated) and K562‐STI‐R cells cultured in the presence of 25 μm IM, 25 μm U0126, 25 μm PS‐1145, 100 nm dasatinib, the combination of 100 nm dasatinib and 25 μm PS‐1145, the combination of 25 μm U0126 and 25 μm PS‐1145, the combination of 100 nm das...

Fig. S6. Densitometric analysis of the expression of NF‐κB and phospho‐NF‐κB in (A) K562 and K562‐STI‐R cells and (B) in K562‐STI‐R cells (untreated) and K562‐STI‐R cells cultured in the presence of 25 μm IM, 25 μm U0126, 25 μm PS‐1145, 100 nm dasatinib and combinations of 100 nm dasatinib and 25 μm PS‐1145, 25 μm U0126 and 25 μm PS‐1145, 100 nm da...

Table S2. Comparison of the abundances of MAPK‐ERK superpath related phosphopeptides in K562 vs. K562‐STI‐R cells.

Table S3. Tpl2 expression patterns in various cancers based on the data from The Cancer Genome Atlas (TCGA) datasets.

Motivation: Oxidative stress and protein damage have been associated with over 200 human ailments including cancer, stroke, neuro-degenerative diseases, and aging (Fedorova et al., 2014. Mass Spectrom. Rev., 33, 79-97). Protein carbonylation, a chemically diverse oxidative post-translational modification (PTM), is widely considered as the biomarke...

The introduction of tyrosine kinase inhibitors (TKI) has transformed chronic myeloid leukemia (CML) into a chronic disease with long-term survival exceeding 85%. However, resistance of CML stem cells to TKI may contribute to the 50% relapse rate observed after TKI discontinuation in molecular remission. We previously described a model of resistance...

Biological significance: Comparative label-free proteomics was used to characterize an AtPPI-2T-DNA knockdown mutant. The complex, reduced growth phenotype supports the notion that AtPPI-2 is a global regulator of TOPPs, and possibly other proteins. Comparative proteomics revealed a range of differences in protein abundance from various cellular p...

Despite the success of tyrosine kinase inhibitor (TKI) therapy in chronic myelogenous leukemia (CML), leukemic stem/progenitor cells remain detectable even in the state of deep molecular remission. Mechanisms that allow them to persist despite continued kinase inhibition remain unclear. We have previously shown that prolonged exposure to imatinib m...

Plant mitochondria perform a wide range of functions in the plant cell ranging from providing energy and metabolic intermediates, via coenzyme biosynthesis and their own biogenesis to retrograde signaling and programmed cell death. To perform these functions, they contain a proteome of >2000 different proteins expressed in some cells under some con...

Unlabelled: Allergen levels in fresh and processed foods can vary dynamically. As different sources of foods can cause different types of allergic reactions, the food industry and regulatory bodies urgently require reliable detection and absolute quantitation methods for allergen detection in complex food products to effectively safeguard the food...

Metabolite composition is strongly affected by genotype, environment, and interactions between genotype and environment, although the extent of variation caused by these factors may depend upon the type of metabolite. To characterize the complexity of genotype, environment, and their interaction in hybrid seeds, 50 genetically diverse non-genetical...

The rhizome is responsible for the invasiveness and competitiveness of many plants with great economic and agricultural impact worldwide. Besides its value as an invasive organ, the rhizome plays a role in the establishment and massive growth of forage, providing biomass for biofuel production. Despite these features, little is known about the mole...

Oxidation of methionine (Met) to Met sulfoxide (MetSO) is a frequently found reversible posttranslational modification. It has been presumed that the major functional role for oxidation-labile Met residues is to protect proteins/cells from oxidative stress. However, Met oxidation has been established as a key mechanism for direct regulation of a wi...

The goal of metabolomics data pre-processing is to eliminate systematic variation, such that biologically-related metabolite signatures are detected by statistical pattern recognition. Although several methods have been developed to tackle the issue of batch-to-batch variation, each method has its advantages and disadvantages. In this study, we use...

Among post-translational modifications, there are some conceptual similarities between Lys-N𝜀-acetylation and Ser/Thr/Tyr O-phosphorylation. Herein we present a bioinformatics-based overview of reversible protein Lys-acetylation, including some comparisons with reversible protein phosphorylation. The study of Lys-acetylation of plant proteins has l...

Lys-N(ɛ)-acetylation (PKA) has recently ascended from a post-translational modification (PTM) of limited distribution to one approaching the abundance of O-phosphorylation. Thousands of KAC proteins have been identified in Archaea, bacteria, and Eukarya, and the KAC system of acetyltransferases, deacetylases, and binding proteins is superficially c...

One way to study the function of plant mitochondria is to extract them from plant tissues in an uncontaminated, intact and functional form. The reductionist assumption is that the components present in such a preparation and the in vitro measurable functions or activities reliably reflect the in vivo properties of the organelle inside the plant cel...

Mitochondria are called the powerhouses of the cell. To better understand the role of mitochondria in maintaining and regulating metabolism in storage tissues, highly purified mitochondria were isolated from dormant potato tubers (Solanum tuberosum L. cv. Folva) and their proteome investigated. Proteins were resolved by one-dimensional gel electrop...

Background Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are typically studied individually, herein we describe the potential for cross-talk and hierarchical regulation. Results The proximit...

The current method for reconstructing gene regulatory networks faces a dilemma concerning the study of bio-medical problems. On the one hand, static approaches assume that genes are expressed in a steady state and thus cannot exploit and describe the dynamic patterns of an evolving process. On the other hand, approaches that can describe the dynami...

A crucial work of investigating the mechanisms of cancer development is to unraveling the dynamic nature of gene regulation during the disease process. However, reconstruction of dynamic gene regulatory network requires time-sequence samples of a biological process, which are not available for many bio-medical problems. In this paper, we propose a...

Many recent high throughput technologies have enabled large-scale discoveries of new phosphorylation sites and phosphoproteins. Although they have provided a number of insights into protein phosphorylation and the related processes, an inclusive analysis on the nature of phosphorylated sites in proteins is currently lacking. We have therefore analy...

Proteins are targets for modification by reactive oxygen species, and carbonylation is an important irreversible modification that increases during oxidative stress. While information on protein carbonylation is accumulating, its pattern is not yet understood. We have made a meta-analysis of the available literature data (456 carbonylation sites on...

Proteins can become oxidatively modified in many different ways, either by direct oxidation of amino acid side chains and protein backbone or indirectly by conjugation with oxidation products of polyunsaturated fatty acids and carbohydrates. While reversible oxidative modifications are thought to be relevant in physiological processes, irreversible...

Protein N-glycosylation requires the presence of asparagine (N) in the consensus tri-peptide NXS/T (where X is any amino acid, S is serine and T is threonine). Several factors affect the glycosylation potential of NXS/T sequons and one such factor is the type of amino acid at position X. While proline was shown to negatively affect N-glycosylation,...

Poa pratensis, a type species for the grass family (Poaceae), is an important cool season grass that accumulates fructans as a polysaccharide reserve. We studied fructan contents and expression of candidate fructan metabolism genes during cold acclimation in three varieties of P. pratensis adapted to different environments: Northern Norway, Denmark...

Many viruses are known to undergo rapid evolutionary changes under selective pressures. The HIV-1 envelope glycoprotein 120 (gp120) shows extreme selection for NXS/T sequons, the potential sites of N-glycosylation. Although the average number of sequons in gp120 appears to be relatively stable in the recent past, even slight changes in the distribu...

Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underlying causes have largely been unexplored. We computed...

Many viruses are known to undergo rapid evolutionary changes under selective pressures. The HIV-1 envelope glycoprotein 120 (gp120) shows extreme selection for NXS/T sequons, the potential sites of N-glycosylation. Although the average number of sequons in gp120 appears to be relatively stable in the recent past, even slight changes in the distribu...

Water-soluble feruloyl arabinoxylans (feraxans), isolated from native and malted (96 h) rice (Oryza sativa) and ragi (Eleusine coracana) grains, were fractionated on DEAE-cellulose, followed by purification on Sephacryl S-300 and the homogeneity was ascertained by high performance size exclusion chromatography, cellulose acetate and capillary elect...

Water-soluble non-starch polysaccharides (NSP) were isolated from native and malted rice and ragi. The effects of addition of water-soluble NSP on dough rheological characteristics and baking quality were investigated. Water-soluble NSP had low relative viscosity and showed no gelling activity despite considerable amount of ferulic acid ($492.5–528...

Roads and traffic are the central features of human development, but a severe threat to forest and wildlife. In this study we have assessed the extent of insect road kills in two national parks and a suburb-scrubland. The diversity and abundance of insect casualties were enumerated and compared across sites. Dragonflies and butterflies were the maj...

Water-soluble non-starch polysaccharides (NSP) were isolated from native and malted rice and ragi. The effects of addition of water-soluble NSP on dough rheological characteristics and baking quality were investigated. Water-soluble NSP had low relative viscosity and showed no gelling activity despite considerable amount of ferulic acid (∼492.5–528...

The objective of this study is to determine the changes brought about by germination on water soluble feruloyl arabinoxylans (feraxans), one of the major components of soluble fibre from rice and ragi and their consequence on antioxidant activity. Soluble feraxans, isolated from native and malted rice and ragi were fractionated on DEAE-cellulose. F...

Non-starch polysaccharide–phenolic acid complexes were isolated from native and germinated (96 h) cereals, such as rice, maize, wheat and millet-ragi. They were designated as water extractable (WEPs, yield: 0.60–3.56%) and water-unextractable (WUPs, yield: 7.49–37.8%) non-starch polysaccharides, which consisted mainly of arabinose, xylose and gluco...