Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.

Background: Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.

microGalaxy: A gateway to tools, workflows, and training for reproducible and FAIR analysis of microbial data.

Microbial research generates vast and complex data from diverse omics technologies, necessitating innovative analytical solutions. microGalaxy (Galaxy for Microbiology) addresses these needs with a user-friendly platform that integrates >220 tool suites and >65 curated workflows for microbial analyses, including taxonomic profiling, assembly, annotation, and functional analysis. Hosted on the main EU Galaxy server (microgalaxy.

Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.

Within ovarian cancer research, patient-derived xenograft (PDX) models recapitulate histologic features and genomic aberrations found in original tumors. However, conflicting data from published studies have demonstrated significant transcriptional differences between PDXs and original tumors, challenging the fidelity of these models. We employed a quantitative mass spectrometry-based proteomic approach coupled with generation of patient-specific databases using RNA-seq data to investigate the proteogenomic landscape of serially-passaged PDX models established from two patients with distinct subtypes of ovarian cancer.

QbD-guided phospholipid-tagged nanonized boswellic acid naturosomal delivery for effective rheumatoid arthritis treatment.

Studies have reported the potential role of Boswellic acids (BAs), bioactive pentacyclic triterpenes from (BS), in treating rheumatoid arthritis (RA). However, poor water solubility and limited oral absorption are restricting factors for its better therapeutic efficacy. Based on these assumptions, the current study aimed to develop naturosomal delivery of BAs to boost their extremely low bioavailability, colloidal stability, and water solubility.

Comprehensive protease specificity profiling.

Protease enzymes are of great importance in medicine, industry, and as research tools. Despite the crucial need for detailed knowledge of their proteolytic cleavage specificity, many proteases are poorly characterized. We present a method for fully characterizing the cleavage specificity of proteases through the comprehensive profiling of all possible permutations of octamer peptide substrates in a single experiment.

Discovering Novel Proteoforms Using Proteogenomic Workflows Within the Galaxy Bioinformatics Platform.

Proteogenomics is a growing "multi-omics" research area that combines mass spectrometry-based proteomics and high-throughput nucleotide sequencing technologies. Proteogenomics has helped in genomic annotation for organisms whose complete genome sequences became available by using high-throughput DNA sequencing technologies. Apart from genome annotation, this multi-omics approach has also helped researchers confirm expression of variant proteins belonging to unique proteoforms that could have resulted from single-nucleotide polymorphism (SNP), insertion and deletions (Indels), splice isoforms, or other genome or transcriptome variations.

Regulation and mechanisms of action of RNA helicases.

RNA helicases are an evolutionary conserved class of nucleoside triphosphate dependent enzymes found in all kingdoms of life. Their cellular functions range from transcription regulation up to maintaining genomic stability and viral defence. As dysregulation of RNA helicases has been shown to be involved in several cancers and various diseases, RNA helicases are potential therapeutic targets.

Exploring Niclosamide as a Multi-target Drug Against SARS-CoV-2: Molecular Dynamics Simulation Studies on Host and Viral Proteins.

Niclosamide has emerged as a promising repurposed drug against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In vitro studies suggested that niclosamide inhibits the host transmembrane protein 16F (hTMEM16F), crucial for lipid scramblase activity, which consequently reduces syncytia formation that aids viral spread. Based on other in vitro reports, niclosamide may also target viral proteases such as papain-like protease (PLpro) and main protease (Mpro), essential for viral replication and maturation.

Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.

Mass spectrometry (MS)-based metaproteomics is used to identify and quantify proteins in microbiome samples, with the frequently used methodology being Data-Dependent Acquisition mass spectrometry (DDA-MS). However, DDA-MS is limited in its ability to reproducibly identify and quantify lower abundant peptides and proteins. To address DDA-MS deficiencies, proteomics researchers have started using Data-Independent Acquisition Mass Spectrometry (DIA-MS) for reproducible detection and quantification of peptides and proteins.

Novel approach to exploring protease activity and targets in HIV-associated obstructive lung disease using combined proteomic-peptidomic analysis.

Background: Obstructive lung disease (OLD) is increasingly prevalent among persons living with HIV (PLWH). However, the role of proteases in HIV-associated OLD remains unclear.

Methods: We combined proteomics and peptidomics to comprehensively characterize protease activities.

Nanoprimers in sustainable seed treatment: Molecular insights into abiotic-biotic stress tolerance mechanisms for enhancing germination and improved crop productivity.

Abiotic and biotic stresses during seed germination are typically managed with conventional agrochemicals, known to harm the environment and reduce crop yields. Seeking sustainable alternatives, nanotechnology-based agrochemicals leverage unique physical and chemical properties to boost seed health and alleviate stress during germination. Nanoprimers in seed priming treatment are advanced nanoscale materials designed to enhance seed germination, growth, and stress tolerance by delivering bioactive compounds and nutrients directly to seeds.

Metaproteomics for Coinfections in the Upper Respiratory Tract: The Case of COVID-19.

The upper respiratory tract (URT) is home to a diverse range of microbial species. Respiratory infections disturb the microbial flora in the URT, putting people at risk of secondary infections. The potential dangers and clinical effects of bacterial and fungal coinfections with SARS-CoV-2 support the need to investigate the microbiome of the URT using clinical samples.

An integrated metaproteomics workflow for studying host-microbe dynamics in bronchoalveolar lavage samples applied to cystic fibrosis disease.

Airway microbiota are known to contribute to lung diseases, such as cystic fibrosis (CF), but their contributions to pathogenesis are still unclear. To improve our understanding of host-microbe interactions, we have developed an integrated analytical and bioinformatic mass spectrometry (MS)-based metaproteomics workflow to analyze clinical bronchoalveolar lavage (BAL) samples from people with airway disease. Proteins from BAL cellular pellets were processed and pooled together in groups categorized by disease status (CF vs.

Novel Approach to Exploring Protease Activity and Targets in HIV-associated Obstructive Lung Disease using Combined Proteomic-Peptidomic Analysis.

Background: Obstructive lung disease (OLD) is increasingly prevalent among persons living with HIV (PLWH). However, the role of proteases in HIV-associated OLD remains unclear.

Methods: We combined proteomics and peptidomics to comprehensively characterize protease activities.

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.

Unlabelled: Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification, and prioritization of microbial proteins, enabling targeted assay development to investigate host-microbe dynamics in disease.

Pd-catalysed synthesis of oxomalonamides through adjacent triple carbonylation of tertiary amines.

The monocarbonylation and dicarbonylation reactions are well-established reactions in carbonylation chemistry. This work reports unusual oxidative adjacent triple carbonylation of the tertiary amine towards oxomalonamide synthesis using a Pd catalyst. The protocol involves the use of inert tertiary amines as an active reservoir of secondary amines through sp C-N bond activation using O as an ideal oxidant.

Fundamental Sex Differences in Cocaine-Induced Plasticity of Dopamine D1 Receptor- and D2 Receptor-Expressing Medium Spiny Neurons in the Mouse Nucleus Accumbens Shell.

Background: Cocaine-induced plasticity in the nucleus accumbens shell of males occurs primarily in dopamine D receptor-expressing medium spiny neurons (D1R-MSNs), with little if any impact on dopamine D receptor-expressing medium spiny neurons (D2R-MSNs). In females, the effect of cocaine on accumbens shell D1R- and D2R-MSN neurophysiology has yet to be reported, nor have estrous cycle effects been accounted for.

Methods: We used a 5-day locomotor sensitization paradigm followed by a 10- to 14-day drug-free abstinence period.

Assessing frailty in older Indian patients before cancer treatment: Comparative analysis of three scales and their implications for overall survival.

Introduction: Frailty, characterized by ageing-related vulnerability, influences outcomes in older adults. Our study aimed to investigate the relationship between frailty and clinical outcomes in older Indian patients with cancer.

Materials And Methods: Our observational single-centre study, conducted at Tata Memorial Hospital from February 2020 to July 2022, enrolled participants aged 60 years and above with cancer.

A Novel Dual-Function Nitric Oxide Donor Therapy for Preeclampsia-A Proof-of-Principle Study in a Murine Model.

: Preeclampsia (PE) is a hypertensive disorder of pregnancy that is associated with substantial morbidity and mortality for the mother and fetus. Reduced nitric oxide bioavailability and oxidative stress contribute to the maternal and fetal pathophysiology of PE. In this study, we evaluated the efficacy of a novel dual-function nitric oxide donor/redox modulator, AKT-1005, in reducing PE symptoms in a mouse model of PE.

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease.

Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, which are usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification and prioritization of microbial and host proteins, enabling targeted assay development to investigate host-microbe dynamics in disease.

Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless.

RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We explored the interplay between the RecA and auxiliary domains of the RNA helicase maleless (MLE) from Drosophila using structural and functional studies.

The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).

Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation, data acquisition, and bioinformatics workflows have greatly contributed to progress in this field. In 2020, the Association of Biomolecular Research Facilities Proteome Informatics Research Group launched a collaborative study to assess the bioinformatics options available for metaproteomics research.

A Galaxy of informatics resources for MS-based proteomics.

Introduction: Continuous advances in mass spectrometry (MS) technologies have enabled deeper and more reproducible proteome characterization and a better understanding of biological systems when integrated with other 'omics data. Bioinformatic resources meeting the analysis requirements of increasingly complex MS-based proteomic data and associated multi-omic data are critically needed. These requirements included availability of software that would span diverse types of analyses, scalability for large-scale, compute-intensive applications, and mechanisms to ease adoption of the software.

A Novel Dual-Function Redox Modulator Relieves Oxidative Stress and Anti-Angiogenic Response in Placental Villus Explant Exposed to Hypoxia-Relevance for Preeclampsia Therapy.

Background: Preeclampsia (PE) is a severe, life-threatening complication during pregnancy (~5-7%), and no causative treatment is available. Early aberrant spiral artery remodeling is associated with placental stress and the release of oxygen radicals and other reactive oxygen species (ROS) in the placenta. This precedes the production of anti-angiogenic factors, which ultimately leads to endothelial and trophoblast damage and the key features of PE.

Cu-Mediated Tandem 2,3-Disubstituted Indole Synthesis from Simple Anilines and Internal Alkynes C-H Annulation.

A simple, cost-effective, and straightforward method for the synthesis of 2,3-disubstituted indole scaffolds has been developed. The present protocol involves copper-mediated tandem hydroamination followed by C-H annulation of unprotected anilines with a wide range of internal alkynes. In the presence of Cu(OAc)·HO and trifluoroacetic acid (TFA), the reaction proceeds well to afford a variety of substituted indole derivatives in moderate to good yields.