Applications of Nanotechnology for Spatial Omics: Biological Structures and Functions at Nanoscale Resolution.

Spatial omics methods are extensions of traditional histological methods that can illuminate important biomedical mechanisms of physiology and disease by examining the distribution of biomolecules, including nucleic acids, proteins, lipids, and metabolites, at microscale resolution within tissues or individual cells. Since, for some applications, the desired resolution for spatial omics approaches the nanometer scale, classical tools have inherent limitations when applied to spatial omics analyses, and they can measure only a limited number of targets. Nanotechnology applications have been instrumental in overcoming these bottlenecks.

Mapping dynamic molecular changes in hippocampal subregions after traumatic brain injury through spatial proteomics.

Background: Traumatic brain injury (TBI) often results in diverse molecular responses, challenging traditional proteomic studies that measure average changes at tissue levels and fail to capture the complexity and heterogeneity of the affected tissues. Spatial proteomics offers a solution by providing insights into sub-region-specific alterations within tissues. This study focuses on the hippocampal sub-regions, analyzing proteomic expression profiles in mice at the acute (1 day) and subacute (7 days) phases of post-TBI to understand subregion-specific vulnerabilities and long-term consequences.

Integrated proteomic profiling identifies amino acids selectively cytotoxic to pancreatic cancer cells.

Pancreatic adenocarcinoma (PDAC) is one of the most deadly cancers, characterized by extremely limited therapeutic options and a poor prognosis, as it is often diagnosed during late disease stages. Innovative and selective treatments are urgently needed, since current therapies have limited efficacy and significant side effects. Through proteomics analysis of extracellular vesicles, we discovered an imbalanced distribution of amino acids secreted by PDAC tumor cells.

Circulating Plasma Exosomal Proteins of Either SHIV-Infected Rhesus Macaque or HIV-Infected Patient Indicates a Link to Neuropathogenesis.

Despite the suppression of human immunodeficiency virus (HIV) replication by combined antiretroviral therapy (cART), 50-60% of HIV-infected patients suffer from HIV-associated neurocognitive disorders (HAND). Studies are uncovering the role of extracellular vesicles (EVs), especially exosomes, in the central nervous system (CNS) due to HIV infection. We investigated links among circulating plasma exosomal (crExo) proteins and neuropathogenesis in simian/human immunodeficiency virus (SHIV)-infected rhesus macaques (RM) and HIV-infected and cART treated patients (Patient-Exo).

Targeted proteomics using parallel reaction monitoring confirms salivary proteins indicative of metastatic triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is the most aggressive subtype due to the absence of hormonal receptors. Our study aimed to identify and determine the effectiveness of salivary proteins as candidate markers for metastatic TNBC subtype using parallel reaction monitoring mass spectrometry (PRM-MS). Three salivary proteins (lipocalin-1, SMR3B, and plastin-2) that showed significant differential expression in label-free quantitation (LFQ) between TNBC (N = 6) and health subjects (HS; N = 6) were selected for further validation.

BoMiProt 2.0: An update of the bovine milk protein database.

Milk is a biofluid with various functions, containing carbohydrates, lipids, proteins, vitamins, and minerals. Owing to its importance and availability of vast proteomics information, our research group designed a database for bovine milk proteins (N = 3159) containing the primary and secondary information called BoMiProt. Due to the gaining interest and intensively published literature in the last three years, BoMiProt has been upgraded with newer identified proteins (N = 7459) from peer-reviewed journals, significantly expanding the database from different milk fractions (e.

PD-L1 interacts with Frizzled 6 to activate β-catenin and form a positive feedback loop to promote cancer stem cell expansion.

Cancer stem cells (CSCs) drive tumor initiation, progression, metastasis, and drug resistance. We report here that programmed cell death ligand 1 (PD-L1) is constitutively expressed in cancer cells to maintain and expand CSC through a novel mechanism in addition to promoting cancer cell immune evasion. We discovered that PD-L1 interacts with receptor Frizzled 6 to activate β-catenin signaling and increase β-catenin-targeted gene expression, such as a putative stem cell marker leucine-rich-repeat-containing G-protein-coupled receptor 5.

Integrated Metabolomics and Proteomics Dynamics of Serum Samples Reveals Dietary Zeolite Clinoptilolite Supplementation Restores Energy Balance in High Yielding Dairy Cows.

Dairy cows can suffer from a negative energy balance (NEB) during their transition from the dry period to early lactation, which can increase the risk of postpartum diseases such as clinical ketosis, mastitis, and fatty liver. Zeolite clinoptilolite (CPL), due to its ion-exchange property, has often been used to treat NEB in animals. However, limited information is available on the dynamics of global metabolomics and proteomic profiles in serum that could provide a better understanding of the associated altered biological pathways in response to CPL.

Integrated physiological and comparative proteomics analysis of contrasting genotypes of pearl millet reveals underlying salt-responsive mechanisms.

Salinity stress poses a significant risk to plant development and agricultural yield. Therefore, elucidation of stress-response mechanisms has become essential to identify salt-tolerance genes in plants. In the present study, two genotypes of pearl millet (Pennisetum glaucum L.

Deciphering the enigma of missing DNA binding domain of LacI family transcription factors.

Catabolite repressor activator (Cra) is a member of the LacI family transcriptional regulator distributed across a wide range of bacteria and regulates the carbon metabolism and virulence gene expression. In numerous studies to crystallize the apo form of the LacI family transcription factor, the N-terminal domain (NTD), which functions as a DNA-binding domain, has been enigmatically missing from the final resolved structures. It was speculated that the NTD is disordered or unstable and gets cleaved during crystallization.

Mammary microbial dysbiosis leads to the zoonosis of bovine mastitis: a One-Health perspective.

Bovine mastitis is a prototypic emerging and reemerging bacterial disease that results in cut-by-cut torture to animals, public health and the global economy. Pathogenic microbes causing mastitis have overcome a series of hierarchical barriers resulting in the zoonotic transmission from bovines to humans either by proximity or remotely through milk and meat. The disease control is challenging and has been attributed to faulty surveillance systems to monitor their emergence at the human-animal interface.

Quantitative alterations in bovine milk proteome from healthy, subclinical and clinical mastitis during S. aureus infection.

Bovine mastitis, caused by Staphylococcus aureus, is a major impediment to milk production and lacks markers to indicate disease progression in cows and buffaloes. Thus, the focus of this study was to identify proteins marking the transition from subclinical to clinical mastitis. Whey proteins were isolated from 6 group's i.

BoMiProt: A database of bovine milk proteins.

Bovine milk has become an important biological fluid for proteomic research due to its nutritional and immunological benefits. To date, over 300 publications have reported changes in bovine milk protein composition based on seasons, lactation stages, breeds, health status and milk fractions while there are no reports on consolidation or overlap of data between studies. Thus, we have developed a literature-based, manually curated open online database of bovine milk proteome, BoMiProt (http://bomiprot.

Quantitative proteomics of milk whey reveals breed and season specific variation in protein abundance in Holstein Friesian cow and Murrah buffalo.

Bovine milk contains different components with nutritional and immunological benefits. It is easily accessible and a rich source of potential markers reflective of pathophysiological conditions; however, little is known about the changes in protein abundance associated with variation across breeds and seasons. In this study, we performed a comprehensive proteomic profiling of whey proteins from Holstein Friesian cow and Murrah buffalo across summer and winter seasons.

Protein glycosylation: Sweet or bitter for bacterial pathogens?

Protein glycosylation systems in many bacteria are often associated with crucial biological processes like pathogenicity, immune evasion and host-pathogen interactions, implying the significance of protein-glycan linkage. Similarly, host protein glycosylation has been implicated in antimicrobial activity as well as in promoting growth of beneficial strains. In fact, few pathogens notably modulate host glycosylation machineries to facilitate their survival.