Simulated LC-MS Data Set for Assessing the Metabolomics Data Processing Pipeline Implemented into MVAPACK.

Metabolomics commonly relies on using one-dimensional (1D) H NMR spectroscopy or liquid chromatography-mass spectrometry (LC-MS) to derive scientific insights from large collections of biological samples. NMR and MS approaches to metabolomics require, among other issues, a data processing pipeline. Quantitative assessment of the performance of these software platforms is challenged by a lack of standardized data sets with "known" outcomes.

Analysis of Plasma Proteins Involved in Inflammation, Immune Response/Complement System, and Blood Coagulation upon Admission of COVID-19 Patients to Hospital May Help to Predict the Prognosis of the Disease.

The development of new approaches allowing for the early assessment of COVID-19 cases that are likely to become critical and the discovery of new therapeutic targets are urgently required. In this prospective cohort study, we performed proteomic and laboratory profiling of plasma from 163 COVID-19 patients admitted to Bauru State Hospital (Brazil) between 4 May 2020 and 4 July 2020. Plasma samples were collected upon admission for routine laboratory analyses and shotgun quantitative label-free proteomics.

Leveraging the Structure of DNAJA1 to Discover Novel Potential Pancreatic Cancer Therapies.

Pancreatic cancer remains one of the deadliest forms of cancer with a 5-year survival rate of only 11%. Difficult diagnosis and limited treatment options are the major causes of the poor outcome for pancreatic cancer. The human protein DNAJA1 has been proposed as a potential therapeutic target for pancreatic cancer, but its cellular and biological functions remain unclear.

Peptidomics analysis reveals changes in small urinary peptides in patients with interstitial cystitis/bladder pain syndrome.

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic and debilitating pain disorder of the bladder and urinary tract with poorly understood etiology. A definitive diagnosis of IC/BPS can be challenging because many symptoms are shared with other urological disorders. An analysis of urine presents an attractive and non-invasive resource for monitoring and diagnosing IC/BPS.

A reversed phase ultra-high-performance liquid chromatography-data independent mass spectrometry method for the rapid identification of mycobacterial lipids.

A rapid reversed-phase ultra-high-performance liquid chromatography-high resolution mass spectrometry based mycobacterial lipidomics approach is described. This method enables the separation of various lipid classes including lipids specific to mycobacterial, such as methoxy mycolic acid and α-mycolic acid. Lipid separation occurs during a relatively short runtime of 14 min on a charged surface hybrid C column.

New Insights into the Mechanism of Action of the Cyclopalladated Complex (CP2) in : Calcium Dysregulation, Mitochondrial Dysfunction, and Cell Death.

The current treatment of leishmaniasis is based on a few drugs that present several drawbacks, such as high toxicity, difficult administration route, and low efficacy. These disadvantages raise the necessity to develop novel antileishmanial compounds allied with a comprehensive understanding of their mechanisms of action. Here, we elucidate the probable mechanism of action of the antileishmanial binuclear cyclopalladated complex [Pd(dmba)(μ-N)] (CP2) in Leishmania amazonensis.

Radiation exposure induces cross-species temporal metabolic changes that are mitigated in mice by amifostine.

Exposure to acute, damaging radiation may occur through a variety of events from cancer therapy and industrial accidents to terrorist attacks and military actions. Our understanding of how to protect individuals and mitigate the effects of radiation injury or Acute Radiation Syndrome (ARS) is still limited. There are only a few Food and Drug Administration-approved therapies for ARS; whereas, amifostine is limited to treating low dose (0.

Outer Membrane Vesicle-Mediated Codelivery of the Antifungal HSAF Metabolites and Lytic Polysaccharide Monooxygenase in the Predatory .

are new biocontrol agents known for their prolific production of lytic enzymes and bioactive metabolites. is a predator of fungi and produces several structurally distinct antimicrobial compounds, such as the antifungal HSAF (heat stable antifungal factor) and analogs. The mechanism by which interacts with fungal prey is not well understood.

Global Proteomic Profile Integrated to Quantitative and Morphometric Assessment of Enteric Neurons: Investigation of the Mechanisms Involved in the Toxicity Induced by Acute Fluoride Exposure in the Duodenum.

The enteric nervous system is responsible for controlling the gastrointestinal tract (GIT) functions. Enteric neuropathies are highly correlated to the development of several intestinal disturbances. Fluoride (F) is extensively applied for dental health improvement and its ingestion can promote systemic toxicity with mild to severe GIT symptomatology and neurotoxicity.

Proteomic analysis and antibacterial resistance mechanisms of Salmonella Enteritidis submitted to the inhibitory effect of Origanum vulgare essential oil, thymol and carvacrol.

Biological properties of natural products are an important research target and essential oils (EO) from aromatic plants with antimicrobial properties are well documented. However, their uses are limited, and the mechanisms underlying their antibacterial activity are still not well known. Therefore, our objective was to evaluate the antibacterial activities of Origanum vulgare EO, thymol and carvacrol against Salmonella Enteritidis ATCC 13076 strain, particularly regarding the bacterial proteic profile, enzymatic activities and DNA synthesis.

Identification of Zinc Absorption Biomarkers in Muscle Tissue of Nile Tilapia Fed with Organic and Inorganic Sources of Zinc Using Metallomics Analysis.

The development of metallomics techniques has allowed for metallomics analysis of biological systems, enabling a better understanding of the response mechanisms for different stimuli, their relationship to metallic species, and the characterization of biomarkers. In this study, a metallomics analysis of the muscle tissue of Nile tilapia was used to aid the understanding of the molecular mechanisms involved in zinc absorption in this fish species when fed organic and/or inorganic sources of zinc and to identify possible biomarkers for the absorption of this micromineral. To accomplish this, the fish were separated into three groups of 24 g, 74 g, and 85 g initial weights, and each group, respectively, was fed a zinc-free diet (control group, G1), a diet containing zinc found in organic sources (treatment 1, G2), and a diet containing zinc from an inorganic source (treatment 2, G3).

Analysis of Polymorphisms in Genes Differentially Expressed in the Enamel of Mice with Different Genetic Susceptibilities to Dental Fluorosis.

Genes expressed during amelogenesis are candidates to increase the risk of dental fluorosis (DF). Thus, this study aimed to evaluate the association between polymorphisms in enamel development genes and susceptibility to DF in mice. Mice of both sexes, representing strains 129P3/J (n = 20; resistant to DF) and A/J (n = 20; susceptible to DF), were divided into 2 groups.

Inferring putative virulence factors for Pythium insidiosum by proteomic approach.

Pythium insidiosum is the etiologic agent of pythiosis, a life-threatening disease that affects human and animals, has difficult diagnosis, and therapy. Studies on protein characterization of P. insidiosum are scarce, so we aimed to determine the protein profile of P.

Correction to: Mercury Exposure: Protein Biomarkers of Mercury Exposure in Jaraqui Fish from the Amazon Region.

In the affiliation section, Luiz Fabricio Zara's affiliation "Pontifical Catholic University of Goiás (PUC), Goiânia, GO, Brazil" was incorrect. The correct affiliation is College of Planaltina, UnB - University of Brasília, Distrito Federal, Brazil.

Mercury Exposure: Protein Biomarkers of Mercury Exposure in Jaraqui Fish from the Amazon Region.

This study presents data on the extraction and characterization of proteins associated with mercury in the muscle and liver tissues of jaraqui (Semaprochilodus spp.) from the Madeira River in the Brazilian Amazon. Protein fractionation was carried out by two-dimensional electrophoresis (2D-PAGE).

Oxidative Biochemistry Disbalance and Changes on Proteomic Profile in Salivary Glands of Rats Induced by Chronic Exposure to Methylmercury.

Methylmercury (MeHg) is one of the most toxic mercury species, which can cause many systemic damages, but little is known about its effect in the salivary glands. This study aimed to analyze the mercury levels, oxidative stress, and proteomic profile in parotid, submandibular, and sublingual salivary glands of rats, after chronic MeHg intoxication. Two groups of twenty male Wistar rats (90 days of age) were used on the experiment.

Effect of gels containing chlorhexidine or epigallocatechin-3-gallate on the protein composition of the acquired enamel pellicle.

Objective: This study evaluated changes in protein profile of the acquired enamel pellicle (AEP) formed in vivo, after application of gels containing chlorhexidine or EGCG and further challenge with citric acid.

Design: AEP was formed in 9 volunteers for 2h and then treated with one of the following gels: placebo, 400μM EGCG or 0.012% chlorhexidine.

Metalloproteomic and differential expression in plasma in a rat model of type 1 diabetes.

Type 1 diabetes is characterized by hyperglycemia, which in the chronic stage is associated with abnormalities in lipids, protein and, carbohydrate metabolism, as well as oxidative stress. New strategies for prevention and treatment are needed, as type 1 diabetes affects life quality and survival, and involves high-cost treatment. Proteomic and metalloproteomic studies can elucidate the functional and physiological aspects of biomolecules.

Enteric innervation combined with proteomics for the evaluation of the effects of chronic fluoride exposure on the duodenum of rats.

Ingested fluoride (F) is absorbed mainly in the small intestine, which is controlled by the Enteric Nervous System (ENS). Although important intestinal symptomatology has been described after excessive F exposure, there have been no studies reporting the effects of F on the ENS. In this study, the effects of chronic F exposure were evaluated on the duodenums of rats through proteomic and morphological analyses.

The proteomic profile of the acquired enamel pellicle according to its location in the dental arches.

Objective: This study evaluated the variation in the protein profile of the acquired enamel pellicle (AEP) formed in vivo according to its location in the dental arches.

Design: The AEP was formed for 120min in 9 volunteers. Pellicle formed at upper+lower anterior facial (ULAFa; teeth 13-23 and 33-43), upper anterior palatal (UAPa; teeth 13-23), lower anterior lingual (LALi; teeth 33-43), upper+lower posterior facial (ULPFa; teeth 14-17 24-27, 34-37 and 44-47), upper posterior palatal (UPPa; teeth 14-17 and 24-27) and lower posterior lingual (LPLi; teeth 34-37 and 44-47) regions were collected separately and processed for analysis by label-free LC-ESI-MS/MS.

A proteomic approach to identify metalloproteins and metal-binding proteins in liver from diabetic rats.

Proteins play crucial roles in biological systems, thus studies comparing the protein pattern present in a healthy sample with an affected sample have been widely used for disease biomarker discovery. Although proteins containing metal ions constitute only a small proportion of the proteome, they are essential in a multitude of structural and functional processes. The correct association between metal ions and proteins is essential because this binding can significantly interfere with normal protein function.