Proteomic Analysis of a Rat Streptozotocin Model Shows Dysregulated Biological Pathways Implicated in Alzheimer's Disease.

Alzheimer's Disease (AD) is an age-related neurodegenerative disorder characterized by progressive memory loss and cognitive impairment, affecting 35 million individuals worldwide. Intracerebroventricular (ICV) injection of low to moderate doses of streptozotocin (STZ) in adult male Wistar rats can reproduce classical physiopathological hallmarks of AD. This biological model is known as ICV-STZ.

SpliceProt 2.0: A Sequence Repository of Human, Mouse, and Rat Proteoforms.

SpliceProt 2.0 is a public proteogenomics database that aims to list the sequence of known proteins and potential new proteoforms in human, mouse, and rat proteomes. This updated repository provides an even broader range of computationally translated proteins and serves, for example, to aid with proteomic validation of splice variants absent from the reference UniProtKB/SwissProt database.

Identification of Novel Genes and Proteoforms in through a Proteogenomic Approach.

RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA).

Proteogenomics Reveals Orthologous Alternatively Spliced Proteoforms in the Same Human and Mouse Brain Regions with Differential Abundance in an Alzheimer's Disease Mouse Model.

Alternative splicing (AS) may increase the number of proteoforms produced by a gene. Alzheimer's disease (AD) is a neurodegenerative disease with well-characterized AS proteoforms. In this study, we used a proteogenomics strategy to build a customized protein sequence database and identify orthologous AS proteoforms between humans and mice on publicly available shotgun proteomics (MS/MS) data of the corpus callosum (CC) and olfactory bulb (OB).

Optimal Virulence, Diffusion and Tradeoffs.

In this work we propose a variant of a classical SIR epidemiological model where pathogens are characterized by a (phenotypic) mutant trait x. Imposing that the trait x mutates according to a random walk process and that it directly influences the epidemiological components of the pathogen, we studied its evolutionary development by interpreting the tenet of maximizing the basic reproductive number of the pathogen as an optimal control problem. Pontryagin's maximum principle was used to identify the possible optimal evolutionary strategies of the pathogen.

The Challenge to Search for New Nervous System Disease Biomarker Candidates: the Opportunity to Use the Proteogenomics Approach.

Alzheimer's disease, Parkinson's disease, prion diseases, schizophrenia, and multiple sclerosis are the most common nervous system diseases, affecting millions of people worldwide. The current scientific literature associates these pathological conditions to abnormal expression levels of certain proteins, which in turn improved the knowledge concerning normal and affected brains. However, there is no available cure or preventive therapy for any of these disorders.

Physiological and biochemical characterization of Azospirillum brasilense strains commonly used as plant growth-promoting rhizobacteria.

Azospirillum is a plant growth-promoting rhizobacteria (PGPR) genus vastly studied and utilized as agriculture inoculants. Isolation of new strains under different environmental conditions allows the access to the genetic diversity and improves the success of inoculation procedures. Historically, the isolation of this genus has been performed by the use of some traditional culture media.

Treatment outcomes in a cohort of patients with chronic hepatitis B and human immunodeficiency virus co-infection in Mumbai, India.

Treatment experiences with patients co-infected with human immunodeficiency virus (HIV) and hepatitis B virus (HBV) in resource-limited settings remain poorly documented. This study aimed to evaluate the treatment outcomes in a cohort of HIV/HBV co-infected individuals receiving tenofovir/lamivudine (TDF/3TC)-based antiretroviral therapy (ART) in a programmatic setting in Mumbai, India. Additionally, a cross-sectional laboratory study was carried out measuring serologic and virologic parameters.

HPV infection, cervical abnormalities, and cancer in HIV-infected women in Mumbai, India: 12-month follow-up.

Background: HIV-infected women are at a higher risk of cervical intraepithelial neoplasia (CIN) and cancer than women in the general population, partly due to a high prevalence of persistent human papillomavirus (HPV) infection. The aim of the study was to assess the burden of HPV infection, cervical abnormalities, and cervical cancer among a cohort of HIV-infected women as part of a routine screening in an urban overpopulated slum setting in Mumbai, India.

Methods: From May 2010 to October 2010, Médecins Sans Frontières and Tata Memorial Hospital Mumbai offered routine annual Pap smears and HPV DNA testing of women attending an antiretroviral therapy (ART) clinic and a 12-month follow-up.

Prognostic value of stress hyperglycemia for in-hospital outcome in acute coronary artery disease.

Background: In acute coronary syndrome (ACS), admission hyperglycemia is associated with adverse cardiovascular events in diabetic and nondiabetic patients.

Objective: To assess the prognostic value of stress hyperglycemia for the in-hospital outcome of patients admitted due to ACS.

Methods: This study included 152 patients admitted to the chest pain unit of a tertiary hospital diagnosed with ACS, who had admission blood glucose data, from September 2005 to February 2010.

Adverse events among HIV/MDR-TB co-infected patients receiving antiretroviral and second line anti-TB treatment in Mumbai, India.

Background: Significant adverse events (AE) have been reported in patients receiving medications for multidrug- and extensively-drug-resistant tuberculosis (MDR-TB & XDR-TB). However, there is little prospective data on AE in MDR- or XDR-TB/HIV co-infected patients on antituberculosis and antiretroviral therapy (ART) in programmatic settings.

Methods: Médecins Sans Frontières (MSF) is supporting a community-based treatment program for drug-resistant tuberculosis in HIV-infected patients in a slum setting in Mumbai, India since 2007.

Ambulatory multi-drug resistant tuberculosis treatment outcomes in a cohort of HIV-infected patients in a slum setting in Mumbai, India.

Background: India carries one quarter of the global burden of multi-drug resistant TB (MDR-TB) and has an estimated 2.5 million people living with HIV. Despite this reality, provision of treatment for MDR-TB is extremely limited, particularly for HIV-infected individuals.

Interactions of anionic dyes with silica-aminopropyl 1. A quantitative multivariate analysis of equilibrium adsorption and adsorption Gibbs free energies.

In this work silica-aminopropyl (Sil-NH2) was synthesized and employed to evaluate the quantitative roles of temperature, pH, dye concentration, and Hg(II) or anionic surfactant SDB interferents in the adsorptions of blue and red remazol dyes in aqueous medium using four distinct 2(4) factorial designs. The results were analyzed statistically using multiple regressions, Student's t-test, analysis of variance, and F-test. Polynomial modelings were used to define the most important factors affecting dye adsorption.