All Articles

Testing Maternal-Fetal Genotype Incompatibility with Mother-Offspring Pair Data

Abstract:

Maternal-fetal genotype (MFG) incompatibility has been shown to be strongly associated with a number of genetic diseases. Most current methods for the MFG test rely on parents-offspring trio genotype data and do not apply to mother-offspring pair data where paternal genotype is unavailable. In this paper, we developed a two-stage method for testing the allelic effect of given SNP through subgroup analysis of compatible MFG pairs and further tested the MFG incompatibility effect according to different scenarios determined by the allelic effect. Simulation studies demonstrated that this novel two-stage model is powerful in detecting the MFG incompatibility effect. This method can be implemented through publicly available statistical software, such as SAS, R, etc. We demonstrate with a case-control study of small for gestational age neonates that the method identified a SNP in the IGF2R gene with a significant allelic effect (p = 0.037), and a SNP in the IGF1 gene wi...

Quantitative Proteomics Using 15N SILAC Mouse

Abstract:

In biomedical research the use of mammalian tissues is crucial to increase our understanding of complex human diseases. Mass spectrometry-based proteomic approach has become the most powerful tool of studying large-scale protein expression profiles in mammalian tissues. To perform global proteome analysis quantification of mammalian tissues, we generated ¹⁵N SILAC mice to obtain tissue-matched labeled peptide libraries for mass spectrometry-based quantitative proteomic analysis. We developed a new labeling protocol to circumvent adverse effects of introducing ¹⁵N labeled diet to mice, and showed that the new labeling scheme has no significant effect on the fertility and reproduction of C57/BL6 mice. Using labeled tissues from these mice, we compared the reproducibility of mass spectrometry-based quantification with or without ¹⁵N labeled internal standards among biological replicates of young and old brains. We found that labeled-...

Differences in the Alveolar Macrophage Proteome in Transgenic Mice Expressing Human SP-A1 and SP-A2

Abstract:

Surfactant protein A (SP-A) plays a number of roles in lung host defense and innate immunity. There are two human genes, SFTPA1 and SFTPA2, and evidence indicates that the function of SP-A1 and SP-A2 proteins differ in several respects. To investigate the impact of SP-A1 and SP-A2 on the alveolar macrophage (AM) phenotype, we generated humanized transgenic (hTG) mice on the SP-A knockout (KO) background, each expressing human SP-A1 or SP-A2. Using two-dimensional difference gel electrophoresis (2D-DIGE) we studied the AM cellular proteome. We compared mouse lines expressing high levels of SP-A1, high levels of SP-A2, low levels of SP-A1, and low levels of SP-A2, with wild type (WT) and SP-A KO mice. AM from mice expressing high levels of SP-A2 were the most similar to WT mice, particularly for proteins related to actin and the cytoskeleton, as well as proteins regulated by Nrf2. The expression patterns from mouse lines expressing ...

Editorial for Journal of Proteomics and Genomics Research: Second Issue

Abstract:

An editorial for the second issue highlights notable contributions and reaffirms peer review and openness as pillars for the field.

Correlation of Cryptococcal Antigen Assay with C-reactive Protein as Serum and Urine Biomarker in Cryptococcal Meningitis: Experience in a Tertiary Hospital

Abstract:

The incidence of cryptococcal meningitis caused by Cryptococcus neoformans has risen markedly over the past 20 years as a result of theHIV epidemic and increasing use of immunosuppressive therapies. The objectives of this study were to isolate and identify Cryptococcus neoformans from clinically suspected cases of fungal meningitis by conventional techniques and evaluate the role of C-reactive protein (CRP) as a serum or urine biomarker for the diagnosis and monitoring of patients with cryptococcal meningitis.

Pattern of Use of Highly Active Antiretroviral Therapy Regimens and Pattern of Occurrence of Adverse Drug Reactions in an Indian Human Immunodeficiency Virus Positive Patients

Abstract:

In India, Human immunodeficiency (HIV) infected patients with highly active antiretroviral therapy (HAART) are at higher risk of developing adverse drug reactions (ADRs).

When and How Should we be Measuring Adherence to Antiretroviral Therapy in Resource-Limited Settings?

Abstract:

This perspective reviews practical approaches to measuring ART adherence in resource‑limited settings. It weighs self‑report, pill counts, pharmacy refill data, and biologic measures, emphasizing feasibility, bias, and programmatic integration to support sustainable HIV care.

Prevalence and Factors Associated with Disclosure of HIV Diagnosis to Infected Children Receiving Antiretroviral Treatment in Public Health Care Facilities in Gauteng, South Africa

Abstract:

HIV infected children who started antiretroviral therapy (ART) in public health facilities in South Africa have survived to older age and disclosure has become an essential part of their care. Available data on HIV disclosure to children were collected much earlier in the provision of ART in South Africa. The aim of the study was to (a) determine the characteristics of caregivers of pediatric HIV patients in Gauteng, South Africa, (b) estimate the prevalence and timing of HIV disclosure among these patients, and (c) assess the factors associated with disclosure status. A cross-sectional study was conducted among 286 caregivers of paediatric ART children aged 4–17 in two centres in Gauteng, South Africa. Bivariate and multivariate logistic regression analyses were carried out. The highest proportion of care givers were biological mothers (n=140, 49.3%). The mean age of the children was 8.5 years, (range 4-17 years). More than a third (n=99, 34%) were disclosed th...

Single Nucleotide Polymorphisms associated with alimentary fatty liver disease are not genetic risk factors for treatment-associated hepatic steatosis in HIV patients on HAART

Abstract:

Analyzing SNPs linked to fatty liver disease, this study finds no association with HAART‑related hepatic steatosis in HIV patients. The work underscores the multifactorial nature of antiretroviral toxicity and points to metabolic and pharmacologic contributors beyond common variants.

Demographics, Clinical Profile and Outcome among the HIV Infected Persons Hospitalized in the HAART Era in Barbados.

Abstract:

HAART has resulted in significant decline in morbidity and mortality from HIV. However, it is unclear if the trends have continued in the current HAART era. An understanding of healthcare utilization patterns is important for optimization of care and resource allocation. We examined the diagnoses for hospitalizations of patients with HIV and their clinical and demographic profile years after the introduction of HAART.