Publications

Membrane proteins serve as cellular gatekeepers, regulators, and sensors. Prior studies have explored the functional breadth and evolution of proteins and families of particular interest, such as the diversity of transport-associated membrane protein families in prokaryotes and eukaryotes, the composition of integral membrane proteins, and family classification of all human G-protein coupled receptors. However, a comprehensive analysis of the content and evolutionary associations between membrane proteins and families in a diverse set of genomes is lacking. Here, a membrane protein annotation pipeline was developed to define the integral membrane genome and associations between 21,379 proteins from 34 genomes; most, but not all of these proteins belong to 598 defined families. The pipeline was used to provide target input for a structural genomics project that successfully cloned, expressed, and purified 61 of our first 96 selected targets in yeast. Furthermore, the methodology was applied (1) to explore the evolutionary history of the substrate-binding transmembrane domains of the human ABC transporter superfamily, (2) to identify the multidrug resistance-associated membrane proteins in whole genomes, and (3) to identify putative new membrane protein families.

BACKGROUND

Human immunodeficiency virus type 1 (HIV-1) elite controllers are able to control virus replication to levels below the limits of detection by commercial assays, but the actual level of viremia in these individuals is not well defined. Here, we quantify plasma HIV-1 RNA in elite controllers and correlate this with specific immunologic parameters.

METHODS

Plasma HIV-1 RNA levels were quantified in 90 elite controllers with use of a real time reverse-transcriptase polymerase chain reaction assay with a sensitivity of 0.2 copies/mL. HIV-1-specific immune responses and longitudinal CD4(+) T cell counts were examined.

RESULTS

The median plasma HIV-1 RNA level was 2 copies/mL (interquartile range, 0.2-14 copies/mL). A longitudinal analysis of 31 elite controllers demonstrated 2-5-fold fluctuations in viremia in the majority of individuals; 6 had persistent levels below 1 copy/mL. Viremia correlated directly with HIV-1-specific neutralizing antibodies and Western blot reactivity but not with CD8(+) T cell responses. Absolute CD4(+) T cell decrease was more common among individuals with detectable viremia (P = .04).

CONCLUSIONS

Low-level viremia is present in the majority of elite controllers and is associated with higher HIV-1-specific antibody responses. Absolute CD4(+) T cell loss is more common among viremic individuals, suggesting that even very low-level viremia has negative consequences over time.

BACKGROUND

Nonalcoholic fatty liver disease (NAFLD) in children can lead to steatohepatitis, cirrhosis, and end-stage liver disease. The cause of NAFLD is unknown, but it is commonly associated with obesity, insulin resistance, and dyslipidemia.

OBJECTIVES

TONIC is conducted to test whether treatment with metformin, an insulin sensitizer, or vitamin E, a naturally available antioxidant, will lead to improvements in biochemical and histological features of nondiabetic children with biopsy-proven NAFLD.

DESIGN

TONIC is a randomized, multicenter, double-masked, placebo-controlled trial of 96 weeks of treatment with metformin or vitamin E. The primary outcome measure chosen for the trial is improvement in serum alanine aminotransferase (ALT) levels with treatment as compared to placebo. An improvement in ALT is defined as reduction in serum ALT levels to below 50% of the baseline values or into the normal range (40 U/L or less) during the last 48 weeks of treatment. Histological improvement is defined by changes in liver histology between a baseline and end-of-treatment liver biopsy in regards to (1) steatohepatitis, (2) NAFLD Activity Score, consisting of scores for steatosis, lobular inflammation, and hepatocellular injury (ballooning), and (3) fibrosis score.

METHODS

Between September 2005 and September 2007, 173 children were enrolled into TONIC at 10 clinical centers in the United States. Participants were randomized to receive either metformin (500 mg b.i.d.), vitamin E (400 IU b.i.d.), or placebo for 96 weeks. This protocol was approved by all participating center Institutional Review Boards (IRBs) and an independent Data and Safety Monitoring Board (DSMB). (ClinicalTrials.gov number, NCT00063635.).

BACKGROUND

As malaria control efforts intensify, it is critical to monitor trends in disease burden and measure the impact of interventions. A key surveillance indicator is the incidence of malaria. Yet measurement of incidence is challenging. The slide positivity rate (SPR) has been used as a surrogate measure of malaria incidence, but limited data exist on the relationship between SPR and the incidence of malaria.

METHODS

A cohort of 690 children aged 1-10 years at enrollment were followed for all their health care needs over a four-year period in Kampala, Uganda. All children with fever underwent laboratory testing, allowing us to measure the incidence of malaria and non-malaria fevers. A formula was derived to estimate relative changes in the incidence of malaria (rDeltaIm) based on changes in the SPR and the assumption that the incidence of non-malaria fevers was consistent over time. Observed and estimated values of rDeltaIm were compared over two, six, and 12 month time intervals after restricting the analysis to children contributing observation time between the ages of 4-10 years to control for aging of the cohort.

RESULTS

Over the four-year observation period the incidence of malaria declined significantly from 0.93 episodes per person-year in 2005 to 0.39 episodes per person-year in 2008 (p < 0.0001) and the incidence of non-malaria fevers declined significantly from 2.31 episodes per person-year in 2005 to 1.31 episodes per person-year in 2008 (p < 0.0001). Younger age was associated with a significantly greater incidence of malaria and the incidence of malaria was significantly higher during seasonal peaks occurring each January-February and May-June. Changes in SPR produced reasonably accurate estimates of rDeltaIm over all time intervals. The average absolute difference in observed and estimated values of rDeltaIm was lower for six-month intervals (0.13) than it was for two-month (0.21) or 12 month intervals (0.21).

CONCLUSION

Changes in SPR provided a useful estimate of changes in the incidence of malaria in a well defined cohort; however, a gradual decline in the incidence of non-malaria fevers introduced some bias in these estimates.