Temporal Improvements in Long-term Outcome in Care Among HIV-infected Children Enrolled in Public Antiretroviral Treatment Care: An Analysis of Outcomes From 2004 to 2012 in Zimbabwe.

BACKGROUND: Increasing numbers of children are requiring long-term HIV care and antiretroviral treatment (ART) in public ART programs in Africa, but temporal trends and long-term outcomes in care remain poorly understood. METHODS: We analyzed outcomes in a longitudinal cohort of infants (<2 years of age) and children (2-10 years of age) enrolling in a public tertiary ART center in Zimbabwe over an 8-year period (2004-2012). RESULTS: The clinic enrolled 1644 infants and children; the median age at enrollment was 39 months (interquartile range: 14-79), with a median CD4% of 17.0 (interquartile range: 11-24) in infants and 15.0 (9%-23%) in children (P = 0.0007). Among those linked to care, 33.5% dropped out of care within the first 3 months of enrollment. After implementation of revised guidelines in 2009, decentralization of care and increased access to prevention of mother to child transmission services, we observed an increase in infants (48.9%-68.3%; P < 0.0001) and children (48.9%-68.3%; P < 0.0001) remaining in care for more than 3 months. Children enrolled from 2009 were younger, had lower World Health Organization clinical stage, improved baseline CD4 counts than those who enrolled in 2004-2008. Long-term retention in care also improved with decreasing risk of loss from care at 36 months for infants enrolled from 2009 (aHR: 0.57; 95% confidence interval: 0.34-0.95; P = 0.031). ART eligibility at enrollment was a significant predictor of long-term retention in care, while delayed ART initiation after 5 years of age resulted in failure to fully reconstitute CD4 counts to age-appropriate levels despite prolonged ART. CONCLUSIONS: Significant improvements have been made in engaging and retaining children in care in public ART programs in Zimbabwe. Guideline and policy changes that increase access and eligibility will likely to continue to support improvement in pediatric HIV outcomes.

Automethylation activities within the mixed lineage leukemia-1 (MLL1) core complex reveal evidence supporting a "two-active site" model for multiple histone H3 lysine 4 methylation.

The mixed lineage leukemia-1 (MLL1) core complex predominantly catalyzes mono- and dimethylation of histone H3 at lysine 4 (H3K4) and is frequently altered in aggressive acute leukemias. The molecular mechanisms that account for conversion of mono- to dimethyl H3K4 (H3K4me1,2) are not well understood. In this investigation, we report that the suppressor of variegation, enhancer of zeste, trithorax (SET) domains from human MLL1 and Drosophila Trithorax undergo robust intramolecular automethylation reactions at an evolutionarily conserved cysteine residue in the active site, which is inhibited by unmodified histone H3. The location of the automethylation in the SET-I subdomain indicates that the MLL1 SET domain possesses significantly more conformational plasticity in solution than suggested by its crystal structure. We also report that MLL1 methylates Ash2L in the absence of histone H3, but only when assembled within a complex with WDR5 and RbBP5, suggesting a restraint for the architectural arrangement of subunits within the complex. Using MLL1 and Ash2L automethylation reactions as probes for histone binding, we observed that both automethylation reactions are significantly inhibited by stoichiometric amounts of unmethylated histone H3, but not by histones previously mono-, di-, or trimethylated at H3K4. These results suggest that the H3K4me1 intermediate does not significantly bind to the MLL1 SET domain during the dimethylation reaction. Consistent with this hypothesis, we demonstrate that the MLL1 core complex assembled with a catalytically inactive SET domain variant preferentially catalyzes H3K4 dimethylation using the H3K4me1 substrate. Taken together, these results are consistent with a "two-active site" model for multiple H3K4 methylation by the MLL1 core complex.

Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing.

BACKGROUND: Aptamers are oligonucleotides that bind proteins and other targets with high affinity and selectivity. Twenty years ago elements of natural selection were adapted to in vitro selection in order to distinguish aptamers among randomized sequence libraries. The primary bottleneck in traditional aptamer discovery is multiple cycles of in vitro evolution. METHODOLOGY/PRINCIPAL FINDINGS: We show that over-representation of sequences in aptamer libraries and deep sequencing enables acyclic identification of aptamers. We demonstrated this by isolating a known family of aptamers for human α-thrombin. Aptamers were found within a library containing an average of 56,000 copies of each possible randomized 15mer segment. The high affinity sequences were counted many times above the background in 2-6 million reads. Clustering analysis of sequences with more than 10 counts distinguished two sequence motifs with candidates at high abundance. Motif I contained the previously observed consensus 15mer, Thb1 (46,000 counts), and related variants with mostly G/T substitutions; secondary analysis showed that affinity for thrombin correlated with abundance (K(d) = 12 nM for Thb1). The signal-to-noise ratio for this experiment was roughly 10,000∶1 for Thb1. Motif II was unrelated to Thb1 with the leading candidate (29,000 counts) being a novel aptamer against hexose sugars in the storage and elution buffers for Concanavilin A (K(d) = 0.5 µM for α-methyl-mannoside); ConA was used to immobilize α-thrombin. CONCLUSIONS/SIGNIFICANCE: Over-representation together with deep sequencing can dramatically shorten the discovery process, distinguish aptamers having a wide range of affinity for the target, allow an exhaustive search of the sequence space within a simplified library, reduce the quantity of the target required, eliminate cycling artifacts, and should allow multiplexing of sequencing experiments and targets.