Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms. In one subject we combined these genetic data with detailed immunological analyses to comprehensively evaluate viral evolution and immune escape during the acute phase of HIV-1 infection. The majority of early, low frequency mutations represented viral adaptation to host CD8+ T cell responses, evidence of strong immune selection pressure occurring during the early decline from peak viremia. CD8+ T cell responses capable of recognizing these low frequency escape variants coincided with the selection and evolution of more effective secondary HLA-anchor escape mutations. Frequent, and in some cases rapid, reversion of transmitted mutations was also observed across the viral genome. When located within restricted CD8 epitopes these low frequency reverting mutations were sufficient to prime de novo responses to these epitopes, again illustrating the capacity of the immune response to recognize and respond to low frequency variants. More importantly, rapid viral escape from the most immunodominant CD8+ T cell responses coincided with plateauing of the initial viral load decline in this subject, suggestive of a potential link between maintenance of effective, dominant CD8 responses and the degree of early viremia reduction. We conclude that the early control of HIV-1 replication by immunodominant CD8+ T cell responses may be substantially influenced by rapid, low frequency viral adaptations not detected by conventional sequencing approaches, which warrants further investigation. These data support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia.

There is growing appreciation for the importance of non-protein-coding genes in development and disease. Although much is known about microRNAs, limitations in bioinformatic analyses of RNA sequencing have precluded broad assessment of other forms of small-RNAs in humans. By analysing sequencing data from plasma-derived RNA from 40 individuals, here we identified over a thousand human extracellular RNAs including microRNAs, piwi-interacting RNA (piRNA), and small nucleolar RNAs. Using a targeted quantitative PCR with reverse transcription approach in an additional 2,763 individuals, we characterized almost 500 of the most abundant extracellular transcripts including microRNAs, piRNAs and small nucleolar RNAs. The presence in plasma of many non-microRNA small-RNAs was confirmed in an independent cohort. We present comprehensive data to demonstrate the broad and consistent detection of diverse classes of circulating non-cellular small-RNAs from a large population.

Background Biomarkers that predict response to cardiac resynchronization therapy (CRT) in heart failure patients with dyssynchrony (HFDYS) would be clinically important. Circulating extracellular microRNAs (miRNAs) have emerged as novel biomarkers that may also play important functional roles, but their relevance as markers for CRT response has not been examined. Methods and Results Comprehensive miRNA PCR arrays were used to assess baseline levels of 766 plasma miRNA in patients undergoing clinically indicated CRT in an initial discovery set (n=12) with and without subsequent echocardiographic improvement at 6 months after CRT. Validation of candidate miRNAs in 61 additional patients confirmed that baseline plasma miR-30d was associated with CRT response (defined as increase in LVEF≥10%). MiR-30d was enriched in coronary sinus (CS) blood and increased in late-contracting myocardium in a canine model of HFDYS, indicating cardiac origin with maximal expression in areas of high mechanical stress. We examined the functional effects of miR-30d in cultured cardiomyocytes (CMs), and determined that miR-30d is expressed in CMs and released in vesicles in response to mechanical stress. Overexpression of miR-30d in cultured CMs led to CM growth and protected against apoptosis by targeting the mitogen-associated kinase 4 (MAP4K4), a downstream effector of tumor necrosis factor (TNF). In HFDYS patients, miR-30d plasma levels inversely correlated with high sensitivity Troponin T, a marker of myocardial necrosis. Conclusions Baseline plasma miR-30d level is associated with response to CRT in HFDYS in this translational pilot study. MiR-30d increase in CMs correlates with areas of increased wall stress in HFDYS, and is protective against deleterious TNF signaling.

Although the coordination chemistry of N-heterocyclic carbenes (NHCs) with transition metals has been explored for half a century, only in the past ten years has the chemistry of metallosupramolecular assemblies based on poly-NHC ligands been studied more extensively. Remarkable discrete assemblies featuring poly-NHC ligands including two-dimensional metallacycles and three-dimensional metallaprisms/cages have since emerged. These assemblies are mostly obtained starting from various imidazolium or benzimidazolium salts. Driven by the increasing interest in new supramolecular architectures from carbon donor ligands, design, and construction of poly-NHC metal assemblies has become a rapidly growing area of research. The metal-carbene bond length is fixed to approximately 2.0 Å in linear NHC-M-NHC complexes. This allows the use of such complexes bearing olefin-substituted NHC ligands as templates for subsequent photochemical [2 + 2] cycloaddition reactions. The postassembly modification of such assemblies has been actively explored in recent years. In this review, we focus on the synthetic methods, characterization, structural features, and postassembly modifications of metallosupramolecular assemblies obtained from poly-NHC ligands.