Regulated superinfection may help HIV adaptation on rugged landscape.

Human immunodeficiency virus (HIV) is highly adaptable to a, changing environment, including host immune response and antiviral drugs. Superinfection occurs when several HIV proviruses share the same host cell. We previously proposed that HIV may regulate the rate of its superinfection, which would help the virus to adapt (Leontiev et al., 2008). In this paper we, investigate the effect of regulated superinfection in HIV on complex, adaptation on rugged fitness landscapes. We present the results of our in silico experiments that suggest that regulated superinfection facilitates HIV, adaptation on rugged fitness landscapes and that the advantage of regulated, superinfection increases with the ruggedness of the landscape.

Drug induced superinfection in HIV and the evolution of drug resistance.

The rapid evolution of HIV drug resistance is a major cause of AIDS treatment failure. Superinfection, the infection of an already infected cell by additional virions, can be a major factor contributing to the evolution of drug resistance. However, the pattern and consequences of superinfection in HIV populations are far from fully understood. In this paper we study the implications of the fact that superinfection is regulated by HIV. We propose that superinfection is negatively associated with the success of the virus, so that more successful viruses are less likely to allow superinfection. We use computational models to investigate the effect that regulated superinfection would have on the evolution of drug resistance in HIV population. We find that regulated, fitness-associated superinfection can provide a distinct advantage to the virus in adapting to anti-HIV drugs in comparison with unregulated superinfection. Based on the results of the computational models and on current biological evidence, we suggest that the mechanism of fitness-associated regulation of coinfection in HIV is plausible, and that its investigation can lead to new ways to fight viral drug resistance.

Transcript annotation prioritization and screening system (TrAPSS) for mutation screening.

When searching for disease-causing mutations with polymerase chain reaction (PCR)-based methods, candidate genes are usually screened in their entirety, exon by exon. Genomic resources (i.e. www.ncbi.nih.gov, www.ensembl.org, and genome.ucsc.edu) largely support this paradigm for mutation screening by making it easy to view and access sequence data associated with genes in their genomic context. However, the administrative burden of conducting mutation screening in potentially hundreds of genes and thousands of exons in thousands of patients is significant, even with the use of public genome resources. For example, the manual design of oligonucleotide primers for all exons of the 10 Leber's congenital amaurosis (LCA) genes (149 exons) represents a significant information management challenge. The Transcript Annotation Prioritization and Screening System (TrAPSS) is designed to accelerate mutation screening by (1) providing a gene-based local cache of candidate disease genes in a genomic context, (2) automating tasks associated with optimizing candidate disease gene screening and information management, and (3) providing the implementation of an algorithmic technique to utilize large amounts of heterogeneous genome annotation (e.g. conserved protein functional domains) so as to prioritize candidate genes.

Wnt-3A/beta-catenin signaling induces transcription from the LEF-1 promoter.

Members of the Wnt family of secreted molecules have been established as key factors in determining cell fate and morphogenic signaling. It has long been recognized that Wnt induces morphogenic signaling through the Tcf/LEF-1 cascade by regulating free intracellular levels of beta-catenin, a co-factor for Tcf/LEF-1 transcription factors. In the present study, we have demonstrated that Wnt-3A can also directly induce transcription from the LEF-1 promoter. This induction was dependent on glycogen synthase kinase 3beta inactivation, a rise in free intracellular beta-catenin, and a short 110-bp Wnt-responsive element (WRE) in the LEF-1 promoter. Linear and internal deletion of this WRE led to a dramatic increase in constitutive LEF-1 promoter activity and loss of Wnt-3A responsiveness. In isolation, the 110-bp WRE conferred context-independent Wnt-3A or beta-catenin(S37A) responsiveness to a heterologous SV40 promoter. Studies expressing dominant active and negative forms of LEF-1, beta-catenin, GSK-3beta, and beta-catenin/LEF-1 fusions suggest that Wnt-3A activates the LEF-1 promoter through a beta-catenin-dependent and LEF-1-independent process. Wnt-3A expression also induced multiple changes in the binding of factors to the WRE and suggests that regulatory mechanisms may involve modulation of a multiprotein complex. In summary, these results provide evidence for transcriptional regulation of the LEF-1 promoter by Wnt and enhance the mechanistic understanding of Wnt/beta-catenin signaling in the regulation of LEF-1-dependent developmental processes.

Mechanisms of submucosal gland morphogenesis in the airway.

Submucosal glands (SMGs) are thought to play an important role in the pathogenesis of a number of hypersecretory lung diseases including cystic fibrosis, asthma, and chronic bronchitis. In such diseases, severe SMG hypertrophy and hyperplasia is characteristic of disease progression. Our laboratory has focused efforts on defining both the mechanism of SMG morphogenesis and the identification of SMG stem cells. To this end, we have identified a transcription factor (LEF1) that is temporally and spatially uniquely regulated in SMG progenitors during the initial stages of gland development. LEF1 expression is absolutely required for SMG development in mouse and ferret tracheas, but is insufficient to induce de novo gland development in the absence of other unknown co-factors. In an effort to delineate the transcriptional cascades responsible for inducing LEF1 expression and subsequent SMG development in the airway, we have begun to dissect the regulation of the LEF1 promoter using cell line and transgenic mouse models. Current efforts are focused on defining the cis-acting elements and transcriptional binding factors responsible for Wnt induction of the LEF1 promoter and determining whether the Wnt/beta catenin cascade plays a role in submucosal gland development in vivo.