Patterns of conserved gp120 epitope presentation on attached HIV-1 virions.

A complete picture of HIV antigenicity during early replication is needed to elucidate the full range of options for controlling infection. Such information is frequently gained through analyses of isolated viral envelope antigens, host CD4 receptors, and cognate antibodies. However, direct examination of viral particles and virus-cell interactions is now possible via advanced microscopy techniques and reagents.

Conserved molecular signatures in gp120 are associated with the genetic bottleneck during simian immunodeficiency virus (SIV), SIV-human immunodeficiency virus (SHIV), and HIV type 1 (HIV-1) transmission.

Unlabelled: Human immunodeficiency virus (HIV) transmission typically results from infection by a single transmitted/founder (T/F) variant. Are T/F variants chosen uniformly at random from the donor pool, or are they selected based on advantageous traits facilitating transmission? Finding evidence for selection during transmission is of particular interest, because it would indicate that phenotypic and/or genetic properties of the viruses might be harnessed as potential vaccine targets or immunotherapies. Here, we systematically evaluated the differences between the Env proteins of simian immunodeficiency virus/simian HIV (SIV/SHIV) stock and T/F variants in search of "signature" sites of transmission.

Domain analysis of symbionts and hosts (DASH) in a genome-wide survey of pathogenic human viruses.

Background: In the coevolution of viruses and their hosts, viruses often capture host genes, gaining advantageous functions (e.g. immune system control).

Chapter 4: Protein interactions and disease.

Proteins do not function in isolation; it is their interactions with one another and also with other molecules (e.g. DNA, RNA) that mediate metabolic and signaling pathways, cellular processes, and organismal systems.

RefProtDom: a protein database with improved domain boundaries and homology relationships.

Unlabelled: RefProtDom provides a set of divergent query domains, originally selected from Pfam, and full-length proteins containing their homologous domains, with diverse architectures, for evaluating pair-wise and iterative sequence similarity searches. Pfam homology and domain boundary annotations in the target library were supplemented using local and semi-global searches, PSI-BLAST searches, and SCOP and CATH classifications.

Availability: RefProtDom is available from http://faculty.

Homologous over-extension: a challenge for iterative similarity searches.

We have characterized a novel type of PSI-BLAST error, homologous over-extension (HOE), using embedded PFAM domain queries on searches against a reference library containing Pfam-annotated UniProt sequences and random synthetic sequences. PSI-BLAST makes two types of errors: alignments to non-homologous regions and HOE alignments that begin in a homologous region, but extend beyond the homology into neighboring sequence regions. When the neighboring sequence region contains a non-homologous domain, PSI-BLAST can incorporate the unrelated sequence into its position specific scoring matrix, which then finds non-homologous proteins with significant expectation values.