Research Highlights

Recent advances in sequencing technology have enabled highly sensitive measurement of whole transcriptomes. In the September 2011 issue of mBio, the Katze Lab reported the first use of next-generation sequencing to measure changes in total mRNA from an HIV-1-infected T cell line. This approach identified novel viral RNA splice variants and was able to detect small changes in mRNA abundance, including the suppression of cellular genes associated with T cell activation early after infection. In addition, HIV-1 infection resulted in the altered expression of multiple forms of noncoding RNAs, providing insights into the regulation of microRNAs. These findings give new insights into the panoply of changes that occur in host cells infected with HIV-1 and provide the groundwork for using new sequencing technologies in future studies investigating the host response to virus infection.

The STEP HIV-1 vaccine trial was concluded in 2009 and involved 3,000 volunteers from 34 sites worldwide. Overall, the vaccine failed to protect people from infection. In the February 2011 issue of Nature Medicine, the Mullins Lab reported on the results of a large viral genome sequencing and analysis effort to determine whether the vaccine nevertheless provided a benefit that may have been overshadowed by the negative effects of the formulation. They found that the vaccine did indeed exert a partially protective effect by blocking strains of HIV antigenically similar to the vaccine. Their results were the first to demonstrate a positive impact of a vaccine on HIV-1 infection. Although the selective pressures detected were not sufficient to prevent infection, they do provide a new benchmark to evaluate the impact of forthcoming vaccines and provide impetus for designing novel vaccine inserts to block a larger segment of the HIV population from infecting vaccine recipients. A parallel study was conducted on breakthrough infections that occurred in the most recent HIV vaccine trial called RV144, one that did have a small protective effect, with the gene sequencing results due to be released in Spring 2012.

The molecular motor myosin drives the contraction of muscle, but doesn't just produce force along the axis of shortening. Models of muscle contraction have primarily treated myosin as a simple spring oriented parallel to its direction of movement. This assumption does not allow prediction of the relationship between the forces produced and the spacing between contractile filaments or of radial forces, perpendicular to the axis of shortening, that are observed during muscle contraction. In the December 2010 issue of PLoS Computational Biology, C. Dave Williams, Mike Regnier, and Tom Daniel developed an alternative model, still computationally efficient enough to be used in simulations, that incorporates springs that are both extensional and torsional (angle-dependent, like those found in a watch). Their model captures much of the spacing-dependent kinetics and forces that are missing from single-spring models.

The two most common diseases in humans that cause irreversible damage, destructive periodontitis and dental caries, involve disturbance of the interface between protein and hydroxyapatite surfaces. In the October 2010 issue of Pattern Recognition Letters, the Samudrala Lab created a variety of bioinformatic protein sequence analysis methods designed to identify functional mechanisms of mineralization proteins. They applied these methods to define meta-functional signatures that describe the form and function of amelogenin, a protein highly conserved across vertebrates but with unique sequence and function with respect to other proteins in nature. They predicted physiologic mechanisms of amelogenin that were prospectively verified in the laboratory, including nucleation of calcium phosphate seed crystals, maturation, and physiologic binding of enamel hydroxyapatite.

The Qian Lab works on biochemical reaction systems in small volumes such as cells, in which many important proteins have small copy numbers and reaction kinetics are stochastic and discrete. In the September 2010 issue of the Journal of Physical Chemistry B they proposed a new mechanism for regulating protein functions called Cyclic Conformational Modification. In contrast to the classical ligand-induced conformational change, Cyclic Conformational Modification only requires a catalytic amount of ligand as an activator, with an associated energy expenditure.

In the June 2010 issue of Nature Biotechnology, Xiaoyu Chen and Martin Tompa assessed four expert ENCODE alignments, each of which aligns 28 vertebrate sequences on 554,000,000 base-pairs of total input sequence. They reported a disturbing lack of agreement among the alignments not only in species distant from human, but even in mouse, a well-studied model organism. Overall, the assessment showed that the Pecan alignment method produced the most accurate or nearly most accurate alignment in all species and genomic location categories, while still providing coverage comparable to or better than that of the other alignments.

Genomic DNA is tightly packaged by histone proteins to form nucleosomes, which must be mobilized to allow regulatory proteins to bind and polymerases to replicate and transcribe DNA. These active processes can cause the histones to turn over. A study published in the May 2010 issue of Science by the Henikoff Lab describes a new method for measuring histone turnover genome-wide using a metabolic labeling approach. Termed "CATCH-IT", for Covalent Attachment of Tags to Capture Histones and Identify Turnover, this method was used to show that histones at epigenetic regulatory elements turn over much faster than a single cell cycle. This implies that histone marks do not themselves transmit epigenetic information, but rather are continually replenished during the cell cycle.

One of the best-studied transcription factors, MyoD, is a master regulator of myogenesis, the process by which precursor cells differentiate into skeletal muscle cells. Indeed, expressing this one protein in a fibroblast (skin cell) causes extensive remodeling of the cell, resulting in a facsimile of a muscle cell. In the April 2010 issue of Developmental CellWalter L. Ruzzo and collaborators at the Fred Hutchinson Cancer Research Center assayed genome-wide MyoD binding in differentiating and mature muscle cells. They used "ChIP-seq" technology -- chromatin immunoprecipitation followed by next-gen sequencing. As expected, MyoD is found near start sites of the several hundred genes that are known to be driven by this powerful regulator. Surprisingly, however, these sites comprise only a tiny fraction of the sites bound by MyoD, many thousands of which occur far from any gene. These data suggest that MyoD is unexpectedly multifunctional, initiating changes in chromatin state that result in broad reprogramming of the cell, in addition to its canonical role in activating genes immediately adjacent to some of its target sites.

Nuclear Magnetic Resonance (NMR) is a powerful method for determining protein structures in the physiologically relevant solution state. For larger proteins, however, the NMR spectrum gets extremely crowded, rendering it virtually impossible to assign the spectrum. In the February 2010 issue of Science, the Baker Lab demonstrated that sparse, backbone-only NMR data can be combined with the Rosetta protein structure prediction program to computationally determine large NMR structures up to 200 amino acids.

Hepatitis C virus is notorious for its ability to stay under the immune system radar and cause chronic and often debilitating liver disease. In the January 2010 issue of PLoS Pathogens, the Katze Lab showed how the virus disrupts the normal metabolic functioning of the liver. This was the first study to use sensitive mass spectrometry and computational methods to analyze changes in the protein and lipid profiles of liver cells during hepatitis C virus infection. The approach led to the identification of mitochondrial fatty acid enzymes as key cellular proteins targeted by hepatitis C virus. These findings raise the prospect that these enzymes may be useful as diagnostic indicators or possibly even as drug targets.

Studying genomic patterns of human population structure provides important insights into human evolutionary history and the relationship among populations, and it has significant practical implications for disease-gene mapping. In the May 2009 issue of The American Journal of Human Genetics, the Akey Lab used principal component analysis to study intra-continental population structure in humans. Their methodology was applied to a dataset of 650,000 SNPs genotyped in 944 unrelated individuals from 52 populations. They demonstrated that substantial information about population structure is contained in the lower-ranked principal components. In total, they identified 18 significant principal components, some of which distinguish individual populations. They also estimated the set of all SNPs significantly correlated with each of the most informative axes of variation. These polymorphisms, unlike ancestry-informative markers, constitute a much larger set of loci that drive genomic signatures of population structure.