Analysis of temporal structure in spike trains of visual cortical area MT

The temporal structure of neuronal spike trains in the visual cortex can provide detailed information about the stimulus and about the neuronal implementation of visual processing. Spike trains recorded from the macaque motion area MT in previous studies (Newsome et al., 1989a; Britten et al., 1992; Zohary et al., 1994) are analyzed here in the context of the dynamic random dot stimulus which was used to evoke them. If the stimulus is incoherent, the spike trains can be highly modulated and precisely locked in time to the stimulus. In contrast, the coherent motion stimulus creates little or no temporal modulation and allows us to study patterns in the spike train that may be intrinsic to the cortical circuitry in area MT. Long gaps in the spike train evoked by the preferred direction motion stimulus are found, and they appear to be symmetrical to bursts in the response to the anti-preferred direction of motion. A novel cross-correlation technique is used to establish that the gaps are correlated between pairs of neurons. Temporal modulation is also found in psychophysical experiments using a modified stimulus. A model is made that can account for the temporal modulation in terms of the computational theory of biological image motion processing. A frequency domain analysis of the stimulus reveals that it contains a repeated power spectrum that may account for psychophysical and electrophysiological observations.

Some neurons tend to fire bursts of action potentials while others avoid burst firing. Using numerical and analytical models of spike trains as Poisson processes with the addition of refractory periods and bursting, we are able to account for peaks in the power spectrum near 40 Hz without assuming the existence of an underlying oscillatory signal. A preliminary examination of the local field potential reveals that stimulus-locked oscillation appears briefly at the beginning of the trial.

Biophysics of V(D)J recombination and Genome Packaging: In singulo studies on RAG, HMGB1, and TFAM

The recombination-activating gene products, RAG1 and RAG2, initiate V(D)J recombination during lymphocyte development by cleaving DNA adjacent to conserved recombination signal sequences (RSSs). The reaction involves DNA binding, synapsis, and cleavage at two RSSs located on the same DNA molecule and results in the assembly of antigen receptor genes. Since their discovery full-length, RAG1 and RAG2 have been difficult to purify, and core derivatives are shown to be most active when purified from adherent 293-T cells. However, the protein yield from adherent 293-T cells is limited. Here we develop a human suspension cell purification and change the expression vector to boost RAG production 6-fold. We use these purified RAG proteins to investigate V(D)J recombination on a mechanistic single molecule level. As a result, we are able to measure the binding statistics (dwell times and binding energies) of the initial RAG binding events with or without its co-factor high mobility group box protein 1 (HMGB1), and to characterize synapse formation at the single-molecule level yielding insights into the distribution of dwell times in the paired complex and the propensity for cleavage upon forming the synapse. We then go on to investigate HMGB1 further by measuring it compact single DNA molecules. We observed concentration dependent DNA compaction, differential DNA compaction depending on the divalent cation type, and found that at a particular HMGB1 concentration the percentage of DNA compacted is conserved across DNA lengths. Lastly, we investigate another HMGB protein called TFAM, which is essential for packaging the mitochondrial genome. We present crystal structures of TFAM bound to the heavy strand promoter 1 (HSP1) and to nonspecific DNA. We show TFAM dimerization is dispensable for DNA bending and transcriptional activation, but is required for mtDNA compaction. We propose that TFAM dimerization enhances mtDNA compaction by promoting looping of mtDNA.

The Mechanical Genome in Regulation and Infection

Biological information storage and retrieval is a dynamic process that requires the genome to undergo dramatic structural rearrangements. Recent advances in single-molecule techniques have allowed precise quantification of the nano-mechanical properties of DNA [1, 2], and direct in vivo observation of molecules in action [3]. In this work, we will examine elasticity in protein-mediated DNA looping, whose structural rearrangement is essential for transcriptional regulation in both prokaryotes and eukaryotes. We will look at hydrodynamics in the process of viral DNA ejection, which mediates information transfer and exchange and has prominent implications in evolution. As in the case of Kepler's laws of planetary motion leading to Newton's gravitational theory, and the allometric scaling laws in biology revealing the organizing principles of complex networks [4], experimental data collapse in these biological phenomena has guided much of our studies and urged us to find the underlying physical principles.