Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

The hybridization kinetics for a series of designed 25mer probe�target pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, respectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments. Specifically, addition of three intramolecular base pairs in the probe and target structure slow hybridization by a factor of two. For individual strands containing four or more intramolecular base pairs, hybridization cannot be described by a traditional two-state model in solution-phase nor on the surface. Surface hybridization rates are also 20- to 40-fold slower than solution-phase rates for identical sequences and conditions. These quantitative findings may have implications for the design of better biosensors, particularly those using probes with deliberate secondary structure.

BU Computer Science 1998 Proxy Trace: Release Notes

In a recent paper (Changes in Web Client Access Patterns: Characteristics and Caching Implications by Barford, Bestavros, Bradley, and Crovella) we performed a variety of analyses upon user traces collected in the Boston University Computer Science department in 1995 and 1998. A sanitized version of the 1995 trace has been publicly available for some time; the 1998 trace has now been sanitized, and is available from: http://www.cs.bu.edu/techreports/1999-011-usertrace-98.gz ftp://ftp.cs.bu.edu/techreports/1999-011-usertrace-98.gz This memo discusses the format of this public version of the log, and includes additional discussion of how the data was collected, how the log was sanitized, what this log is and is not useful for, and areas of potential future research interest.

Neuropeptide Co-Release with Gaba May Explain Functional Non-Monotonic Uncertainty Responses in Dopamine Neurons

Co-release of the inhibitory neurotransmitter GABA and the neuropeptide substance-P (SP) from single axons is a conspicuous feature of the basal ganglia, yet its computational role, if any, has not been resolved. In a new learning model, co-release of GABA and SP from axons of striatal projection neurons emerges as a highly efficient way to compute the uncertainty responses that are exhibited by dopamine (DA) neurons when animals adapt to probabilistic contingencies between rewards and the stimuli that predict their delivery. Such uncertainty-related dopamine release appears to be an adaptive phenotype, because it promotes behavioral switching at opportune times. Understanding the computational linkages between SP and DA in the basal ganglia is important, because Huntington's disease is characterized by massive SP depletion, whereas Parkinson's disease is characterized by massive DA depletion.