Helicase delivery and activation by DnaA and TrfA proteins during the initiation of replication of the broad host range plasmid RK2

Specific binding of the plasmid-encoded protein, TrfA, and the Escherichia coli DnaA protein to the origin region (oriV) is required for the initiation of replication of the broad host range plasmid RK2. It has been shown that the DnaA protein which binds to DnaA boxes upstream of the TrfA-binding sites (iterons) cannot by itself form an open complex, but it enhances the formation of the open complex by TrfA (Konieczny, I., Doran, K. S., Helinski, D. R., Blasina, A. (1997) J. Biol. Chem. 272, 20173). In this study an in vitro replication system is reconstituted from purified TrfA protein and E. coli proteins. With this system, a specific interaction between the DnaA and DnaB proteins is required for delivery of the helicase to the RK2 origin region. Although the DnaA protein directs the DnaB-DnaC complex to the plasmid replication origin, it cannot by itself activate the helicase. Both DnaA and TrfA proteins are required for DnaB-induced template unwinding. We propose that specific changes in the nucleoprotein structure mediated by TrfA result in a repositioning of the DnaB helicase within the open origin region and an activation of the DnaB protein for template unwinding.     

The Transmogrifier-2: a 1 million gate rapid-prototyping system

This paper describes the Transmogrifier-2 (TM-2), a second-generation multifield programmable gate array (FPGA) rapid-prototyping system. The largest version of the system will comprise 16 boards that each contain two Altera 10K50 FPGA's, four I-Cube interconnect chips, and up to 8 Mbytes of memory. The inter-FPGA routing architecture of the TM-2 uses a novel interconnect structure, a nonuniform partial crossbar, that provides a constant delay between any two FPGA's in the system. The TM-2 architecture is modular and scalable, meaning that systems of various sizes can be constructed from copies of the same board, while maintaining routability and the constant delay feature. Other features include a system-level programmable clock that allows single-cycle access to off-chip memory, and programmable clock waveforms with edge resolution of 10 ns. The first Transmogrifier-2 boards have been manufactured and are functional. They have recently been used successfully in some simple graphics acceleration applications     

HoxA is a transcriptional regulator for expression of the hup structural genes in free-living Bradyrhizobium japonicum

A chromosomally integrated Bradyrhizobium japonicum hoxA mutant is unable to oxidize hydrogen in free-living conditions. Derepressing conditions that induce hydrogenase activity in free-living, wild-type B. japonicum cells cannot induce expression of the hydrogenase structural genes in the hoxA mutant. The DNA-binding capacity of HoxA at the hup promoter region was studied by means of gel retardation. Both heterotrophically growing cells and cells induced to express hydrogenase activity contain a protein that specifically binds to the hup promoter region. Crude protein extracts isolated from a B. japonicum hoxA mutant do not contain this binding compound. The HoxA protein was overexpressed in E. coli and isolated in the form of a maltose-binding protein (MBP)-HoxA fusion. The MBP-HoxA hybrid protein specifically bound to a 50 bp region of the hupSL promoter known to be important for regulation of hupSL expression.     

Increased expression of peripheral benzodiazepine receptors in the facial nucleus following motor neuron axotomy

Peripheral benzodiazepine receptors (PBRs) are expressed in a variety of tissues but are normally found at low levels in the brain. Following various types of nerve injury, a reactive gliosis results that exhibits a high expression of this receptor. To further characterize the expression of PBRs following neuronal injury, we evaluated PBR expression in the facial nucleus following facial nerve axotomy (FNA). Injury to a peripheral nerve results in a complex series of metabolic and morphological changes around the injured neuron. Transections of the facial nerve results in a rapid activation of both astrocytes and microglia around axotomized motor neurons. FNA resulted in an increase in the staining for both astrocytes (glial fibrillary acidic protein) and activated microglia (OX42). There was also a reduction in synaptic contacts with the motor nucleus as evidenced by reduced staining for the synaptic marker, synaptophysin. In sections labeled with [3H]-PK11195, the subsequent autoradiograms displayed marked increases in the labeling for PBRs. This increase was observed at 5, 7 and 10 days after nerve transection. The increase was primarily in the level of expression (Bmax), with no change in the affinity of the ligand (Kd). The increase in PBR expression after FNA supports the hypothesis that PBRs can be used as a sensitive marker for CNS injury.     

Nitric oxide synthase-immunoreactive neurons in human and porcine respiratory tract

The presence of nitric oxide synthase (NO-synthase), the enzyme responsible for the production of nitric oxide (NO) from L-arginine, is shown immunocytochemically in the intrinsic neurons of the human and porcine respiratory tract. NO-synthase immunoreactivity is demonstrated in a subpopulation of neurons of the microganglia present in the wall of the extra- and intrapulmonary bronchi as well as in the hilar region of the lung in relation to blood vessels. The immunostaining was also found in some nerve fibers of the respiratory nervous system. Human and porcine lung gave similar results. The possible involvement of NO in the nonadrenergic noncholinergic (NANC) nervous regulation of the lung is discussed.     

Subspace-based signal analysis using singular value decomposition

A unified approach is presented to the related problems of recovering signal parameters from noisy observations and identifying linear system model parameters from observed input/output signals, both using singular value decomposition (SVD) techniques. Both known and new SVD-based identification methods are classified in a subspace-oriented scheme. The SVD of a matrix constructed from the observed signal data provides the key step in a robust discrimination between desired signals and disturbing signals in terms of signal and noise subspaces. The methods that are presented are distinguished by the way in which the subspaces are determined and how the signal or system model parameters are extracted from these subspaces. Typical examples, such as the direction-of-arrival problem and system identification from input/output measurements, are elaborated upon, and some extensions to time-varying systems are given     

Nanocell logic gates for molecular computing

Molecular electronics seeks to build electrical devices to implement computation - logic and memory - using individual or small collections of molecules. These devices have the potential to reduce device size and fabrication costs, by several orders of magnitude, relative to conventional CMOS. However, the construction of a practical molecular computer will require the molecular switches and their related interconnect technologies to behave as large-scale diverse logic, with input/output wires scaled to molecular dimensions. It is unclear whether it is necessary or even. possible to control the precise regular placement and interconnection of these diminutive molecular systems. This paper describes genetic algorithm-based simulations of molecular device structures in a nanocell where placement and connectivity of the internal molecular switches are not specifically directed and the internal topology is generally disordered. With some simplifying assumptions, these results show that it is possible to use easily fabricated nanocells as logic devices by setting the internal molecular switch states after the topological molecular assembly is complete. Simulated logic devices include an inverter, a NAND gate, an XOR gate and a 1-bit adder. Issues of defect and fault tolerance are addressed.     

The Generic Bilinear Calibration-Estimation Problem

We identify a very general, recurring pattern in a number of well known problems in biological and machine vision. Many problems are of a peculiar double-sided nature: One attempts to estimate certain properties of the environment using a certain type of equipment and simultaneously one attempts to calibrate the same equipment on the structure of the environment. At first sight this appears the kind of the chicken and the egg problem that might well prove to be insoluble. However, due to basic constraints that universally apply (e.g., the world is only three-dimensional), a solution—up to a certain class of ambiguity transformations—often exists. The more complicated the problem is, the less important the remaining ambiguity will be, at least in a relative sense. Many well known problems are special in that they can be cast in bilinear form, sometimes after transformation or the introduction of dummy variables. Instances include photometric stereo, photometric estimations (e.g., of lightness), local (differential) image operators, a variety of photogrammetric problems, etc. It turns out that many of these problems—and together these make up a large fraction of the generic problems in machine vision today—can be cast in a simple universal framework. This framework enables one to handle arbitrarily large (that is, not minimal, consistent configurations), noisy (thus inconsistent) date sets automatically. The level at which prior information (either of a deterministic or a statistical nature) is used (assumptions such as constant albedo, rigidity, uniform distributions, etc.) is clearly separated as an additional, typically nonlinear, stage.     

Acute aortic outflow obstruction by diminution of bulboventricular foramen size after volume unloading in univentricular physiology

A young child with [S, L, L] segmental anatomy, double-inlet left ventricle, transposition of the great arteries, rudimentary right ventricle, and mildly restrictive bulboventricular foramen is reported, in whom intraoperative temporary snaring of the modified Blalock-Taussig shunt resulted in instantaneous and dramatic volume contraction of the left ventricle, decrease in bulboventricular foramen size, and increase of the gradient across the latter from 10 mm Hg preoperatively to 50 mm Hg. A modified Damus-Stansel-Kaye procedure using autogenous aortic tissue resulted in unobstructed aortic outflow; in addition, a bidirectional cavopulmonary shunt was performed. The importance of early relief of actual or potential aortic outflow obstruction in hearts with restrictive bulboventricular foramen is emphasized.     

The entry of antiviral and antiretroviral drugs into the central nervous system

The ability of antiviral and antiretroviral drugs to enter the brain is a critical issue in the treatment of many viral brain diseases, including HIV-related neurologic disease. Much of the literature concerning nucleoside analog entry into the nervous system focuses on drug levels in the cerebrospinal fluid (CSF), equating these with drug levels in the brain extracellular fluid (ECF) as though the two compartments intermix freely. We review the anatomic and physiologic aspects of drug entry into CSF and into brain ECF, as well as the exchange processes between these two compartments. In most instances drug concentrations in the CSF and ECF compartments bear little relationship to one another and using CSF concentrations to extrapolate brain ECF concentrations may significantly overestimate the latter. Accepted terminology and methodology for making measurements of blood-brain barrier function are discussed. Studies of brain uptake that express results as brain:plasma ratios, or that have used microdialysis, may overestimate the amount of drug reaching the brain. Using published data, we present an estimate of the time course of Zidovudine (AZT) concentrations in brain ECF and show that brain concentrations of AZT will likely be below that necessary to inhibit HIV-1 replication when AZT is administered systemically. Antiviral nucleosides and oligonucleotides appear to have limited entry into the brain when given systemically, which may hinder therapy of viral brain diseases, while some of the protease inhibitors may enter the brain more readily. Alternative methods for increasing antiviral and antiretroviral drug delivery to brain are discussed.