A computer program for the analysis of protein complex formation.

Motivation: We needed an efficient way to explore the binding reactions leading to protein complexes of known composition and structure.

Results: A new program is described that allows the user to define a set of protein elements and to link these elements into an oligomeric 'ball-and-stick' assembly in a graphical interface. Once the structure of the oligomer has been defined, the program then employs a novel algorithm to deduce the binding reactions and intermediate complexes needed to make the oligomer from its starting protein components.

Factors affecting the performance of simulated large herringbone and parallel milking parlors.

A simulation model of double-16 and double-20 herringbone and parallel milking parlors and double-32 and double-40 parallel milking parlors was used to examine the effects of size, design, operating characteristics of the milking system, management strategies, and milk yield on parlor performance. Analysis of factorial experiments indicated that smaller parlors were more efficient. Turns per hour and milk per stall per hour for double-16, -20, -32, and -40 parallel parlors were 5.

A network simulation model of large herringbone and parallel milking parlors.

A network simulation model of herringbone and parallel milking parlors was built. Parlor performance was predicted based on the number of cows milked per hour and the amount of milk harvested per shift. Modeled parlors operated using a task-oriented milking routine.

Fathers of children with disabilities comment on health services.

Aim: A study to investigate the experiences of fathers of children with disabilities generated comments about hospital-based services received around the time of diagnosis.

Methods: Fifteen fathers were interviewed in-depth using an inductive qualitative methodology. Interview transcripts were subjected to computer-assisted analysis in order to identify patterns, themes and categories.

Implementing a directly observed therapy program in an urban community hospital.

St. Clare's Health and Hospital Center has implemented a directly observed therapy (DOT) program for a challenging urban population of largely HIV+ patients in response to a need for the prevention of the spread of multidrug-resistant tuberculosis in the population. Identified treatment barriers are needs of patient subgroups within the population.

The dynamics of growing axons. Membrane biophysics.

Experiments with laser optical tweezers throw light on the old question of where membrane is added in a growing nerve axon.

Computer analysis of the binding reactions leading to a transmembrane receptor-linked multiprotein complex involved in bacterial chemotaxis.

The chemotactic response of bacteria is mediated by complexes containing two molecules each of a transmembrane receptor and the intracellular signaling proteins CheA and CheW. Mutants in which one or the other of the proteins of this complex are absent, inactive, or expressed at elevated amounts show altered chemotactic behavior and the phenotypes are difficult to interpret for some overexpression mutants. We have examined the possibility that these unexpected phenotypes might arise from the binding steps that lead to active complex formation.

Protein molecules as computational elements in living cells.

Many proteins in living cells appear to have as their primary function the transfer and processing of information, rather than the chemical transformation of metabolic intermediates or the building of cellular structures. Such proteins are functionally linked through allosteric or other mechanisms into biochemical 'circuits' that perform a variety of simple computational tasks including amplification, integration and information storage.

Changes to alveolar macrophage phenotype in HIV infected individuals with normal CD4 counts and no respiratory disease.

Background: It has previously been shown that HIV infected individuals with pneumonitis have identifiable abnormalities in alveolar macrophages obtained by bronchoalveolar lavage (BAL). In particular, alterations in the expression of alveolar macrophage surface antigens associated with macrophage function have been reported. To determine whether these changes reflect HIV infection or the respiratory episode itself, a population of HIV infected patients with no respiratory disease was studied.

Effectiveness of short-term cooling and vitamin E for alleviation of infertility induced by heat stress in dairy cows.

Four experiments were performed to determine whether cooling cows during final maturation of oocytes and early embryonic development or injection of vitamin E at AI prevented adverse effects of heat stress on pregnancy rates in lactating Holstein dairy cows. In Experiment 1, cows were placed in a cooling facility containing sprinklers and forced ventilation or received shade only from 2 to 3 d before until 5 to 6 d after breeding. Although cooling had no effect on detection of estrus, pregnancy rates were increased slightly for cooled cows (8 of 50 cows; 16.

Rapid numerical integration algorithm for finding the equilibrium state of a system of coupled binding reactions.

We have adapted a simple method of numerical integration to predict the equilibrium state of a population of components undergoing reversible association according to the Law of Mass Action. Its particular application is to populations of protein molecules in aqueous solution. The method is based on Euler integration but employs an adaptive step size: the time increment being reduced if it would make the concentration of any component negative and increased while the concentration of any component changes at greater than a specified rate.

Computer simulated evolution of a network of cell-signaling molecules.

We have trained a computer model of a simple cell-signaling pathway to give specified responses to a pulse of an extracellular ligand. The pathway consists of two initially identical membrane receptors, each of which relays the concentration of the ligand to the level of phosphorylation of an intracellular molecule. Application of random "mutational" changes to the rate constants of the pathway, followed by selection in favor of certain outputs, generates a variety of wave forms and dose-response curves.

Measuring intramuscular fat in beef with ultrasonic frequency analysis.

Frequency analysis of Fourier spectra from ultrasonic signals was used for predicting intramuscular fat content of beef tissue. The most significant parameter in the frequency domain for predicting intramuscular fat concentration in beef was the number of local maxima. It represents the discontinuity of the Fourier spectrum caused by inhomogeneous fat concentrations in the longissimus muscle, which had the correlation coefficient .

An ultrasonic attenuation parameter for investigating the holding power of non-threaded fixation pins in canine femur (in vitro).

External skeletal fixation (ESF) is a widely used method of fracture treatment but often produces medical complications in the patient. The most serious complication, pin loosening, may lead to pain, poor limb usage, pin tract infection, fracture instability and non-union. Studies of pin loosening are based primarily on pin extraction force measurements, which are destructive in nature.

Comparison of hexamethyldisilazane (HMDS), Peldri II, and critical-point drying methods for scanning electron microscopy of biological specimens.

Three different drying methods, critical-point drying (CPD), Peldri II, and hexamethyldisilazane (HMDS), were compared using representative animal (rat kidney, trachea, duodenum, lung, and red blood cells) and plant (leaves from ten species of monocotyledons and dicotyledons) specimens. All three drying methods produced identical results with animal specimens. Plant specimens showed signs of shrinkage regardless of which drying method was employed.

Ultrastructural immunolocalization of type-VI collagen and chondroitin sulphate in ligament.

Immunological methods were used to determine the identity of the major components comprising a network of electron-dense seams (described by the authors in a previous work) within the extracellular matrix of medial collateral ligament (MCL) from humans and rabbits. Tissue obtained from MCL midsubstance was subjected to pre-embedding labelling with colloidal gold at the electron microscopic level with monoclonal antibodies (MAbs) against type-VI collagen and chondroitin sulphate (CS), before and after digestion with chondroitinase ABC and testicular hyaluronidase. Tissue labelled with anti-type-VI MAbs showed gold conjugates attached to the microfilamentous component of the seams both before and after enzyme digestion, which confirmed the identity of the beaded microfilaments as type-VI collagen.

Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis.

We have developed a computer program that simulates the intracellular reactions mediating the rapid (nonadaptive) chemotactic response of Escherichia coli bacteria to the attractant aspartate and the repellent Ni2+ ions. The model is built from modular units representing the molecular components involved, which are each assigned a known value of intracellular concentration and enzymatic rate constant wherever possible. The components are linked into a network of coupled biochemical reactions based on a compilation of widely accepted mechanisms but incorporating several novel features.

Antiretroviral treatment reverses HIV-induced reduction in the expression of surface antigens on alveolar macrophages in AIDS patients.

MoAbs and immunoperoxidase methods were used to identify antigen-presenting and phagocytic cells and to assess expression of HLA-DR molecules on cells obtained by bronchoalveolar lavage (BAL) from 33 AIDS patients and nine normal volunteers. In 17 patients, not receiving antiretroviral therapy, the expression of HLA-DR molecules (MoAb RFDR1) as well as the percentages of cells expressing RFD1 marker for antigen-presenting cells and RFD7 marker for mature phagocytes were significantly reduced. However, in BAL obtained after commencing treatment with zidovudine (AZT) in 21 patients or with 2',3'-dideoxyinosine (DDI) in five patients, the expression of the markers studied was found to have returned to levels of expression seen in normal lavages.

Low response of BALB/c macrophages to priming and activating signals.

Trehalose dimycolate (TDM), a mycobacterial glycolipid, is a powerful macrophage-priming agent. However, its efficiency seems limited in the case of BALB/c mice. Peritoneal macrophages harvested from TDM-treated BALB/c mice did not control BCG growth in vitro as efficiently as similar macrophages from two other mouse strains, (B6 x D2)F1 and C57BL/6, which are respectively Bcgr and Bcgs.

Actin depolymerizing factor is a component of slow axonal transport.

We examined the low molecular weight proteins transported with actin in the chicken sciatic nerve after injection of [35S]methionine into the lumbar spinal cord. A prominent component of slow axonal transport with apparent molecular mass 19 kDa comigrated on two-dimensional gels with chicken actin depolymerizing factor (ADF), previously shown to be a major actin-binding protein in brain. There was comparatively little radioactivity associated with the actin monomer sequestering proteins, profilin or cofilin, and examination of the rapid component of axonal transport failed to reveal appreciable quantities of actin, ADF, profilin, or cofilin.

Alveolar macrophage populations are distorted in immunocompromised patients with pneumonitis.

Alveolar macrophages (AM) were obtained by bronchoalveolar lavage (BAL) from patients presenting with pneumonitis: 30 human immunodeficiency virus (HIV)-infected individuals and 12 transplant recipients. Nine normal volunteers acted as controls. The cells were washed and cytospins prepared.

Collagen fibril diameters in the healing adult rabbit medial collateral ligament.

This study was carried out to test the hypothesis that improvements in ligament scar mechanical behavior during healing may be related, in part, to increases in collagen fibril diameters. Forty-eight adult female New Zealand White rabbits had standardized midsubstance gap injuries created in their right medial collateral ligaments (MCLs) and were allowed normal cage activity until sacrifice in groups of 12 at 3, 6, 14 or 40 weeks post-injury. Eight animals in each group had both MCLs tested biomechanically while 4 animals had transmission EM investigation of midsubstance collagen fibril diameters by a standardized protocol.

A new phloroglucinol derivative from Hypericum calycinum with antifungal and in vitro antimalarial activity.

The new phloroglucinol derivative 1 has been isolated from the light petroleum ether extract of the aerial parts of Hypericum calycinum. Its structure has been established by means of 1H- and 13C-NMR spectroscopy and by nOe, MHQC, and HMBC experiments on its monomethyl ether derivative 3. Compound 1 was fungicidal against Cladosporium cucumerinum in a TLC bioassay.

Radiation dose rates from paediatric patients undergoing 99Tcm investigations.

Infants or children undergoing nuclear medicine investigations may subsequently come into close contact with nurses or parents responsible for their care. In order to estimate the radiation dose to these individuals, and to formulate appropriate recommendations, dose rates were measured at distances of 0.1, 0.