Variation in genomic alu repeat density as a basis for rapid construction of low resolution physical maps of human chromosomes

Human DNA restriction fragments containing high numbers of Alu repeat sequences can be preferentially detected in the presence of other human DNA restriction fragments in DNA from human:rodent somatic cell hybrids when the DNA is fragmented with enzymes that cleave mammalian DNA infrequently. This ability to lower the observed human DNA complexity allowed us to develop an approach to order rapidly somatic hybrid cell lines retaining overlapping human genomic domains. The ordering process also generates a relative physical map of the human fragments detected with Alu probe DNA. This process can generate physical mapping information for human genomic domains as large as an entire chromosome (100,000 kb). The strategy is demonstrated by ordering Alu-detected NotI fragments in a panel of mouse:human hybrid cells that span the entire long arm of human chromosome 17.by L. Manuelidis     

Effects of changing heart rate on electrophysiological and hemodynamic function in the dog

Cardiovascular parameters were measured in dogs after RR interval was changed from 0.25 s to 1.2 s with atropine and graded doses of zatebradine, an I(f)-channel blocker. Left ventricular (LV) pre-ejection period (PEP), systemic vascular resistance, tau (an estimate of myocardial stiffness), PQ, QTc, dLVP/dt(max) and dLVP/dt(min), aortic pressure, and right atrial pressure did not change when each parameter was plotted against RR interval (r(2)'s < or = 0.5). LV end-diastolic pressure, stroke volume index, LV ejection time (ET), and QT all increased either linearly or curvilinearly as RR interval prolonged. Cardiac output index and PEP/ET decreased curvilinearly. When heart rate (HR) was fixed by pacing, and graded doses of zatebradine were given, changes in cardiovascular function were minimal. Thus zatebradine affects cardiovascular function principally by changing HR and not by affecting function directly. This study provides data on the effects of changing HR, alone, on cardiovascular parameters measured frequently during pharmacological and toxicological studies. It should prove useful when physiological variables, including HR, change, and there is need to know what change in HR, alone, contributes.     

Statistical approach for the estimation of daily physical activity levels using the probability density function of heart rate

An investigation was undertaken into the statistical properties of heart rate during daily physical activity. The probability density function of the heart rate was estimated using the Gram-Charlier series. In addition, the probability density was separated into two Gaussian distributions: relatively low and relatively high heart rates. The former appeared to correspond to the metabolic rate associated with basic daily living and the latter appeared to be associated with more active physical activity of the type necessary to sustain or elevate the level of physical fitness. The higher heart rate distribution of five subjects occupied 8.72 ± 2.15% of a period of waking. The validity of the statistical approach was confirmed with fractional estimation error of 1.22 ± 0.62%.     

Assembling global maps of cellular function through integrative analysis of physical and genetic networks

To take full advantage of high-throughput genetic and physical interaction mapping projects, the raw interactions must first be assembled into models of cell structure and function. PanGIA (for physical and genetic interaction alignment) is a plug-in for the bioinformatics platform Cytoscape, designed to integrate physical and genetic interactions into hierarchical module maps. PanGIA identifies 'modules' as sets of proteins whose physical and genetic interaction data matches that of known protein complexes. Higher-order functional cooperativity and redundancy is identified by enrichment for genetic interactions across modules. This protocol begins with importing interaction networks into Cytoscape, followed by filtering and basic network visualization. Next, PanGIA is used to infer a set of modules and their functional inter-relationships. This module map is visualized in a number of intuitive ways, and modules are tested for functional enrichment and overlap with known complexes. The full protocol can be completed between 10 and 30 min, depending on the size of the data set being analyzed.     

Towards the physical basis of how intrinsic disorder mediates protein function

Intrinsically disordered proteins (IDPs) are an important class of functional proteins that is highly prevalent in biology and has broad association with human diseases. In contrast to structured proteins, free IDPs exist as heterogeneous and dynamical conformational ensembles under physiological conditions. Many concepts have been discussed on how such intrinsic disorder may provide crucial functional advantages, particularly in cellular signaling and regulation. Establishing the physical basis of these proposed phenomena requires not only detailed characterization of the disordered conformational ensembles, but also mechanistic understanding of the roles of various ensemble properties in IDP interaction and regulation. Here, we review the experimental and computational approaches that may be integrated to address many important challenges of establishing a "structural" basis of IDP function, and discuss some of the key emerging ideas on how the conformational ensembles of IDPs may mediate function, especially in coupled binding and folding interactions.     

Cryo-EM density maps adjustment for subtraction,consensus and sharpening

Electron cryomicroscopy (cryo-EM) has emerged as a powerful structural biology instrument to solve near-atomic three-dimensional structures. Despite the fast growth in the number of density maps generated from cryo-EM data, comparison tools among these reconstructions are still lacking. Current proposals to compare cryo-EM data derived volumes perform map subtraction based on adjustment of each volume grey level to the same scale. We present here a more sophisticated way of adjusting the volumes before comparing, which implies adjustment of grey level scale and spectrum energy, but keeping phases intact inside a mask and imposing the results to be strictly positive. The adjustment that we propose leaves the volumes in the same numeric frame, allowing to perform operations among the adjusted volumes in a more reliable way. This adjustment can be a preliminary step for several applications such as comparison through subtraction, map sharpening, or combination of volumes through a consensus that selects the best resolved parts of each input map. Our development might also be used as a sharpening method using an atomic model as a reference. We illustrate the applicability of this algorithm with the reconstructions derived of several experimental examples. This algorithm is implemented in Xmipp software package and its applications are user-friendly accessible through the cryo-EM image processing framework Scipion.     

Effects of hippotherapy on brain function,BDNF level,and physical fitness in children with ADHD

[Purpose]

The purpose of this study was to examine the effects of hippotherapy on brain function and levels of blood-derived neurotrophic factor (BDNF) in children with attention deficit and/or hyperactivity disorder (ADHD).

[Methods]

The hippotherapy group (HRG) included twenty children with ADHD and the control group (CG) included 19 children. All participants’ physical fitness, fMRI brain scans, and blood BDNF levels were measured at baseline and after 32 weeks of participating in hippotherapy.

[Results]

After 32 weeks of participating in hippotherapy, the body fat of the HRG was significantly decreased (-1.12 ± 4.20%) and the body fat of the CG was increased (2.38 ± 6.35%) (p=0.049). There was no significant difference of physical fitness in both groups (p>0.05). Although there was a higher decrease in the activated insular area in the HRG (-1.59 ± 0.99) than in the CG (-1.14 ± 1.41), there was no significant difference between the two groups (p>0.05) Also, there was a higher increase in the activated cerebellum area in the HRG (1.97 ± 1.45) than in the CG (1.92 ± 1.81). However, there was no significant difference between the two groups (p>0.05). BDNF levels showed an increased tendency in the HRG (166.29 ± 277.52pg) compared to the CG (21.13 ± 686.33pg); otherwise, there was not any significant difference in these blood levels between the two groups (p>0.05). It can be assumed that big individual differences in the level of ADHD in the study participants might not cause any significant results, although there might be positive changes in the brain function of children with ADHD.

[Conclusion]

Therefore, this study suggests that hippotherapy training would need to be modified and developed to increase the efficacy of hippotherapy in children with ADHD.     

Map2mod--a server for evaluation of crystallographic models and their agreement with electron density maps

Here we report on recent developments of the map2mod server. It has been designed for validation of protein models created by X-ray data interpretation. It can also be used during the refinement process since it is able to indicate problem regions in the model. Apart from evaluation of model quality, it has an option to remove atoms of side chains, which are not consistent with the maps as well as improperly placed water molecules. There are two additional options: checking the B-factors of atoms in the provided model and comparison of R and R(free) values obtained as the result of refinement with the averages characteristic for the data resolution shell.     

Nonparametric density estimation and regression achieved with topographic maps maximizing the information-theoretic entropy of their outputs

We introduce an unsupervised competitive learning rule, called the extended Maximum Entropy learning Rule (eMER), for topographic map formation. Unlike Kohonen's Self-Organizing Map (SOM) algorithm, the presence of a neighborhood function is not a prerequisite for achieving topology-preserving mappings, but instead it is intended: (1) to speed up the learning process and (2) to perform nonparametric regression. We show that, when the neighborhood function vanishes, the neural weigh t density at convergence approaches a linear function of the input density so that the map can be regarded as a nonparametric model of the input density. We apply eMER to density estimation and compare its performance with that of the SOM algorithm and the variable kernel method. Finally, we apply the ‘batch’ version of eMER to nonparametric projection pursuit regression and compare its performance with that of back-propagation learning, projection pursuit learning, constrained topolog ical mapping, and the Heskes and Kappen approach. Received: 12 August 1996 / Accepted in revised form: 9 April 1997     

Fast 3D motif search of EM density maps using a locally normalized cross-correlation function

Three-dimensional motif search is becoming increasingly important both in the search for molecular signatures within a tomographic reconstruction, at low resolution, and in the search for atomic structures within high-resolution cryo-EM maps of macromolecular complexes. The present work describes the implementation of a fast local correlation algorithm suitable for template matching in the SPIDER environment. Two examples are given, one in each of the areas of application: (i). within a 7.8A single-particle reconstruction of the Escherichia coli ribosome, four proteins and one RNA structure were located with high accuracy; (ii). within a cryo-tomogram of sarcoplasmic reticulum vesicles, ryanodine receptors were located in positions that agreed with expert knowledge.     

Glyceride lipases in nerve endings of guinea-pig brain and their stimulation by noradrenaline, 5-hydroxytryptamine and adrenaline

1. Combined guinea-pig cortex and cerebellum was shown to contain triglyceride lipase, diglyceride lipase and monoglyceride lipase, which were assayed by the release of [1-(14)C]palmitate from [1-(14)C]palmitoylglycerol esters. Triglyceride lipase and diglyceride lipase were found in all particulate fractions. 2. With osmotically ruptured synaptosomes the rates of release of palmitate from glyceryl tripalmitate and glyceryl dipalmitate were 7-25mumol/h per g of protein and 0.18-0.69mmol/h per g of protein respectively. The logarithm of the rate of hydrolysis of glyceryl monopalmitate increased linearly with the logarithm of protein concentration. The pH optima of triglyceride lipase and diglyceride lipase were between 7 and 8. The pH optimum for monoglyceride lipase was approx. 8. 3. Triglyceride lipase and diglyceride lipase of osmotically ruptured synaptosomes were stimulated by noradrenaline, 5-hydroxytryptamine and adrenaline. Triglyceride lipase of isolated synaptic membranes was stimulated by 0.01-1mm-noradrenaline. Aging of membranes at 0 degrees C decreased activity, which could still be stimulated by noradrenaline. Diglyceride lipase of isolated membranes was stimulated by 1mum-1mm-noradrenaline. The activity of triglyceride lipase in isolated synaptic vesicles was diminished by 1mm-5-hydroxytryptamine.     

Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis

The methods of continuum electrostatics are used to calculate the binding free energies of a set of protein-protein complexes including experimentally determined structures as well as other orientations generated by a fast docking algorithm. In the native structures, charged groups that are deeply buried were often found to favor complex formation (relative to isosteric nonpolar groups), whereas in nonnative complexes generated by a geometric docking algorithm, they were equally likely to be stabilizing as destabilizing. These observations were used to design a new filter for screening docked conformations that was applied, in conjunction with a number of geometric filters that assess shape complementarity, to 15 antibody-antigen complexes and 14 enzyme-inhibitor complexes. For the bound docking problem, which is the major focus of this paper, native and near-native solutions were ranked first or second in all but two enzyme-inhibitor complexes. Less success was encountered for antibody-antigen complexes, but in all cases studied, the more complete free energy evaluation was able to identify native and near-native structures. A filter based on the enrichment of tyrosines and tryptophans in antibody binding sites was applied to the antibody-antigen complexes and resulted in a native and near-native solution being ranked first and second in all cases. A clear improvement over previously reported results was obtained for the unbound antibody-antigen examples as well. The algorithm and various filters used in this work are quite efficient and are able to reduce the number of plausible docking orientations to a size small enough so that a final more complete free energy evaluation on the reduced set becomes computationally feasible.     

Differences in electrophysiological properties of motor and sensory nerve fibres

Differences in the electrophysiological properties of amphibian motor and sensory nerve fibres are reviewed. It is concluded that the differences are mainly due to an altered K-conduction system which suggests the presence of different K channels in the two types of nerve fibres.     

A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps

For many species, multiple maps are available, often constructed independently by different research groups using different sets of markers and different source material. Integration of these maps provides a higher density of markers and greater genome coverage than is possible using a single study. In this article, we describe a novel approach to comparing and integrating maps by using abstract graphs. A map is modeled as a directed graph in which nodes represent mapped markers and edges define the order of adjacent markers. Independently constructed graphs representing corresponding maps from different studies are merged on the basis of their common loci. Absence of a path between two nodes indicates that their order is undetermined. A cycle indicates inconsistency among the mapping studies with regard to the order of the loci involved. The integrated graph thus produced represents a complete picture of all of the mapping studies that comprise it, including all of the ambiguities and inconsistencies among them. The objective of this representation is to guide additional research aimed at interpreting these ambiguities and inconsistencies in locus order rather than presenting a "consensus order" that ignores these problems.