Relations for lipid bilayers. Connection of electron density profiles to other structural quantities.

Three relations are derived that connect low angle diffraction/scattering results obtained from lipid bilayers to other structural quantities of interest. The first relates the area along the surface of the bilayer, the measured specific volume, and the zeroth order structure factor, F(0). The second relates the size of the trough in the center of the electron density profile, the volume of the terminal methyl groups, and the volume of the methylene groups in the fatty acid chains. The third relates the size of the headgroup electron density peak, the volume of the headgroup, and the volumes of water and hydrocarbon in the headgroup region. These relations, which are easily modified for neutron diffraction, are useful for obtaining structural quantities from electron density profiles obtained by fitting model profiles to measured low angle x-ray intensities.     

Methods for generating high-resolution structural models from electron microscope tomography data

Reconstructed volumes generated by tilt-image electron-microscope tomography offer the best spatial resolution currently available for studying cell structures in situ. Analysis is often accomplished by creating surface models that delineate grayscale contrast boundaries. Here, we introduce a specialized and convenient sequence of segmentation operations for making such models that greatly improves their reliability and spatial resolution as compared to current approaches, providing a basis for making accurate measurements. To assess the reliability of the surface models, we introduce a spatial uncertainty measurement based on grayscale gradient scale length. The model generation and measurement methods are validated by applying them to synthetic data, and their utility is demonstrated by using them to characterize macromolecular architecture of active zone material at the frog's neuromuscular junction.     

YUP.SCX: coaxing atomic models into medium resolution electron density maps

The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.     

Alternative models of organisation are needed.

Anyone considering a fundamental rethink of the role of consultants risks exposing tensions in the medical profession that have characterised the development of medical practice since the 18th century. That tense story was one of beds and money, power and domination. Rethinking the role of consultants must now take into account the relationship between consultants and their specialist colleagues and general practitioners; examine the distribution of work between consultants and junior doctors; and relate the contribution of the consultant as specialist to that of other health professionals. After half a century of a national health service characterised by equity of access to care, we urgently need to debate the roles of those who work in it and in doing so to focus primarily on the needs of patients.     

Alternative models of counseling for genetic disorders

Abstract

A sample survey was conducted of a nationwide voluntary association whose purpose is to challenge societal pressures to have children and to provide support for those choosing to remain childless. The membership was predominantly under 35 years of age and married, almost entirely Caucasian, disproportionately concentrated in the higher education and income categories, and not committed to religion. Asked to rate the importance of various reasons for their decision not to have children, members under 35 years of age most frequently cited the deleterious effect of children on personal independence, the responsibility of rearing a child, and the interference of children with the marital relationship. Two out of three members under 35 intending to have no children reported pressures to have children, with the media, friends, and coworkers (but not parents) most often named as the leading sources.     

The structural biochemistry of the superoxide dismutases

The discovery of superoxide dismutases (SODs), which convert superoxide radicals to molecular oxygen and hydrogen peroxide, has been termed the most important discovery of modern biology never to win a Nobel Prize. Here, we review the reasons this discovery has been underappreciated, as well as discuss the robust results supporting its premier biological importance and utility for current research. We highlight our understanding of SOD function gained through structural biology analyses, which reveal important hydrogen-bonding schemes and metal-binding motifs. These structural features create remarkable enzymes that promote catalysis at faster than diffusion-limited rates by using electrostatic guidance. These architectures additionally alter the redox potential of the active site metal center to a range suitable for the superoxide disproportionation reaction and protect against inhibition of catalysis by molecules such as phosphate. SOD structures may also control their enzymatic activity through product inhibition; manipulation of these product inhibition levels has the potential to generate therapeutic forms of SOD. Markedly, structural destabilization of the SOD architecture can lead to disease, as mutations in Cu,ZnSOD may result in familial amyotrophic lateral sclerosis, a relatively common, rapidly progressing and fatal neurodegenerative disorder. We describe our current understanding of how these Cu,ZnSOD mutations may lead to aggregation/fibril formation, as a detailed understanding of these mechanisms provides new avenues for the development of therapeutics against this so far untreatable neurodegenerative pathology.     

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.     

Alternative models for species replacement of pelagic fishes

It is well known that the stock abundance of a pelagic fish usually fluctuates and a species of pelagic fish which was dominant in abundance is often taken over by another species. Several alternative models for species replacement among pelagic fishes are presented and analyzed: (A) environmental fluctuation, (B) strong density-dependent reproduction rate, (C) a two-species system with phase variation (density-dependent change of life history traits), (D) a two-species competition system with environmental fluctuation, (E) cyclic advantage relationship among three competitive species, and (F) a two-prey, one-predator system. Different model requires different number of species for the occurrence of species replacement. Three criteria to test each hypothesis from qualitative properties of species replacement are proposed. Possible management policies to decrease the amplitude of stock fluctuations are discussed. As a result, if the catching effort to mackerels which is rare now is large, or if the catching effort to the sardine is still large when it begins to decline in stock abundance, fisheries may be strong destabilizing effect on the stock abundance.     

Plant models to replace classical biochemistry practicals

The object of this general article is simply to suggest alternative inexpensive and novel procedures for biochemistry laboratory demonstrators and stil     

Residual-based diagnostics for structural equation models

Summary .  Classical diagnostics for structural equation models are based on aggregate forms of the data and are ill suited for checking distributional or linearity assumptions. We extend recently developed goodness-of-fit tests for correlated data based on subject-specific residuals to structural equation models with latent variables. The proposed tests lend themselves to graphical displays and are designed to detect misspecified distributional or linearity assumptions. To complement graphical displays, test statistics are defined; the null distributions of the test statistics are approximated using computationally efficient simulation techniques. The properties of the proposed tests are examined via simulation studies. We illustrate the methods using data from a study of in utero lead exposure.     

Alternative mitochondrial electron transfer as a novel strategy for neuroprotection

Neuroprotective strategies, including free radical scavengers, ion channel modulators, and anti-inflammatory agents, have been extensively explored in the last 2 decades for the treatment of neurological diseases. Unfortunately, none of the neuroprotectants has been proved effective in clinical trails. In the current study, we demonstrated that methylene blue (MB) functions as an alternative electron carrier, which accepts electrons from NADH and transfers them to cytochrome c and bypasses complex I/III blockage. A de novo synthesized MB derivative, with the redox center disabled by N-acetylation, had no effect on mitochondrial complex activities. MB increases cellular oxygen consumption rates and reduces anaerobic glycolysis in cultured neuronal cells. MB is protective against various insults in vitro at low nanomolar concentrations. Our data indicate that MB has a unique mechanism and is fundamentally different from traditional antioxidants. We examined the effects of MB in two animal models of neurological diseases. MB dramatically attenuates behavioral, neurochemical, and neuropathological impairment in a Parkinson disease model. Rotenone caused severe dopamine depletion in the striatum, which was almost completely rescued by MB. MB rescued the effects of rotenone on mitochondrial complex I-III inhibition and free radical overproduction. Rotenone induced a severe loss of nigral dopaminergic neurons, which was dramatically attenuated by MB. In addition, MB significantly reduced cerebral ischemia reperfusion damage in a transient focal cerebral ischemia model. The present study indicates that rerouting mitochondrial electron transfer by MB or similar molecules provides a novel strategy for neuroprotection against both chronic and acute neurological diseases involving mitochondrial dysfunction.     

Cloned myogenic cells during differentiation: membrane biochemistry and fine structural observations.

Isolated membranes from clones of a permanent line of myogenic cells, L₆, were studied during three temporally consecutive stages of growth: (1) exponentially growing cells, (2) intermediate phase cells, and (3) fused cells. Membrane fractions have been isolated on a sucrose gradient and studied with respect to morphology, enzymatic activity, density, and α-bungarotoxin binding. Changes as a function of differentiation were seen both in the density of the fractions and in the specific activities of several proteins. Membranes characterized by specific enzyme markers generally sediment at higher densities when isolated from exponentially growing cells than when isolated from fused cells. The change in density is especially pronounced for the 5′ nucleotidase, TPNH-dependent cytochrome c reductase, and β-N-acetylglucosaminidase. The specific activity of adenylate cyclase increases in the intermediate phase cells and remains high in the fused cells; that of TPNH-dependent cytochrome c reductase decreases in the intermediate phase cells and remains low in the fused cells. The binding of α-bungarotoxin increases dramatically following fusion. On the other hand, there was little change, less than a factor of two, in the specific activities of a number of enzymes during growth or following fusion. In this group are hexose-6-phosphatase, acid phosphatase, Na⁺,K⁺-activated ATPase, and 5′ nucleotidase. Both our morphological and our biochemical studies suggest that in the exponentially growing cells, the ribosomes are associated largely with membranes, whereas in the fused cells, the ribosomes are largely free.     

Low density lipoprotein receptor regulation. Kinetic models

The macromolecular species distribution in a receptor-mediated endocytotic pathway was computer simulated based on kinetic data reported in the literature. In the proposed model, the rapidity with which the recycled receptor is shuttled to the cell surface is indicated by the magnitude of k-3, the shuttling constant. The magnitude of k-3 will vary with the experimental conditions, but when this value is large, the internalized receptor is shuttled back to the cell surface with a traverse time of 14 min. Under steady-state conditions, after the cells have been incubated in the presence of LDL for 5 h (M.S. Brown and J.L. Goldstein, Cell 9 (1976) 663), the time required for a receptor to traverse the entire endocytotic pathway is 52 min. Our simulation suggests that normal LDL binding in such a short-term experiment may be independent of receptor synthesis. Thus, the degradation of LDL and resultant build-up of cholesterol would have no apparent inhibitory effect on the down-regulation of receptor synthesis.     

Alternative time representation in dopamine models

Dopaminergic neuron activity has been modeled during learning and appetitive behavior, most commonly using the temporal-difference (TD) algorithm. However, a proper representation of elapsed time and of the exact task is usually required for the model to work. Most models use timing elements such as delay-line representations of time that are not biologically realistic for intervals in the range of seconds. The interval-timing literature provides several alternatives. One of them is that timing could emerge from general network dynamics, instead of coming from a dedicated circuit. Here, we present a general rate-based learning model based on long short-term memory (LSTM) networks that learns a time representation when needed. Using a naïve network learning its environment in conjunction with TD, we reproduce dopamine activity in appetitive trace conditioning with a constant CS-US interval, including probe trials with unexpected delays. The proposed model learns a representation of the environment dynamics in an adaptive biologically plausible framework, without recourse to delay lines or other special-purpose circuits. Instead, the model predicts that the task-dependent representation of time is learned by experience, is encoded in ramp-like changes in single-neuron activity distributed across small neural networks, and reflects a temporal integration mechanism resulting from the inherent dynamics of recurrent loops within the network. The model also reproduces the known finding that trace conditioning is more difficult than delay conditioning and that the learned representation of the task can be highly dependent on the types of trials experienced during training. Finally, it suggests that the phasic dopaminergic signal could facilitate learning in the cortex.     

Protein structural models for nucleic acid interactions

It is proposed that particular segments of some ribosomal, histone and plant viral capsid proteins adopt a helical structural mode for interaction with nucleic acid. The amino acid regions were determined by three probes applied to 26 protein sequences: searches for helical wheels displaying asymmetric basic charge distributions, secondary structural predictions, and searches for primary structural homologies. In 11 of the protein sequences examined, homologous heptapeptides were found in the residue spans delineated by the three probes. A helical wheel analysis of the oligopeptide amino acids showed a distinct positive charge clustering. It is suggested that the basic amino acid side chains on the hydrophilic helical side interact with nucleic acid negative phosphate groups while the somewhat hydrophobic side is available for interaction within the protein or possibly with the major groove of double-stranded nucleic acid.