Structural study of the development of ocularity domains using a neural network model

We present a model for the development of ocularity domains in the visual cortex of mammals during the embryonic stage. We model the thalamo-cortical pathway with a self-organising neural network with two source layers, each of them serving different retinae, and one target layer, where the connections end. The connectivity between the source layers and the target layer is driven by Hebbian learning. In both the source layers and the target layer we assume excitatory lateral signal diffusion between proximal neurons that causes them to be correlated. According to the developmental state being modelled, we do not consider either correlation or anti-correlation between the signals originated in neurons of different retinae. The basic assumptions made are proved to be sufficient to attain a distribution of connections arranged in ocularity domains. The dependence of the geometry of the ocularity domains on the parameters of the model is analysed and a correlation between the width of the signal diffusion and the extent of the domains is found. The generality of the assumptions made allows an easy translation of the model to explain the development of other elements of the sensory nervous system.     

ProteinArchitect: Protein Evolution above the Sequence Level

Background

While many authors have discussed models and tools for studying protein evolution at the sequence level, molecular function is usually mediated by complex, higher order features such as independently folding domains and linear motifs that are based on or embedded in a particular arrangment of features such as secondary structure elements, transmembrane domains and regions with intrinsic disorder. This ‘protein architecture’ can, in its most simplistic representation, be visualized as domain organization cartoons that can be used to compare proteins in terms of the order of their mostly globular domains.

Methodology

Here, we describe a visual approach and a webserver for protein comparison that extend the domain organization cartoon concept. By developing an information-rich, compact visualization of different protein features above the sequence level, potentially related proteins can be compared at the level of propensities for secondary structure, transmembrane domains and intrinsic disorder, in addition to PFAM domains. A public Web server is available at www.proteinarchitect.net, while the code is provided at protarchitect.sourceforge.net.

Conclusions/Significance

Due to recent advances in sequencing technologies we are now flooded with millions of predicted proteins that await comparative analysis. In many cases, mature tools focused on revealing hits with considerable global or local similarity to well-characterized proteins will not be able to lead us to testable hypotheses about a protein''s function, or the function of a particular region. The visual comparison of different types of protein features with ProteinArchitect will be useful when assessing the relevance of similarity search hits, to discover subgroups in protein families and superfamilies, and to understand protein regions with conserved features outside globular regions. Therefore, this approach is likely to help researchers to develop testable hypotheses about a protein''s function even if is somewhat distant from the more characterized proteins, by facilitating the discovery of features that are conserved above the sequence level for comparison and further experimental investigation.     

Molecular Mechanism of Active Zone Organization at Vertebrate Neuromuscular Junctions

Organization of presynaptic active zones is essential for development, plasticity, and pathology of the nervous system. Recent studies indicate a trans-synaptic molecular mechanism that organizes the active zones by connecting the pre- and the postsynaptic specialization. The presynaptic component of this trans-synaptic mechanism is comprised of cytosolic active zone proteins bound to the cytosolic domains of voltage-dependent calcium channels (P/Q-, N-, and L-type) on the presynaptic membrane. The postsynaptic component of this mechanism is the synapse organizer (laminin β2) that is expressed by the postsynaptic cell and accumulates specifically on top of the postsynaptic specialization. The pre- and the postsynaptic components interact directly between the extracellular domains of calcium channels and laminin β2 to anchor the presynaptic protein complex in front of the postsynaptic specialization. Hence, the presynaptic calcium channel functions as a scaffolding protein for active zone organization and as an ion-conducting channel for synaptic transmission. In contrast to the requirement of calcium influx for synaptic transmission, the formation of the active zone does not require the calcium influx through the calcium channels. Importantly, the active zones of adult synapses are not stable structures and require maintenance for their integrity. Furthermore, aging or diseases of the central and peripheral nervous system impair the active zones. This review will focus on the molecular mechanisms that organize the presynaptic active zones and summarize recent findings at the neuromuscular junctions and other synapses.     

The C-Terminal Domain of the Virulence Factor MgtC Is a Divergent ACT Domain

MgtC is a virulence factor of unknown function important for survival inside macrophages in several intracellular bacterial pathogens, including Mycobacterium tuberculosis. It is also involved in adaptation to Mg²⁺ deprivation, but previous work suggested that MgtC is not a Mg²⁺ transporter. In this study, we demonstrated that the amount of the M. tuberculosis MgtC protein is not significantly increased by Mg²⁺ deprivation. Members of the MgtC protein family share a conserved membrane N-terminal domain and a more divergent cytoplasmic C-terminal domain. To get insights into MgtC functional and structural organization, we have determined the nuclear magnetic resonance (NMR) structure of the C-terminal domain of M. tuberculosis MgtC. This structure is not affected by the Mg²⁺ concentration, indicating that it does not bind Mg²⁺. The structure of the C-terminal domain forms a βαββαβ fold found in small molecule binding domains called ACT domains. However, the M. tuberculosis MgtC ACT domain differs from canonical ACT domains because it appears to lack the ability to dimerize and to bind small molecules. We have shown, using a bacterial two-hybrid system, that the M. tuberculosis MgtC protein can dimerize and that the C-terminal domain somehow facilitates this dimerization. Taken together, these results indicate that M. tuberculosis MgtC does not have an intrinsic function related to Mg²⁺ uptake or binding but could act as a regulatory factor based on protein-protein interaction that could be facilitated by its ACT domain.     

Diversity concept in ecology

Hierarchy of systems organization is used as a framework in advancing methodological guidelines for posing correct questions related to ecological diversity.Diversity if defined in general terms as a property of a set of elements dependent on and determines: by the epistemological perspective. Ontological diversity, because it is indefinite, is regarded as unmeasurable.Ecological diversity — be it species, spatial, reproductive or trophic, is a particular case of diversity of matter and must be precisely defined on the studied level of system organization.Diversity measurements combining more than one level of organization are information-void, for data become irretrievable as a result of such a treatment.Hypotheses explaining diversity sources are briefly surveyed. An integrated model interrelating them is constructed as a result of some basic views on the structure of matter coupled with the empirical knowledge of involved factors. The model reflects hierarchies of systems, their dynamics, and the complexities of factors affecting diversity. The model's properties suggest that it is conceptually related to an imaginary model of organization of ecological systems. Parameters recognized as invariant components of this complexity are: habitat differentiation, ecological specialization of species, ambiental changes, and integration of this system.Finally, it is shown that the peculiar shape of the species abundances curve is a necessary consequence of stratification of the system structure, which is an intrinsic attribute of hierarchical organization.     

Effect of nerve compression on the morphogenesis of the cholinesterase containing structures of the rat myoneural junction

Summary The sciatic nerve of the newborn rat was unilaterally compressed to cause temporary denervation and subsequent re-innervation of immature myoneural junctions prior to the development of postsynaptic infoldings in the rat tibialis anterior muscle. Subsequent changes in the postsynaptic structure were followed by histochemical demonstration of acetylcholinesterase activity.It was found that postsynaptic infoldings into the myoneural junctions appeared between 16–21 days of age on the temporarily denervated side but already at 5 days of age on the contralateral unoperated side. Also further development on the operated side was delayed by 10–15 days as compared to the control side.The observations indicate that the nerve-ending exerts a stimulating influence on the development of the postsynaptic structures and, in addition, that this action is long-lasting, as compared to the more transitory induction of myoneural acetylcholinesterase activity shown earlier to take place in the rat embryo at the 18-day stage.     

GKAP, a Novel Synaptic Protein That Interacts with the Guanylate Kinase-like Domain of the PSD-95/SAP90 Family of Channel Clustering Molecules

The molecular mechanisms underlying the organization of ion channels and signaling molecules at the synaptic junction are largely unknown. Recently, members of the PSD-95/SAP90 family of synaptic MAGUK (membrane-associated guanylate kinase) proteins have been shown to interact, via their NH₂-terminal PDZ domains, with certain ion channels (NMDA receptors and K⁺ channels), thereby promoting the clustering of these proteins. Although the function of the NH₂-terminal PDZ domains is relatively well characterized, the function of the Src homology 3 (SH3) domain and the guanylate kinase-like (GK) domain in the COOH-terminal half of PSD-95 has remained obscure. We now report the isolation of a novel synaptic protein, termed GKAP for guanylate kinase-associated protein, that binds directly to the GK domain of the four known members of the mammalian PSD-95 family. GKAP shows a unique domain structure and appears to be a major constituent of the postsynaptic density. GKAP colocalizes and coimmunoprecipitates with PSD-95 in vivo, and coclusters with PSD-95 and K⁺ channels/ NMDA receptors in heterologous cells. Given their apparent lack of guanylate kinase enzymatic activity, the fact that the GK domain can act as a site for protein– protein interaction has implications for the function of diverse GK-containing proteins (such as p55, ZO-1, and LIN-2/CASK).     

A critical step for postsynaptic F‐actin organization: Regulation of Baz/Par‐3 localization by aPKC and PTEN

Actin remodeling has emerged as a critical process during synapse development and plasticity. Thus, understanding the regulatory mechanisms controlling actin organization at synapses is exceedingly important. Here, we used the highly plastic Drosophila neuromuscular junction (NMJ) to understand mechanisms of actin remodeling at postsynaptic sites. Previous studies have suggested that the actin‐binding proteins Spectrin and Coracle play a critical role in NMJ development and the anchoring of glutamate receptors most likely through actin regulation. Here, we show that an additional determinant of actin organization at the postsynaptic region is the PDZ protein Baz/Par‐3. Decreasing Baz levels in postsynaptic muscles has dramatic consequences for the size of F‐actin and spectrin domains at the postsynaptic region. In turn, proper localization of Baz at this site depends on both phosphorylation and dephosphorylation events. Baz phosphorylation by its binding partner, atypical protein kinase C (aPKC), is required for normal Baz targeting to the postsynaptic region. However, the retention of Baz at this site depends on its dephosphorylation mediated by the lipid and protein phosphatase PTEN. Misregulation of the phosphorylation state of Baz by genetic alterations in PTEN or aPKC activity has detrimental consequences for postsynaptic F‐actin and spectrin localization, synaptic growth, and receptor localization. Our results provide a novel mechanism of postsynaptic actin regulation through Baz, governed by the antagonistic actions of aPKC and PTEN. Given the conservation of these proteins from worms to mammals, these results are likely to provide new insight into actin organization pathways. © 2009 Wiley Periodicals, Inc. Develop Neurobiol 2009     

Calsyntenin-3 Molecular Architecture and Interaction with Neurexin 1α

Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. However, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca²⁺, and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca²⁺ and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function.     

Reproduction and the central project of evolutionary theory

In much of the discourse of evolutionary theory, reproduction is treated as an autonomous function of the individual organism — even in discussions of sexually reproducing organisms. In this paper, I examine some of the functions and consequences of such manifestly peculiar language. In particular, I suggest that it provides crucial support for the central project of evolutionary theory — namely that of locating causal efficacy in intrinsic properties of the individual organism. Furthermore, I argue that the language of individual reproduction is maintained by certain methodological conventions that both obscure many of the problems it generates and serve to actively impede attempts to redress those difficulties that can be identified. Finally, I suggest that inclusion of the complexities introduced by sexual reproduction — in both language and methodology — may radically undermine the individualist focus of evolutionary theory.I am indepted to the Rockefeller Foundation for a Humanities Fellowship that supported this research during the spring of 1986. I am also grateful to Richard Lewontin, Diane Paul, and Lisa Lloyd for many extremely helpful conversations.     

A specific chromosome element,the telomere of Drosophila polytene chromosomes

The submicroscopic organization of terminal chromosome regions of Drosophila hydei polytene chromosomes is described. A compact region composed of tightly packed fibrils of 100 to 125 Å diameter embedded in an amorphous material is located at each of the chromosome ends of the 5 long chromosome arms. From this compact region, sometimes containing cavities, fibrils extend onto the nearest normal band region. The diameter of the extending fibrils is 100–125 Å, 200–250 Å or 400 Å. Pronase digestion of fixed and squashed chromosomes reduced the electron density of the amorphous matrix in the compact regions but failed to affect the diameter of the fibrils. The extending fibrils, however, showed a decrease in diameter after pronase digestion. The most frequently observed diameter values were 100–125 Å. — The volume of the terminal structures, including the compact region as well as the extending fibrils, is characteristically different for the various elements of the karyotype. Chromosome 2 displays the largest terminal structure, whereas chromosome 4 only occasionally shows the presence of compact regions. — End to end association of the long chromosome arms involves the fusion of the compact terminal structures. The non-random distribution of end to end association seems to be correlated with the volume of the terminal structures. Chromosome 2 which contains the largest compact terminal region is more frequently involved in end to end associations than any other chromosome arm. — The terminal regions show replication of DNA. They belong to the group of regions which display a discontinuous labeling pattern along the chromosomes, representing a late phase of the replication cycle. — The unique structural organization of the terminal chromosome regions, which is never observed at any other location of the genome supports the idea that they are morphological manifestations of the postulated telomeres.     

The fine structure of the kinetochore of a mammalian cell in vitro

The chromosomes of Chinese hamster cells were examined with the electron microscope and the following observations were made concerning the structure and organization of the kinetochore. — The kinetochore consists of a dense core 200–300 Å in diameter surrounded hy a less dense zone 200–600 Å wide. The dense core consists of a pair of axial fibrils 50–80 Å in diameter which may be coiled together in a cohelical manner. The less dense zone about the axial elements is composed of numerous microfibrils which loop out at right angles to the axial fibrils. Together the structures comprise a lampbrush-like filament which extends along the surface of each chromatid. Some sections suggested that two such filaments may be present on each chromatid. The fine structure of kinetochores associated with spindle filaments was essentially the same as those free of filaments. The structure and organization of the kinetochore of these mammalian cells was compared to that of lampbrush chromosomes of certain amphibian oöcytes, dipteran polytene chromosome puffs, and the synaptinemal complex seen during meiotic prophase.The authors also wish to thank Dr. Arthur Cole of the Department of Physics for the use of his electron microscope facilities and for his helpful criticism.     

Space-time variability in mediterranean pastures analyzed with diversity parameters

Different parameters of diversity and spatial niche amplitude (Piclou, 1975, Pineda et al., 1981b) have been used to describe the spatial organization of mediterranean grasslands in Central Spain. A slope sampled by 480 contiguous 8×8 cm quadrats proved to have a homogeneous floristic distribution when it was divided into 160 parts and maximum heterogeneity when divided into 4 sectors. These sectors corresponded to different geomorphological zones of the slope. The complexity of vegetation distribution on the slope was reflected by differences in organization — measured by diversity parameter A=H(P/E)/log₂ N (number of plots) between the parts obtained by division. The presence of low-entropy species — specialists - and high entropy species — generalists — was related to the different scales of slope organization. The spatial distribution of plants was compared for different successional stages. Multivariate analysis of sampling plots confirmed previously identified organizational characteristics and clarified the nature of transitions between communities of different floristic composition or structure.     

Effects of α-latrotoxin on synaptic transmission between identified neurons in the snail central nervous system

The effects of -latrotoxin — a component of black widow spider venom — on an identified monosynaptic peptidergic synapse were investigated in the central nervous system ofHelix pomatia. Extracellular and intracellular application of the toxin was found to increase and block postsynaptic current respectively. Current induced by intracellular injection of cAMP which imitates postsynaptic current was inhibited, irrespective of the mode of toxin application. It was concluded on the basis of the experiments performed that -latrotoxin manifests its reinforcing effect, acting on the transmitter release system in the presynaptic neuron. It can also induce an inhibitory effect, however, operating on the postsynaptic cell direct — an effect which may be mediated by the cAMP system.A. A. Bogomolets Institute of Physiology, Ukrainian Academy of Sciences, Kiev. A. A. Bogomolets Medical Institute of Biochemistry, Ukrainian Academy of Sciences, Kiev. Translated from Neirofiziologiya, Vol. 24, No. 4, pp. 430–437, July–August, 1992.     

A Comparative Study and a Phylogenetic Exploration of the Compositional Architectures of Mammalian Nuclear Genomes

For the past four decades the compositional organization of the mammalian genome posed a formidable challenge to molecular evolutionists attempting to explain it from an evolutionary perspective. Unfortunately, most of the explanations adhered to the “isochore theory,” which has long been rebutted. Recently, an alternative compositional domain model was proposed depicting the human and cow genomes as composed mostly of short compositionally homogeneous and nonhomogeneous domains and a few long ones. We test the validity of this model through a rigorous sequence-based analysis of eleven completely sequenced mammalian and avian genomes. Seven attributes of compositional domains are used in the analyses: (1) the number of compositional domains, (2) compositional domain-length distribution, (3) density of compositional domains, (4) genome coverage by the different domain types, (5) degree of fit to a power-law distribution, (6) compositional domain GC content, and (7) the joint distribution of GC content and length of the different domain types. We discuss the evolution of these attributes in light of two competing phylogenetic hypotheses that differ from each other in the validity of clade Euarchontoglires. If valid, the murid genome compositional organization would be a derived state and exhibit a high similarity to that of other mammals. If invalid, the murid genome compositional organization would be closer to an ancestral state. We demonstrate that the compositional organization of the murid genome differs from those of primates and laurasiatherians, a phenomenon previously termed the “murid shift,” and in many ways resembles the genome of opossum. We find no support to the “isochore theory.” Instead, our findings depict the mammalian genome as a tapestry of mostly short homogeneous and nonhomogeneous domains and few long ones thus providing strong evidence in favor of the compositional domain model and seem to invalidate clade Euarchontoglires.     

Protein tyrosine phosphatases ε and α perform nonredundant roles in osteoclasts

Female mice lacking protein tyrosine phosphatase ε (PTP ε) are mildly osteopetrotic. Osteoclasts from these mice resorb bone matrix poorly, and the structure, stability, and cellular organization of their podosomal adhesion structures are abnormal. Here we compare the role of PTP ε with that of the closely related PTP α in osteoclasts. We show that bone mass and bone production and resorption, as well as production, structure, function, and podosome organization of osteoclasts, are unchanged in mice lacking PTP α. The varying effects of either PTP on podosome organization in osteoclasts are caused by their distinct N-termini. Osteoclasts express the receptor-type PTP α (RPTPa), which is absent from podosomes, and the nonreceptor form of PTP ε (cyt-PTPe), which is present in these structures. The presence of the unique 12 N-terminal residues of cyt-PTPe is essential for podosome regulation; attaching this sequence to the catalytic domains of PTP α enables them to function in osteoclasts. Serine 2 within this sequence regulates cyt-PTPe activity and its effects on podosomes. We conclude that PTPs α and ε play distinct roles in osteoclasts and that the N-terminus of cyt-PTPe, in particular serine 2, is critical for its function in these cells.     

Transmission Efficacy and Plasticity in Glutamatergic Synapses Formed by Excitatory Interneurons of the Substantia Gelatinosa in the Rat Spinal Cord

Background

Substantia gelatinosa (SG, lamina II) is a spinal cord region where most unmyelinated primary afferents terminate and the central nociceptive processing begins. The glutamatergic excitatory interneurons (EINs) form the majority of the SG neuron population, but little is known about the mechanisms of signal processing in their synapses.

Methodology

To describe the functional organization and properties of excitatory synapses formed by SG EINs, we did non-invasive recordings from 183 pairs of monosynaptically connected neurons. An intact presynaptic SG EIN was specifically stimulated through the cell-attached pipette while the evoked EPSCs/EPSPs were recorded through perforated-patch from a postsynaptic neuron (laminae I-III).

Principal Findings

We found that the axon of an SG EIN forms multiple functional synapses on the dendrites of a postsynaptic neuron. In many cases, EPSPs evoked by stimulating an SG EIN were sufficient to elicit spikes in a postsynaptic neuron. EPSCs were carried through both Ca²⁺-permeable (CP) and Ca²⁺-impermeable (CI) AMPA receptors (AMPARs) and showed diverse forms of functional plasticity. The synaptic efficacy could be enhanced through both activation of silent synapses and strengthening of already active synapses. We have also found that a high input resistance (R_IN, >0.5 GΩ) of the postsynaptic neuron is necessary for resolving distal dendritic EPSCs/EPSPs and correct estimation of their efficacy.

Conclusions/Significance

We conclude that the multiple synapses formed by an SG EIN on a postsynaptic neuron increase synaptic excitation and provide basis for diverse forms of plasticity. This functional organization can be important for sensory, i.e. nociceptive, processing in the spinal cord.     

The postnatal development of the synapse: A morphological approach utilizing synaptosomes

Summary Synaptosomes derived from 2–21 days postnatal rat cerebral cortex have been examined following glutaraldehyde fixation and block PTA staining, with the aim of investigating the maturation of the paramembranous densities at the contact region between the pre- and postsynaptic components. The internal coats of pre- and postsynaptic membranes first appear as undifferentiated plaque-like thickenings, which gradually develop into, or are replaced by, dense projections and postsynaptic focal densities respectively. Both sets of densities pass through an interconnected phase before starting to emerge as discrete entities at 5–7 days. The external coats of the pre- and postsynaptic membranes coalesce to form a plate-like structure which breaks down during development to form the cleft densities or transverse bars of the adult contact region. Although for the first few days of postnatal development only one type of synaptosome can be identified, from 5 days onwards two types corresponding to types A and B of adult life become recognizable.Increase in height of the dense projections has been correlated with increase in the number of synaptic vesicles per synaptosome during postnatal development, indicating that the synaptic vesicles may play a role in the formation and maturation of dense projections. The possible importance of other factors in this process is also discussed.We would like to thank Professors J. Z. Young, F. R. S., and E. G. Gray for their advice, and Mr. S. Waterman for expert photographic assistance.     

Supramolecular Organization of the Repetitive Backbone Unit of the Streptococcus pneumoniae Pilus

Streptococcus pneumoniae, like many other Gram-positive bacteria, assembles long filamentous pili on their surface through which they adhere to host cells. Pneumococcal pili are formed by a backbone, consisting of the repetition of the major component RrgB, and two accessory proteins (RrgA and RrgC). Here we reconstruct by transmission electron microscopy and single particle image reconstruction method the three dimensional arrangement of two neighbouring RrgB molecules, which represent the minimal repetitive structural domain of the native pilus. The crystal structure of the D2-D4 domains of RrgB was solved at 1.6 Å resolution. Rigid-body fitting of the X-ray coordinates into the electron density map enabled us to define the arrangement of the backbone subunits into the S. pneumoniae native pilus. The quantitative fitting provide evidence that the pneumococcal pilus consists uniquely of RrgB monomers assembled in a head-to-tail organization. The presence of short intra-subunit linker regions connecting neighbouring domains provides the molecular basis for the intrinsic pilus flexibility.