Erythropoietin processing in erythropoietic system and central nervous system

We describe possible functions of carbohydrates attached to growth factors and strategies to examine the functions, concentrating on erythropoietin, a major regulator of erythropoiesis. Erythropoietin in erythropoiesis functions as an endocrine hormone; it is produced by kidney cells and transferred into the circulation to hemopoietic sites. In the brain, erythropoietin acts on neurons in a paracrine fashion. Comparison of glycosylation has been made between kidney and brain erythropoietins.Abbreviations BHK Baby Hamster Kidney - Epo Erythropoietin - Epo-R erythropoietin receptor     

The brain as a distributed intelligent processing system: an EEG study

Background

Various neuroimaging studies, both structural and functional, have provided support for the proposal that a distributed brain network is likely to be the neural basis of intelligence. The theory of Distributed Intelligent Processing Systems (DIPS), first developed in the field of Artificial Intelligence, was proposed to adequately model distributed neural intelligent processing. In addition, the neural efficiency hypothesis suggests that individuals with higher intelligence display more focused cortical activation during cognitive performance, resulting in lower total brain activation when compared with individuals who have lower intelligence. This may be understood as a property of the DIPS.

Methodology and Principal Findings

In our study, a new EEG brain mapping technique, based on the neural efficiency hypothesis and the notion of the brain as a Distributed Intelligence Processing System, was used to investigate the correlations between IQ evaluated with WAIS (Whechsler Adult Intelligence Scale) and WISC (Wechsler Intelligence Scale for Children), and the brain activity associated with visual and verbal processing, in order to test the validity of a distributed neural basis for intelligence.

Conclusion

The present results support these claims and the neural efficiency hypothesis.     

DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI

Background  

Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the de novo assembly in terms of assembly quality and scalability for large-scale short read datasets.     

A widely distributed antigen developmentally regulated in the nervous system

We have identified a glycoprotein (BEN) of 95-100 x 10(3) Mr using a monoclonal antibody. This protein is transiently expressed at the cell surface of the peripherally projecting neurons, i.e. motoneurons of the spinal cord and cranial nuclei, sensory neurons of the dorsal root and cranial sensory ganglia and sympathetic, parasympathetic and enteric neurons. In vitro cultures of dorsal root and sympathetic ganglia have shown that BEN is expressed on neurons but not on glial cells. On motor and sensory neurons, BEN first appears at the level of the cell body just after withdrawal from the cell cycle. Soon afterwards, expression of the antigen extends to the elongating axon. After a few days, BEN is no longer expressed by the motor and sensory neurons, disappearing first from the cell body and then progressively from the fibres. The loss of expression is concomitant with the onset of intense proliferation of satellite and Schwann cells. This modulated expression within the nervous system is unlike that of any surface glycoprotein so far described in vertebrates. Preliminary biochemical analysis indicates that, although it bears the adhesion-associated epitope HNK-1, BEN does not share characteristics with any previously described axonal glycoprotein. Consequently, we speculate that this glycoprotein might be a novel molecule implicated in selective adhesion phenomena, such as axonal fasciculation.     

Intracellular signalling as a parallel distributed process

Living cells respond to their environment by means of an interconnected network of receptors, second messengers, protein kinases and other signalling molecules. This article suggests that the performance of cell signalling pathways taken as a whole has similarities to that of the parallel distributed process networks (PDP networks) used in computer-based pattern recognition. Using the response of hepatocytes to glucagon as an example, a procedure is described by which a PDP network could simulate a cell signalling pathway. This procedure involves the following steps: (a) a bounded set of molecules is defined that carry the signals of interest; (b) each of these molecules is represented by a PDP-type of unit, with input and output functions and connection weights corresponding to specific biochemical parameters; (c) a "learning algorithm" is applied in which small random changes are made in the parameters of the cell signalling units and the new network is then tested by a selection procedure in favour of a specific input-output relationship. The analogy with PDP networks shows how living cells can recognize combinations of environmental influences, how cell responses can be stabilized and made resistant to damage, and how novel cell signalling pathways might appear during evolution.     

Peach: a simple Perl-based system for distributed computation and its application to cryo-EM data processing

A simple distributed processing system named "Peach" was developed to meet the rising computational demands of modern structural biology (and other) laboratories without additional expense by using existing hardware resources more efficiently. A central server distributes jobs to idle workstations in such a way that each computer is used maximally, but without disturbing intermittent interactive users. As compared to other distributed systems, Peach is simple, easy to install, easy to administer, easy to use, scalable, and robust. While it was designed to queue and distribute large numbers of small tasks to participating computers, it can also be used to send single jobs automatically to the fastest currently available computer and/or survey the activity of an entire laboratory's computers. Tests of robustness and scalability are reported, as are three specific electron cryomicroscopy applications where Peach enabled projects that would not otherwise have been feasible without an expensive, dedicated cluster.     

Evolution of structure and information processing in the nervous system: Part IV of a general theory

Starting from fundamental principles, evolution of the nervous system is modelled as a random walk process in a multidimensional representation space (the F-space). This space is not flat, it is highly structured in terms of step probability. Fundamental considerations of evolutionary speed, efficiency of information processing, and priorities lead to specific theoretical predictions of the most probable pathways of evolution of the nervous system and its mechanisms of information processing. These processes are represented as vector paths (F-paths) in the F-space. Cognition becomes a process of correlations of the input signal to information stored in memories. Higher level brain processes involve extrapolation and interpolation along F-paths, input data reduction by clearly specifiable abstraction methods, and a unique process using abstracted analogs. These processes define and limit what the brain does and how it can do it. These considerations lead to certain inevitable conclusions (consequences of the fundamental principles) for the basis of our logical reasoning, decision-making, the process of dreaming (conscious and sleep), and explicit definitions of consciousness, unconsciousness, and personality. Detailed applications of this theory for analyzing empirical findings are suggested in the final paragraphs.     

ClustalW-MPI: ClustalW analysis using distributed and parallel computing

ClustalW is a tool for aligning multiple protein or nucleotide sequences. The alignment is achieved via three steps: pairwise alignment, guide-tree generation and progressive alignment. ClustalW-MPI is a distributed and parallel implementation of ClustalW. All three steps have been parallelized to reduce the execution time. The software uses a message-passing library called MPI (Message Passing Interface) and runs on distributed workstation clusters as well as on traditional parallel computers.     

Scheduling parallel applications in distributed networks

Prophet is a run-time scheduling system designed to support the efficient execution of parallel applications written in the Mentat programming language (Grimshaw, 1993). Prior results demonstrated that SPMD applications could be scheduled automatically in an Ethernet-based local-area workstation network with good performance (Weissman and Grimshaw, 1994 and 1995). This paper describes our recent efforts to extend Prophet along several dimensions: improved overhead control, greater resource sharing, greater resource heterogeneity, wide-area scheduling, and new application types. We show that both SPMD and task parallel applications can be scheduled effectively in a shared heterogeneous LAN environment containing ethernet and ATM networks by exploiting the application structure and dynamic run-time information. This revised version was published online in July 2006 with corrections to the Cover Date.     

SSK-DDoS: distributed stream processing framework based classification system for DDoS attacks

Cluster Computing - Distributed denial of service (DDoS) is an immense threat for Internet based-applications and their resources. It immediately floods the victim system by transmitting a large...     

The neural mechanisms of gustation: a distributed processing code

Whenever food is placed in the mouth, taste receptors are stimulated. Simultaneously, different types of sensory fibre that monitor several food attributes such as texture, temperature and odour are activated. Here, we evaluate taste and oral somatosensory peripheral transduction mechanisms as well as the multi-sensory integrative functions of the central pathways that support the complex sensations that we usually associate with gustation. On the basis of recent experimental data, we argue that these brain circuits make use of distributed ensemble codes that represent the sensory and post-ingestive properties of tastants.     

RNA splicing: Advantages of parallel processing

Parallel and sequential modes of RNA processing are systematically compared by an analysis of the relevant kinetic reaction schemes. The parallel mode is shown to be superior in the sense that it allows molecules to be processed with larger numbers of introns, smaller losses of immature intermediates, and shorter processing times. It also is more sensitive to variations in the rate constants for individual splice-reactions, and hence more amenable to evolutionary refinements. Quantitatively, the parallel mode agrees well with published experimental data.     

Energy systems concepts and self-organization: a rebuttal

Tadpoles in small, ephemeral pools whose duration and food content are unpredictable can potentially encounter substantial variation in diet composition and availability. We compared the effects of 10 days of food deprivation occurring early, midway and late in ontogeny on the metamorphic size and bioenergetic properties of Hyla chrysoscelis tadpoles. Tadpoles fed throughout ontogeny were controls. Metamorphs from tadpoles starved early and midway in ontogeny had the same snout-vent length and dry mass as controls, but the time to metamorphosis was extended by 8 and 19% respectively. Metamorphs of tadpoles starved late in development attained 85% of the length and 55% of the mass of controls, metamorphosed at the same time as controls, and suffered mortality 15 times greater than other treatments, perhaps because they were near the absolute minimum necessary level of energy reserves. There were no significant differences in percent organic matter, percent tissue water, condition index, and protein or glycogen concentrations between any experimental and control treatments. If food deprivation occurred early in development, the tadpoles caught up to the size of controls, but an extended developmental time would increase the risk of predation or habitat loss. If food reductions occur late in development, perhaps magnified by pond desiccation, tadpoles are stimulated to metamorphose at the same time as controls but at a smaller size. The bioenergetic composition of tadpoles at metamorphosis is unaffected by time of food deprivation.     

Evolution in parallel: new insights from a classic system

Neo-darwinists have long argued that parallel evolution, the repeated evolution of similar phenotypes in closely related lineages, is caused by the action of similar environments on alleles at many loci of small effect. A more controversial possibility is that the genetic architecture of traits initiates parallelism, sometimes through fixation of alleles of large effect. Recent research (by Cole et al., Colosimo et al., Cresko et al., and Shapiro et al.) offers the surprising insight that reduction in two armor traits of threespine stickleback is governed by independently segregating major loci as well as additional quantitative trait loci (QTL), and that alleles at the same major loci are associated with parallel phenotypes in globally distributed populations. This research suggests the emergence of a new and exciting vertebrate model system for evolutionary genetics.     

Neuronal evolution: analysis of regulatory genes in a first-evolved nervous system, the hydra nervous system

Cnidarians represent the first animal phylum with an organized nervous system and a complex active behavior. The hydra nervous system is formed of sensory-motoneurons, ganglia neurons and mechanoreceptor cells named nematocytes, which all differentiate from a common stem cell. The neurons are organized as a nerve net and a subset of neurons participate in a more complex structure, the nerve ring that was identified in most cnidarian species at the base of the tentacles. In order to better understand the genetic control of this neuronal network, we analysed the expression of evolutionarily conserved regulatory genes in the hydra nervous system. The Prd-class homeogene prdl-b and the nuclear orphan receptor hyCOUP-TF are expressed at strong levels in proliferating nematoblasts, a lineage where they were found repressed during patterning and morphogenesis, and at low levels in distinct subsets of neurons. Interestingly, Prd-class homeobox and COUP-TF genes are also expressed during neurogenesis in bilaterians, suggesting that mechanoreceptor and neuronal cells derive from a common ancestral cell. Moreover, the Prd-class homeobox gene prdl-a, the Antp-class homeobox gene msh, and the thrombospondin-related gene TSP1, which are expressed in distinct subset of neurons in the adult polyp, are also expressed during early budding and/or head regeneration. These data strengthen the fact that two distinct regulations, one for neurogenesis and another for patterning, already apply to these regulatory genes, a feature also identified in bilaterian related genes.     

Autowave processes in a distributed chemical system

The autowave processes with a characteristic wavelength and oscillation period may arise under some initial conditions in a uniform active medium. The wavelength and period depend on the chemical and physical parameters of the system and are independent of the initial and boundary conditions and of the system linear size. The processes occur in a homogeneous solution in the course of an oscillating chemical reaction. Similar processes may play an important role in the phenomena of short-term memory, cardiac arrhythmia, morphogenesis and prebiological evolution.Different types of structures are discussed, and experimental data and mathematical models are presented.     

Dopamine in a molluscan nervous system: Synthesis and fluorescence histochemistry

The nervous system of the pond snail, Helisoma trivolvis, was investigated for its ability to synthesize and accumulate ³H-catecholamines from ³H-tyrosine. ³H-Dopamine, but not ³H-norepinephrine, was synthesized by several ganglia. The highest accumulations were found in the cerebral, pedal, and buccal ganglia. The Falck-Hillarp and glyoxylic acid fluorescence histochemical techniques were applied to the buccal ganglia to visualize dopamine-containing cells. Fluorescing cells were found on both dorsal and ventral sides of the ganglion. Peripheral nerves of the buccal ganglia also displayed catecholamine fluorescence and accumulated ³H-dopamine. However, no ³H-dopamine synthesis occurred in the cerebral-buccal connectives, which connect the buccal ganglia with the rest of the central nervous system. Therefore, we conclude that there is a dopaminergic system intrinsic to the buccal ganglia and their peripheral targets.