Control of alternative pre-mRNA splicing by distributed pentameric repeats

Multiple copies of the hexamer TGCATG have been shown to regulate fibronectin pre-mRNA alternative splicing. GCATG repeats also are clustered near the regulated calcitonin-specific 3′ splice site in the rat calcitonin/CGRP gene. Specific mutagenesis of these repeats in calcitonin/CGRP pre-mRNA resulted in the loss of calcitonin-specific splicing, suggesting that the native repeats act to enhance alternative exon inclusion. Mutation of subsets of these elements implies that alternative splicing requires a minimum of two repeats, and that the combination of one intronic and one exonic repeat is necessary for optimal cell-specific splicing. However, multimerized intronic repeats inhibited calcitonin-specific splicing in both the wild-type context and in a transcript lacking endogenous repeats. These results suggest that both the number and distribution of repeats may be important features for the regulation of tissue-specific alternative splicing. Further, RNA containing a single repeat bound cell-specific protein complexes, but tissue-specific differences in protein binding were not detected by using multimerized repeats. Together, these data support a novel model for alternative splicing regulation that requires the cell-specific recognition of multiple, distributed sequence elements.

Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes

The positions of ≈4,800 individual miniature inverted-repeat transposable element (MITE)-like repeats from four families were mapped on the Caenorhabditis elegans chromosomes. These families represent 1–2% of the total sequence of the organism. The four MITE families (Cele1, Cele2, Cele14, and Cele42) displayed distinct chromosomal distribution profiles. For example, the Cele14 MITEs were observed clustering near the ends of the autosomes. In contrast, the Cele2 MITEs displayed an even distribution through the central autosome domains, with no evidence for clustering at the ends. Both the number of elements and the distribution patterns of each family were conserved on all five C. elegans autosomes. The distribution profiles indicate chromosomal polarity and suggest that the current genetic and physical maps of chromosomes II, III, and X are inverted with respect to the other chromosomes. The degree of conservation of both the number and distribution of these elements on the five autosomes suggests a role in defining specific chromosomal domains.

Mutations in HYAL1, a member of a tandemly distributed multigene family encoding disparate hyaluronidase activities, cause a newly described lysosomal disorder, mucopolysaccharidosis IX

Hyaluronan (HA), a large glycosaminoglycan abundant in the extracellular matrix, is important in cell migration during embryonic development, cellular proliferation, and differentiation and has a structural role in connective tissues. The turnover of HA requires endoglycosidic breakdown by lysosomal hyaluronidase, and a congenital deficiency of hyaluronidase has been thought to be incompatible with life. However, a patient with a deficiency of serum hyaluronidase, now designated as mucopolysaccharidosis IX, was recently described. This patient had a surprisingly mild clinical phenotype, including notable periarticular soft tissue masses, mild short stature, an absence of neurological or visceral involvement, and histological and ultrastructural evidence of a lysosomal storage disease. To determine the molecular basis of mucopolysaccharidosis IX, we analyzed two candidate genes tandemly distributed on human chromosome 3p21.3 and encoding proteins with homology to a sperm protein with hyaluronidase activity. These genes, HYAL1 and HYAL2, encode two distinct lysosomal hyaluronidases with different substrate specificities. We identified two mutations in the HYAL1 alleles of the patient, a 1412G → A mutation that introduces a nonconservative amino acid substitution (Glu268Lys) in a putative active site residue and a complex intragenic rearrangement, 1361del37ins14, that results in a premature termination codon. We further show that these two hyaluronidase genes, as well as a third recently discovered adjacent hyaluronidase gene, HYAL3, have markedly different tissue expression patterns, consistent with differing roles in HA metabolism. These data provide an explanation for the unexpectedly mild phenotype in mucopolysaccharidosis IX and predict the existence of other hyaluronidase deficiency disorders.

Localization of the central rhythm generator involved in spontaneous consummatory licking in rats: functional ablation and electrical brain stimulation studies.

Localization of the central rhythm generator (CRG) of spontaneous consummatory licking was studied in freely moving rats by microinjection of tetrodotoxin (TTX) into the pontine reticular formation. Maximum suppression of spontaneous water consumption was elicited by TTX (1 ng) blockade of the oral part of the nucleus reticularis gigantocellularis (NRG), whereas TTX injections into more caudal or rostral locations caused significantly weaker disruption of drinking. To verify the assumption that TTX blocked the proper CRG of licking rather than some relay in its output, spontaneously drinking thirsty rats were intracranially stimulated via electrodes chronically implanted into the oral part of the NRG. Lick-synchronized stimulation (a 100-ms train of 0.1-ms-wide rectangular pulses at 100 Hz and 25-150 microA) applied during continuous licking (after eight regular consecutive licks) caused a phase shift of licks emitted after stimulus delivery. The results suggest that the stimulation has reset the CRG of licking without changing its frequency. The reset-inducing threshold current was lowest during the tongue retraction and highest during the tongue protrusion period of the lick cycle. It is concluded that the CRG of licking is located in the oral part of NRG.

How are close residues of protein structures distributed in primary sequence?

Structurally neighboring residues are categorized according to their separation in the primary sequence as proximal (1-4 positions apart) and otherwise distal, which in turn is divided into near (5-20 positions), far (21-50 positions), very far ( > 50 positions), and interchain (from different chains of the same structure). These categories describe the linear distance histogram (LDH) for three-dimensional neighboring residue types. Among the main results are the following: (i) nearest-neighbor hydrophobic residues tend to be increasingly distally separated in the linear sequence, thus most often connecting distinct secondary structure units. (ii) The LDHs of oppositely charged nearest-neighbors emphasize proximal positions with a subsidiary maximum for very far positions. (iii) Cysteine-cysteine structural interactions rarely involve proximal positions. (iv) The greatest numbers of interchain specific nearest-neighbors in protein structures are composed of oppositely charged residues. (v) The largest fraction of side-chain neighboring residues from beta-strands involves near positions, emphasizing associations between consecutive strands. (vi) Exposed residue pairs are predominantly located in proximal linear positions, while buried residue pairs principally correspond to far or very far distal positions. The results are principally invariant to protein sizes, amino acid usages, linear distance normalizations, and over- and underrepresentations among nearest-neighbor types. Interpretations and hypotheses concerning the LDHs, particularly those of hydrophobic and charged pairings, are discussed with respect to protein stability and functionality. The pronounced occurrence of oppositely charged interchain contacts is consistent with many observations on protein complexes where multichain stabilization is facilitated by electrostatic interactions.

Estradiol and the inhibition of hypothalamic gonadotropin-releasing hormone pulse generator activity in the rhesus monkey.

In mammals, gonadal function is controlled by a hypothalamic signal generator that directs the pulsatile release of gonadotropin-releasing hormone (GnRH) and the consequent pulsatile secretion of luteinizing hormone. In female rhesus monkeys, the electrophysiological correlates of GnRH pulse generator activity are abrupt, rhythmic increases in hypothalamic multiunit activity (MUA volleys), which represent the simultaneous increase in firing rate of individual neurons. MUA volleys are arrested by estradiol, either spontaneously at midcycle or after the administration of the steroid. Multiunit recordings, however, provide only a measure of total neuronal activity, leaving the behavior of the individual cells obscure. This study was conducted to determine the mode of action of estradiol at the level of single neurons associated with the GnRH pulse generator. Twenty-three such single units were identified by cluster analysis of multiunit recordings obtained from a total of six electrodes implanted in the mediobasal hypothalamus of three ovariectomized rhesus monkeys, and their activity was monitored before and after estradiol administration. The bursting of all 23 units was arrested within 4 h of estradiol administration although their baseline activity was maintained. The bursts of most units reappeared at the same time as the MUA volleys, the recovery of some was delayed, and one remained inhibited for the duration of the study (43 days). The results indicate that estradiol does not desynchronize the bursting of single units associated with the GnRH pulse generator but that it inhibits this phenomenon. The site and mechanism of action of estradiol in this regard remain to be determined.

Fault location in power distribution networks with distributed generation.

This research presents the development and implementation of fault location algorithms in power distribution networks with distributed generation units installed along their feeders. The proposed algorithms are capable of locating the fault based on voltage and current signals recorded by intelligent electronic devices installed at the end of the feeder sections, information to compute the loads connected to these feeders and their electric characteristics, and the operating status of the network. In addition, this work presents the study of analytical models of distributed generation and load technologies that could contribute to the performance of the proposed fault location algorithms. The validation of the algorithms was based on computer simulations using network models implemented in ATP, whereas the algorithms were implemented in MATLAB.

Particle Swarm Optimization Based Reactive Power Dispatch for Power Networks with Distributed Generation

Reactive power is critical to the operation of the power networks on both safety aspects and economic aspects. Unreasonable distribution of the reactive power would severely affect the power quality of the power networks and increases the transmission loss. Currently, the most economical and practical approach to minimizing the real power loss remains using reactive power dispatch method. Reactive power dispatch problem is nonlinear and has both equality constraints and inequality constraints. In this thesis, PSO algorithm and MATPOWER 5.1 toolbox are applied to solve the reactive power dispatch problem. PSO is a global optimization technique that is equipped with excellent searching capability. The biggest advantage of PSO is that the efficiency of PSO is less sensitive to the complexity of the objective function. MATPOWER 5.1 is an open source MATLAB toolbox focusing on solving the power flow problems. The benefit of MATPOWER is that its code can be easily used and modified. The proposed method in this thesis minimizes the real power loss in a practical power system and determines the optimal placement of a new installed DG. IEEE 14 bus system is used to evaluate the performance. Test results show the effectiveness of the proposed method.

Modeling a mobile robot using a grammatical model

Virtual Worlds Generator is a grammatical model that is proposed to define virtual worlds. It integrates the diversity of sensors and interaction devices, multimodality and a virtual simulation system. Its grammar allows the definition and abstraction in symbols strings of the scenes of the virtual world, independently of the hardware that is used to represent the world or to interact with it. A case study is presented to explain how to use the proposed model to formalize a robot navigation system with multimodal perception and a hybrid control scheme of the robot.

Multi-agent system for control of robots inspired on the distributed activity and hormonal regulation of humans

Robotics is an emerging field with great activity. Robotics is a field that presents several problems because it depends on a large number of disciplines, technologies, devices and tasks. Its expansion from perfectly controlled industrial environments toward open and dynamic environment presents a many new challenges. New uses are, for example, household robots or professional robots. To facilitate the low cost, rapid development of robotic systems, reusability of code, its medium and long term maintainability and robustness are required novel approaches to provide generic models and software systems who develop paradigms capable of solving these problems. For this purpose, in this paper we propose a model based on multi-agent systems inspired by the human nervous system able to transfer the control characteristics of the biological system and able to take advantage of the best properties of distributed software systems. Specifically, we model the decentralized activity and hormonal variation.

A grammatical approach to the modeling of an autonomous robot

Virtual Worlds Generator is a grammatical model that is proposed to define virtual worlds. It integrates the diversity of sensors and interaction devices, multimodality and a virtual simulation system. Its grammar allows the definition and abstraction in symbols strings of the scenes of the virtual world, independently of the hardware that is used to represent the world or to interact with it. A case study is presented to explain how to use the proposed model to formalize a robot navigation system with multimodal perception and a hybrid control scheme of the robot. The result is an instance of the model grammar that implements the robotic system and is independent of the sensing devices used for perception and interaction. As a conclusion the Virtual Worlds Generator adds value in the simulation of virtual worlds since the definition can be done formally and independently of the peculiarities of the supporting devices.

Fast pseudorandom generator based on packed matrices

Pseudorandom generators are a basic foundation of many cryptographic services and information security protocols. We propose a modification of a previously published matricial pseudorandom generator that significantly improves performance and security. The resulting generator is successfully compared to world class standards.

An optimized pseudorandom generator using packed matrices

Most cryptographic services and information security protocols require a dependable source of random data; pseudorandom generators are convenient and efficient for this application working as one of the basic foundation blocks on which to build the required security infrastructure. We propose a modification of a previously published matricial pseudorandom generator that significantly improves performance and security by using word packed matrices and modifying key scheduling and bit extraction schemes. The resulting generator is then successfully compared to world class standards.

PCDD/F Emissions from Light-Duty Diesel Vehicles Operated under Highway Conditions and a Diesel-Engine Based Power Generator

PCDD/F emissions from three light-duty diesel vehicles–two vans and a passenger car–have been measured in on-road conditions. We propose a new methodology for small vehicles: a sample of exhaust gas is collected by means of equipment based on United States Environmental Protection Agency (U.S. EPA) method 23A for stationary stack emissions. The concentrations of O2, CO, CO2, NO, NO2 and SO2 have also been measured. Six tests were carried out at 90-100 km/h on a route 100 km long. Two additional tests were done during the first 10 minutes and the following 60 minutes of the run to assess the effect of the engine temperature on PCDD/F emissions. The emission factors obtained for the vans varied from 1800 to 8400 pg I-TEQ/Nm3 for a 2004 model year van and 490-580 pg I-TEQ/Nm3 for a 2006 model year van. Regarding the passenger car, one run was done in the presence of a catalyst and another without, obtaining emission factors (330-880 pg I-TEQ/Nm3) comparable to those of the modern van. Two other tests were carried out on a power generator leading to emission factors ranging from 31 to 78 pg I-TEQ/Nm3. All the results are discussed and compared with literature.

A Matrix PRNG with S-Box Output Filtering

We describe a modification to a previously published pseudorandom number generator improving security while maintaining high performance. The proposed generator is based on the powers of a word-packed block upper triangular matrix and it is designed to be fast and easy to implement in software since it mainly involves bitwise operations between machine registers and, in our tests, it presents excellent security and statistical characteristics. The modifications include a new, key-derived s-box based nonlinear output filter and improved seeding and extraction mechanisms. This output filter can also be applied to other generators.