Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome

Following transcription and splicing, each mRNA of a mammalian cell passes into the cytoplasm where its fate is in the hands of a complex network of ribonucleoproteins (mRNPs). The success or failure of a gene to be expressed depends on the performance of this mRNP infrastructure. The entry, gating, processing, and transit of each mRNA through an mRNP network helps determine the composition of a cell's proteome. The machinery that regulates storage, turnover, and translational activation of mRNAs is not well understood, in part, because of the heterogeneous nature of mRNPs. Recently, subsets of cellular mRNAs clustered as members of mRNP complexes have been identified by using antibodies reactive with RNA-binding proteins, including ELAV/Hu, eIF-4E, and poly(A)-binding proteins. Cytoplasmic ELAV/Hu proteins are involved in the stability and translation of early response gene (ERG) transcripts and are expressed predominately in neurons. mRNAs recovered from ELAV/Hu mRNP complexes were found to have similar sequence elements, suggesting a common structural linkage among them. This approach opens the possibility of identifying transcripts physically clustered in vivo that may have similar fates or functions. Moreover, the proteins encoded by physically organized mRNAs may participate in the same biological process or structural outcome, not unlike operons and their polycistronic mRNAs do in prokaryotic organisms. Our goal is to understand the organization and flow of genetic information on an integrative systems level by analyzing the collective properties of proteins and mRNAs associated with mRNPs in vivo.

Participation of Mitochondrial Metabolism in Photorespiration1 : Reconstituted System of Peroxisomes and Mitochondria from Spinach Leaves

In this study the interplay of mitochondria and peroxisomes in photorespiration was simulated in a reconstituted system of isolated mitochondria and peroxisomes from spinach (Spinacia oleracea L.) leaves. The mitochondria oxidizing glycine produced serine, which was reduced in the peroxisomes to glycerate. The required reducing equivalents were provided by the mitochondria via the malate-oxaloacetate (OAA) shuttle, in which OAA was reduced in the mitochondrial matrix by NADH generated during glycine oxidation. The rate of peroxisomal glycerate formation, as compared with peroxisomal protein, resembled the corresponding rate required during leaf photosynthesis under ambient conditions. When the reconstituted system produced glycerate at this rate, the malate-to-OAA ratio was in equilibrium with a ratio of NADH/NAD of 8.8 × 10−3. This low ratio is in the same range as the ratio of NADH/NAD in the cytosol of mesophyll cells of intact illuminated spinach leaves, as we had estimated earlier. This result demonstrates that in the photorespiratory cycle a transfer of redox equivalents from the mitochondria to peroxisomes, as postulated from separate experiments with isolated mitochondria and peroxisomes, can indeed operate under conditions of the very low reductive state of the NADH/NAD system prevailing in the cytosol of mesophyll cells in a leaf during photosynthesis.

Sensitive detection of bacterial transcription initiation sites and differentiation from RNA processing sites in the pheromone-induced plasmid transfer system of Enterococcus faecalis.

A method was developed to detect 5' ends of bacterial RNAs expressed at low levels and to differentiate newly initiated transcripts from processed transcripts produced in vivo. The procedure involves use of RNA ligase to link a specific oligoribonucleotide to the 5' ends of cellular RNAs, followed by production of cDNA and amplification of the gene of interest by PCR. The method was used to identify the precise sites of transcription initiation within a 10-kb region of the pheromone-inducible conjugative plasmid pCF10 of Enterococcus faecalis. Results confirmed the 5' end of a very abundant, constitutively produced transcript (from prgQ) that had been mapped previously by primer extension and defined the initiation point of a less abundant, divergently transcribed message (from prgX). The method also showed that the 5' end of a pheromone-inducible transcript (prgB) that had been mapped by primer extension was generated by processing rather than new initiation. In addition, the results provided evidence for two promoters, 3 and 5 kb upstream of prgB, and indicated that only the transcripts originating 5 kb upstream may be capable of extending to prgB.

Amygdala activity at encoding correlated with long-term, free recall of emotional information.

Positron emission tomography of cerebral glucose metabolism in adult human subjects was used to investigate amygdaloid complex (AC) activity associated with the storage of long-term memory for emotionally arousing events. Subjects viewed two videos (one in each of two separate positron emission tomography sessions, separated by 3-7 days) consisting either of 12 emotionally arousing film clips ("E" film session) or of 12 relatively emotionally neutral film clips ("N" film session), and rated their emotional reaction to each film clip immediately after viewing it. Three weeks after the second session, memory for the videos was assessed in a free recall test. As expected, the subjects' average emotional reaction to the E films was higher than that for the N films. In addition, the subjects recalled significantly more E films than N films. Glucose metabolic rate of the right AC while viewing the E films was highly correlated with the number of E films recalled. AC activity was not significantly correlated with the number of N films recalled. The findings support the view derived from both animal and human investigations that the AC is selectively involved with the formation of enhanced long-term memory associated with emotionally arousing events.

The invariant system of coordinates of antibody molecules: prediction of the "standard" C alpha framework of VL and VH domains.

A new approach of comparing protein structures that does not involve the procedure of superposition is suggested. An invariant system of coordinates for immunoglobulin molecules that is based on the geometrical symmetry inherent to the variable domain light-chain (VL)-heavy-chain (VH) complex is described. The coordinates of the Calpha atoms in 22 immunoglobulin structures are calculated in the invariant system of coordinates. We found that 76 identical positions in this Calpha framework are symmetrical about the twofold axis. Comparison of the identical positions in these molecules allows us to select 96 positions in the light chains and 87 positions in the heavy chains whose Calpha atom coordinates are approximately the same. To check whether the average coordinates of Calpha atoms in these positions complies with the stereochemical requirements, we calculated Calpha-Calpha distances. Seventy-three positions of the light chains and 72 positions of the heavy chains satisfy the Calpha-Calpha distance criterion. The Calpha atoms in these positions are used for constructing the "standard" Calpha framework of VL and VH complexes. The average coordinates of Calpha atoms are presented.

Functional activation of the human ventrolateral frontal cortex during mnemonic retrieval of verbal information.

Regional cerebral blood flow was measured with positron emission tomography during the performance of a verbal free recall task, a verbal paired associate task, and tasks that required the production of verbal responses either by speaking or writing. Examination of the differences in regional cerebral blood flow between these conditions demonstrated that the left ventrolateral frontal cortical area 45 is involved in the recall of verbal information from long-term memory, in addition to its contribution to speech. The act of writing activated a network of areas involving posterior parietal cortex and sensorimotor areas but not ventrolateral frontal cortex.

The Ste locus, a component of the parasitic cry-Ste system of Drosophila melanogaster, encodes a protein that forms crystals in primary spermatocytes and mimics properties of the beta subunit of casein kinase 2.

Males of Drosophila melanogaster lacking the Y chromosome-linked crystal locus show multiple meiotic alterations including chromosome disorganization and prominent crystal formation in primary spermatocytes. These alterations are due to the derepression of the X chromosome-linked Stellate sequences. To understand how the derepression of the Stellate elements gives rise to these abnormalities, we have expressed the protein encoded by the Stellate sequences in bacteria and produced an antibody against the fusion protein. Immunostaining of crystal- testes has clearly shown that the Stellate protein is a major component of the crystals. Moreover, in vitro experiments have shown that this protein can interact with the catalytic alpha subunit of casein kinase 2 enzyme, altering its activity.

Spatial organization of retinal information about the direction of image motion.

The visual stimuli that elicit neural activity differ for different retinal ganglion cells and these cells have been categorized by the visual information that they transmit. If specific visual information is conveyed exclusively or primarily by a particular set of ganglion cells, one might expect the cells to be organized spatially so that their sampling of information from the visual field is complete but not redundant. In other words, the laterally spreading dendrites of the ganglion cells should completely cover the retinal plane without gaps or significant overlap. The first evidence for this sort of arrangement, which has been called a tiling or tessellation, was for the two types of "alpha" ganglion cells in cat retina. Other reports of tiling by ganglion cells have been made subsequently. We have found evidence of a particularly rigorous tiling for the four types of ganglion cells in rabbit retina that convey information about the direction of retinal image motion (the ON-OFF direction-selective cells). Although individual cells in the four groups are morphologically indistinguishable, they are organized as four overlaid tilings, each tiling consisting of like-type cells that respond preferentially to a particular direction of retinal image motion. These observations lend support to the hypothesis that tiling is a general feature of the organization of information outflow from the retina and clearly implicate mechanisms for recognition of like-type cells and establishment of mutually acceptable territories during retinal development.

Role of the monkey ventrolateral prefrontal cortex in the integration of contextual information for the selection and understanding of goal-directed actions

Action selection and organization are very complex processes that need to exploit contextual information and the retrieval of previously memorized information, as well as the integration of these different types of data. On the basis of anatomical connection with premotor and parietal areas involved in action goal coding, and on the data about the literature it seems appropriate to suppose that one of the most candidate involved in the selection of neuronal pools for the selection and organization of intentional actions is the prefrontal cortex. We recorded single ventrolateral prefrontal (VLPF) neurons activity while monkeys performed simple and complex manipulative actions aimed at distinct final goals, by employing a modified and more strictly controlled version of the grasp-to-eat(a food pellet)/grasp-to-place(an object) paradigm used in previous studies on parietal (Fogassi et al., 2005) and premotor neurons (Bonini et al., 2010). With this task we have been able both to evaluate the processing and integration of distinct (visual and auditory) contextual sequentially presented information in order to select the forthcoming action to perform and to examine the possible presence of goal-related activity in this portion of cortex. Moreover, we performed an observation task to clarify the possible contribution of VLPF neurons to the understanding of others’ goal-directed actions. Simple Visuo Motor Task (sVMT). We found four main types of neurons: unimodal sensory-driven, motor-related, unimodal sensory-and-motor, and multisensory neurons. We found a substantial number of VLPF neurons showing both a motor-related discharge and a visual presentation response (sensory-and-motor neurons), with remarkable visuo-motor congruence for the preferred target. Interestingly the discharge of multisensory neurons reflected a behavioural decision independently from the sensory modality of the stimulus allowing the monkey to make it: some encoded a decision to act/refraining from acting (the majority), while others specified one among the four behavioural alternatives. Complex Visuo Motor Task (cVMT). The cVMT was similar to the sVMT, but included a further grasping motor act (grasping a lid in order to remove it, before grasping the target) and was run in two modalities: randomized and in blocks. Substantially, motor-related and sensory-and-motor neurons tested in the cVMTrandomized were activated already during the first grasping motor act, but the selectivity for one of the two graspable targets emerged only during the execution of the second grasping. In contrast, when the cVMT was run in block, almost all these neurons not only discharged during the first grasping motor act, but also displayed the same target selectivity showed in correspondence of the hand contact with the target. Observation Task (OT). A great part of the neurons active during the OT showed a firing rate modulation in correspondence with the action performed by the experimenter. Among them, we found neurons significantly activated during the observation of the experimenter’s action (action observation-related neurons) and neurons responding not only to the action observation, but also to the presented cue stimuli (sensory-and-action observation-related neurons. Among the neurons of the first set, almost the half displayed a target selectivity, with a not clear difference between the two presented targets; Concerning to the second neuronal set, sensory-and-action related neurons, we found a low target selectivity and a not strictly congruence between the selectivity exhibited in the visual response and in the action observation.

Detection of concealed information using event-related potentials

Existe un interés considerable en hallar métodos que nos ayuden a saber cuándo una persona miente y cuándo dice la verdad desde un punto de vista forense. Actualmente, una de las líneas de investigación se inclina hacia el uso de potenciales relacionados con eventos. Se pretende hacer una revisión de los artículos que estudian estos procedimientos mediante distintos métodos: propiedades, fiabilidad, validez y limitaciones. Los resultados indican tasas de acierto en la discriminación de culpables en un rango de 7 al 100 por ciento, y en la de inocentes de 31 a 100 por ciento. La gran variabilidad y la posibilidad de “falsear” las respuestas llevan a cuestionar la inexactitud utilizada en algunos círculos mediáticos respecto a las cualidades y finalidades de dicha prueba. Se concluye la necesidad de profundizar más la posibilidad de que esta prueba sea utilizada con fines forenses.

Stop, Collaborate & Listen: How the Librarian/Publisher Relationship Can Facilitate the Development of the Information Literacy Curriculum

A librarian from the Florida Gulf Coast University (FGCU) and the Library Communications Manager at Taylor & Francis Group partnered to launch a collaborative information literacy pilot program focusing on assisting FGCU students and faculty navigate and understand the scholarly publishing process. This article describes how the idea was created, as well as steps involved in developing the publishing toolkit to help FGCU patrons. An overview of the pilot program was presented during the 2015 Charleston Conference as a poster session.

Model of Competencies for Decomposition of Human Behavior: Application to Control System of Robots

Humans and machines have shared the same physical space for many years. To share the same space, we want the robots to behave like human beings. This will facilitate their social integration, their interaction with humans and create an intelligent behavior. To achieve this goal, we need to understand how human behavior is generated, analyze tasks running our nerves and how they relate to them. Then and only then can we implement these mechanisms in robotic beings. In this study, we propose a model of competencies based on human neuroregulator system for analysis and decomposition of behavior into functional modules. Using this model allow separate and locate the tasks to be implemented in a robot that displays human-like behavior. As an example, we show the application of model to the autonomous movement behavior on unfamiliar environments and its implementation in various simulated and real robots with different physical configurations and physical devices of different nature. The main result of this study has been to build a model of competencies that is being used to build robotic systems capable of displaying behaviors similar to humans and consider the specific characteristics of robots.

Os Sistemas de Informação Geográfica como ferramenta de apoio à decisão em Protecção Civil

Dissertação apresentada à Escola Superior Agrária do Instituto Politécnico de Castelo Branco para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Sistemas de Informação Geográfica - Recursos Agro-Florestais e Ambientais.