Strategies for Enhancing Communication Between Students, Academics and Researchers Participating in Large-Scale Undergraduate Research Projects

Spreading the word about science and inspiring people to connect with the processes and outcomes of science, whether as researchers, educators, students, industry professionals or consumers, is essential in forging stronger links among scientists and with the communities that stand to benefit from their work. How do we nurture inspirational scientific communication in the context of university undergraduate science education, particularly in large cohort settings that are often more mind-numbing than soul-stirring? Communicating your own discoveries effectively is the zenith of scientific endeavour. We have developed a large-scale original research experience for second or third year undergraduate biomedical science students. The students undertake ‘mini’ projects and present their research outcomes verbally, visually and in a written format suitable for journal publication. This helps students understand how science works and develops their ability to explain scientific concepts to their peers and others. To promote ‘original research’ to students in ways that inspire and motivate participation, we have also evolved strategies to help instructors and researchers communicate successfully with large student cohorts, including a wiki for secure data storage, FAQ sheets and databases of bioinformatics tools. Introduction of the research experience has improved survey scores overall and on items relating to communication. These strategies are applicable to any course seeking to introduce students to the practice of research and communication of research outcomes. Our experience suggests optimal multidimensional communication may be best achieved through instructors, researchers and students working together to develop effective stratagems for surviving and thriving in the information-dense, digital world

Post-Transcriptional Trafficking and Regulation of Neuronal Gene Expression

Intracellular messenger RNA (mRNA) traffic and translation must be highly regulated, both temporally and spatially, within eukaryotic cells to support the complex functional partitioning. This capacity is essential in neurons because it provides a mechanism for rapid input-restricted activity-dependent protein synthesis in individual dendritic spines. While this feature is thought to be important for synaptic plasticity, the structures and mechanisms that support this capability are largely unknown. Certainly specialized RNA binding proteins and binding elements in the 3′ untranslated region (UTR) of translationally regulated mRNA are important, but the subtlety and complexity of this system suggests that an intermediate “specificity” component is also involved. Small non-coding microRNA (miRNA) are essential for CNS development and may fulfill this role by acting as the guide strand for mediating complex patterns of post-transcriptional regulation. In this review we examine post-synaptic gene regulation, mRNA trafficking and the emerging role of post-transcriptional gene silencing in synaptic plasticity

Roles of post-transcriptional gene silencing in the functional regulation of neuronal gene expression and plasticity

Research Doctorate - Doctor of Philosophy (PhD)The phenomenon of synaptic plasticity in neurons is poorly understood, but is known to rely on appropriate temporo-spatial availability of mRNA. The complexity of neuronal cytoarchitecture necessitates an exquisite regulatory matrix that begins with the establishment of subcellular compartments during differentiation, however the molecular mechanisms that support trafficking and translational control are not well defined. The class of short, non-coding RNA molecules known as microRNA (miRNA) have well-established roles in neuronal differentiation and development, and growing evidence suggests that miRNA-mediated post-transcriptional gene silencing (PTGS) may be an important mediator of synaptic plasticity. To investigate this in a human genetic context, techniques were established for isolating distinct subcellular fractions of the SH-SY5Y neuroblastoma cell line and examining genome-wide miRNA and mRNA responses to neuronal cues such as differentiation and depolarisation. These studies identified a pattern of activity-associated miRNA expression changes unique to the neurites that was revealed to be connected to the release of exosomes from this compartment. Interestingly, some miRNA were found to be preferentially enriched in the nucleus. A motif detected within these sequences lead to the unexpected identification of putative transcription factor binding elements within their precursors, showing support for novel roles of miRNA outside PTGS. Connecting these findings was the unanticipated contribution of primate-specific miRNA, resulting in significant ontological enrichment of neuronal functionality. This demonstrates the importance and relevance of these cells as a vehicle for explicating the mechanisms underlying higher brain functions. Ultimately, substantial evidence was obtained to support a role for miRNA and the components of PTGS in the functional compartmentalisation of neurons and the response to activity, though further methodological developments are required to elaborate the novel mechanisms of miRNA function and investigate the direct contribution of miRNA-mediated PTGS to enabling real-time, activity-driven synaptic modification

miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif

While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons

BDNF and the maturation of posttranscriptional regulatory networks in human SH-SY5Y neuroblast differentiation

The SH-SY5Y culture system is a convenient neuronal model with the potential to elaborate human/primate-specific transcription networks and pathways related to human cognitive disorders. While this system allows for the exploration of specialized features in the human genome, there is still significant debate about how this model should be implemented, and its appropriateness for answering complex functional questions related to human neural architecture. In view of these questions we sought to characterize the posttranscriptional regulatory structure of the two-stage ATRA differentiation, BDNF maturation protocol proposed by Encinas et al. (2000) using integrative whole-genome gene and microRNA (miRNA) expression analysis. We report that ATRA-BDNF induced significant increases in expression of key synaptic genes, brain-specific miRNA and miRNA biogenesis machinery, and in AChE activity, compared with ATRA alone. Functional annotation clustering associated BDNF more significantly with neuronal terms, and with synaptic terms not found in ATRA-only clusters. While our results support use of SH-SY5Y as a neuronal model, we advocate considered selection of the differentiation agent/s relative to the system being modeled

miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif

Tesis (Ingeniero Mecánico Eléctrico)--Universidad de Piura. Facultad de Ingeniería. Programa Académico de Ingeniería Mecánico Eléctrica, 2015.El objetivo de la investigación es desarrollar un sistema de supervisión y control de pivotes centrales de riego integrando herramientas y tecnologías acorde a la necesidad del proyecto. Para ello, se explica a detalle el protocolo Modbus, la forma en que se construye una trama de comunicación y la sintaxis del mismo, además se usan equipos de automatización, ejemplo de ellos son los PLCs. Todo esto basado en el proyecto de irrigación Agrolmos. Finalmente, el estudio ha permitido la integración de varios sistemas para implementar el actual sistema de control de riego del proyecto Agrolmos asegurando una buena producción y rentabilidad de estos terrenos

miRNA Enriched in Human Neuroblast Nuclei Bind the MAZ Transcription Factor and Their Precursors Contain the MAZ Consensus Motif

While the cytoplasmic function of microRNA (miRNA) as post-transcriptional regulators of mRNA has been the subject of significant research effort, their activity in the nucleus is less well characterized. Here we use a human neuronal cell model to show that some mature miRNA are preferentially enriched in the nucleus. These molecules were predominantly primate-specific and contained a sequence motif with homology to the consensus MAZ transcription factor binding element. Precursor miRNA containing this motif were shown to have affinity for MAZ protein in nuclear extract. We then used Ago1/2 RIP-Seq to explore nuclear miRNA-associated mRNA targets. Interestingly, the genes for Ago2-associated transcripts were also significantly enriched with MAZ binding sites and neural function, whereas Ago1-transcripts were associated with general metabolic processes and localized with SC35 spliceosomes. These findings suggest the MAZ transcription factor is associated with miRNA in the nucleus and may influence the regulation of neuronal development through Ago2-associated miRNA induced silencing complexes. The MAZ transcription factor may therefore be important for organizing higher order integration of transcriptional and post-transcriptional processes in primate neurons

Ontogeny of small RNA in the regulation of mammalian brain development

Background: MicroRNAs (miRNAs) play a pivotal role in coordinating messenger RNA (mRNA) transcription and stability in almost all known biological processes, including the development of the central nervous system. Despite our broad understanding of their involvement, we still have a very sparse understanding of specifically how miRNA contribute to the strict regional and temporal regulation of brain development. Accordingly, in the current study we have examined the contribution of miRNA in the developing rat telencephalon and mesencephalon from just after neural tube closure till birth using a genome-wide microarray strategy. Results: We identified temporally distinct expression patterns in both the telencephalon and mesencephalon for both miRNAs and their target genes. We demonstrate direct miRNA targeting of several genes involved with the migration, differentiation and maturation of neurons. Conclusions: Our findings suggest that miRNA have significant implications for the development of neural structure and support important mechanisms that if disrupted, may contribute to or drive neurodevelopmental disorders