Evolutionary conservation and ontogenetic emergence of neural algorithms

1998 ◽  
Vol 21 (2) ◽  
pp. 285-286
Author(s):  
Hermann Wagner ◽  
Dirk Kautz
Keyword(s):  
Molecular Mechanisms ◽  
Evolutionary Conservation ◽  
Computational Problem ◽  
Different Shapes ◽  
Plausible Scheme

Neural algorithms are conserved during evolution. Neurons with different shapes and using different molecular mechanisms can perform the same computation. However, evolutionary conservation of neural algorithms is not sufficient for claiming the realization of an algorithm for a specific computational problem. A plausible scheme for ontogenetic emergence of the structure of the algorithm must also be provided.

scholarly journals Transgenic Epigenetics: Using Transgenic Organisms to Examine Epigenetic Phenomena

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
Lori A. McEachern
Keyword(s):  
Molecular Mechanisms ◽  
Model Organism ◽  
Evolutionary Conservation ◽  
Model Organisms ◽  
Valuable Insight ◽  
Epigenetic Control ◽  
Transgenic Organisms ◽  
Epigenetic Analysis ◽  
Insight Into ◽  
Epigenetic Processes

Non-model organisms are generally more difficult and/or time consuming to work with than model organisms. In addition, epigenetic analysis of model organisms is facilitated by well-established protocols, and commercially-available reagents and kits that may not be available for, or previously tested on, non-model organisms. Given the evolutionary conservation and widespread nature of many epigenetic mechanisms, a powerful method to analyze epigenetic phenomena from non-model organisms would be to use transgenic model organisms containing an epigenetic region of interest from the non-model. Interestingly, while transgenic Drosophila and mice have provided significant insight into the molecular mechanisms and evolutionary conservation of the epigenetic processes that target epigenetic control regions in other model organisms, this method has so far been under-exploited for non-model organism epigenetic analysis. This paper details several experiments that have examined the epigenetic processes of genomic imprinting and paramutation, by transferring an epigenetic control region from one model organism to another. These cross-species experiments demonstrate that valuable insight into both the molecular mechanisms and evolutionary conservation of epigenetic processes may be obtained via transgenic experiments, which can then be used to guide further investigations and experiments in the species of interest.

scholarly journals Evolutionary Conservation of Reactions in Translation

2002 ◽  
Vol 66 (3) ◽  
pp. 460-485 ◽  
Author(s):  
M. Clelia Ganoza ◽  
Michael C. Kiel ◽  
Hiroyuki Aoki
Keyword(s):  
Molecular Mechanisms ◽  
Tertiary Structure ◽  
Evolutionary Conservation ◽  
Initiation Factor ◽  
Structural Studies ◽  
X Ray Diffraction ◽  
X Ray ◽  
Common Features ◽  
New Information ◽  
And Function

SUMMARY Current X-ray diffraction and cryoelectron microscopic data of ribosomes of eubacteria have shed considerable light on the molecular mechanisms of translation. Structural studies of the protein factors that activate ribosomes also point to many common features in the primary sequence and tertiary structure of these proteins. The reconstitution of the complex apparatus of translation has also revealed new information important to the mechanisms. Surprisingly, the latter approach has uncovered a number of proteins whose sequence and/or structure and function are conserved in all cells, indicating that the mechanisms are indeed conserved. The possible mechanisms of a new initiation factor and two elongation factors are discussed in this context.

scholarly journals Identification of Putative Programmed −1 Ribosomal Frameshift Signals in Large DNA Databases

1999 ◽  
Vol 9 (5) ◽  
pp. 417-427 ◽  
Author(s):  
Amy B. Hammell ◽  
Ronald C. Taylor ◽  
Stuart W. Peltz ◽  
Jonathan D. Dinman
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Evolutionary Conservation ◽  
Preliminary Survey ◽  
Ribosomal Frameshift ◽  
Cellular Gene ◽  
Ribosomal Frameshifting ◽  
Dna Databases ◽  
Homologous Genes ◽  
Normal Expression

The cis-acting elements that promote efficient ribosomal frameshifting in the −1 (5′) direction have been well characterized in several viral systems. Results from many studies have convincingly demonstrated that the basic molecular mechanisms governing programmed −1 ribosomal frameshifting are almost identical from yeast to humans. We are interested in testing the hypothesis that programmed −1 ribosomal frameshifting can be used to control cellular gene expression. Toward this end, a computer program was designed to search large DNA databases for consensus −1 ribosomal frameshift signals. The results demonstrated that consensus programmed −1 ribosomal frameshift signals can be identified in a substantial number of chromosomally encoded mRNAs and that they occur with frequencies from two- to sixfold greater than random in all of the databases searched. A preliminary survey of the databases resulting from the computer searches found that consensus frameshift signals are present in at least 21 homologous genes from different species, 2 of which are nearly identical, suggesting evolutionary conservation of function. We show that four previously described missense alleles of genes that are linked to human diseases would disrupt putative programmed −1 ribosomal frameshift signals, suggesting that the frameshift signal may be involved in the normal expression of these genes. We also demonstrate that signals found in the yeastRAS1 and the human CCR5 genes were able to promote significant levels of programmed −1 ribosomal frameshifting. The significance of these frameshifting signals in controlling gene expression is not known, however.

scholarly journals Evolutionary conservation of mechanisms for neural regionalization, proliferation and interconnection in brain development

2008 ◽  
Vol 5 (1) ◽  
pp. 112-116 ◽  
Author(s):  
Heinrich Reichert
Keyword(s):  
Brain Development ◽  
Molecular Mechanisms ◽  
Evolutionary Conservation ◽  
Model Systems ◽  
Embryonic Patterning ◽  
Developmental Control ◽  
Central Nervous Systems ◽  
Invertebrate Model ◽  
Circuit Formation ◽  
The Brain

Comparative studies of brain development in vertebrate and invertebrate model systems demonstrate remarkable similarities in expression and action of developmental control genes during embryonic patterning, neural proliferation and circuit formation in the brain. Thus, comparable sets of developmental control genes are involved in specifying the early brain primordium as well as in regionalized patterning along its anteroposterior and dorsoventral axes. Furthermore, similar cellular and molecular mechanisms underlie the formation and proliferation of neural stem cell-like progenitors that generate the neurons in the central nervous systems. Finally, neural identity and some complex circuit interconnections in specific brain domains appear to be comparable in vertebrates and invertebrates and may depend on similar developmental control genes.

Blood vessel differentiation and growth

2018 ◽  
Author(s):  
Rui Benedito ◽  
Arndt F. Siekmann
Keyword(s):  
Vascular Function ◽  
Molecular Mechanisms ◽  
Vascular System ◽  
Evolutionary Conservation ◽  
Model Systems ◽  
Molecular Pathways ◽  
Life And Death ◽  
Cellular Processes ◽  
Origin Life ◽  
Lines Of Evidence

A variety of diseases are related to or dependent on the vascular system. Several lines of evidence show that adequate manipulation of the vascular function in disease requires targeting and interfering with the same molecular pathways and cellular processes that act to form vessels during embryo or organ development. Therefore an understanding of the mechanisms that regulate vascular development in this non-pathological context is of major importance, since it may lead to better ways of treating vascular-related pathologies. This chapter covers the most significant cellular and molecular mechanisms involved in the origin, life, and death of the endothelial cellwhich is involved in several important developmental and pathological processes. Most of the mechanisms described were identified in animal model systems. However, owing to the high evolutionary conservation of these, they are likely be very similar to those occurring in humans and in disease.

scholarly journals Poly(ADP-Ribose) Polymerase-3 Regulates Regeneration in Planarians

2020 ◽  
Vol 21 (3) ◽  
pp. 875
Author(s):  
Paul G. Barghouth ◽  
Peter Karabinis ◽  
Andie Venegas ◽  
Néstor J. Oviedo
Keyword(s):  
Large Scale ◽  
Molecular Mechanisms ◽  
Evolutionary Conservation ◽  
Covalent Attachment ◽  
Post Translational Modification ◽  
Cellular Events ◽  
Adult Body ◽  
Scale Regeneration ◽  
The Central Nervous System ◽  
Transcription And Replication

Protein ADP-ribosylation is a reversible post-translational modification (PTM) process that plays fundamental roles in cell signaling. The covalent attachment of ADP ribose polymers is executed by PAR polymerases (PARP) and it is essential for chromatin organization, DNA repair, cell cycle, transcription, and replication, among other critical cellular events. The process of PARylation or polyADP-ribosylation is dynamic and takes place across many tissues undergoing renewal and repair, but the molecular mechanisms regulating this PTM remain mostly unknown. Here, we introduce the use of the planarian Schmidtea mediterranea as a tractable model to study PARylation in the complexity of the adult body that is under constant renewal and is capable of regenerating damaged tissues. We identified the evolutionary conservation of PARP signaling that is expressed in planarian stem cells and differentiated tissues. We also demonstrate that Smed-PARP-3 homolog is required for proper regeneration of tissues in the anterior region of the animal. Furthermore, our results demonstrate, Smed-PARP-3(RNAi) disrupts the timely location of injury-induced cell death near the anterior facing wounds and also affects the regeneration of the central nervous system. Our work reveals novel roles for PARylation in large-scale regeneration and provides a simplified platform to investigate PARP signaling in the complexity of the adult body.

scholarly journals Snrk-1 is involved in multiple steps of angioblast development and acts via notch signaling pathway in artery-vein specification in vertebrates

Blood ◽  
2009 ◽  
Vol 113 (5) ◽  
pp. 1192-1199 ◽  
Author(s):  
Chang Z. Chun ◽  
Sukhbir Kaur ◽  
Ganesh V. Samant ◽  
Ling Wang ◽  
Kallal Pramanik ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Essential Role ◽  
Molecular Mechanisms ◽  
Human Gene ◽  
Evolutionary Conservation ◽  
Notch Signaling Pathway ◽  
Loss Of Function ◽  
Arteries And Veins

Abstract In vertebrates, molecular mechanisms dictate angioblasts' migration and subsequent differentiation into arteries and veins. In this study, we used a microarray screen to identify a novel member of the sucrose nonfermenting related kinase (snrk-1) family of serine/threonine kinases expressed specifically in the embryonic zebrafish vasculature and investigated its function in vivo. Using gain- and loss-of-function studies in vivo, we show that Snrk-1 plays an essential role in the migration, maintenance, and differentiation of angioblasts. The kinase function of Snrk-1 is critical for migration and maintenance, but not for the differentiation of angioblasts. In vitro, snrk-1 knockdown endothelial cells show only defects in migration. The snrk-1 gene acts downstream or parallel to notch and upstream of gridlock during artery-vein specification, and the human gene compensates for zebrafish snrk-1 knockdown, suggesting evolutionary conservation of function.

Transcription factor/DNA interactions visualized by electron spectroscopic imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 450-451
Author(s):  
David P. Bazett-Jones ◽  
Mark L. Brown
Keyword(s):  
Transcription Factor ◽  
Dna Sequences ◽  
Transcription Initiation ◽  
Molecular Mechanisms ◽  
Phosphorus Content ◽  
Spectroscopic Imaging ◽  
Electron Spectroscopic Imaging ◽  
Dna Backbone ◽  
Two Parameters ◽  
High Level

A multisubunit RNA polymerase enzyme is ultimately responsible for transcription initiation and elongation of RNA, but recognition of the proper start site by the enzyme is regulated by general, temporal and gene-specific trans-factors interacting at promoter and enhancer DNA sequences. To understand the molecular mechanisms which precisely regulate the transcription initiation event, it is crucial to elucidate the structure of the transcription factor/DNA complexes involved. Electron spectroscopic imaging (ESI) provides the opportunity to visualize individual DNA molecules. Enhancement of DNA contrast with ESI is accomplished by imaging with electrons that have interacted with inner shell electrons of phosphorus in the DNA backbone. Phosphorus detection at this intermediately high level of resolution (≈lnm) permits selective imaging of the DNA, to determine whether the protein factors compact, bend or wrap the DNA. Simultaneously, mass analysis and phosphorus content can be measured quantitatively, using adjacent DNA or tobacco mosaic virus (TMV) as mass and phosphorus standards. These two parameters provide stoichiometric information relating the ratios of protein:DNA content.

Dissection of the molecular mechanisms of protein targeting to the peroxisome using immunofluorescence and immunocryoelectron microscopies

1990 ◽  
Vol 48 (3) ◽  
pp. 44-45
Author(s):  
G-A. Keller ◽  
S. J. Gould ◽  
S. Subramani ◽  
S. Krisans
Keyword(s):  
Mammalian Cells ◽  
Molecular Mechanisms ◽  
Protein Targeting ◽  
Firefly Luciferase ◽  
Peroxisomal Enzyme ◽  
Transfected Cells ◽  
Peroxisomal Targeting ◽  
Targeting Signal ◽  
Series Of Experiments ◽  
Peroxisomal Targeting Signal

Subcellular compartments within eukaryotic cells must each be supplied with unique sets of proteins that must be directed to, and translocated across one or more membranes of the target organelles. This transport is mediated by cis- acting targeting signals present within the imported proteins. The following is a chronological account of a series of experiments designed and carried out in an effort to understand how proteins are targeted to the peroxisomal compartment.-We demonstrated by immunocryoelectron microscopy that the enzyme luciferase is a peroxisomal enzyme in the firefly lantern. -We expressed the cDNA encoding firefly luciferase in mammalian cells and demonstrated by immunofluorescence that the enzyme was transported into the peroxisomes of the transfected cells. -Using deletions, linker insertions, and gene fusion to identify regions of luciferase involved in its transport to the peroxisomes, we demonstrated that luciferase contains a peroxisomal targeting signal (PTS) within its COOH-terminal twelve amino acid.

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