GENE NETWORKS UNIQUE TO HUMAN BRAINS SHED LIGHT ON EVOLUTIONARY DIVERGENCE FROM CHIMPANZEES

2006 ◽  
Vol 6 (24) ◽  
pp. 6-7
Author(s):  
Kurt Samson
Keyword(s):  
Gene Networks ◽  
Evolutionary Divergence ◽  
Human Brains ◽  
Shed Light

scholarly journals The evolutionary development of plant body plans

2009 ◽  
Vol 36 (8) ◽  
pp. 682 ◽  
Author(s):  
Karl J. Niklas ◽  
Ulrich Kutschera
Keyword(s):  
Gene Networks ◽  
Functional Divergence ◽  
Evolutionary Developmental Biology ◽  
The Body ◽  
Regulatory Mechanisms ◽  
Evolutionary Development ◽  
Evolutionary Divergence ◽  
Early Maturation ◽  
Photosynthetic Eukaryotes ◽  
Cladistic Analyses

Evolutionary developmental biology, cladistic analyses, and paleontological insights make it increasingly clear that regulatory mechanisms operating during embryogenesis and early maturation tend to be highly conserved over great evolutionary time scales, which can account for the conservative nature of the body plans in the major plant and animal clades. At issue is whether morphological convergences in body plans among evolutionarily divergent lineages are the result of adaptive convergence or ‘genome recall’ and ‘process orthology’. The body plans of multicellular photosynthetic eukaryotes (‘plants’) are reviewed, some of their important developmental/physiological regulatory mechanisms discussed, and the evidence that some of these mechanisms are phyletically ancient examined. We conclude that endosymbiotic lateral gene transfers, gene duplication and functional divergence, and the co-option of ancient gene networks were key to the evolutionary divergence of plant lineages.

Using Functional Linkage Gene Networks to Study Human Diseases

2011 ◽  
pp. 275-293
Author(s):  
Bolan Linghu ◽  
Guohui Liu ◽  
Yu Xia
Keyword(s):  
Gene Networks ◽  
Molecular Mechanisms ◽  
Common Disease ◽  
Disease Genes ◽  
New Disease ◽  
Cellular Functions ◽  
Proteomic Data ◽  
Functional Linkage ◽  
Disease Associations ◽  
Shed Light

A major challenge in the post-genomic era is to understand the specific cellular functions of individual genes and how dysfunctions of these genes lead to different diseases. As an emerging area of systems biology, gene networks have been used to shed light on gene function and human disease. In this chapter, first the existence of functional association for genes working in a common biological process or implicated in a common disease is demonstrated. Next, approaches to construct the functional linkage gene network (FLN) based on genomic and proteomic data integration are reviewed. Finally, two FLN-based applications related to diseases are reviewed: prediction of new disease genes and therapeutic targets, and identification of disease-disease associations at the molecular level. Both of these applications bring new insights into the molecular mechanisms of diseases, and provide new opportunities for drug discovery.

scholarly journals Exome Sequencing Landscape Analysis in Ovarian Clear Cell Carcinoma Shed Light on Key Chromosomal Regions and Mutation Gene Networks

2017 ◽  
Vol 187 (10) ◽  
pp. 2246-2258 ◽  
Author(s):  
Ryusuke Murakami ◽  
Noriomi Matsumura ◽  
J.B. Brown ◽  
Koichiro Higasa ◽  
Takanobu Tsutsumi ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Exome Sequencing ◽  
Gene Networks ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Landscape Analysis ◽  
Ovarian Clear Cell Carcinoma ◽  
Shed Light

scholarly journals Conserved developmental processes and the formation of evolutionary novelties: examples from butterfly wings

2008 ◽  
Vol 363 (1496) ◽  
pp. 1549-1556 ◽  
Author(s):  
Suzanne V Saenko ◽  
Vernon French ◽  
Paul M Brakefield ◽  
Patrícia Beldade
Keyword(s):  
Gene Networks ◽  
Evolutionary Developmental Biology ◽  
Model Organisms ◽  
Bicyclus Anynana ◽  
Developmental Processes ◽  
Key Issues ◽  
Or Gene ◽  
Morphological Novelties ◽  
Shed Light ◽  
Evolutionary Novelties

The origin and diversification of evolutionary novelties—lineage-specific traits of new adaptive value—is one of the key issues in evolutionary developmental biology. However, comparative analysis of the genetic and developmental bases of such traits can be difficult when they have no obvious homologue in model organisms. The finding that the evolution of morphological novelties often involves the recruitment of pre-existing genes and/or gene networks offers the potential to overcome this challenge. Knowledge about shared developmental processes obtained from extensive studies in model organisms can then be used to understand the origin and diversification of lineage-specific structures. Here, we illustrate this approach in relation to eyespots on the wings of Bicyclus anynana butterflies. A number of spontaneous mutations isolated in the laboratory affect eyespots, lepidopteran-specific features, and also processes that are shared by most insects. We discuss how eyespot mutants with disturbed embryonic development may help elucidate the genetic pathways involved in eyespot formation, and how venation mutants with altered eyespot patterns might shed light on mechanisms of eyespot development.

scholarly journals Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa

2021 ◽  
Author(s):  
Olayinka S Okoh ◽  
Nicholas Israel Nii-Trebi ◽  
Abdulrokeeb Jakkari ◽  
Tosin Titus Olaniran ◽  
Tosin Yetunde Senbadejo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Likelihood Inference ◽  
Evolutionary Divergence ◽  
African Countries ◽  
Protein Motifs ◽  
Large Heterogeneity ◽  
One Year ◽  
Inference Methods ◽  
Shed Light

COVID-19 disease dynamics have been widely studied in different settings around the globe, but little is known about these patterns in the African continent. To investigate the epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa, more than 2400 complete genomes from 33 African countries were retrieved from the GISAID database and analyzed. We investigated their diversity using various clade and lineage nomenclature systems, reconstructed their evolutionary divergence and history using maximum likelihood inference methods, and studied the case and death trends in the continent. We also examined potential repeat patterns and motifs across the sequences. In this study, we show that after almost one year of the COVID-19 pandemic, only 143 out of the 782 Pango lineages found worldwide circulated in Africa, with five different lineages dominating in distinct periods of the pandemic. Analysis of the number of reported deaths in Africa also revealed large heterogeneity across the continent. Phylogenetic analysis revealed that African viruses cluster closely with those from all continents but more notably with viruses from Europe. However, the extent of viral diversity observed among African genomes is closest to that of the Oceania outbreak, most likely due to genomic under-surveillance in Africa. We also identified two motifs that could function as integrin-binding sites and N-glycosylation domains. These results shed light on the evolutionary dynamics of the circulating viral strains in Africa, elucidate the functions of protein motifs present in the genome sequences, and emphasize the need to expand genomic surveillance efforts in the continent to better understand the molecular, evolutionary, epidemiological, and spatiotemporal dynamics of the COVID-19 pandemic in Africa.

scholarly journals Transcriptional and morpho-physiological responses of Marchantia polymorpha upon phosphate starvation

2020 ◽  
Author(s):  
Felix Rico-Reséndiz ◽  
Sergio Alan Cervantes-Pérez ◽  
Annie Espinal-Centeno ◽  
Melissa Dipp-Álvarez ◽  
Araceli Oropeza-Aburto ◽  
...  
Keyword(s):  
Gene Networks ◽  
Regulatory Element ◽  
Phosphate Starvation ◽  
Plant Evolution ◽  
Marchantia Polymorpha ◽  
Phylogenomic Analysis ◽  
Physiological Level ◽  
Plant Phylogeny ◽  
Pi Starvation ◽  
Shed Light

AbstractPhosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (eg. PHR1-SPX1 and STOP1-ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes and MpMYB14, an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting preference for citrate exudation. Analysis of MpPHR1 binding sequences (P1BS) shows enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.Significance StatementThis study unravels the transcriptional and morphophysiological mechanisms executed by the non-vascular, and rootless, plant Marchantia polymorpha upon phosphate starvation conditions. The findings in this study shed light on the mechanisms that early land plants may have developed for the conquest of substrates poor in available phosphate, some of which are still conserved by current-day plants. Moreover, our results open several working hypotheses and novel perspectives for the study of Pi-starvation responses along plant evolution.

scholarly journals Integrated multi-omics analysis reveals common and distinct dysregulated pathways for genetic subtypes of Frontotemporal Dementia

2021 ◽  
Author(s):  
Kevin Menden ◽  
Margherita Francescatto ◽  
Tenzin Niyma ◽  
Cornelis Blauwendraat ◽  
Ashutosh Dhingra ◽  
...  
Keyword(s):  
Frontotemporal Dementia ◽  
Molecular Mechanisms ◽  
Neuronal Cell ◽  
Rna Seq ◽  
Data Resource ◽  
Cellular Models ◽  
Patient Groups ◽  
Cellular Pathways ◽  
Human Brains ◽  
Shed Light

Abstract Understanding the molecular mechanisms underlying frontotemporal dementia (FTD) is essential for the development of successful therapies. Here we integrated transcriptomic and epigenomic analyses of postmortem human brains of FTD patients with mutations in MAPT, GRN and C9orf72 and detected common and distinct dysregulated cellular pathways between patient groups. Our results highlight that excitatory neurons are the most vulnerable neuronal cell type and that vascular aberrations are a common hallmark in FTD. Via integration of multi-omics data, we detected several transcription factors and pathways which regulate the strong neuroinflammation observed in FTD-GRN. Small RNA-seq data and verification experiments in cellular models identified up-regulated miRNAs that inhibit cellular trafficking pathways in FTD and lead to microglial activation. These findings shed light on novel mechanistic and pathophysiological hallmarks of FTD. The data represent the 1st phase of a multi-omics, multi-model data resource for FTD research which allows in-depth molecular research into disease mechanisms that will further mechanistic FTD research.

Concluding Remarks

2021 ◽  
pp. 123-128
Author(s):  
Susan D. Healy
Keyword(s):  
Geographical Location ◽  
Ecological Factors ◽  
Brain Regions ◽  
The Other ◽  
Cognitive Test ◽  
Fitness Benefits ◽  
Multiple Species ◽  
Human Brains ◽  
Shed Light

In this chapter, I conclude that ecology has been shown to explain variation in the size of brain regions in multiple species, which is not the case for any of the other hypotheses. I go on to suggest the steps that need to be taken to collect the requisite data: collecting data on size of brain regions with identifiable function, choosing the appropriate cognitive test and collecting data from appropriate species, better quantification of ecological factors along with data collected from individuals that differ in age, sex, and geographical location, and demonstration that better cognition confers fitness benefits. Each of these is in both principle and practice feasible, if challenging to assemble for one hypothesis/taxonomic group. With these data, we may eventually be able to shed light on what has caused human brains to become relatively large.

Elucidating cyclic AMP signaling in subcellular domains with optogenetic tools and fluorescent biosensors

2019 ◽  
Vol 47 (6) ◽  
pp. 1733-1747 ◽  
Author(s):  
Christina Klausen ◽  
Fabian Kaiser ◽  
Birthe Stüven ◽  
Jan N. Hansen ◽  
Dagmar Wachten
Keyword(s):  
Cyclic Amp ◽  
Adenosine Monophosphate ◽  
Adenylyl Cyclases ◽  
Temporal Precision ◽  
Fluorescent Biosensors ◽  
Subcellular Domains ◽  
Spatio Temporal ◽  
Hydrolysis Of ◽  
Shed Light ◽  
Cyclic Amp Signaling

The second messenger 3′,5′-cyclic nucleoside adenosine monophosphate (cAMP) plays a key role in signal transduction across prokaryotes and eukaryotes. Cyclic AMP signaling is compartmentalized into microdomains to fulfil specific functions. To define the function of cAMP within these microdomains, signaling needs to be analyzed with spatio-temporal precision. To this end, optogenetic approaches and genetically encoded fluorescent biosensors are particularly well suited. Synthesis and hydrolysis of cAMP can be directly manipulated by photoactivated adenylyl cyclases (PACs) and light-regulated phosphodiesterases (PDEs), respectively. In addition, many biosensors have been designed to spatially and temporarily resolve cAMP dynamics in the cell. This review provides an overview about optogenetic tools and biosensors to shed light on the subcellular organization of cAMP signaling.

Sentence-Based Experience Logging in New Hearing Aid Users

2020 ◽  
Vol 29 (3S) ◽  
pp. 631-637
Author(s):  
Katja Lund ◽  
Rodrigo Ordoñez ◽  
Jens Bo Nielsen ◽  
Dorte Hammershøi
Keyword(s):  
Hearing Aid ◽  
Patient Experiences ◽  
Online Tool ◽  
Rehabilitation Process ◽  
Hearing Rehabilitation ◽  
Clinical Observations ◽  
Hearing Aid Use ◽  
Wide Range ◽  
Insight Into ◽  
Shed Light

Purpose The aim of this study was to develop a tool to gain insight into the daily experiences of new hearing aid users and to shed light on aspects of aided performance that may not be unveiled through standard questionnaires. Method The tool is developed based on clinical observations, patient experiences, expert involvement, and existing validated hearing rehabilitation questionnaires. Results An online tool for collecting data related to hearing aid use was developed. The tool is based on 453 prefabricated sentences representing experiences within 13 categories related to hearing aid use. Conclusions The tool has the potential to reflect a wide range of individual experiences with hearing aid use, including auditory and nonauditory aspects. These experiences may hold important knowledge for both the patient and the professional in the hearing rehabilitation process.

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