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Gene network evolution

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https://www.readbyqxmd.com/read/28818668/a-bipolar-role-of-the-transcription-factor-erg-for-cnidarian-germ-layer-formation-and-apical-domain-patterning
#1
Aldine R Amiel, Hereroa Johnston, Taylor Chock, Paul Dahlin, Marta Iglesias, Michael Layden, Eric Röttinger, Mark Q Martindale
Germ layer formation and axial patterning are biological processes that are tightly linked during embryonic development of most metazoans. In addition to canonical WNT, it has been proposed that ERK-MAPK signaling is involved in specifying oral as well as aboral territories in cnidarians. However, the effector and the molecular mechanism underlying latter phenomenon is unknown. By screening for potential effectors of ERK-MAPK signaling in both domains, we identified a member of the ETS family of transcription factors, Nverg that is bi-polarily expressed prior to gastrulation...
August 14, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28816684/a-multiobjective-evolutionary-algorithm-based-on-structural-and-attribute-similarities-for-community-detection-in-attributed-networks
#2
Zhangtao Li, Jing Liu, Kai Wu
Most of the existing community detection algorithms are based on vertex connectivity. While in many real networks, each vertex usually has one or more attributes describing its properties which are often homogeneous in a cluster. Such networks can be modeled as attributed graphs, whose attributes sometimes are equally important to topological structure in graph clustering. One important challenge is to detect communities considering both topological structure and vertex properties simultaneously. To this propose, a multiobjective evolutionary algorithm based on structural and attribute similarities (MOEA-SA) is first proposed to solve the attributed graph clustering problems in this paper...
August 16, 2017: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/28811313/a-key-role-for-foxq2-in-anterior-head-and-central-brain-patterning-in-insects
#3
Peter Kitzmann, Matthias Weißkopf, Magdalena Ines Schacht, Gregor Bucher
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the red flour beetle Tribolium castaneum ortholog of foxQ2 (Tc-foxQ2) as a novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression...
August 15, 2017: Development
https://www.readbyqxmd.com/read/28809832/phagocytosis-assay-for-apoptotic-cells-in-drosophila-embryos
#4
Saori Nonaka, Aki Hori, Yoshinobu Nakanishi, Takayuki Kuraishi
The molecular mechanisms underlying the phagocytosis of apoptotic cells need to be elucidated in more detail because of its role in immune and inflammatory intractable diseases. We herein developed an experimental method to investigate phagocytosis quantitatively using the fruit fly Drosophila, in which the gene network controlling engulfment reactions is evolutionally conserved from mammals. In order to accurately detect and count engulfing and un-engulfing phagocytes using whole animals, Drosophila embryos were homogenized to obtain dispersed cells including phagocytes and apoptotic cells...
August 3, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28809429/dissection-of-the-module-network-implementation-lemontree-enhancements-towards-applications-in-metagenomics-and-translation-in-autoimmune-maladies
#5
Youtao Lu, Xiaoyuan Zhou, Christine Nardini
Under the current deluge of omics, module networks distinctively emerge as methods capable of not only identifying inherently coherent groups (modules), thus reducing dimensionality, but also hypothesizing cause-effect relationships between modules and their regulators. Module networks were first designed in the transcriptomic era and further exploited in the multi-omic context to assess (for example) miRNA regulation of gene expression. Despite a number of available implementations, expansion of module networks to other omics is constrained by a limited characterization of the solutions' (modules plus regulators) accuracy and stability - an immediate need for the better characterization of molecular biology complexity in silico...
August 15, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28808102/recruitment-of-pre-existing-networks-during-the-evolution-of-c4-photosynthesis
#6
REVIEW
Ivan Reyna-Llorens, Julian M Hibberd
During C4 photosynthesis, CO2 is concentrated around the enzyme RuBisCO. The net effect is to reduce photorespiration while increasing water and nitrogen use efficiencies. Species that use C4 photosynthesis have evolved independently from their C3 ancestors on more than 60 occasions. Along with mimicry and the camera-like eye, the C4 pathway therefore represents a remarkable example of the repeated evolution of a highly complex trait. In this review, we provide evidence that the polyphyletic evolution of C4 photosynthesis is built upon pre-existing metabolic and genetic networks...
September 26, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28808032/mechanical-constraint-from-growing-jaw-facilitates-mammalian-dental-diversity
#7
Elodie Renvoisé, Kathryn D Kavanagh, Vincent Lazzari, Teemu J Häkkinen, Ritva Rice, Sophie Pantalacci, Isaac Salazar-Ciudad, Jukka Jernvall
Much of the basic information about individual organ development comes from studies using model species. Whereas conservation of gene regulatory networks across higher taxa supports generalizations made from a limited number of species, generality of mechanistic inferences remains to be tested in tissue culture systems. Here, using mammalian tooth explants cultured in isolation, we investigate self-regulation of patterning by comparing developing molars of the mouse, the model species of mammalian research, and the bank vole...
August 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28801915/manganese-and-1-methyl-4-phenylpyridinium-mpp-induced-neurotoxicity-indicate-differences-in-morphological-electrophysiological-and-genome-wide-alterations-implications-for-idiopathic-parkinson-s-disease
#8
Rajeswara Babu Mythri, Narayana Reddy Raghunath, Santosh Chandrakant Narwade, Mirazkar DasharathaRao Pandareesh, Kollarkandi Rajesh Sabitha, Mohamad Aiyaz, Bipin Chand, Manas Sule, Krittika Ghosh, Senthil Kumar, Bhagyalakshmi Shankarappa, Soundarya Soundararajan, Phalguni Anand Alladi, Meera Purushottam, Narayanappa Gayathri, Deepti Dileep Deobagkar, Thenkanidiyoor Rao Laxmi, Srinivas Bharath Muchukunte Mukunda
Idiopathic Parkinson's disease (iPD) and manganese-induced atypical Parkinsonism are characterized by movement disorder and nigrostriatal pathology. Although clinical features, brain region involved and responsiveness to levodopa distinguish both, differences at the neuronal level are largely unknown. We studied the morphological, neurophysiological and molecular differences in dopaminergic neurons exposed to the PD toxin 1-methyl-4-phenylpyridinium ion (MPP(+) ) and manganese (Mn) followed by validation in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and Mn mouse models...
August 12, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28800289/viral-master-circuits-from-discovery-to-new-therapy-targets
#9
Anand Pai, Leor S Weinberger
Current antivirals effectively target diverse viruses at various stages of their life cycles. Nevertheless, curative therapy has remained elusive for important pathogens, such as human immunodeficiency virus type 1 (HIV-1) and herpesviruses, in large part due to viral latency and the evolution of resistance to existing therapies. Here, we review the discovery of viral master circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression programs (i.e., between active, latent, and abortive fates)...
August 11, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28798667/the-foxp2-driven-network-in-developmental-disorders-and-neurodegeneration
#10
Franz Oswald, Patricia Klöble, André Ruland, David Rosenkranz, Bastian Hinz, Falk Butter, Sanja Ramljak, Ulrich Zechner, Holger Herlyn
The transcription repressor FOXP2 is a crucial player in nervous system evolution and development of humans and songbirds. In order to provide an additional insight into its functional role we compared target gene expression levels between human neuroblastoma cells (SH-SY5Y) stably overexpressing FOXP2 cDNA of either humans or the common chimpanzee, Rhesus monkey, and marmoset, respectively. RNA-seq led to identification of 27 genes with differential regulation under the control of human FOXP2, which were previously reported to have FOXP2-driven and/or songbird song-related expression regulation...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28790313/evolution-of-new-regulatory-functions-on-biophysically-realistic-fitness-landscapes
#11
Tamar Friedlander, Roshan Prizak, Nicholas H Barton, Gašper Tkačik
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28790205/comparative-genomics-of-bacillus-thuringiensis-reveals-a-path-to-specialized-exploitation-of-multiple-invertebrate-hosts
#12
Jinshui Zheng, Qiuling Gao, Linlin Liu, Hualin Liu, Yueying Wang, Donghai Peng, Lifang Ruan, Ben Raymond, Ming Sun
Understanding the genetic basis of host shifts is a key genomic question for pathogen and parasite biology. The Bacillus cereus group, which encompasses Bacillus thuringiensis and Bacillus anthracis, contains pathogens that can infect insects, nematodes, and vertebrates. Since the target range of the essential virulence factors (Cry toxins) and many isolates is well known, this group presents a powerful system for investigating how pathogens can diversify and adapt to phylogenetically distant hosts. Specialization to exploit insects occurs at the level of the major clade and is associated with substantial changes in the core genome, and host switching between insect orders has occurred repeatedly within subclades...
August 8, 2017: MBio
https://www.readbyqxmd.com/read/28767659/mitochondrial-and-nuclear-dna-reveals-reticulate-evolution-in-hares-lepus-spp-lagomorpha-mammalia-from-ethiopia
#13
Zelalem Tolesa, Endashaw Bekele, Kassahun Tesfaye, Hichem Ben Slimen, Juan Valqui, Abebe Getahun, Günther B Hartl, Franz Suchentrunk
For hares (Lepus spp., Leporidae, Lagomorpha, Mammalia) from Ethiopia no conclusive molecular phylogenetic data are available. To provide a first molecular phylogenetic model for the Abyssinian Hare (Lepus habessinicus), the Ethiopian Hare (L. fagani), and the Ethiopian Highland Hare (L. starcki) and their evolutionary relationships to hares from Africa, Eurasia, and North America, we phylogenetically analysed mitochondrial ATPase subunit 6 (ATP6; n = 153 / 416bp) and nuclear transferrin (TF; n = 155 / 434bp) sequences of phenotypically determined individuals...
2017: PloS One
https://www.readbyqxmd.com/read/28767643/bow-tie-signaling-in-c-di-gmp-machine-learning-in-a-simple-biochemical-network
#14
Jinyuan Yan, Maxime Deforet, Kerry E Boyle, Rayees Rahman, Raymond Liang, Chinweike Okegbe, Lars E P Dietrich, Weigang Qiu, Joao B Xavier
Bacteria of many species rely on a simple molecule, the intracellular secondary messenger c-di-GMP (Bis-(3'-5')-cyclic dimeric guanosine monophosphate), to make a vital choice: whether to stay in one place and form a biofilm, or to leave it in search of better conditions. The c-di-GMP network has a bow-tie shaped architecture that integrates many signals from the outside world-the input stimuli-into intracellular c-di-GMP levels that then regulate genes for biofilm formation or for swarming motility-the output phenotypes...
August 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28760746/insights-into-the-evolution-and-function-of-auxin-signaling-f-box-proteins-in-arabidopsis-thaliana-through-synthetic-analysis-of-natural-variants
#15
R Clay Wright, Mollye L Zahler, Stacey R Gerben, Jennifer L Nemhauser
The evolution of complex body plans in land plants has been paralleled by gene duplication and divergence within nuclear auxin-signaling networks. A deep mechanistic understanding of auxin signaling proteins therefore may allow rational engineering of novel plant architectures. Towards that end, we analyzed natural variation in the auxin receptor F-box family of wild accessions of the reference plant Arabidopsis thaliana and used this information to populate a structure/function map. We employed a synthetic assay to identify natural hypermorphic F-box variants, and then assayed auxin-associated phenotypes in accessions expressing these variants...
July 31, 2017: Genetics
https://www.readbyqxmd.com/read/28759647/connectivity-in-gene-coexpression-networks-negatively-correlates-with-rates-of-molecular-evolution-in-flowering-plants
#16
Rishi R Masalia, Adam J Bewick, John M Burke
Gene coexpression networks are a useful tool for summarizing transcriptomic data and providing insight into patterns of gene regulation in a variety of species. Though there has been considerable interest in studying the evolution of network topology across species, less attention has been paid to the relationship between network position and patterns of molecular evolution. Here, we generated coexpression networks from publicly available expression data for seven flowering plant taxa (Arabidopsis thaliana, Glycine max, Oryza sativa, Populus spp...
2017: PloS One
https://www.readbyqxmd.com/read/28754660/selection-during-maize-domestication-targeted-a-gene-network-controlling-plant-and-inflorescence-architecture
#17
Anthony J Studer, Huai Wang, John F Doebley
Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is composed of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, teosinte branched1 (tb1), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of genes that lie downstream of tb1 in a gene network regulating both plant and inflorescence architecture...
July 28, 2017: Genetics
https://www.readbyqxmd.com/read/28751903/evolution-of-daily-gene-co-expression-patterns-from-algae-to-plants
#18
Pedro de Los Reyes, Francisco J Romero-Campero, M Teresa Ruiz, José M Romero, Federico Valverde
Daily rhythms play a key role in transcriptome regulation in plants and microalgae orchestrating responses that, among other processes, anticipate light transitions that are essential for their metabolism and development. The recent accumulation of genome-wide transcriptomic data generated under alternating light:dark periods from plants and microalgae has made possible integrative and comparative analysis that could contribute to shed light on the evolution of daily rhythms in the green lineage. In this work, RNA-seq and microarray data generated over 24 h periods in different light regimes from the eudicot Arabidopsis thaliana and the microalgae Chlamydomonas reinhardtii and Ostreococcus tauri have been integrated and analyzed using gene co-expression networks...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28744706/the-evolution-of-a-g1-s-transcriptional-network-in-yeasts
#19
REVIEW
Adi Hendler, Edgar M Medina, Nicolas E Buchler, Robertus A M de Bruin, Amir Aharoni
The G1-to-S cell cycle transition is promoted by the periodic expression of a large set of genes. In Saccharomyces cerevisiae G1/S gene expression is regulated by two transcription factor (TF) complexes, the MBF and SBF, which bind to specific DNA sequences, the MCB and SCB, respectively. Despite extensive research little is known regarding the evolution of the G1/S transcription regulation including the co-evolution of the DNA binding domains with their respective DNA binding sequences. We have recently examined the co-evolution of the G1/S TF specificity through the systematic generation and examination of chimeric Mbp1/Swi4 TFs containing different orthologue DNA binding domains in S...
July 25, 2017: Current Genetics
https://www.readbyqxmd.com/read/28743801/foxq2-has-a-key-role-in-anterior-head-and-central-brain-patterning-in-insects
#20
Peter Kitzmann, Matthias Weißkopf, Magdalena Ines Schacht, Gregor Bucher
Anterior patterning of animals is based on a set of highly conserved transcription factors but the interactions within the protostome anterior gene regulatory network (aGRN) remain enigmatic. Here, we identify the foxQ2 ortholog of the red flour beetle Tribolium castaneum as novel upstream component of the aGRN. It is required for the development of the labrum and higher order brain structures, namely the central complex and the mushroom bodies. We reveal Tc-foxQ2 interactions by RNAi and heat shock-mediated misexpression...
July 25, 2017: Development
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