Evolutionary trends of neuropeptide signaling in beetles - A comparative analysis of Coleopteran transcriptomic and genomic data

2019 ◽  
Vol 114 ◽  
pp. 103227 ◽  
Author(s):  
Aniruddha A. Pandit ◽  
Shireen-Anne Davies ◽  
Guy Smagghe ◽  
Julian A.T. Dow
Keyword(s):  
Comparative Analysis ◽  
Genomic Data ◽  
Evolutionary Trends

scholarly journals Continuous-trait probabilistic model for comparing multi-species functional genomic data

2018 ◽  
Author(s):  
Yang Yang ◽  
Quanquan Gu ◽  
Yang Zhang ◽  
Takayo Sasaki ◽  
Julianna Crivello ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Molecular Mechanisms ◽  
Probabilistic Models ◽  
Phenotypic Diversity ◽  
Genomic Data ◽  
Primate Species ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Continuous Trait ◽  
A Genome

SummaryA large amount of multi-species functional genomic data from high-throughput assays are becoming available to help understand the molecular mechanisms for phenotypic diversity across species. However, continuous-trait probabilistic models, which are key to such comparative analysis, remain underexplored. Here we develop a new model, called phylogenetic hidden Markov Gaussian processes (Phylo-HMGP), to simultaneously infer heterogeneous evolutionary states of functional genomic features in a genome-wide manner. Both simulation studies and real data application demonstrate the effectiveness of Phylo-HMGP. Importantly, we applied Phylo-HMGP to analyze a new cross-species DNA replication timing (RT) dataset from the same cell type in five primate species (human, chimpanzee, orangutan, gibbon, and green monkey). We demonstrate that our Phylo-HMGP model enables discovery of genomic regions with distinct evolutionary patterns of RT. Our method provides a generic framework for comparative analysis of multi-species continuous functional genomic signals to help reveal regions with conserved or lineage-specific regulatory roles.

scholarly journals Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses

2021 ◽  
Author(s):  
Han Mei ◽  
Sergei Kosakovsky Pond ◽  
Anton Nekrutenko
Keyword(s):  
Comparative Analysis ◽  
Secondary Structure ◽  
Nucleotide Substitution ◽  
Genomic Data ◽  
Signatures Of Selection ◽  
Slippery Sequence ◽  
Stepwise Evolution ◽  
Reading Frames

Abstract The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for propagation of coronaviruses. The overlap between the two reading frames, a slippery sequence, and an ensemble of secondary structure elements places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these features. Here we performed a comparative analysis of all available coronaviral genomic data available to date to demonstrate exceptional conservation and detect signatures of selection within the PFE region.

scholarly journals CONFIGURATIONS OF KNOWLEDGE-INTENSIVE ENTREPRENEURIAL ECOSYSTEMS

2019 ◽  
Vol 59 (4) ◽  
pp. 242-257 ◽  
Author(s):  
ANDRE CHERUBINI ALVES ◽  
BRUNO FISCHER ◽  
NICHOLAS SPYRIDON VONORTAS ◽  
SÉRGIO ROBLES REIS DE QUEIROZ
Keyword(s):  
Comparative Analysis ◽  
Capital Market ◽  
Research Universities ◽  
Qualitative Comparative Analysis ◽  
Entrepreneurial Activity ◽  
Evolutionary Trends ◽  
Entrepreneurial Ecosystems ◽  
Business Dynamics ◽  
Heterogeneous Nature ◽  
Knowledge Intensive

ABSTRACT The dominant discourse on Entrepreneurial Ecosystems (EE) remains focused on the profile of a handful of successful locations. This has hindered a deeper comprehension of the economic mechanisms that shape evolutionary trends in entrepreneurial activity and how they operate in distinct places. We propose that EE have regularities, but they can also assume different configurations, i.e., varying combinations of influential dimensions. Through fuzzy set qualitative comparative analysis, we address this issue with data from the State of São Paulo, Brazil. This research focuses on five EE dimensions: Science & Technology, Human Capital, Market Dynamics, Business Dynamics, and Infrastructure. Findings point at the heterogeneous nature of EE distributed in three different paths. While configurations’ vary in terms of causal conditions, research universities, knowledge-intensive jobs and wider credit operations are core-causal conditions. Proximity to the main economic hub appears as a key differentiator among ecosystems.

Sequence and comparative analysis of the MIP gene in Chinese straw mushroom, Volvariella volvacea

Genome ◽  
2012 ◽  
Vol 55 (09) ◽  
pp. 667-672 ◽  
Author(s):  
Bing-Zhi Chen ◽  
Fu Gui ◽  
Bao-Gui Xie ◽  
Feng Zou ◽  
Yu-Ji Jiang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Analysis ◽  
Genomic Data ◽  
Volvariella Volvacea ◽  
Phylogeny Analysis ◽  
Blast Analysis ◽  
Mitochondrial Intermediate Peptidase ◽  
Straw Mushroom ◽  
Motif Searching ◽  
Cloning Technology

The mitochondrial intermediate peptidase (MIP) gene is conserved in fungi. It is linked closely with the mating-type A (mtA) gene. In this study, a fragment of the MIP gene in Volvariella volvacea (Bull. ex Fr.) Singer was first cloned by homologue-based cloning technology. Subsequently, the entire MIP DNA sequence (PYd21-MIP) was obtained after the fragment was compared with the genomic data through BLAST analysis. The PYd21-MIP sequence appeared to be homologous with the MIP gene in other fungi. Phylogenetic analysis of PYd21-MIP and other MIP sequences from diverse fungi agreed with the current organism phylogeny. Analysis of protein domains by InterProScan software and motif searching demonstrated that PYd21-MIP encodes a homologous MIP protein. These data support the hypothesis that the PYd21-MIP protein is a Hog-MIP protein homologue from V. volvacea.

Revision of the Malagasy genus Lechius Iwan, 1995 (Coleoptera: Tenebrionidae: Pedinini)

Zootaxa ◽  
2012 ◽  
Vol 3399 (1) ◽  
pp. 23 ◽  
Author(s):  
DARIUSZ IWAN ◽  
MARCIN JAN KAMIŃSKI
Keyword(s):  
Comparative Analysis ◽  
Identification Key ◽  
Female Genitalia ◽  
Evolutionary Trends ◽  
Male And Female ◽  
Taxonomic Concept ◽  
Genus Two ◽  
Coleoptera Tenebrionidae

The taxonomic concept of the genus Lechius Iwan, 1995 and the hypotheses of all its species, are tested basing on newlyavailable material from Madagascar. Comparative analysis showed that the male and female genitalia most apparently re-flect the evolutionary trends within this genus. Two new Lechius species are described: L. aalbui sp. nov. and Lechiuslongiclavis sp. nov. A distributional map is presented with complete faunistic data on the genus. An identification key is provided to all known species of Lechius.

scholarly journals Elucidation of Mechanisms of Ceftazidime Resistance among Clinical Isolates of Pseudomonas aeruginosa by Using Genomic Data

2016 ◽  
Vol 60 (6) ◽  
pp. 3856-3861 ◽  
Author(s):  
Veronica N. Kos ◽  
Robert E. McLaughlin ◽  
Humphrey A. Gardner
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Comparative Analysis ◽  
Resistance Mechanism ◽  
Genomic Data ◽  
Clinical Isolates ◽  
Whole Genome ◽  
Content Type ◽  
Sequence Types

Ceftazidime is one of the few cephalosporins with activity againstPseudomonas aeruginosa. Using whole-genome comparative analysis, we set out to determine the prevalent mechanism(s) of resistance to ceftazidime (CAZ) using a set of 181 clinical isolates. These isolates represented various multilocus sequence types that consisted of both ceftazidime-susceptible and -resistant populations. A presumptive resistance mechanism against ceftazidime was identified in 88% of the nonsusceptible isolates using this approach.

COMPARATIVE ANALYSIS OF GENOMIC DATA: A GLOBAL LOOK AT STRUCTURAL AND REGULATORY FEATURES

1993 ◽  
Author(s):  
George S. Michaels ◽  
Ronald Taylor ◽  
Ray Hagstrom ◽  
Morgan Price ◽  
Ross Overbeek
Keyword(s):  
Comparative Analysis ◽  
Genomic Data
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