scholarly journals Phylostratigraphic Analysis Shows the Earliest Origination of the Stress Associated Genes in A. thaliana

2018 ◽  
Author(s):  
Zakhar Mustafin ◽  
Dmitry Konstantinov ◽  
Vladimir Zamyatin ◽  
Alexey Doroshkov ◽  
Sergey Lashin ◽  
...  
Keyword(s):  
Heat Stress ◽  
Gene Networks ◽  
Gene Network ◽  
Common Ancestor ◽  
Cold Water ◽  
Light Stress ◽  
Graphical Analysis ◽  
Last Common Ancestor ◽  
Molecular Processes ◽  
Different Response

Phylostratigraphic analysis is a way to look anew on phylogenetic data in the evolutionary aspect. It allows counting the evolutionary age based on the analysis of genes, their orthologs and finding the last common ancestor. We performed phylostratigraphic analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) determined by the Gene Ontology annotation. Comparison of the distributions of ages of genes associated with stresses of different type has shown the heat stress to involve older genes while the light stress – younger genes. At the same time, all types of stress are characterized by a significantly higher proportion of old genes (common to all eukaryotes) compared to the whole set of A.thaliana genes. This can be explained by the involvement of basic molecular processes in plant cells into the stress response. Reconstruction and graphical analysis of the gene network of the heat stress educed several clusters associated with different response functions. Some of these clusters contain only ancient genes. The results obtained show that the phylostratigraphic analysis reveals the fundamental features of the organization of gene networks and their evolution.

scholarly journals Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Evy van Berlo ◽  
Alejandra P. Díaz-Loyo ◽  
Oscar E. Juárez-Mora ◽  
Mariska E. Kret ◽  
Jorg J. M. Massen
Keyword(s):  
Experimental Evidence ◽  
Common Ancestor ◽  
Great Apes ◽  
Pongo Pygmaeus ◽  
Last Common Ancestor ◽  
Contagious Yawning ◽  
Proximate Mechanism ◽  
Social Species ◽  
Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

scholarly journals Recombinant transfer in the basic genome ofEscherichia coli

2015 ◽  
Vol 112 (29) ◽  
pp. 9070-9075 ◽  
Author(s):  
Purushottam D. Dixit ◽  
Tin Yau Pang ◽  
F. William Studier ◽  
Sergei Maslov
Keyword(s):  
Common Ancestor ◽  
Recipient Cell ◽  
Gene Clusters ◽  
Selective Advantage ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Basic Genome ◽  
Single Base Pair ◽  
Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

A study of structural properties of gene network graphs for mathematical modeling of integrated mosaic gene networks

2017 ◽  
Vol 15 (02) ◽  
pp. 1650045 ◽  
Author(s):  
Olga V. Petrovskaya ◽  
Evgeny D. Petrovskiy ◽  
Inna N. Lavrik ◽  
Vladimir A. Ivanisenko
Keyword(s):  
Mathematical Modeling ◽  
Gene Regulatory Networks ◽  
Gene Networks ◽  
Gene Network ◽  
Regulatory Networks ◽  
Network Modeling ◽  
Computer Experiments ◽  
Linear Control ◽  
Expression Of Genes ◽  
Gene Regulatory

Gene network modeling is one of the widely used approaches in systems biology. It allows for the study of complex genetic systems function, including so-called mosaic gene networks, which consist of functionally interacting subnetworks. We conducted a study of a mosaic gene networks modeling method based on integration of models of gene subnetworks by linear control functionals. An automatic modeling of 10,000 synthetic mosaic gene regulatory networks was carried out using computer experiments on gene knockdowns/knockouts. Structural analysis of graphs of generated mosaic gene regulatory networks has revealed that the most important factor for building accurate integrated mathematical models, among those analyzed in the study, is data on expression of genes corresponding to the vertices with high properties of centrality.

scholarly journals On Robust State Estimation of Gene Networks

2010 ◽  
Vol 2 ◽  
pp. 117959721000200 ◽  
Author(s):  
Chia-Hua Chuang ◽  
Chun-Liang Lin
Keyword(s):  
Parameter Estimation ◽  
Kalman Filter ◽  
Quantitative Analysis ◽  
State Estimation ◽  
Gene Networks ◽  
Gene Network ◽  
Biological Systems ◽  
Uncertain Process ◽  
Network Systems ◽  
Internal States

Gene networks in biological systems are not only nonlinear but also stochastic due to noise corruption. How to accurately estimate the internal states of the noisy gene networks is an attractive issue to researchers. However, the internal states of biological systems are mostly inaccessible by direct measurement. This paper intends to develop a robust extended Kalman filter for state and parameter estimation of a class of gene network systems with uncertain process noises. Quantitative analysis of the estimation performance is conducted and some representative examples are provided for demonstration.

Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

2021 ◽  
Author(s):  
Ksenia Juravel ◽  
Luis Porras ◽  
Sebastian Hoehna ◽  
Davide Pisani ◽  
Gert Wörheide
Keyword(s):  
Common Ancestor ◽  
Sister Group ◽  
The Other ◽  
Gene Content ◽  
Statistical Hypothesis ◽  
Phylogenetic Position ◽  
Last Common Ancestor ◽  
Statistical Hypothesis Testing ◽  
Animal Phylogeny ◽  
Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

Inductive patterning of the embryonic brain in Drosophila

Development ◽  
2002 ◽  
Vol 129 (9) ◽  
pp. 2121-2128
Author(s):  
Damon T. Page
Keyword(s):  
Brain Development ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Embryonic Brain ◽  
Germ Layers ◽  
Brain Anomaly ◽  
Prechordal Plate ◽  
Foregut Endoderm ◽  
The Brain ◽  
Brain Patterning

In vertebrates (deuterostomes), brain patterning depends on signals from adjacent tissues. For example, holoprosencephaly, the most common brain anomaly in humans, results from defects in signaling between the embryonic prechordal plate (consisting of the dorsal foregut endoderm and mesoderm) and the brain. I have examined whether a similar mechanism of brain development occurs in the protostome Drosophila, and find that the foregut and mesoderm act to pattern the fly embryonic brain. When the foregut and mesoderm of Drosophila are ablated, brain patterning is disrupted. The loss of Hedgehog expressed in the foregut appears to mediate this effect, as it does in vertebrates. One mechanism whereby these defects occur is a disruption of normal apoptosis in the brain. These data argue that the last common ancestor of protostomes and deuterostomes had a prototype of the brains present in modern animals, and also suggest that the foregut and mesoderm contributed to the patterning of this ‘proto-brain’. They also argue that the foreguts of protostomes and deuterostomes, which have traditionally been assigned to different germ layers, are actually homologous.

Mouse Hox-3.4: homeobox sequence and embryonic expression patterns compared with other members of the Hox gene network

Development ◽  
1990 ◽  
Vol 109 (2) ◽  
pp. 329-339 ◽  
Author(s):  
S.J. Gaunt ◽  
P.L. Coletta ◽  
D. Pravtcheva ◽  
P.T. Sharpe
Keyword(s):  
Gene Network ◽  
Common Ancestor ◽  
Expression Patterns ◽  
Homeobox Gene ◽  
Predicted Amino Acid Sequence ◽  
Chromosome 15 ◽  
Hox Gene ◽  
The Central Nervous System ◽  
Genomic Organisation

A putative mouse homeobox gene (Hox-3.4) was previously identified 4kb downstream of the Hox-3.3 (Hox-6.1)* gene (Sharpe et al. 1988). We have now sequenced the Hox-3.4 homeobox region. The predicted amino acid sequence shows highest degree of homology in the mouse with Hox-1.3 and -2.1. This, together with similarities in the genomic organisation around these three genes, suggests that they are comembers of a subfamily, derived from a common ancestor. Hox-3.4 appears to be a homologue of the Xenopus Xlhbox5 and human cp11 genes (Fritz and De Robertis, 1988; Simeone et al. 1988). Using a panel of mouse-hamster somatic cell hybrids we have mapped the Hox-3.4 gene to chromosome 15. From the results of in situ hybridization experiments, we describe the distribution of Hox-3.4 transcripts within the 12 1/2 day mouse embryo, and we compare this with the distributions of transcripts shown by seven other members of the Hox gene network. We note three consistencies that underlie the patterns of expression shown by Hox-3.4. First, the anterior limits of Hox-3.4 transcripts in the embryo are related to the position of the Hox-3.4 gene within the Hox-3 locus. Second, the anterior limits of Hox-3.4 expression within the central nervous system are similar to those shown by subfamily homologues Hox-2.1 and Hox-1.3, although the tissue-specific patterns of expression for these three genes show many differences. Third, the patterns of Hox-3.4 expression within the spinal cord and the testis are very similar to those shown by a neighbouring Hox-3 gene (Hox-3.3), but they are quite different from those shown by Hox-1 genes (Hox-1.2, -1.3 and -1.4).

A NEW METHOD OF DETERMINING THRESHOLD OF GENE NETWORK BASED ON PHENOTYPES

2011 ◽  
Vol 19 (04) ◽  
pp. 607-616
Author(s):  
YUANYUAN ZHANG ◽  
SHUDONG WANG ◽  
MEIXI YANG ◽  
DASHUN XU ◽  
DAZHI MENG
Keyword(s):  
Gene Networks ◽  
Gene Network ◽  
Structural Parameters ◽  
Network Modeling ◽  
Genetic Diseases ◽  
Disease Stage ◽  
External Representation ◽  
Functional Relationships ◽  
Disease Phenotypes ◽  
Significant Difference

With the rapid growth of microarray data, it has become a hot topic to reveal complex behaviors and functions of life system by studying the relationships among genes. In the process of reverse network modeling, the relationships with less relevance are generally not considered by determining a threshold when the relationships among genes are mined. However, there are no effective methods to determine the threshold up to now. It is worthwhile to note that the phenotypes of genetic diseases are generally regarded as external representation of the functions of genes. Therefore, two types of phenotype networks are constructed from gene and disease views, respectively, and through comparing these two types of phenotype networks, the threshold of gene network corresponding to a certain disease can be determined when their similarity reaches to maximum. Because the gene network is determined based on the relationships among phenotypes and phenotypes are external representation of the functions of genes, it is considered that relationships in the gene network may show functional relationships among genes in biological system. In this work, the thresholds 0.47 and 0.48 of gene network are determined based on Parkinson disease phenotypes. Furthermore, the validity of these thresholds is verified by the specificity and susceptibility of phenotype networks. Also, through comparing the structural parameters of gene networks for normal and disease stage at different thresholds, significant difference between the two gene networks at threshold 0.47 or 0.48 is found. The significant difference of structural parameters further verifies the efficiency of this method.

Natural history of ABC systems: not only transporters

2011 ◽  
Vol 50 ◽  
pp. 19-42 ◽  
Author(s):  
Elie Dassa
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Last Common Ancestor ◽  
Abc Proteins ◽  
Hypothetical Scenario ◽  
History Of ◽  
Phylogenetic Perspective ◽  
Living Organisms

In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.

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