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.

Evolution of the Internet’s Support for Chinese Enterprises’ Innovation Based on Big Data

2021 ◽  
pp. 2159042
Author(s):  
Cuilan Wang ◽  
Deji Wang ◽  
Yu Wang ◽  
Fangyuan Jiao
Keyword(s):  
Development Process ◽  
Organizational Innovation ◽  
Learning Algorithm ◽  
Innovation System ◽  
Development Trend ◽  
Recall Rate ◽  
The Body ◽  
Evolutionary Development ◽  
Chinese Enterprises ◽  
Enterprise Innovation

In order to study the development trend of the Internet’s role in supporting enterprise innovation, a new method based on deep learning algorithm and knowledge graph technology is proposed. Experiments show that the accuracy, F1 value, recall rate and precision of the algorithm are distinctly improved compared with the existing algorithms. A new algorithm is applied to analyze the innovation evolution of Chinese enterprises, using papers, patents and other documents between 1905 and 2020 as data sources. Based on the experimental results, the development stages can be divided into five stages. The research focus is on product R&D innovation, manufacturing innovation, marketing innovation, resource allocation innovation and organizational innovation. It can be seen that the development process of the Internet supporting enterprise innovation system is an evolutionary development process from point to line, to surface, to the body, and to the ecosystem.

scholarly journals Transcription Factors and microRNA Genes Regulatory Network Construction Under Drought Stress in Sesame (Sesamum indicum L.)

2020 ◽  
Author(s):  
Mohammad Amin Baghery ◽  
Seyed Kamal Kazemitabar ◽  
Ali Dehestani ◽  
Pooyan Mehrabanjoubani ◽  
Mohammad Mehdi Naghizadeh ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Drought Stress ◽  
Gene Networks ◽  
Regulatory Networks ◽  
Regulatory Gene ◽  
Sesamum Indicum ◽  
Regulatory Mechanisms ◽  
Oilseed Crop ◽  
Sesame Genotypes ◽  
Almost All

Abstract Background: Drought is one of the most common environmental stresses affecting crops yield and quality. Sesame is an important oilseed crop that most likely faces drought during its growth due to growing in semi-arid and arid areas. Plants responses to drought controlled by regulatory mechanisms. Despite this importance, there is little information about Sesame regulatory mechanisms against drought stress. Results: 458 drought-related genes were identified using comprehensive RNA-seq data analysis of two susceptible and tolerant sesame genotypes under drought stress. These drought-responsive genes were included secondary metabolites biosynthesis-related Like F3H, sucrose biosynthesis-related like SUS2, transporters like SUC2, and protectives like LEA and HSP families. Interactions between identified genes and regulators including TFs and miRNAs were predicted using bioinformatics tools and related regulatory gene networks were constructed. Key regulators and relations of Sesame under drought stress were detected by network analysis. TFs belonged to DREB (DREB2D), MYB (MYB63), ZFP (TFIIIA), bZIP (bZIP16), bHLH (PIF1), WRKY (WRKY30) and NAC (NAC29) families were found among key regulators. mRNAs like miR399, miR169, miR156, miR5685, miR529, miR395, miR396, and miR172 also found as key drought regulators. Furthermore, a total of 117 TFs and 133 miRNAs that might be involved in drought stress were identified with this approach. Conclusions: Most of the identified TFs and almost all of the miRNAs are introduced for the first time as potential regulators of drought response in Sesame. These regulators accompany with identified drought-related genes could be valuable candidates for future studies and breeding programs on Sesame under drought stress. Keywords: Sesamum indicum, Drought stress, Regulatory networks, miRNA, Transcription Factors.

scholarly journals Arrdc2 and Arrdc3 elicit divergent changes in gene expression in skeletal muscle following anabolic and catabolic stimuli

2019 ◽  
Vol 51 (6) ◽  
pp. 208-217 ◽  
Author(s):  
Bradley S. Gordon ◽  
Michael L. Rossetti ◽  
Alexey M. Eroshkin
Keyword(s):  
Skeletal Muscle ◽  
Muscle Mass ◽  
Tibialis Anterior ◽  
Gene Networks ◽  
Tibialis Anterior Muscle ◽  
The Body ◽  
Molecular Networks ◽  
Expression Of Genes ◽  
Consistent Change ◽  
Mechanical Overload

Skeletal muscle is a highly plastic organ regulating various processes in the body. As such, loss of skeletal muscle underlies the increased morbidity and mortality risk that is associated with numerous conditions. However, no therapies are available to combat the loss of muscle mass during atrophic conditions, which is due in part to the incomplete understanding of the molecular networks altered by anabolic and catabolic stimuli. Thus, the current objective was to identify novel gene networks modulated by such stimuli. For this, total RNA from the tibialis anterior muscle of mice that were fasted overnight or fasted overnight and refed the next morning was subjected to microarray analysis. The refeeding stimulus altered the expression of genes associated with signal transduction. Specifically, expression of alpha arrestin domain containing 2 (Arrdc2) and alpha arrestin domain containing 3 (Arrdc3) was significantly lowered 70–85% by refeeding. Subsequent analysis showed that expression of these genes was also lowered 50–75% by mechanical overload, with the combination of nutrients and mechanical overload acting synergistically to lower Arrdc2 and Arrdc3 expression. On the converse, stimuli that suppress growth such as testosterone depletion or acute aerobic exercise increased Arrdc2 and Arrdc3 expression in skeletal muscle. While Arrdc2 and Arrdc3 exhibited divergent changes in expression following anabolic or catabolic stimuli, no other member of the Arrdc family of genes exhibited the consistent change in expression across the analyzed conditions. Thus, Arrdc2 and Arrdc3 are a novel set of genes that may be implicated in the regulation of skeletal muscle mass.

On the life history of Ascaris devosi and its development in the white mouse and the domestic ferret

Parasitology ◽  
1953 ◽  
Vol 42 (3-4) ◽  
pp. 244-258 ◽  
Author(s):  
J. F. A. Sprent
Keyword(s):  
Life History ◽  
Intermediate Host ◽  
White Mouse ◽  
The Body ◽  
Stage Larva ◽  
Evolutionary Development ◽  
Food Material ◽  
Mature Adult ◽  
Mouse Tissues ◽  
History Of

The development of Ascaris devosi, a parasite of the fisher and marten, was followed from the egg to the adult stage using the white mouse and the ferret as the intermediate and final hosts respectively. The eggs contained motile 1st stage larvae 6 days after cleavage and were infective at 12 days, the 1st moult having already occurred. The eggs remained infective for at least 1 year. The 2nd stage larva after hatching from the egg in the intestine of the mouse passes through the intestinal wall to the liver and mesenteric tissues. At 3 days after infection they were recovered from the heart, lungs, brain, kidneys and from the carcass. The larvae grow and store food material during the 2nd stage and between 8 and 12 days after infection they undergo the 2nd moult. The mouse shows the most severe pulmonary symptoms on the 3rd and 4th days after infection, the lungs showing complete red hepatization at this time. The 3rd stage larva is relatively inactive and becomes encapsulated in various tissues, particularly in the muscular and subcutaneous tissues of the neck, shoulders and thorax. The chief developmental changes, apart from growth, which occur in the 2nd and 3rd stage larvae are: (i) the intestine develops from a single row of cells to a multi-cellular tube; (ii) the body cavity appears; (iii) the excretory lobes appear, the nucleus on the left side becoming prominent at the end of the 2nd stage; (iv) the cuticle shows transverse striations at the end of the 2nd stage; (v) the lateral lines become prominent.The encapsulated 3rd stage larvae remained alive for at least six months in the tissues of mice and at 25 days after infection of the mouse they were able to develop in the young ferret following killing and ingestion of the mouse. No infection of ferrets was obtained through oral administration of embryonated eggs or 3rd stage larvae digested from mouse tissues.The 3rd moult occurred in the intestine of the young ferret 3–4 days after infection; in adult ferrets the 3rd stage larvae were evidently unable to gain a hold and were passed out in the faeces. In the next 2–3 weeks the larva grew from about 2 to 16 mm. the 4th moult occurring between 2 and 3 weeks after infection. During the 4th stage the lips develop into the adult form and sexual differentiation occurs. In the female the genital rudiment moves forward and becomes differentiated into the vagina, uteri and ovaries. The vulva remains closed throughout the 4th stage.The adult parasites had developed to sexual maturity by 56 days after infection, but they continued to grow and were considerably longer at 6 months after infection. The position of the vulva relative to the body length was found to move from about midway along the body in the 4th stage larva to a position at the junction of the anterior and middle third of the body in the mature adult.The life history of this parasite is discussed in relation to that of A. lumbricoides and other species. It is considered that the life history of A. devosi, requiring as it does a true intermediate host for its completion, provides further information on the evolutionary development of the ascaris group. This work accordingly supports the hypothesis that the earliest members of this group utilized an intermediate host and does not support that which supposes that ascaris parasites are descended from skin-penetrating forms.During this investigation the writer has benefited considerably from correspondence with Dr J. D. Tiner, Department of Zoology, University of Illinois, Urbana, Illinois, U.S.A. His thanks are also due to Dr H. B. Speakman and Dr A. M. Fallis for their encouragement, guidance and help.This work was supported by the Province of Ontario on the recommendation of the Research Council of Ontario.Grateful acknowledgement is made to Mr Cliff Smith of the Connaught Medical Research Laboratories of the University of Toronto for photographic work.

scholarly journals ECMarker: interpretable machine learning model identifies gene expression biomarkers predicting clinical outcomes and reveals molecular mechanisms of human disease in early stages

2020 ◽  
Author(s):  
Ting Jin ◽  
Nam D Nguyen ◽  
Flaminia Talos ◽  
Daifeng Wang
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Lung Cancer ◽  
Cancer Patients ◽  
Human Disease ◽  
Gene Networks ◽  
Regulatory Mechanisms ◽  
Disease Development ◽  
Lung Cancer Patients ◽  
Machine Learning Model

Abstract Motivation Gene expression and regulation, a key molecular mechanism driving human disease development, remains elusive, especially at early stages. Integrating the increasing amount of population-level genomic data and understanding gene regulatory mechanisms in disease development are still challenging. Machine learning has emerged to solve this, but many machine learning methods were typically limited to building an accurate prediction model as a ‘black box’, barely providing biological and clinical interpretability from the box. Results To address these challenges, we developed an interpretable and scalable machine learning model, ECMarker, to predict gene expression biomarkers for disease phenotypes and simultaneously reveal underlying regulatory mechanisms. Particularly, ECMarker is built on the integration of semi- and discriminative-restricted Boltzmann machines, a neural network model for classification allowing lateral connections at the input gene layer. This interpretable model is scalable without needing any prior feature selection and enables directly modeling and prioritizing genes and revealing potential gene networks (from lateral connections) for the phenotypes. With application to the gene expression data of non-small-cell lung cancer patients, we found that ECMarker not only achieved a relatively high accuracy for predicting cancer stages but also identified the biomarker genes and gene networks implying the regulatory mechanisms in the lung cancer development. In addition, ECMarker demonstrates clinical interpretability as its prioritized biomarker genes can predict survival rates of early lung cancer patients (P-value < 0.005). Finally, we identified a number of drugs currently in clinical use for late stages or other cancers with effects on these early lung cancer biomarkers, suggesting potential novel candidates on early cancer medicine. Availabilityand implementation ECMarker is open source as a general-purpose tool at https://github.com/daifengwanglab/ECMarker. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

Physiological Roles and Regulation of Mammalian Sulfate Transporters

2001 ◽  
Vol 81 (4) ◽  
pp. 1499-1533 ◽  
Author(s):  
Daniel Markovich
Keyword(s):  
Normal Function ◽  
The Body ◽  
Regulatory Mechanisms ◽  
Sulfur Source ◽  
Sulfate Transporter ◽  
Structural And Functional Properties ◽  
Congenital Chloride Diarrhea ◽  
Sat 1 ◽  
Inorganic Sulfate

All cells require inorganic sulfate for normal function. Sulfate is among the most important macronutrients in cells and is the fourth most abundant anion in human plasma (300 μM). Sulfate is the major sulfur source in many organisms, and because it is a hydrophilic anion that cannot passively cross the lipid bilayer of cell membranes, all cells require a mechanism for sulfate influx and efflux to ensure an optimal supply of sulfate in the body. The class of proteins involved in moving sulfate into or out of cells is called sulfate transporters. To date, numerous sulfate transporters have been identified in tissues and cells from many origins. These include the renal sulfate transporters NaSi-1 and sat-1, the ubiquitously expressed diastrophic dysplasia sulfate transporter DTDST, the intestinal sulfate transporter DRA that is linked to congenital chloride diarrhea, and the erythrocyte anion exchanger AE1. These transporters have only been isolated in the last 10–15 years, and their physiological roles and contributions to body sulfate homeostasis are just now beginning to be determined. This review focuses on the structural and functional properties of mammalian sulfate transporters and highlights some of regulatory mechanisms that control their expression in vivo, under normal physiological and pathophysiological states.

scholarly journals Two SecA/SecY Systems with Distinct Roles in the Ecological Adaptations of Bacteria

2017 ◽  
Author(s):  
Xiaowei Jiang ◽  
Mario A. Fares
Keyword(s):  
Pathogenic Bacteria ◽  
Atp Hydrolysis ◽  
Functional Divergence ◽  
Evolutionary Divergence ◽  
Ecological Diversity ◽  
Secretion Systems ◽  
Membrane Pore ◽  
Functional Changes ◽  
Ecological Diversification ◽  
Ecological Adaptations

AbstractBacteria interact with their environment through the secretion of a specific set of proteins (known as secretome) through various secretion systems. Molecular modifications of these secretion systems may lead to the emergence of new bacterial-environment interactions, although this remains unexplored. In this study we investigate the possible link between molecular and functional changes in secretion proteins and the ecological diversity of bacteria. We studied functional modifications in secretion proteins by identifying events of functional evolutionary divergence—that is, changes at the molecular level that have driven changes of protein’s function. We present data supporting that these functional diversifications occurred in essential secretion proteins in bacteria. In particular, functional divergence of the two most important secretion proteins SecA and SecY in pathogenic bacteria suggests that molecular changes at these proteins are responsible for their adaptations to the host. Functional divergence has mainly occurred at protein domains involved in ATP hydrolysis in SecA and membrane pore formation in SecY. This divergence is stronger in pathogenic bacteria for protein copies resulting from the duplication of SecA/SecY, known as SecA2/SecY2. In concert with these results, we find that the secretome of bacteria with the strongest functional divergence is enriched for proteins specialized in the interaction with specific environments. We unravel evolutionary signatures that link mutations at secretion proteins to the ecological diversification of bacteria.

scholarly journals Humanization of yeast genes with multiple human orthologs reveals principles of functional divergence between paralogs

2019 ◽  
Author(s):  
Jon M. Laurent ◽  
Riddhiman K. Garge ◽  
Ashley I. Teufel ◽  
Claus O. Wilke ◽  
Aashiq H. Kachroo ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Gene Families ◽  
Evolutionary Divergence ◽  
Orthologous Genes ◽  
Specific Expression ◽  
Human Genes ◽  
Human Orthologs ◽  
Human Proteins ◽  
Yeast Genes ◽  
Opening Up

AbstractDespite over a billion years of evolutionary divergence, several thousand human genes possess clearly identifiable orthologs in yeast, and many have undergone lineage-specific duplications in one or both lineages. The ortholog conjecture postulates that orthologous genes between species retain ancestral functions despite divergence over vast timescales, but duplicated genes will be free to diverge in function. However, the retention of ancestral functions among co-orthologs between species and within gene families has been difficult to test experimentally at scale. In order to investigate how ancestral functions are retained or lost post-duplication, we systematically replaced hundreds of essential yeast genes with their human orthologs from gene families that have undergone lineage-specific duplications, including those with single duplications (one yeast gene to two human genes, 1:2) or higher-order expansions (1:>2) in the human lineage. We observe a variable pattern of replaceability across different ortholog classes, with an obvious trend towards differential replaceability inside gene families, rarely observing replaceability by all members of a family. We quantify the ability of various properties of the orthologs to predict replaceability, showing that in the case of 1:2 orthologs, replaceability is predicted largely by the divergence and tissue-specific expression of the human co-orthologs, i.e. the human proteins that are less diverged from their yeast counterpart and more ubiquitously expressed across human tissues more often replace their single yeast ortholog. These trends were consistent with in silico simulations demonstrating that when only one ortholog is replaceable, it tends to be the least diverged of the pair. Replaceability of yeast genes having more than two human co-orthologs was marked by retention of orthologous interactions in functional or protein networks as well as by more ancestral subcellular localization. Overall, we performed >400 human gene replaceability assays revealing 56 new human-yeast complementation pairs, thus opening up avenues to further functionally characterize these human genes in a simplified organismal context.

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