scholarly journals Retroposed New Genes Out of the X in Drosophila

2002 ◽  
Vol 12 (12) ◽  
pp. 1854-1859
Author(s):  
Esther Betrán ◽  
Kevin Thornton ◽  
Manyuan Long
Keyword(s):  
Population Genetics ◽  
Molecular Mechanisms ◽  
Sequence Data ◽  
Evolutionary Process ◽  
Significant Excess ◽  
Link Type ◽  
New Genes ◽  
Asymmetric Pattern ◽  
Unpublished Information

New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the wholeDrosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.[The sequence data from this study have been submitted to GenBank under accession nos. AY150701–AY150797. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: M.-L. Wu, F. Lemeunier, and P. Gibert.]

scholarly journals The Power of Yeast in Modelling Human Nuclear Mutations Associated with Mitochondrial Diseases

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 300
Author(s):  
Camilla Ceccatelli Berti ◽  
Giulia di Punzio ◽  
Cristina Dallabona ◽  
Enrico Baruffini ◽  
Paola Goffrini ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Mitochondrial Diseases ◽  
Yeast Saccharomyces Cerevisiae ◽  
Genome Data ◽  
New Genes ◽  
Eukaryotic Organism ◽  
Novel Variants ◽  
Therapeutic Molecules ◽  
Nuclear Mutations

The increasing application of next generation sequencing approaches to the analysis of human exome and whole genome data has enabled the identification of novel variants and new genes involved in mitochondrial diseases. The ability of surviving in the absence of oxidative phosphorylation (OXPHOS) and mitochondrial genome makes the yeast Saccharomyces cerevisiae an excellent model system for investigating the role of these new variants in mitochondrial-related conditions and dissecting the molecular mechanisms associated with these diseases. The aim of this review was to highlight the main advantages offered by this model for the study of mitochondrial diseases, from the validation and characterisation of novel mutations to the dissection of the role played by genes in mitochondrial functionality and the discovery of potential therapeutic molecules. The review also provides a summary of the main contributions to the understanding of mitochondrial diseases emerged from the study of this simple eukaryotic organism.

scholarly journals Molecular mechanisms of autophagy and its role in cancer development

2016 ◽  
Vol 64 (3) ◽  
pp. 529
Author(s):  
Kathleen Salazar-Ramírez ◽  
Jhonny Molinares-Rodríguez ◽  
Samir Bolívar-González
Keyword(s):  
Cancer Patients ◽  
Tumor Cells ◽  
Therapeutic Efficacy ◽  
Molecular Mechanisms ◽  
Evolutionary Process ◽  
Cancer Development ◽  
Cell Homeostasis ◽  
Pathological Conditions ◽  
Extracellular Stimuli

Autophagy is an evolutionary process preserved in eukaryotes, which removes harmful components and maintains cell homeostasis in response to a variety of extracellular stimuli. It is involved in both physiological and pathological conditions, including cancer.The role of autophagy in the treatment of cancer is described as a “double-edged sword”, which reflects its involvement in tumor suppression, survival and subsequent proliferation of tumor cells. Recent advances are useful for planning appropriate adjustments to inhibit or promote autophagy in order to obtain therapeutic efficacy in cancer patients. The objectives of this review are to clarify the role of autophagy in cancer and to highlight the need for more research in the field.

scholarly journals P*R*O*P: a web application to perform phylogenetic analysis considering the effect of gaps

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Takuma Nishimaki ◽  
Keiko Sato
Keyword(s):  
Phylogenetic Analysis ◽  
Web Application ◽  
Sequence Data ◽  
Genetic Difference ◽  
Evolutionary Process ◽  
Genetic Differences ◽  
Amino Acid Sequences ◽  
Evolutionary Information ◽  
Evolutionary Models ◽  
Link Type

Abstract Background Phylogenetic analysis strongly depends on evolutionary models. Most evolutionary models for estimating genetic differences and phylogenetic relationships do not treat gap sites in the alignment of sequences. Appropriately incorporating evolutionary information of sites containing insertions and deletions into genetic difference measures will be improve the accuracy of phylogenetic estimates. Results We introduced a new measure for estimating genetic differences, and presented P*R*O*P, a web application for performing phylogenetic analysis based on genetic difference considering the effect of gaps. As an example of phylogenetic analysis using P*R*O*P, we used complete p53 amino acid sequences of 31 organisms and illustrated that the genetic differences with and without information on sites containing gaps result in trees with different topologies. Conclusions P*R*O*P is available at https://www.rs.tus.ac.jp/bioinformatics/prop and the user can perform phylogenetic analysis by uploading sequence data on the website. The most distinctive feature of P*R*O*P is its genetic difference that is estimated without eliminating gap sites for alignment sequences, which helps users detect meaningful difference in an evolutionary process. The source code is available in GitHub: https://github.com/TUS-Satolab/PROP.

scholarly journals A Random Sequencing Approach for the Analysis of the Trypanosoma cruzi Genome: General Structure, Large Gene and Repetitive DNA Families, and Gene Discovery

2000 ◽  
Vol 10 (12) ◽  
pp. 1996-2005
Author(s):  
Fernán Agüero ◽  
Ramiro E. Verdún ◽  
Alberto Carlos C. Frasch ◽  
Daniel O. Sánchez
Keyword(s):  
Trypanosoma Cruzi ◽  
Repetitive Dna ◽  
Sequence Data ◽  
Random Sequence ◽  
General Structure ◽  
Gc Content ◽  
Haploid Genome ◽  
Additional Information ◽  
Link Type ◽  
New Genes

A random sequence survey of the genome of Trypanosoma cruzi, the agent of Chagas disease, was performed and 11,459 genomic sequences were obtained, resulting in ∼4.3 Mb of readable sequences or ∼10% of the parasite haploid genome. The estimated total GC content was 50.9%, with a high representation of A and T di- and trinucleotide repeats. Out of the estimated 5000 parasite genes, 947 putative new genes were identified. Another 1723 sequences corresponded to genes detected previously in T. cruzi through expression sequence tag analysis. 7735 sequences had no matches in the database, but the presence of open reading frames that passed Fickett's test suggests that some might contain coding DNA. The survey was highly redundant, with ∼35% of the sequences included in a few large sequence families. Some of them code for protein families present in dozens of copies, including proteins essential for parasite survival and retrotransposons. Other sequence families include repetitive DNA present in thousands of copies per haploid genome. Some families in the latter group are new, parasite-specific, repetitive DNAs. These results suggest that T. cruzi could constitute an interesting model to analyze gene and genome evolution due to its plasticity in terms of sequence amplification and divergence. Additional information can be found at http://www.iib.unsam.edu.ar/tcruzi.gss.html.[The sequence data described in this paper have been submitted to the dbGSS database under the following GenBank accession nos.:AQ443439–AQ443513, AQ443743–AQ445667, AQ902981–AQ911366,AZ049857–AZ051184, and AZ302116–AZ302563.]

scholarly journals Analysis of the Placental Tissue Transcriptome of Normal and Preeclampsia Complicated Pregnancies

Acta Naturae ◽  
2014 ◽  
Vol 6 (2) ◽  
pp. 71-83 ◽  
Author(s):  
E. A. Trifonova ◽  
T. V. Gabidulina ◽  
N. I. Ershov ◽  
V. N. Serebrova ◽  
A. Yu. Vorozhishcheva ◽  
...  
Keyword(s):  
Intracellular Signaling ◽  
Molecular Mechanisms ◽  
Ischemia Reperfusion ◽  
Placental Tissue ◽  
Immunological Tolerance ◽  
Leading Role ◽  
New Genes ◽  
Genome Wide ◽  
Differential Gene

Preeclampsia is one of the most severe gestational complications which is one of the leading causes of maternal and perinatal morbidity and mortality. A growth in the incidence of severe and combined forms of the pathology has been observed in recent years. According to modern concepts, inadequate cytotrophoblast invasion into the spiral arteries of the uterus and development of the ischemia-reperfusion syndrome in the placental tissue play the leading role in the development of preeclampsia, which is characterized by multipleorgan failure. In this regard, our work was aimed at studying the patterns of placental tissue transcriptome that are specific to females with PE and with physiological pregnancy, as well as identifying the potential promising biomarkers and molecular mechanisms of this pathology. We have identified 63 genes whose expression proved to differ significantly in the placental tissue of females with PE and with physiological pregnancy. A cluster of differentially expressed genes (DEG) whose expression level is increased in patients with preeclampsia includes not only the known candidate genes that have been identified in many other genome-wide studies (e.g., LEP, BHLHB2, SIGLEC6, RDH13, BCL6), but also new genes (ANKRD37, SYDE1, CYBA, ITGB2, etc.), which can be considered as new biological markers of preeclampsia and are of further interest. The results of a functional annotation of DEG show that the development of preeclampsia may be related to a stress response, immune processes, the regulation of cell-cell interactions, intracellular signaling cascades, etc. In addition, the features of the differential gene expression depending on preeclampsia severity were revealed. We have found evidence of the important role of the molecular mechanisms responsible for the failure of immunological tolerance and initiation of the pro-inflammatory cascade in the development of severe preeclampsia. The results obtained elaborate the concept of the pathophysiology of preeclampsia and contain the information necessary to work out measures for targeted therapy of this disease.

scholarly journals Comparative Sequence Analysis of the X-Inactivation Center Region in Mouse, Human, and Bovine

2000 ◽  
Vol 12 (6) ◽  
pp. 894-908 ◽  
Author(s):  
Corinne Chureau ◽  
Marine Prissette ◽  
Agnès Bourdet ◽  
Valérie Barbe ◽  
Laurence Cattolico ◽  
...  
Keyword(s):  
Transcriptional Activity ◽  
Sequence Data ◽  
Cpg Islands ◽  
Comparative Sequence Analysis ◽  
X Inactivation ◽  
Asymmetric Distribution ◽  
Repeat Elements ◽  
Link Type ◽  
New Genes ◽  
Intergenic Regions

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including theXist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5′ of Xist that was recently shown to attract histone modification early after the onset of X inactivation.[The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AJ421478, AJ421479, AJ421480, andAJ421481. Online supplemental data are available athttp://pbil.univ-lyon1.fr/datasets/Xic2002/data.html andwww.genome.org.]

scholarly journals The Importance of Ion Homeostasis and Nutrient Status in Seed Development and Germination

Agronomy ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 504 ◽  
Author(s):  
María del Carmen Martínez-Ballesta ◽  
Catalina Egea-Gilabert ◽  
Encarnación Conesa ◽  
Jesús Ochoa ◽  
María José Vicente ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Seed Development ◽  
Molecular Mechanisms ◽  
Ion Homeostasis ◽  
Nutrient Status ◽  
Seed Vigor ◽  
Nutrient Deficiencies ◽  
Seed Formation ◽  
New Genes

Seed is the dissemination unit of plants initiating an important stage in the life cycle of plants. Seed development, comprising two phases: embryogenesis and seed maturation, may define the quality of sown seed, especially under abiotic stress. In this review we have focused on the recent advances in the molecular mechanisms underlying these complex processes and how they are controlled by distinct environmental factors regulating ion homeostasis into the seed tissues. The role of transporters affecting seed embryogenesis and first stages of germination as imbibition and subsequent radicle protrusion and extension were revised from a molecular point of view. Seed formation depends on the loading of nutrients from the maternal seed coat to the filial endosperm, a process of which the efflux is not clear and where different ions and transporters are involved. The clear interrelation between soil nutrients, presence of heavy metals and the ion capacity of penetration through the seed are discussed in terms of ion effect during different germination stages. Results concerning seed priming techniques used in the improvement of seed vigor and radicle emergence are shown, where the use of nutrients as a novel way of osmopriming to alleviate abiotic stress effects and improve seedlings yield is discussed. Novel approaches to know the re-translocation from source leaves to developing seeds are considered, as an essential mechanism to understand the biofortification process of certain grains in order to cope with nutrient deficiencies, especially in arid and semiarid areas. Finally, the role of new genes involved in hormone-dependent processes, oxidative response and water uptake into the seeds during their development or germination, have been described as plant mechanisms to deal with abiotic stresses.

How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans?

2020 ◽  
Vol 48 (3) ◽  
pp. 1019-1034 ◽  
Author(s):  
Rachel M. Woodhouse ◽  
Alyson Ashe
Keyword(s):  
Histone Modifications ◽  
Molecular Mechanisms ◽  
Epigenetic Inheritance ◽  
Nematode Caenorhabditis Elegans ◽  
Histone Methyltransferases ◽  
Transgenerational Epigenetic Inheritance ◽  
C Elegans ◽  
Recent Developments ◽  
Gene Regulatory

Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.

Mesophyll conductance: the leaf corridors for photosynthesis

2020 ◽  
Vol 48 (2) ◽  
pp. 429-439 ◽  
Author(s):  
Jorge Gago ◽  
Danilo M. Daloso ◽  
Marc Carriquí ◽  
Miquel Nadal ◽  
Melanie Morales ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Current Knowledge ◽  
Main Role ◽  
Mesophyll Conductance ◽  
Future Studies ◽  
Cell Structures ◽  
Leaf Tissues ◽  
Change Framework ◽  
Chloroplast Stroma

Besides stomata, the photosynthetic CO2 pathway also involves the transport of CO2 from the sub-stomatal air spaces inside to the carboxylation sites in the chloroplast stroma, where Rubisco is located. This pathway is far to be a simple and direct way, formed by series of consecutive barriers that the CO2 should cross to be finally assimilated in photosynthesis, known as the mesophyll conductance (gm). Therefore, the gm reflects the pathway through different air, water and biophysical barriers within the leaf tissues and cell structures. Currently, it is known that gm can impose the same level of limitation (or even higher depending of the conditions) to photosynthesis than the wider known stomata or biochemistry. In this mini-review, we are focused on each of the gm determinants to summarize the current knowledge on the mechanisms driving gm from anatomical to metabolic and biochemical perspectives. Special attention deserve the latest studies demonstrating the importance of the molecular mechanisms driving anatomical traits as cell wall and the chloroplast surface exposed to the mesophyll airspaces (Sc/S) that significantly constrain gm. However, even considering these recent discoveries, still is poorly understood the mechanisms about signaling pathways linking the environment a/biotic stressors with gm responses. Thus, considering the main role of gm as a major driver of the CO2 availability at the carboxylation sites, future studies into these aspects will help us to understand photosynthesis responses in a global change framework.

On the role of conflict in the evolutionary process

2016 ◽  
pp. 87-91
Author(s):  
V.I. Bol’shakov ◽  
◽  
Yu.I. Dubrov ◽  
Keyword(s):  
Evolutionary Process
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