scholarly journals Genomic and physiological responses to strong selective pressure during late organogenesis: few gene expression changes found despite striking morphological differences

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 779 ◽  
Author(s):  
Goran Bozinovic ◽  
Tim L Sit ◽  
Richard Di Giulio ◽  
Lauren F Wills ◽  
Marjorie F Oleksiak
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Physiological Responses ◽  
Strong Selective Pressure ◽  
Morphological Differences

scholarly journals Unearthing LTR retrotransposon gag genes co-opted in the deep evolution of eukaryotes

2021 ◽  
Author(s):  
Jianhua Wang ◽  
Guan-Zhu Han
Keyword(s):  
Gene Expression ◽  
Selective Pressure ◽  
Ltr Retrotransposon ◽  
Ltr Retrotransposons ◽  
Cellular Functions ◽  
The Family ◽  
Family Level ◽  
Gene Expression Analyses ◽  
Comprehensive Picture ◽  
Gypsy Retrotransposons

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes, and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.

scholarly journals Transcriptional analysis of the response of C. elegans to ethanol exposure

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mark G. Sterken ◽  
Marijke H. van Wijk ◽  
Elizabeth C. Quamme ◽  
Joost A. G. Riksen ◽  
Lucinda Carnell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Physiological Response ◽  
Physiological Responses ◽  
Ethanol Exposure ◽  
Transcriptional Analysis ◽  
Transcriptional Responses ◽  
Genetic Pathways ◽  
C Elegans ◽  
Chronic Ethanol Consumption ◽  
Transcriptional Changes

AbstractEthanol-induced transcriptional changes underlie important physiological responses to ethanol that are likely to contribute to the addictive properties of the drug. We examined the transcriptional responses of Caenorhabditis elegans across a timecourse of ethanol exposure, between 30 min and 8 h, to determine what genes and genetic pathways are regulated in response to ethanol in this model. We found that short exposures to ethanol (up to 2 h) induced expression of metabolic enzymes involved in metabolizing ethanol and retinol, while longer exposure (8 h) had much more profound effects on the transcriptome. Several genes that are known to be involved in the physiological response to ethanol, including direct ethanol targets, were regulated at 8 h of exposure. This longer exposure to ethanol also resulted in the regulation of genes involved in cilia function, which is consistent with an important role for the effects of ethanol on cilia in the deleterious effects of chronic ethanol consumption in humans. Finally, we found that food deprivation for an 8-h period induced gene expression changes that were somewhat ameliorated by the presence of ethanol, supporting previous observations that worms can use ethanol as a calorie source.

scholarly journals Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity and temperature, but not dissolved oxygen

2019 ◽  
Vol 222 (13) ◽  
pp. jeb198036 ◽  
Author(s):  
Aimee Lee S. Houde ◽  
Arash Akbarzadeh ◽  
Oliver P. Günther ◽  
Shaorong Li ◽  
David A. Patterson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dissolved Oxygen ◽  
Physiological Responses

scholarly journals Selective Pressure for Biofilm Formation in Bacillus subtilis: Differential Effect of Mutations in the Master Regulator SinR on Bistability

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Jan Kampf ◽  
Jan Gerwig ◽  
Kerstin Kruse ◽  
Robert Cleverley ◽  
Miriam Dormeyer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Biofilm Formation ◽  
Type Strain ◽  
Wild Type Strain ◽  
Selective Pressure ◽  
Wild Type ◽  
Master Regulator ◽  
Form Complex ◽  
Content Type

ABSTRACT Biofilm formation by Bacillus subtilis requires the expression of genes encoding enzymes for extracellular polysaccharide synthesis and for an amyloid-like protein. The master regulator SinR represses all the corresponding genes, and repression of these key biofilm genes is lifted when SinR interacts with its cognate antagonist proteins. The YmdB phosphodiesterase is a recently discovered factor that is involved in the control of SinR activity: cells lacking YmdB exhibit hyperactive SinR and are unable to relieve the repression of the biofilm genes. In this study, we have examined the dynamics of gene expression patterns in wild-type and ymdB mutant cells by microfluidic analysis coupled to time-lapse microscopy. Our results confirm the bistable expression pattern for motility and biofilm genes in the wild-type strain and the loss of biofilm gene expression in the mutant. Moreover, we demonstrated dynamic behavior in subpopulations of the wild-type strain that is characterized by switches in sets of the expressed genes. In order to gain further insights into the role of YmdB, we isolated a set of spontaneous suppressor mutants derived from ymdB mutants that had regained the ability to form complex colonies and biofilms. Interestingly, all of the mutations affected SinR. In some mutants, large genomic regions encompassing sinR were deleted, whereas others had alleles encoding SinR variants. Functional and biochemical studies with these SinR variants revealed how these proteins allowed biofilm gene expression in the ymdB mutant strains. IMPORTANCE Many bacteria are able to choose between two mutually exclusive lifestyles: biofilm formation and motility. In the model bacterium Bacillus subtilis, this choice is made by each individual cell rather than at the population level. The transcriptional repressor SinR is the master regulator in this decision-making process. The regulation of SinR activity involves complex control of its own expression and of its interaction with antagonist proteins. We show that the YmdB phosphodiesterase is required to allow the expression of SinR-repressed genes in a subpopulation of cells and that such subpopulations can switch between different SinR activity states. Suppressor analyses revealed that ymdB mutants readily acquire mutations affecting SinR, thus restoring biofilm formation. These findings suggest that B. subtilis cells experience selective pressure to form the extracellular matrix that is characteristic of biofilms and that YmdB is required for the homeostasis of SinR and/or its antagonists.

C-Myc, but Not Akt, Can Substitute for Notch in Lymphomagenesis.

Blood ◽  
2009 ◽  
Vol 114 (22) ◽  
pp. 7-7
Author(s):  
Mark Y Chiang ◽  
M. Eden Childs ◽  
Candice Romany ◽  
Olga Shestova ◽  
Jon Aster ◽  
...  
Keyword(s):  
T Cell ◽  
Mouse Model ◽  
Selective Pressure ◽  
Conflicts Of Interest ◽  
Lymphoblastic Leukemia ◽  
Gamma Secretase ◽  
Growth And Survival ◽  
Strong Selective Pressure ◽  
Human T Cell ◽  
Notch1 Mutations

Abstract Abstract 7 Notch signaling is activated in ∼70% of human T-cell acute lymphoblastic leukemia/lymphoma (T-ALL) samples and many human and mouse T-ALL cell lines require Notch signals for growth and survival. To gain insight into the role of Notch during induction of T-ALL, we used a fully penetrant, conditional, transgenic KrasG12D mouse model in which ∼80% of T-ALLs acquire activating Notch1 mutations in the endogenous locus. We crossed mice bearing this transgene with Rosa26-DNMAMLf/f mice, which conditionally express the pan-Notch inhibitor DNMAML. T-ALL developed in these mice despite the expression of DNMAML throughout T-cell development. ∼75% of T-ALL tumors acquired activating Notch1 mutations and suppressed expression of DNMAML, which is consistent with frequent “escape” of Notch from inhibition for efficient T-ALL development. We next compared T-ALL cells that lacked DNMAML expression with T-ALL cells that continued to express DNMAML. T-ALL cells lacking DNMAML expressed the direct Notch target c-Myc at higher levels, proliferated at a higher rate, and contained ∼10-fold higher levels of leukemia-initiating cells. Moreover, DNMAML-positive T-ALLs lost DNMAML after transfer into secondary recipients. These data underscore the strong selective pressure for Notch signals during generation and maintenance of T-ALL. We next sought a mechanistic answer for the strong selective pressure for Notch activation. c-Myc and Akt have both been posited to be critical targets of oncogenic Notch signals. To compare the relative contributions of c-Myc and Akt to lymphomagenesis, we overexpressed c-Myc and activated AKT in the KrasG12D-driven mouse model. T-ALLs induced by KrasG12D and Akt acquired activating Notch1 mutations in ∼70% of tumors, which were sensitive to Notch inhibitors (gamma-secretase inhibitors [GSI]). In contrast, T-ALLs induced by KrasG12D and c-Myc did not acquire Notch1 mutations and were resistant to GSI. We conclude that upregulation of c-Myc is sufficient to substitute for Notch in lymphomagenesis, whereas activation of Akt signaling is not. These data identify c-Myc not AKT as the driving force behind Notch-induced lymphomagenesis. These data emphasize the Notch/c-Myc axis as an attractive, rational, therapeutic target in T-ALL. Disclosures: No relevant conflicts of interest to declare.

scholarly journals A Homeodomain Leucine Zipper Gene from Craterostigma plantagineum Regulates Abscisic Acid Responsive Gene Expression and Physiological Responses

2006 ◽  
Vol 61 (3) ◽  
pp. 469-489 ◽  
Author(s):  
Xin Deng ◽  
Jonathan Phillips ◽  
Anne Bräutigam ◽  
Peter Engström ◽  
Henrik Johannesson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abscisic Acid ◽  
Leucine Zipper ◽  
Physiological Responses ◽  
Craterostigma Plantagineum ◽  
Responsive Gene

scholarly journals Genomic signatures of diet-related shifts during human origins

2010 ◽  
Vol 278 (1708) ◽  
pp. 961-969 ◽  
Author(s):  
Courtney C. Babbitt ◽  
Lisa R. Warner ◽  
Olivier Fedrigo ◽  
Christine E. Wall ◽  
Gregory A. Wray
Keyword(s):  
Gene Expression ◽  
New Technologies ◽  
Morphological Changes ◽  
Current Evidence ◽  
Human Origins ◽  
Human Phenotype ◽  
Genomic Signatures ◽  
Profound Influence ◽  
Genomic Studies ◽  
Morphological Differences

There are numerous anthropological analyses concerning the importance of diet during human evolution. Diet is thought to have had a profound influence on the human phenotype, and dietary differences have been hypothesized to contribute to the dramatic morphological changes seen in modern humans as compared with non-human primates. Here, we attempt to integrate the results of new genomic studies within this well-developed anthropological context. We then review the current evidence for adaptation related to diet, both at the level of sequence changes and gene expression. Finally, we propose some ways in which new technologies can help identify specific genomic adaptations that have resulted in metabolic and morphological differences between humans and non-human primates.

Conflict between morphological and molecular data: A case study of Ficus krishnae (Moraceae)

Phytotaxa ◽  
2016 ◽  
Vol 247 (2) ◽  
pp. 143 ◽  
Author(s):  
KUMAR K. ANAND ◽  
SATYA N. JENA ◽  
LAL B. CHAUDHARY ◽  
MUNNA SINGH
Keyword(s):  
Gene Expression ◽  
Molecular Level ◽  
Molecular Data ◽  
Nodal Anatomy ◽  
Aerial Roots ◽  
Dna Contents ◽  
Morphological Differences ◽  
Morphological And Molecular Data ◽  
Peculiar Nature

Ficus krishnae, considered as highly sacred plant species in India, is well known for its peculiar nature of cup-shaped leaves. The species distinctly differs from its allied species F. benghalensis not only in the cup formation in leaves but also in the height of plants, aerial roots, stipules, petiole and its leafy appendages, ostiolar bracts of the receptacle and pollinator wasps, in addition to slight differences in the karyotype, DNA contents, stomatal and parenchymatous cells and nodal anatomy. In spite of having several morphological differences, F. krishnae is considered by some authors as a synonym of F. benghalensis, which does not seem to be convincing. Contrary to the morphological differences, the sequence analysis of nuclear and plastid regions of both the species conducted in the present study does not reveal any significant variations and thus infers no differentiation between the species at molecular level. This may be due to mutations at one or few coding loci or differences in gene expression associated with morphogenesis with significant phenotypic appearance.

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