[The toolbox of developmental evolution or how Mexican cave fishes lost their eyes]. / La boîte à outils de l'évolution développementale ou comment les poissons cavernicoles mexicains ont perdu leurs yeux.

The fish Astyanax mexicanus comes in two very different forms: a "normal" river morph, and a blind, depigmented cave morph, living in the total and permanent darkness of Mexican caves. This species is on the way to becoming a model of choice in evolutionary and comparative biology, both for the study of the evolution of behavior, physiology or morphology, and for molecular genetics or population genetics. Here, I present the advancement of knowledge in the field of the developmental evolution of the eye of the cave morph. By rewinding back in time its development from the eye of the larva to the retinal field at the end of gastrulation, the cave-dwelling Astyanax embryo reveals mechanisms and processes likely to contribute to evolutionary variations between species, but also to pathological variations in the morphogenesis of the optic region.

Title: La boîte à outils de l'évolution développementale ou comment les poissons cavernicoles mexicains ont perdu leurs yeux. Abstract: Le poisson Astyanax mexicanus se présente sous deux formes très différentes : un morphe de rivière « normal ¼, et un morphe cavernicole, aveugle et dépigmenté, vivant dans l'obscurité totale et permanente de grottes mexicaines. Cette espèce est en passe de devenir un modèle de choix en biologie évolutive et comparée, tant pour l'étude de l'évolution des comportements, de la physiologie ou de la morphologie, que pour la génétique moléculaire ou la génétique des populations. Je présente ici l'avancée des connaissances dans le domaine de l'évolution développementale de l'œil du morphe cavernicole. En remontant dans le temps son développement « à l'envers ¼ depuis l'œil de la larve jusqu'au champ rétinien en fin de gastrulation, l'embryon d'Astyanax cavernicole révèle des mécanismes et processus susceptibles de contribuer aux variations évolutives entre espèces et aux variations pathologiques de la morphogenèse de la région optique.

Genome-wide identification of bZIP transcription factor genes related to starch synthesis in barley (Hordeum vulgare L.).

The basic leucine zipper (bZIP) family of genes encode transcription factors that play key roles in plant growth and development. In this study, a total of 92 HvbZIP genes were identified and compared with previous studies using recently released barley genome data. Two novel genes were characterized in this study, and some misannotated and duplicated genes from previous studies have been corrected. Phylogenetic analysis results showed that 92 HvbZIP genes were classified into 10 groups and three unknown groups. The gene structure and motif distribution of the three unknown groups implied that the genes of the three groups may be functionally different. Expression profiling indicated that the HvbZIP genes exhibited different patterns of spatial and temporal expression. Using qRT-PCR, more than 10 HvbZIP genes were identified with expression patterns similar to those of starch synthase genes in barley. Yeast one-hybrid analysis revealed that two of the HvbZIP genes exhibited in vitro binding activity to the promoter of HvAGP-S. The two HvbZIP genes may be candidate genes for further study to explore the mechanism by which they regulate the synthesis of barley starch.

Advances in visualizing transcription factor - DNA interactions.

At the heart of the transcription process is the specific interaction between transcription factors (TFs) and their target DNA sequences. Decades of molecular biology research have led to unprecedented insights into how TFs access the genome to regulate transcription. In the last 20 years, advances in microscopy have enabled scientists to add imaging as a powerful tool in probing two specific aspects of TF-DNA interactions: structure and dynamics. In this review, we examine how applications of diverse imaging technologies can provide structural and dynamic information that complements insights gained from molecular biology assays. As a case study, we discuss how applications of advanced imaging techniques have reshaped our understanding of TF behavior across the cell cycle, leading to a rethinking in the field of mitotic bookmarking.

FoxO3 transcription factor promotes autophagy after oxidative stress injury in HT22 cells.

Autophagy has been implicated in neurodegenerative diseases. Forkhead box O3 (FoxO3) transcription factors promote autophagy in heart and inhibit oxidative damage. Here we investigate the role of FoxO3 transcription factors in regulating autophagy after oxidative stress injury in immortalized mouse hippocampal cell line (HT22). The present study confirms that hydrogen peroxide (H2O2) injury could induce autophagy and FoxO3 activation in HT22 cells. In addition, overexpression of FoxO3 enhanced H2O2-induced autophagy activation and suppressed neuronal cell damage, while knockdown of FoxO3 reduced H2O2-induced autophagy activation and exacerbated neuronal cell injury. Inhibition of autophagy by 3-methyladenine (3-MA) resulted in reduced cell viability, increased production of reactive oxygen species (ROS), promoted nuclear condensation, and decreased expression of antiapoptotic and autophagy-related proteins, indicating that autophagy may have protective effects on H2O2-induced injury in HT22 cells. Moreover, overexpression of FoxO3 prevented exacerbation of brain damage induced by 3-MA. Taken together, these results show that activation of FoxO3 could induce autophagy and inhibit H2O2-induced damage in HT22 cells. Our study demonstrates the critical role of FoxO3 in regulating autophagy in brain.

Transcriptome analysis of maize reveals potential key genes involved in the response to belowground herbivore Holotrichia parallela larvae feeding.

The larvae of Holotrichia parallela, a destructive belowground herbivore, causes tremendous damages to maize plants. However, little is known if there are any defense mechanisms in maize roots to defend themselves against this herbivore. In the current research, we carried out RNA-sequencing to investigate the changes in gene transcription level in maize roots after H. parallela larvae infestation. A total of 644 up-regulated genes and 474 down-regulated genes was found. In addition, Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed. Weighted gene co-expression network analysis (WGCNA) indicated that peroxidase genes may be the hub genes that regulate maize defenses to H. parallela larvae attack. We also found 105 transcription factors, 44 hormone-related genes, and 62 secondary metabolism-related genes within differentially expressed genes (DEGs). Furthermore, the expression profiles of 12 DEGs from the transcriptome analysis were confirmed by quantitative real-time PCR experiments. This transcriptome analysis provides insights into the molecular mechanisms of the underground defense in maize roots to H. parallela larvae attack and will help to select target genes of maize for defense against belowground herbivory.

Dysregulation of 1-carbon metabolism and muscle atrophy: potential roles of forkhead box O proteins and PPARγ co-activator-1α.

Homocysteine, a non-proteinogenic amino acid but an important metabolic intermediate is generated as an integral component for the "1-carbon metabolism" during normal physiology. It is catabolized to cysteine via the transulfuration pathway resulting in the generation of hydrogen sulfide, a naturally endogenous byproduct. Genetics or metabolic derangement can alter homocysteine concentration leading to hyperhomocysteinemia (HHcy), a physiologically unfavorable condition that causes serious medical conditions including muscle wasting. HHcy environment can derail physiological processes by targeting biomolecules such as Akt; however, not much is known regarding the effects of HHcy on regulation of transcription factors such as forkhead box O (FOXO) proteins. Recently, hydrogen sulfide has been shown to be highly effective in alleviating the effects of HHcy by serving as an antiapoptotic factor, but role of FOXO and its interaction with hydrogen sulfide are yet to be established. In this review, we discuss role(s) of HHcy in skeletal muscle atrophy and how HHcy interact with FOXO and peroxisome proliferator-activated receptor gamma coactivator 1-alpha expressions that are relevant in musculoskeletal atrophy. Further, therapeutic intervention with hydrogen sulfide for harnessing its beneficial effects might help mitigate the dysregulated 1-carbon metabolism that happens to be the hallmark of HHcy-induced pathologies such as muscle atrophy.

High temperature reduces peel color in eggplant (Solanum melongena) as revealed by RNA-seq analysis.

To acquire the eggplant transcriptome under high temperature stress, 18 cDNA libraries were constructed and sequenced. A total of 136.31 Gb of clean data was obtained, and 88.86%-92.35% of the clean reads were mapped to the eggplant reference genome. Under high temperature, the number of down-regulated genes was more than that of up-regulated genes and there were more differentially expressed genes on the 10th day after flowering than on the 15th and 20th days after flowering. On the 10th day after flowering, the key genes CHI, 3GT, F3'5'H, DFR2, ANS, and F3H in anthocyanin synthetic pathway and most ERF, WRKY, bHLH, and MYB transcription factors were all down-regulated. High temperature significantly decreased the total anthocyanin content in peels. The results showed that at the early stage of peel coloring, high temperature inhibited the expressions of key genes in anthocyanin biosynthetic pathways through the regulation of transcription factors, leading to a significant decrease in total anthocyanin content, which might reduce the peel color in eggplant.

Novel molecular therapeutic targets in cardiac fibrosis: a brief overview 1.

Cardiac fibrosis, characterized by excessive accumulation of extracellular matrix, abolishes cardiac contractility, impairs cardiac function, and ultimately leads to heart failure. In recent years, significant evidence has emerged that supports the highly dynamic and responsive nature of the cardiac extracellular matrix. Although our knowledge of cardiac fibrosis has advanced tremendously over the past decade, there is still a lack of specific therapies owing to an incomplete understanding of the disease etiology and process. In this review, we attempt to highlight some of the recently investigated molecular determinants of ischemic and non-ischemic fibrotic remodeling of the myocardium that present as promising avenues for development of anti-fibrotic therapies.

Modification of gene expression in rat cardiomyocytes by linoleic and docosahexaenoic acids 1.

Regulation of cardiac fatty acid metabolism is central to the development of cardiac hypertrophy and heart failure. We investigated the effects of select fatty acids on the expression of genes involved in immediate early as well as inflammatory and hypertrophic responses in adult rat cardiomyocytes. Cardiac remodeling begins with upregulation of immediate early genes for c-fos and c-jun, followed by upregulation of inflammatory genes for nuclear factor kappa B (NF-κB) and nuclear factor of activated T-cells (NFAT). At later stages, genes involved in hypertrophic responses, such as atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP), are upregulated. Adult rat cardiomyocytes were treated with palmitic acid, a saturated fatty acid; oleic acid, a monounsaturated fatty acid; linoleic acid, a polyunsaturated fatty acid belonging to the n-6 class; and docosahexaenoic acid, a polyunsaturated fatty acid belonging to the n-3 class. Linoleic acid produced a greater increase in the mRNA expression of c-fos, c-jun, NF-κB, NFAT3, ANP, and BNP relative to palmitic acid and oleic acid. In contrast, docosahexaenoic acid caused a decrease in the expression of genes involved in cardiac hypertrophy. Our findings suggest that linoleic acid may be a potent inducer of genes involved in cardiac hypertrophy, whereas docosahexaenoic acid may be protective against the cardiomyocyte hypertrophic response.

Higher anthocyanin accumulation associated with higher transcription levels of anthocyanin biosynthesis genes in spinach.

Spinach (Spinacia oleracea L.) is widely cultivated as an economically important green leafy vegetable crop for fresh and processing consumption. The red-purple spinach shows abundant anthocyanin accumulation in the leaf and leaf petiole. However, the molecular mechanisms of anthocyanin synthesis in this species are still undetermined. In the present study, we investigated pigment formation and identified anthocyanin biosynthetic genes in spinach. We also analyzed the expression of these genes in purple and green cultivars by quantitative PCR. The accumulation of anthocyanin showed that it was the dominant pigment resulting in the red coloration in spinach. In total, 22 biosynthesis genes and 25 regulatory genes were identified in spinach, based on the spinach genomic and transcriptomic database. Furthermore, the expression patterns of genes encoding enzymes indicated that SoPAL, SoUFGT3, and SoUFGT4 were possible candidate genes for anthocyanin biosynthesis in red-purple spinach. The expression patterns of transcription factors indicated that two SoMYB genes, three SobHLH genes, and one SoWD40 gene were drastically up-regulated and co-expression in red-purple spinach, suggesting an essential role of regulatory genes in the anthocyanin biosynthesis of spinach. These results will enhance our understanding of the molecular mechanisms of anthocyanin biosynthesis in purple spinach.

RNA sequencing on Amomum villosum Lour. induced by MeJA identifies the genes of WRKY and terpene synthases involved in terpene biosynthesis.

Amomum villosum Lour. is an important Chinese medicinal plant that has diverse medicinal functions, and mainly contains volatile terpenes. This study aims to explore the WRKY transcription factors (TFs) and terpene synthase (TPS) unigenes that might be involved in terpene biosynthesis in A. villosum, and thus providing some new information on the regulation of terpenes in plants. RNA sequencing of A. villosum induced by methyl jasmonate (MeJA) revealed that the WRKY family was the second largest TF family in the transcriptome. Thirty-six complete WRKY domain sequences were expressed in response to MeJA. Further, six WRKY unigenes were highly correlated with eight deduced TPS unigenes. Ultimately, we combined the terpene abundance with the expression of candidate WRKY TFs and TPS unigenes to presume a possible model wherein AvWRKY61, AvWRKY28, and AvWRKY40 might coordinately trans-activate the AvNeoD promoter. We propose an approach to further investigate TF unigenes that might be involved in terpenoid biosynthesis, and identified four unigenes for further analyses.