Chromatin dynamics of the developmentally regulated P. lividus neural alpha tubulin gene

Over 40 years ago, Allfrey and colleagues (1964) suggested that two histone modifications, namely acetylation and methylation, might regulate RNA synthesis. Nowadays it is universally accepted that activation of gene expression strictly depends on enzymatic mechanisms able to dynamically modify chromatin structure. Here, using techniques including DNaseI hypersensitive site analysis, chomatin immunoprecipitation and quantitative PCR analysis, we have analyzed the dynamics of histone post-translation modifications involved in developmentally/spatially controlled activation of the sea urchin PlTalpha2 tubulin gene. We have demonstrated that only when the PlTalpha2 core promoter chromatin is acetylated on H3K9, tri-methylated on H3K4 and not di-methylated on H3K27, RNA pol II can be enrolled. In contrast, we have shown that when chromatin is methylated both on H3K9 (me2/3) and H3K27 (me2) and mono methylated on H3K4 the promoter is not accessible to RNA pol II. Our results suggest that, during P. lividus embryogenesis, both HAT/HDAC and HMT/HDM activities, which are able to regulate accessibility of the PlTalpha2 basal promoter to RNA polymerase II, are coordinately switched-on

In silico characterization of the neural alpha tubulin gene promoter of the sea urchin embryo Paracentrotus lividus by phylogenetic footprinting

During Paracentrotus lividus sea urchin embryo development one alpha and one beta tubulin genes are expressed specifically in the neural cells and they are early end output of the gene regulatory network that specifies the neural commitment. In this paper we have used a comparative genomics approach to identify conserved regulatory elements in the P. lividus neural alpha tubulin gene. To this purpose, we have first isolated a genomic clone containing the entire gene plus 4.5 Kb of 50 upstream sequences. Then, we have shown by gene transfer experiments that its non-coding region drives the spatiotemporal gene expression corresponding substantially to that of the endogenous gene. In addition, we have identified by genome and EST sequence analysis the S. purpuratus alpha tubulin orthologous gene and we propose a revised annotation of some tubulin family members. Moreover, by computational techniques we delineate at least three putative regulatory regions located both in the upstream region and in the first intron containing putative binding sites for Forkhead and Nkx transcription factor families

Renal Insufficiency in Non-Diabetic Subjects: Relationship of MTHFR C677t Gene Polymorphism and Left Ventricular Hypertrophy

Association of methylenetetrahydrofolate reductase (MTHFR) 677CT gene polymorphism with hyperhomocysteinemia, renal failure, and cardiovascular events is controversial. We investigated the relationship of MTHFR 677CT polymorphisms with left ventricular hypertrophy (LVH) and renal insufficiency.Glomerular filtration rate (GFR) and left myocardial ventricular mass/m2 were assessed in 138 non-diabetic subjects (age, 50.93 ± 14.85 years; body mass index, 27.95 ± 5.98 kg/m(2)), 38 no-mutation wild MTHFR C677CC, 52 heterozygous MTHFR C677CT, and 48 homozygous MTHFR C677TT, all with adequate adherence to current international healthy dietary guidelines. Serum homocysteine, insulin resistance, high-sensitivity C-reactive-protein (hsCRP), parathyroid hormone, and renal artery resistive index (RRI) were challenged by odds ratio analysis and multiple linear regression models.MTHFR 677CT polymorphism showed higher GFR (73.8 ± 27.99 vs. 58.64 ± 29.95; p= 0.001) and lower renal failure odds (OR, 0.443; 95% confidence interval, 0.141-1.387) in comparison with wild MTHFR genotype. A favorable effect on GFR of MTHFR polymorphism is presented independently by the negative effects of LVH, increased intra-renal arterial resistance, and hyperparathyroidism; GFR is the significant predictive factor to LVH.Renal insufficiency in non-diabetic subjects is explained by interactions of MTHFR C677T polymorphism mutation with LVH, hsCRP, intact parathyroid hormone (iPTH), and RRI. Sign of these predictive effects is opposite: subjects with MTHFR 677CT polymorphism have lower likelihood of renal insufficiency; differently, wild-type MTHFR genotype subjects have lower GFR and greater hsCRP, iPTH, RRI, and LVH

The nucleic acid-binding protein PcCNBP is transcriptionally regulated during the immune response in red swamp crayfish Procambarus clarkii

Gene family encoding cellular nucleic acid binding proteins (CNBP) is well conserved among vertebrates; however, there is limited knowledge in lower organisms. In this study, a CNBP homolog from the red swamp crayfish Procambarus clarkii was characterised. The full-length cDNA of PcCNBP was of 1257 bp with a 5′-untranslated region (UTR) of 63 bp and a 3′-UTR of 331 bp with a poly (A) tail, and an open-reading frame (ORF) of 864 bp encoding a polypeptide of 287 amino acids with the predicted molecular weight of about 33 kDa. The predicted protein possesses 7 tandem repeats of 14 amino acids containing the CCHC zinc finger consensus sequence, two RGG-rich single-stranded RNA-binding domain and a nuclear localization signal, strongly suggesting that PcCNBP was a homolog of vertebrate CNBP. The PcCNBP transcript was constitutively expressed in all tested tissues of unchallenged crayfish, including hepatopancreas, gill, eyestalk, haemocytes, intestine, stomach and cuticle with highest expression in haemocytes, intestine, gills and hepatopancreas. The mRNA expression of PcCNBP in haemocytes was modulated at transcriptional level by different immune challenges, suggesting its involvement in the immune response of P. clarkii during both bacteria and viruses infection

Indicaxanthin Induces Autophagy in Intestinal Epithelial Cancer Cells by Epigenetic Mechanisms Involving DNA Methylation

Autophagy is an evolutionarily conserved process critical in maintaining cellular homeostasis. Recently, the anticancer potential of autophagy inducers, including phytochemicals, was suggested. Indicaxanthin is a betalain pigment found in prickly pear fruit with antiproliferative and pro-apoptotic activities in colorectal cancer cells associated with epigenetic changes in selected methylation-silenced oncosuppressor genes. Here, we demonstrate that indicaxanthin induces the up-regulation of the autophagic markers LC3-II and Beclin1, and increases autophagolysosome production in Caco-2 cells. Methylomic studies showed that the indicaxanthin-induced pro-autophagic activity was associated with epigenetic changes. In addition to acting as a hypermethylating agent at the genomic level, indicaxanthin also induced significant differential methylation in 39 out of 47 autophagy-related genes, particularly those involved in the late stages of autophagy. Furthermore, in silico molecular modelling studies suggested a direct interaction of indicaxanthin with Bcl-2, which, in turn, influenced the function of Beclin1, a key autophagy regulator. External effectors, including food components, may modulate the epigenetic signature of cancer cells. This study demonstrates, for the first time, the pro-autophagic potential of indicaxanthin in human colorectal cancer cells associated with epigenetic changes and contributes to outlining its potential healthy effect in the pathophysiology of the gastrointestinal tract

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement

Checklist of the birds of Mato Grosso do Sul state, Brazil: diversity and conservation

Several phytogeographic regions (Cerrado, Pantanal, Atlantic Forest, Gran Chaco, and Chiquitano Dry Forests) converge in the state of Mato Grosso do Sul, Brazil, and influence regional biodiversity. Despite a list of birds in the state of Mato Grosso do Sul being published by Nunes et al. (2017), it is necessary to update and critically review avifauna records. In this study, we gathered the results of several records obtained from species lists and online data platforms of the 336 sites in this state over the last decades and grouped them into Main (Primary and Secondary) and Tertiary Lists. The avifauna of Mato Grosso do Sul is composed of 678 species, of which 643 (95%) have records proving their occurrence (Primary List), whereas 34 still lack documentation (Secondary List). The number of related species for Mato Grosso do Sul represents 34% of the Brazilian avifauna. Some species stand out for their unique occurrence in Mato Grosso do Sul, such as Melanerpes cactorum, Celeus lugubris, Phaethornis subochraceus, and Cantorchilus guarayanus, reflecting the influence of different phytogeographic regions of the Chaco and Chiquitano Dry Forests. Migrants represent 20% of the bird community occurring in the state, of which 93 species correspond to migrants from various regions of South America (south and west) and 40 to boreal migrants. Thirty-three species perform nomadic movements across the Pantanal Plain and other regions of the state. Thirty-one species are included in some conservation-threatened categories of global and/or national endangered species lists. Other 30 species are included in the near-threatened category at the global level and 23 at the national level. In addition, species typical of dry forests (in Serra da Bodoquena and Maciço do Urucum) and those from the Atlantic Forest in the south of the state deserve attention due to their restricted distribution and the high anthropogenic pressure on their habitat

Checklist of the birds of Mato Grosso do Sul state, Brazil: diversity and conservation

Several phytogeographic regions (Cerrado, Pantanal, Atlantic Forest, Gran Chaco, and Chiquitano Dry Forests) converge in the state of Mato Grosso do Sul, Brazil, and influence regional biodiversity. Despite a list of birds in the state of Mato Grosso do Sul being published by Nunes et al. (2017), it is necessary to update and critically review avifauna records. In this study, we gathered the results of several records obtained from species lists and online data platforms of the 336 sites in this state over the last decades and grouped them into Main (Primary and Secondary) and Tertiary Lists. The avifauna of Mato Grosso do Sul is composed of 678 species, of which 643 (95%) have records proving their occurrence (Primary List), whereas 34 still lack documentation (Secondary List). The number of related species for Mato Grosso do Sul represents 34% of the Brazilian avifauna. Some species stand out for their unique occurrence in Mato Grosso do Sul, such as Melanerpes cactorum, Celeus lugubris, Phaethornis subochraceus, and Cantorchilus guarayanus, reflecting the influence of different phytogeographic regions of the Chaco and Chiquitano Dry Forests. Migrants represent 20% of the bird community occurring in the state, of which 93 species correspond to migrants from various regions of South America (south and west) and 40 to boreal migrants. Thirty-three species perform nomadic movements across the Pantanal Plain and other regions of the state. Thirty-one species are included in some conservation-threatened categories of global and/or national endangered species lists. Other 30 species are included in the near-threatened category at the global level and 23 at the national level. In addition, species typical of dry forests (in Serra da Bodoquena and Maciço do Urucum) and those from the Atlantic Forest in the south of the state deserve attention due to their restricted distribution and the high anthropogenic pressure on their habitat

Analysis of the effects of co-exposure to antibiotics and cadmium on sea urchin embryos

In order to understand the mechanisms of responses to changes in the physical and chemical environment, as well as the mechanisms of developmental pathways, we investigated by RT-qPCR assays and light microscopy observations the impact of antibiotics and cadmium in P. lividus sea urchin embryos. In particular we inspected development and biomarkers for free radical damage and apoptosis. During development embryos were exposed to an antibiotic mix (Ab mix, usually added to sea urchin cultures) or to sulfamethoxazole/trimethoprim mix (TMP/SMX, usually added to aquacultures) and/or levels of 10-5, 10-4, 10-3 M CdCl2. Even though treatment with TMP/SMX apparently did not affect development, it stimulated a remarkable molecular response to oxidative stress. Moreover, when embryos were exposed to TMP/SMX and CdCl2, even development was seriously impaired and the antioxidant defense was blocked. On the other hand, Ab mix and Cd co-treatment made the cadmium effect on development worse, but the antioxidant molecular defense was unchanged, rising the possibility that another stress pathway is involved. This study leads to the conclusion that co-exposure to antibiotics and cadmium induces synergistic effects on sea urchin embryos. Thus, in cadmium contaminated areas, antibiotic discharge can be an important environmental factor which might play an important role in survival of P. lividus populations

Effects of cadmium exposition on sea urchin development by SSH and RT-qPCR techniques

Cadmium (Cd) is a toxic heavy metal contaminating coastal environments. It has been suggested that the mechanisms of acute Cd toxicity involve the depletion of glutathione and protein-bound sulfhydryl groups, resulting in enhanced production of ROS. Cd-increased ROS in turn produces lipid peroxidation, and results in DNA damage. However, little is known about direct evidence and mechanism for Cd-generated radicals until recently. In order to study the early defense strategies activated by P. lividus 30 hours embryos, in response to exposition to sub-lethal doses of Cd (100μM), we analyzed the induced transcriptome comparing it to that of control embryos by Suppression Subtractive Hybridization (SSH) technique. By this technique, we isolated five metallothionein (MT) cDNA and we analyzed their levels by RT-qPCR at different Cd concentrations. Two MT (MT7 and MT8) isogenes appeared to be constitutively expressed and upregulated upon high Cd concentration treatment (100μM). Three isogenes (MT4/MT6) are not transcribed in control embryos and they are specifically activated in response to low doses of Cd (0.1-1 μM). Moreover, in Cd upregulated group, there were: 10 genes related to intracellular signaling pathway components and transcription factors, 9 to oxidative, reductive and conjugative biotransformation, 7 to RNA maturation and protein synthesis, 6 to metal detoxification (including 5 MTs), 5 conserved hypothetical proteins with unknown functions and 16 unidentified sequences. In Cd down-regulated group, there were: 4 genes related to transcription regulation, 2 to oxidative phosphorilation, 1 to protein synthesis, 3 other hypothetical proteins and 4 unidentified sequences. We analyzed cDNA levels for 20 genes by RT-qPCR. Preliminary results show significant upregulation for apolipoprotein D, molybdopterin oxidoreductase, splicing coactivator subunit and ER lumen protein retaining receptor, TGFβ family receptor and TGFβ-activated kinase