mRNA secondary structure optimization using a correlated stem–loop prediction

Secondary structure of messenger RNA plays an important role in the bio-synthesis of proteins. Its negative impact on translation can reduce the yield of protein by slowing or blocking the initiation and movement of ribosomes along the mRNA, becoming a major factor in the regulation of gene expression. Several algorithms can predict the formation of secondary structures by calculating the minimum free energy of RNA sequences, or perform the inverse process of obtaining an RNA sequence for a given structure. However, there is still no approach to redesign an mRNA to achieve minimal secondary structure without affecting the amino acid sequence. Here we present the first strategy to optimize mRNA secondary structures, to increase (or decrease) the minimum free energy of a nucleotide sequence, without changing its resulting polypeptide, in a time-efficient manner, through a simplistic approximation to hairpin formation. Our data show that this approach can efficiently increase the minimum free energy by >40%, strongly reducing the strength of secondary structures. Applications of this technique range from multi-objective optimization of genes by controlling minimum free energy together with CAI and other gene expression variables, to optimization of secondary structures at the genomic level.     

Neuronal damage and cognitive impairment associated with hypoglycemia: An integrated view

The aim of the present review is to offer a current perspective about the consequences of hypoglycemia and its impact on the diabetic disorder due to the increasing incidence of diabetes around the world. The main consequence of insulin treatment in type 1 diabetic patients is the occurrence of repetitive periods of hypoglycemia and even episodes of severe hypoglycemia leading to coma. In the latter, selective neuronal death is observed in brain vulnerable regions both in humans and animal models, such as the cortex and the hippocampus. Cognitive damage subsequent to hypoglycemic coma has been associated with neuronal death in the hippocampus. The mechanisms implicated in selective damage are not completely understood but many factors have been identified including excitotoxicity, oxidative stress, zinc release, PARP-1 activation and mitochondrial dysfunction. Importantly, the diabetic condition aggravates neuronal damage and cognitive failure induced by hypoglycemia. In the absence of coma prolonged and severe hypoglycemia leads to increased oxidative stress and discrete neuronal death mainly in the cerebral cortex. The mechanisms responsible for cell damage in this condition are still unknown. Recurrent moderate hypoglycemia is far more common in diabetic patients than severe hypoglycemia and currently important efforts are being done in order to elucidate the relationship between cognitive deficits and recurrent hypoglycemia in diabetics. Human studies suggest impaired performance mainly in memory and attention tasks in healthy and diabetic individuals under the hypoglycemic condition. Only scarce neuronal death has been observed under moderate repetitive hypoglycemia but studies suggest that impaired hippocampal synaptic function might be one of the causes of cognitive failure. Recent studies have also implicated altered mitochondrial function and mitochondrial oxidative stress.     

Effect of Acute and Chronic Administration of l-Tyrosine on Nerve Growth Factor Levels in Rat Brain

Most inborn errors of tyrosine catabolism produce hypertyrosinemia. Neurological manifestations are variable and some patients are developmentally normal, while others show different degrees of developmental retardation. Considering that current data do not eliminate the possibility that elevated levels of tyrosine and/or its derivatives may have noxious effects on central nervous system development in some patients, the present study evaluated nerve growth factor (NGF) levels in hippocampus, striatum and posterior cortex of young rats. In our acute protocol, Wistar rats (10 and 30 days old) were killed 1 h after a single intraperitoneal administration of l-tyrosine (500 mg/kg) or saline. Chronic administration consisted of l-tyrosine (500 mg/kg) or saline injections 12 h apart for 24 days in Wistar rats (7 days old); the rats were killed 12 h after the last injection. NGF levels were then evaluated. Our findings showed that acute administration of l-tyrosine decreased NGF levels in striatum of 10-day-old rats. In the 30-day-old rats, NGF levels were decreased in hippocampus and posterior cortex. On the other hand, chronic administration of l-tyrosine increased NGF levels in posterior cortex. Decreased NGF may impair growth, differentiation, survival and maintenance of neurons.     

Decline in local abundance of bottlenose dolphins (Tursiops truncatus) in the Bay of Islands,New Zealand

Regional populations of bottlenose dolphins (Tursiops truncatus) around New Zealand are genetically isolated from each other and the species was recently classified as nationally endangered based on relatively small population sizes and reports of high calf mortality. Here, we estimate the abundance and trends in one of these regional populations, the Bay of Islands, using a photo‐identification database collected from 1997 to 1999 and from 2003 to 2006, containing a total of 3,841 records of 317 individual dolphins. Estimates of abundance obtained with the robust design fluctuated widely but showed a significant decline in the number of dolphins present in the bay over time (7.5% annual rate of decline). Temporary emigration was random and fluctuated considerably (γ  =  0.18, SE = 0.07 to γ  =  0.84, SE = 0.06). Apparent survival was estimated at 0.928 (CI = 0.911–0.942). Seasonal estimates (26 seasons) obtained in POPAN also showed a significant decline in abundance (5.8% annual rate of decline). Despite the decline observed in local abundance, dolphins continue to be found regularly in the Bay of Islands, suggesting that fewer dolphins use the bay on regular basis. Consequently, it seems that a change in habitat use, mortality and possibly low recruitment could underlie the apparent local decline.     

Intestinal Na(+)/Ca(2+) exchanger protein and gene expression are regulated by 1,25(OH)(2)D(3) in vitamin D-deficient chicks

The role of 1,25(OH)(2)D(3) on the intestinal NCX activity was studied in vitamin D-deficient chicks (-D) as well as the hormone effect on NCX1 protein and gene expression and the potential molecular mechanisms underlying the responses. Normal, -D and -D chicks treated with cholecalciferol or 1,25(OH)(2)D(3) were employed. In some experiments, -D chicks were injected with cycloheximide or with cycloheximide and 1,25(OH)(2)D(3) simultaneously. NCX activity was decreased by -D diet, returning to normal values after 50 IU daily of cholecalciferol/10 days or a dose of 1μg calcitriol/kg of b.w. for 15 h. Cycloheximide blocked NCX activity enhancement produced by 1,25(OH)(2)D(3). NCX1 protein and gene expression were diminished by -D diet and enhanced by 1,25(OH)(2)D(3). Vitamin D receptor expression was decreased by -D diet, effect that disappeared after 1,25(OH)(2)D(3) treatment. Rapid effects of 1,25(OH)(2)D(3) on intestinal NCX activity were also demonstrated. The abolition of the rapid effects through addition of Rp-cAMPS and staurosporine suggests that non genomic effects of 1,25(OH)(2)D(3) on NCX activity are mediated by activation of PKA and PKC pathways. In conclusion, 1,25(OH)(2)D(3) enhances the intestinal NCX activity in -D chicks through genomic and non genomic mechanisms.     

Anti-oxidant and anti-inflammatory mechanisms of amlodipine action to improve endothelial cell dysfunction induced by irreversibly glycated LDL

Amlodipine, alone or in combination with other drugs, was successfully used to treat hypertension. Our aim was to evaluate the potential of amlodipine (Am) to restore endothelial dysfunction induced by irreversibly glycated low density lipoproteins (AGE-LDL), an in vitro model mimicking the diabetic condition. Human endothelial cells (HEC) from EA.hy926 line were incubated with AGE-LDL in the presence/absence of Am and the oxidative and inflammatory status of the cells was evaluated along with the p38 MAPK and NF-κB signalling pathways. The cellular NADPH activity, 4-hydroxynonenal (4-HNE) and 3-nitrotyrosine levels in the culture medium and the adhesion of human monocytes to HEC were measured by chemiluminescence, UHPLC, Western Blot and spectrofluorimetric techniques. The gene expression of NADPH subunits (p22^phox, NOX4), eNOS and inflammatory molecules (MCP-1, VCAM-1) were determined by Real Time PCR, while the protein expression of p22^phox, MCP-1, iNOS, phospho-p38 MAPK and phospho-p65 NF-κB subunit were measured by Western Blot. Results showed that in HEC incubated with AGE-LDL, Am led to: (i) decrease of the oxidative stress: by reducing p22^phox, NOX4, iNOS expression, NADPH oxidase activity, 4-HNE and 3-nitrotyrosine levels; (ii) decrease of the inflammatory stress: by the reduction of MCP-1 and VCAM-1 expression, as well as of the number of monocytes adhered to HEC; (iii) inhibition of ROS-sensitive signalling pathways: by decreasing phosphorylation of p38 MAPK and p65 NF-κB subunits. In conclusion, the reported data demonstrate that amlodipine may improve endothelial dysfunction in diabetes through anti-oxidant and anti-inflammatory mechanisms.     

Cholesterol and membrane phospholipid compositions modulate the leakage capacity of the swaposin domain from a potato aspartic protease (StAsp-PSI)

Potato aspartic proteases (StAPs) and their swaposin domain (StAsp-PSI) are proteins with cytotoxic activity which involves plasma membrane destabilization. The ability of these proteins to produce cell death varies with the cellular type. Therefore, StAPs and StAsp-PSI selective cytotoxicity could be attributed to the different membrane lipid compositions of target cells. In this work we investigate the possible mechanism by which StAPs and StAsp-PSI produce selective membrane destabilization. Results obtained from leakage assays show that StAsp-PSI is a potent inducer of the leakage of LUVs containing anionic phospholipids, especially those containing phosphatidylglycerol. Based in these results, we suggest that the cytotoxic activity of StAsp-PSI on pathogenic microorganisms could be mediated by the attraction between the exposed positive domains of StAsp-PSI and the negatively charged microorganism membrane. On the other hand, our circular dichroism spectroscopic measurements and analysis by size exclusion chromatography and followed by electrophoresis, indicate that hydrophobic environment is necessary to StAsp-PSI oligomerization and both StAsp-PSI disulfide bounds and membrane with negative charged phospholipids are required by StAsp-PSI to produce membrane destabilization and then induce cell death in tumors and microorganism cell targets. Additionally, we demonstrate that the presence of cholesterol into the LUV membranes strongly diminishes the capacity of StAsp-PSI to produce leakage. This result suggests that the lack of hemolytic and cytotoxic activities on human lymphocytes of StAsp-PSI/StAPs may be partly due by the presence of cholesterol in these cell membrane types.     

Prostaglandin‐endoperoxide synthase 2 is not required for preimplantation ovine conceptus development in sheep

Conceptus development and elongation is required for successful pregnancy establishment in ruminants and is coincident with the production of interferon τ (IFNT) and prostaglandins (PGs). In both the conceptus trophectoderm and endometrium, PGs are primarily synthesized through a prostaglandin‐endoperoxide synthase 2 (PTGS2) pathway and modify endometrial gene expression and thus histotroph composition in the uterine lumen to promote conceptus growth and survival. Chemical inhibition of PG production by both the endometrium and the conceptus prevented elongation in sheep. However, the contributions of conceptus‐derived PGs to preimplantation conceptus development remain unclear. In this study, CRISPR‐Cas9 genome editing was used to inactivate PTGS2 in ovine embryos to determine the role of PTGS2‐derived PGs in conceptus development and elongation. PTGS2 edited conceptuses produced fewer PGs, but secreted similar amounts of IFNT to their Cas9 control counterparts and elongated normally. Expression of PTGS1 was lower in PTGS2 edited conceptuses, but PPARG expression and IFNT secretion were unaffected. Content of PGs in the uterine lumen was similar as was gene expression in the endometrium of ewes who received either Cas9 control or PTGS2 edited conceptuses. These results support the idea that intrinsic PTGS2‐derived PGs are not required for preimplantation embryo or conceptus survival and development in sheep.     

Antioxidant activity of in vitro plantlets and callus cultures of Randia echinocarpa,a medicinal plant from northwestern Mexico

Randia echinocarpa, an endemic plant to Northwest Mexico, is used as food and in traditional medicine, and several of its biological activities have been demonstrated (antioxidant, antimutagenic, antidiabetic, and immunomodulatory). Plant tissue culture is a safe and scalable system for plant propagation and production of bioactive compounds. Therefore, this study aims to establish protocols for seed germination and callus culture of R. echinocarpa and to evaluate the antioxidant activity of methanol extracts (ME) of plantlets and calli via the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) methods. Seeds were cultured in media with different concentrations of Murashige and Skoog (MS) salts and sucrose, and a higher germination rate and plantlet growth was observed in half-strength MS medium with 15 g L⁻¹ of sucrose. Calli were obtained from cotyledon and hypocotyl explants cultured in MS media with different concentrations of benzyl aminopurine (BAP) and indole-3-acetic acid (IAA). All treatments induced callus formation in 100% of explants; however, the medium containing 1 mg L⁻¹ BAP + 1 mg L⁻¹ IAA was selected because it produced calli with higher biomass and friable texture. The ME of cotyledons showed the highest antioxidant activity values (μmol Trolox per 100 g dry weight) in DPPH (345.5) and ABTS (1166.4) assays, whereas the ME of calli from hypocotyls showed a higher antioxidant activity than the ME of calli from cotyledons in both antioxidant assays. The tissue culture protocols established here will be useful for R. echinocarpa germplasm conservation and propagation, as well as for the production of bioactive compounds.