Mutation screening of multiple genes in Spanish patients with autosomal recessive retinitis pigmentosa by targeted resequencing

Retinitis Pigmentosa (RP) is a heterogeneous group of inherited retinal dystrophies characterised ultimately by the loss of photoreceptor cells. RP is the leading cause of visual loss in individuals younger than 60 years, with a prevalence of about 1 in 4000. The molecular genetic diagnosis of autosomal recessive RP (arRP) is challenging due to the large genetic and clinical heterogeneity. Traditional methods for sequencing arRP genes are often laborious and not easily available and a screening technique that enables the rapid detection of the genetic cause would be very helpful in the clinical practice. The goal of this study was to develop and apply microarray-based resequencing technology capable of detecting both known and novel mutations on a single high-throughput platform. Hence, the coding regions and exon/intron boundaries of 16 arRP genes were resequenced using microarrays in 102 Spanish patients with clinical diagnosis of arRP. All the detected variations were confirmed by direct sequencing and potential pathogenicity was assessed by functional predictions and frequency in controls. For validation purposes 4 positive controls for variants consisting of previously identified changes were hybridized on the array. As a result of the screening, we detected 44 variants, of which 15 are very likely pathogenic detected in 14 arRP families (14%). Finally, the design of this array can easily be transformed in an equivalent diagnostic system based on targeted enrichment followed by next generation sequencing.     

Leaf-litter processing in headwater streams of northern Iberian Peninsula: moderate levels of eutrophication do not explain breakdown rates

Agricultural and urban runoffs result in increased nitrogen and phosphorus inputs in rivers and are the cause of eutrophication. Headwater streams are less frequently affected by these impairments because of the low-to-moderate human activities there. Eutrophication can affect the structure and function of benthic communities in headwater streams, stimulating the activity of heterotrophic microorganisms and macroinvertebrates on a pivotal process such as leaf-litter decomposition. In this study, we monitored the breakdown of alder leaves in six headwater streams that constitute a moderate nutrient enrichment gradient. Breakdown experiments were conducted in autumn–winter and leaf carbon, nitrogen and phosphorus, and associated aquatic hyphomycetes and macroinvertebrates were determined. The increase in nutrient availability in the stream water enhanced leaf-litter quality and led to an increase in the hyphomycete assemblage evenness and a reduction of shredder densities. However, contrary to our expectations, dissolved nutrient availability did not explain the breakdown rates. Thus, the absence of a clear effect of nutrient enrichment of stream water on the leaf breakdown rate highlights the difficulties of predicting the response of this ecosystem process to slight levels of eutrophication in headwater streams.     

Involvement of nitrogen and cytokinins in photosynthetic acclimation to elevated CO2 of spring wheat

Acclimation of photosynthetic capacity to elevated CO₂ involves a decrease of the leaf Rubisco content. In the present study, it was hypothesized that nitrogen uptake and partitioning within the leaf and among different aboveground organs affects the down-regulation of Rubisco. Given the interdependence of nitrogen and cytokinin signals at the whole plant level, it is also proposed that cytokinins affect the nitrogen economy of plants under elevated CO₂, and therefore the acclimatory responses. Spring wheat received varying levels of nitrogen and cytokinin in field chambers with ambient (370 μmol mol⁻¹) or elevated (700 μmol mol⁻¹) atmospheric CO₂. Gas exchange, Rubisco, soluble protein and nitrogen contents were determined in the top three leaves in the canopy, together with total nitrogen contents per shoot. Growth in elevated CO₂ induced decreases in photosynthetic capacity only when nitrogen supply was low. However, the leaf contents of Rubisco, soluble protein and total nitrogen on an area basis declined in elevated CO₂ regardless of nitrogen supply. Total nitrogen in the shoot was no lower in elevated than ambient CO₂, but the fraction of this nitrogen located in flag and penultimate leaves was lower in elevated CO₂. Decreased Rubisco: chlorophyll ratios accompanied losses of leaf Rubisco with CO₂ enrichment. Cytokinin applications increased nitrogen content in all leaves and nitrogen allocation to senescing leaves, but decreased Rubisco contents in flag leaves at anthesis and in all leaves 20 days later, together with the amount of Rubisco relative to soluble protein in all leaves at both growth stages. The results suggest that down regulation of Rubisco in leaves at elevated CO₂ is linked with decreased allocation of nitrogen to the younger leaves and that cytokinins cause a fractional decrease of Rubisco and therefore do not alleviate acclimation to elevated CO₂.     

Comparative analysis of microbial DNA extraction protocols for groundwater samples

A comparative analysis of four different DNA extraction protocols was performed to determine the best choice for groundwater microbial diversity studies using temperature gradient gel electrophoresis (TGGE) analysis. The methods used were a chelex-based method, a modified salting out procedure (MSOP), and the commercial kits Epicentre and FastDNA. Both commercial kits exhibited the greatest reproducibility in their methods; however, their band patterns were very different. The protocol that showed the highest diversity was the chelex-based method, and the one that showed the lowest diversity was the FastDNA kit.     

Coronin 1A promotes a cytoskeletal-based feedback loop that facilitates Rac1 translocation and activation

The activation of the Rac1 GTPase during cell signalling entails its translocation from the cytosol to membranes, release from sequestering Rho GDP dissociation inhibitors (RhoGDI), and GDP/GTP exchange. In addition to those steps, we show here that optimal Rac1 activation during cell signalling requires the engagement of a downstream, cytoskeletal-based feedback loop nucleated around the cytoskeletal protein coronin 1A and the Rac1 exchange factor ArhGEF7. These two proteins form a cytosolic complex that, upon Rac1-driven F-actin polymerization, translocates to juxtamembrane areas where it expands the pool of activated, membrane-bound Rac1. Such activity requires the formation of an F-actin/ArhGEF7-dependent physical complex of coronin 1A with Pak1 and RhoGDIα that, once assembled, promotes the Pak1-dependent dissociation of Rac1 from the Rac1/RhoGDIα complex and subsequent Rac1 activation. Genetic evidence demonstrates that this relay circuit is essential for generating sustained Rac1 activation levels during cell signalling.     

Circadian rhythms of self-feeding and locomotor activity in zebrafish (Danio Rerio)

To investigate daily feeding rhythms in zebrafish, the authors have developed a new self-feeding system with an infrared photocell acting as a food-demand sensor, which lets small-size fish such as zebrafish trigger a self-feeder. In this paper, the authors used eight groups of 20 fish. Locomotor activity rhythms were also investigated by means of infrared sensors. Under a 12?h:12?h light (L)-dark (D) cycle, zebrafish showed a clear nocturnal feeding pattern (88.0% of the total daily food-demands occurring in the dark phase), concentrated during the last 4?h of the dark phase. In contrast, locomotor activity was mostly diurnal (88.2% of total daily activity occurring in the light phase). Moreover, both feeding and locomotor rhythms were endogenously driven, as they persisted under free-running conditions. The average period length (τ) of the locomotor and feeding rhythms was shorter (τ?=?22.9?h) and longer (τ?=?24.6?h) than 24?h, respectively. During the time that food availability was restricted, fish could only feed during ZT0-ZT12 or ZT12-ZT16. This resulted in feeding activity being significantly modified according to feeding time, whereas the locomotor activity pattern remained synchronized to the LD cycle and did not change during this trial. These findings revealed an independent phasing between locomotor and feeding activities (which were mostly nocturnal or diurnal, respectively), thus supporting the concept of multioscillatory control of circadian rhythmicity in zebrafish.     

Caveolin-1 regulates cell polarization and directional migration through Src kinase and Rho GTPases

Development, angiogenesis, wound healing, and metastasis all involve the movement of cells in response to changes in the extracellular environment. To determine whether caveolin-1 plays a role in cell migration, we have used fibroblasts from knockout mice. Caveolin-1–deficient cells lose normal cell polarity, exhibit impaired wound healing, and have decreased Rho and increased Rac and Cdc42 GTPase activities. Directional persistency of migration is lost, and the cells show an impaired response to external directional stimuli. Both Src inactivation and p190RhoGAP knockdown restore the wild-type phenotype to caveolin-1–deficient cells, suggesting that caveolin-1 stimulates normal Rho GTP loading through inactivation of the Src–p190RhoGAP pathway. These findings highlight the importance of caveolin-1 in the establishment of cell polarity during directional migration through coordination of the signaling of Src kinase and Rho GTPases.     

Silent mutations at the 5'-end of the cDNA of actinoporins from the sea anemone Stichodactyla helianthus allow their heterologous overproduction in Escherichia coli

Wild-type actinoporins StnI and StnII from the sea anemone Stichodactyla helianthus, as well as their NH(2)-terminal six-His tagged versions, have been overproduced in Escherichia coli. Overproduction of both wild-type proteins was only possible after introducing silent mutations within the 5'-end of their original cDNA sequences. These mutations would prevent the formation of RNA secondary structures blocking the ribosome-binding site and the initiation codon. The four recombinant proteins were purified to homogeneity in milligrams amount and characterized from spectroscopic and functional points of view. All the isolated proteins behaved as the corresponding natural ones although the six-His tagged variants exhibited a decreased lytic activity. The strategy described will be useful to allow the production of mutant variants of these proteins and probably of other actinoporins.     

Aging impairs neurogenic contraction in guinea pig urinary bladder: role of oxidative stress and melatonin

The incidence of urinary bladder disturbances increases with age, and free radical accumulation has been proposed as a causal factor. Here we investigated the association between changes in bladder neuromuscular function and oxidative stress in aging and the possible benefits of melatonin treatment. Neuromuscular function was assessed by electrical field stimulation (EFS) of isolated guinea pig detrusor strips from adult and aged female guinea pigs. A group of adult and aged animals were treated with 2.5 mg x kg(-1) x day(-1) melatonin for 28 days. Neurotransmitter blockers were used to dissect pharmacologically the EFS-elicited contractile response. EFS induced a neurogenic and frequency-dependent contraction that was impaired by aging. This impairment is in part related to a decrease in detrusor myogenic contractility. Age also decreased the sensitivity of the contraction to pharmacological blockade of purinergic and sensitive fibers but increased the effect of blockade of nitrergic and adrenergic nerves. The density of cholinergic and nitrergic nerves remained unaltered, but aging modified afferent fibers. These changes were associated with an increased level of markers for oxidative stress. Melatonin treatment normalized oxidative levels and counteracted the aging-associated changes in bladder neuromuscular function. In conclusion, these results show that aging modifies neurogenic contraction and the functional profile of the urinary bladder plexus and simultaneously increases the oxidative damage to the organ. Melatonin reduces oxidative stress and improves the age-induced changes in bladder neuromuscular function, which could be of importance in reducing the impact of age-related bladder disorders.     

Rac, membrane heterogeneity, caveolin and regulation of growth by integrins

Anchorage dependence of growth blocks cell proliferation in inappropriate environments, thereby inhibiting cancer cell invasion and metastasis. Inhibition of growth regulatory pathways, including Rac, Erk and PtdIns 3-kinase in non-adherent cells mediates this effect. Here, we review recent work showing that integrin-mediated adhesion controls Rac binding to membranes. Rac binding sites can be found within cholesterol-enriched membrane domains, which are internalized when cells are deprived of adhesion. Endocytosis of these domains is mediated by caveolae and regulated by caveolin-1 phosphorylated on Tyr 14. This mechanism can account for the control of multiple pathways by integrins, thus providing an important mechanism for anchorage dependence of growth.