Mechanism of escape from nonsense-mediated mRNA decay of human beta-globin transcripts with nonsense mutations in the first exon

The degradation of nonsense-mutated β-globin mRNA by nonsense-mediated mRNA decay (NMD) limits the synthesis of C-terminally truncated dominant negative β-globin chains and thus protects the majority of heterozygotes from symptomatic β-thalassemia. β-globin mRNAs with nonsense mutations in the first exon are known to bypass NMD, although current mechanistic models predict that such mutations should activate NMD. A systematic analysis of this enigma reveals that (1) β-globin exon 1 is bisected by a sharp border that separates NMD-activating from NMD-bypassing nonsense mutations and (2) the ability to bypass NMD depends on the ability to reinitiate translation at a downstream start codon. The data presented here thus reconcile the current mechanistic understanding of NMD with the observed failure of a class of nonsense mutations to activate this important mRNA quality-control pathway. Furthermore, our data uncover a reason why the position of a nonsense mutation alone does not suffice to predict the fate of the affected mRNA and its effect on protein expression.     

Extraction and conversion pathways for microalgae to biodiesel: a review focused on energy consumption

Numerous life cycle analysis (LCA) studies of microalgae to fuel have been released over the past 3 years in an attempt to determine the environmental sustainability of this novel concept. Despite numerous issues with these LCA studies, they have highlighted that cultivation and dewatering/drying for extraction and conversion are major energy sinks within the process. This paper provides a critical review of extraction and conversion methods discussed in literature and under commercial investigation. The basis of this review is energy consumption, with its purpose to highlight methods that deserve further attention in research and development. This review concludes with an energetic assessment of four conversion processes including pulsed electric field-assisted extraction followed by transesterification, in situ acid catalysed esterification of dry biomass, in situ hydrolysis and esterification of wet biomass and hydrothermal liquefaction. The analysis highlighted that energetically feasible methods do exist for the conversion of microalgal biomass to fuel; however, all require further research to be applied at commercial scale.     

Investigation of Functional and Morphological Integrity of Freshly Isolated and Cryopreserved Human Hepatocytes

There is a pressing need for alternative therapeutic methods effective in the treatment of patients with liver insufficiency. Isolated human hepatocytes may be a viable alternative or adjunct to orthotopic liver transplantation in such patients. The purpose of this study was to evaluate the viability and functional integrity of freshly isolated and cryopreserved human hepatocytes, in preparation for a multi-center human hepatocyte transplantation trial. We are currently processing transplant-grade human parenchymal liver cells from nondiseased human livers that are obtained through a network of organ procurement organizations (OPOs). Thus far, sixteen hepatocyte transplants have been performed using hepatocytes processed by our methods. At the time of referral all specimens were deemed unsuitable for transplantation due to anatomical anomalies, high fat content, medical history, etc. Hepatocytes were isolated from encapsulated liver sections by a modified two-step perfusion technique. Isolated cells were cryopreserved and stored in liquid nitrogen for one to twelve months. The total yield of freshly isolated hepatocytes averaged 3.7×10⁷ cells per gram of wet tissue. Based on trypan blue exclusion, fresh preparations contained an average of 85% viable hepatocytes vs. 70% in cryopreserved samples. The plating efficiencies of cells seeded immediately after isolation ranged from 87% to 98%, while those of cryopreserved/thawed cells were markedly lower. Flow cytometry analysis of cells labeled with 5,6-carboxyfluorescein diacetate succinimidyl ester (CFSE) showed that there was no significant difference in viability compared with trypan blue staining. Both freshly isolated hepatocytes and those recovered from cryopreservation showed typical and intact morphology as demonstrated by light and electron microscopy. The product of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) reaction was always expressed more intensely in cultures of freshly isolated hepatocytes. Measurements of lactate dehydrogenase (LDH) leakage were inversely correlated with trypan blue exclusion and CFSE labeling. Energy status, evaluated by the intracellular ATP concentration measurements, and various liver-specific functions such as urea synthesis and metabolism of 7-ethoxycoumarin were maintained both in fresh and cryopreserved/thawed hepatocytes. However, the activities were expressed at different levels in thawed cells. These data illustrate the importance and feasibility of human hepatocyte banking. In addition, it is clear that further refinements in the methods of hepatocyte isolation and cryopreservation are needed to utilize more fully these valuable cells in the clinic.     

True water constraint under a rainfall interception experiment in a Mediterranean shrubland (Northern Tunisia): confronting discrete measurements with a plant–soil water budget model

Increased drought length and intensity is expected in the Mediterranean basin under anthropogenic increase in atmospheric CO₂, leading to extreme events not yet encountered in the present climate variability. Understanding ecosystems responses and capturing peculiar ecophysiological processes related to these events have been investigated in the field by rainfall manipulation experiments. Quantifying the actual drought faced by the ecosystem under control and dry plots, or among experiments remain a key challenge for explaining functional impacts on plant growth. Full-profile soil water content can be tricky to assess in rocky soils, and time-consuming plant water potential measurements remain a discrete information unable to capture short rainfall pulses. We propose here to fully investigate the water budget of a total rainfall interception manipulation on a Mediterranean shrubland, coupled with a plant–soil water balance model. We could accurately simulate the seasonal course of plant water status, including small rainfall pulses. We then derived yearly estimates of water stress integral for each water treatment, leading to an estimate of 66–86 % increase of drought intensity for the dry treatment compared to the control. Comparing actual and expected plant water budget from simulations in the dry plots allowed to identify and quantify the impact of methodological issues related to rainfall interception experiments as side effects for intrusive rain drops and subsurface lateral water flow.     

The development and application of molecular markers for abiotic stress tolerance in barley

This article represents some current thinking and objectives in the use of molecular markers to abiotic stress tolerance. Barley has been chosen for study as it is an important crop species, as well as a model for genetic and physiological studies. It is an important crop and, because of its well-studied genetics and physiology, is an excellent candidate in which to devise more efficient breeding methods. Abiotic stress work on cultivated gene pools of small grain cereals frequently shows that adaptive and developmental genes are strongly associated with responses. Developmental genes have strong pleiotropic effects on a number of performance traits, not just abiotic stresses. One concern is that much of the genetic variation for improving abiotic stress tolerance has been lost during domestication, selection and modern breeding, leaving pleiotropic effects of the selected genes for development and adaptation. Such genes are critical in matching cultivars to their target agronomic environment, and since there is little leverage in changing these, other sources of variation may be required. In barley, and many other crops, greater variation to abiotic stresses exists in primitive landraces and related wild species gene pools. Wild barley, Hordeum spontaneum C. Koch is the progenitor of cultivated barley, Hordeum vulgare L. and is easily hybridized to H. vulgare. Genetic fingerprinting of H. spontaneum has revealed genetic marker associations with site-of-origin ecogeographic factors and also experimentally imposed stresses. Genotypes and collection sites have been identified which show the desired variation for particular stresses. Doubled haploid and other segregating populations, including landrace derivatives have been used to map genetically the loci involved. These data can be used in molecular breeding approaches to improve the drought tolerance of barley. One strategy involves screening for genetic markers and physiological traits for drought tolerance, and the associated problem of drought relief-induced mildew susceptibility in naturally droughted fields of North Africa.     

Tracking costs of virulence in natural populations of the wheat pathogen, Puccinia striiformis f.sp. tritici

Background  

Costs of adaptation play an important role in host-parasite coevolution. For parasites, evolving the ability to circumvent host resistance may trade off with subsequent growth or transmission. Such costs of virulence (sensu plant pathology) limit the spread of all-infectious genotypes and thus facilitate the maintenance of genetic polymorphism in both host and parasite. We investigated costs of three virulence factors in Puccinia striiformis f.sp. tritici, a fungal pathogen of wheat (Triticum aestivum).     

Ceratomyxa aegyptiaca n. sp. (Myxozoa: Myxosporea) from the gall-bladder of Solea aegyptiaca Chabanaud (Pleuronectiformes: Soleidae) in a Tunisian coastal lagoon

A new marine myxosporean species, Ceratomyxa aegyptiaca n. sp. is described from the gall-bladder of Solea aegyptiaca Chabanaud collected from the Ghar El Melh Lagoon in northeastern Tunisia. Mature spores are elongate and crescent-shaped, measuring 8-11?μm in length and 48-58?μm in width. The polar capsules are spherical, 3.2-4?μm in diameter and equal in size. Trophozoites are polysporous and float free in the bile or are attached on the epithelium of the gall-bladder. Morphological data and molecular analysis based on 18S rDNA sequences are provided. The 18S rDNA of C. aegyptiaca is readily distinguishable from that of other myxozoan species, as the genetically most similar myxozoan parasite, C. seriolae Yokoyama & Fukuda, 2001 (AB530265) collected from Seriola quinqueradiata Temminck & Schlegel in Japanese waters, shares with it only 67.5% identical nucleotides over a 1,680-bp long fragment of 18S rDNA.     

Evaluation of electrocoagulation,flocculation, and sedimentation harvesting methods on microalgae consortium grown in anaerobically digested abattoir effluent

Microalgae dewatering is a major bottleneck for biomass production in a large-scale microalgal production system which accounts for 20–60% of production cost. In this study, three dewatering systems of electrocoagulation, flocculation, and pH-induced flocculation were evaluated for microalgal consortium grown in anaerobically digested abattoir effluent at pH 6.5 and 9.5. At the shortest time (15 min) and the highest current density (0.08 A cm^?2), the highest microalgae recoveries of 78 and 84% were obtained with the corresponding power consumptions of 1.25 and 1.07 kWh kg^?1 for cultures at pH 6.5 and 9.5. For microalgae suspension at pH 6.5, the highest biomass recovery of 77% was obtained when 100 mg L^?1 of FeCl₃·6H₂O (after 15 min) or 100 mg L^?1 of Al₂(SO₄)₃·18H₂O (after 30 min) was added. However, microalgal recoveries significantly increased when FeCl₃·6H₂O or Al₂(SO₄)₃·18H₂O was used with the culture at pH 9.5. pH-Induced experiments showed that cultures adjusted at pH 10.5 had 36% higher biomass recovery compared to that in cultures at pH 8.5 after 2 h. The results of this study showed that cultures at higher pH (9.5) had a better microalgae recovery in all dewatering systems than cultures at lower pH (6.5).