RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway

RNA interference (RNAi) is widely used to silence genes in plants and animals. It operates through the degradation of target mRNA by endonuclease complexes guided by approximately 21 nucleotide (nt) short interfering RNAs (siRNAs). A similar process regulates the expression of some developmental genes through approximately 21 nt microRNAs. Plants have four types of Dicer-like (DCL) enzyme, each producing small RNAs with different functions. Here, we show that DCL2, DCL3 and DCL4 in Arabidopsis process both replicating viral RNAs and RNAi-inducing hairpin RNAs (hpRNAs) into 22-, 24- and 21 nt siRNAs, respectively, and that loss of both DCL2 and DCL4 activities is required to negate RNAi and to release the plant's repression of viral replication. We also show that hpRNAs, similar to viral infection, can engender long-distance silencing signals and that hpRNA-induced silencing is suppressed by the expression of a virus-derived suppressor protein. These findings indicate that hpRNA-mediated RNAi in plants operates through the viral defence pathway.     

Flavour-active wine yeasts

The flavour of fermented beverages such as beer, cider, saké and wine owe much to the primary fermentation yeast used in their production, Saccharomyces cerevisiae. Where once the role of yeast in fermented beverage flavour was thought to be limited to a small number of volatile esters and higher alcohols, the discovery that wine yeast release highly potent sulfur compounds from non-volatile precursors found in grapes has driven researchers to look more closely at how choice of yeast can influence wine style. This review explores recent progress towards understanding the range of ??flavour phenotypes?? that wine yeast exhibit, and how this knowledge has been used to develop novel flavour-active yeasts. In addition, emerging opportunities to augment these phenotypes by engineering yeast to produce so-called grape varietal compounds, such as monoterpenoids, will be discussed.     

The winemaker's bug: From ancient wisdom to opening new vistas with frontier yeast science

The past three decades have seen a global wine glut. So far, well-intended but wasteful and expensive market-intervention has failed to drag the wine industry out of a chronic annual oversupply of roughly 15%. Can yeast research succeed where these approaches have failed by providing a means of improving wine quality, thereby making wine more appealing to consumers? To molecular biologists Saccharomyces cerevisiae is as intriguing as it is tractable. A simple unicellular eukaryote, it is an ideal model organism, enabling scientists to shed new light on some of the biggest scientific challenges such as the biology of cancer and aging. It is amenable to almost any modification that modern biology can throw at a cell, making it an ideal host for genetic manipulation, whether by the application of traditional or modern genetic techniques. To the winemaker, this yeast is integral to crafting wonderful, complex wines from simple, sugar-rich grape juice. Thus any improvements that we can make to wine, yeast fermentation performance or the sensory properties it imparts to wine will benefit winemakers and consumers. With this in mind, the application of frontier technologies, particularly the burgeoning fields of systems and synthetic biology, have much to offer in their pursuit of "novel" yeast strains to produce high quality wine. This paper discusses the nexus between yeast research and winemaking. It also addresses how winemakers and scientists face up to the challenges of consumer perceptions and opinions regarding the intervention of science and technology; the greater this intervention, the stronger the criticism that wine is no longer "natural." How can wine researchers respond to the growing number of wine commentators and consumers who feel that scientific endeavors favor wine quantity over quality and "technical sophistication, fermentation reliability and product consistency" over "artisanal variation"? This paper seeks to present yeast research in a new light and a new context, and it raises important questions about the direction of yeast research, its contribution to science and the future of winemaking.     

C. elegans BLOC-1 Functions in Trafficking to Lysosome-Related Gut Granules

The human disease Hermansky-Pudlak syndrome results from defective biogenesis of lysosome-related organelles (LROs) and can be caused by mutations in subunits of the BLOC-1 complex. Here we show that C. elegans glo-2 and snpn-1, despite relatively low levels of amino acid identity, encode Pallidin and Snapin BLOC-1 subunit homologues, respectively. BLOC-1 subunit interactions involving Pallidin and Snapin were conserved for GLO-2 and SNPN-1. Mutations in glo-2 and snpn-1,or RNAi targeting 5 other BLOC-1 subunit homologues in a genetic background sensitized for glo-2 function, led to defects in the biogenesis of lysosome-related gut granules. These results indicate that the BLOC-1 complex is conserved in C. elegans. To address the function of C. elegans BLOC-1, we assessed the intracellular sorting of CDF-2::GFP, LMP-1, and PGP-2 to gut granules. We validated their utility by analyzing their mislocalization in intestinal cells lacking the function of AP-3, which participates in an evolutionarily conserved sorting pathway to LROs. BLOC-1(-) intestinal cells missorted gut granule cargo to the plasma membrane and conventional lysosomes and did not have obviously altered function or morphology of organelles composing the conventional lysosome protein sorting pathway. Double mutant analysis and comparison of AP-3(-) and BLOC-1(-) phenotypes revealed that BLOC-1 has some functions independent of the AP-3 adaptor complex in trafficking to gut granules. We discuss similarities and differences of BLOC-1 activity in the biogenesis of gut granules as compared to mammalian melanosomes, where BLOC-1 has been most extensively studied for its role in sorting to LROs. Our work opens up the opportunity to address the function of this poorly understood complex in cell and organismal physiology using the genetic approaches available in C. elegans.     

TNF-α is associated with loss of lean body mass only in already cachectic COPD patients

Background

Systemic inflammation may contribute to cachexia in patients with chronic obstructive pulmonary disease (COPD). In this longitudinal study we assessed the association between circulating C-reactive protein (CRP), tumor necrosis factor (TNF)-α, interleukin (IL)-1ß, and IL-6 levels and subsequent loss of fat free mass and fat mass in more than 400 COPD patients over three years.

Methods

The patients, aged 40–76, GOLD stage II-IV, were enrolled in 2006/07, and followed annually. Fat free mass and fat mass indexes (FFMI & FMI) were calculated using bioelectrical impedance, and CRP, TNF-α, IL-1ß, and IL-6 were measured using enzyme immunoassays. Associations with mean change in FFMI and FMI of the four inflammatory plasma markers, sex, age, smoking, FEV₁, inhaled steroids, arterial hypoxemia, and Charlson comorbidity score were analyzed with linear mixed models.

Results

At baseline, only CRP was significantly (but weakly) associated with FFMI (r = 0.18, p < 0.01) and FMI (r = 0.27, p < 0.01). Univariately, higher age, lower FEV₁, and use of beta2-agonists were the only significant predictors of decline in FFMI, whereas smoking, hypoxemia, Charlson score, and use of inhaled steroids predicted increased loss in FMI. Multivariately, high levels of TNF-α (but not CRP, IL-1ß or IL-6) significantly predicted loss of FFMI, however only in patients with established cachexia at entry.

Conclusion

This study does not support the hypothesis that systemic inflammation is the cause of accelerated loss of fat free mass in COPD patients, but suggests a role for TNF-α in already cachectic COPD patients.     

Lack of somatic alterations of MC1R in primary melanoma

Germline variation of the melanocortin 1 receptor gene (MC1R) is a risk factor for cutaneous melanoma. Recent studies have indicated that the risk is significantly higher for melanomas with somatic BRAF mutations, suggesting that MC1R variants may have a more specific role than their demonstrated effects on skin and hair pigmentation. To address the possibility that MC1R may act like a tumor suppressor gene by creating a permissive condition for melanocytes with specific somatic mutations to proliferate or survive, we analyzed 103 primary melanomas for somatic MC1R mutations and copy number alterations. This cohort included melanomas from skin with and without chronic sun-induced damage, mucosal membranes, and acral skin (palms, soles, and subungual). We did not find somatic mutations or frequent DNA copy number alterations at the MC1R locus, nor any skewed pattern of copy number alterations that would favor one allele type over the other. In conclusion, our findings indicate that MC1R is not a frequent target of somatic alterations in melanoma.     

Plant cation-anion balance as affected by the ionic composition of the growing medium

Plants that remove an excess of cations over anions may cause soil acidification. The acidification potential of plants has been evaluated using solution culture techniques, but the influence of ionic composition of the medium on the plant cation-anion balance remains unclear. Our objective was to determine how electrolyte concentration and salt type affect the cation- anion balance of two test plants [barley (Hordeum vulgare L.) and kochia (Kochia scoparia L. Schrad.)]. Seedlings were grown in sand culture and irrigated with nutrient solution (Hoagland’s solution), which was adjusted to a range of electrolyte concentrations (target electrical conductivity of 7.5, 17.5 and 27.5 dS m⁻¹) using either chloride or sulphate salts. Increase in electrolyte concentration reduced yield of kochia, a salt-tolerant plant, by up to 38%. Total cation (Ca + Mg + K + Na) equivalents in kochia exceeded those of anions (Cl + S + P + NO₃) by 250 to 280 cmol_c kg⁻¹ of dry matter. Electrolyte concentration had no effect on the cation-anion balance of kochia, but excess cation values were significantly greater in the sulphate than in the chloride system. Kochia had a large content of water-soluble oxalate (194 to 226 cmol_c kg⁻¹), which was linearly related to the excess cation content. Growth of barley was severely restricted at the intermediate and high electrolyte concentrations. Cations exceeded anions by 21 to 59 cmol_c kg⁻¹ of barley dry matter. Excess cation content was greater in the sulphate than in the chloride medium, but electrolyte concentration did not have a consistent effect on the cation-anion balance. The small amounts of oxalate found in barley (0.9 to 2.6 cmol_c kg⁻¹) were insufficient to balance the cation excess.     

A yield control approach to assess phytoavailability of Zn and Cu in irradiated,composted sewage sludges and composted manure in field experiments: II. Copper

Organic wastes such as sewage sludges contain copper (Cu). Increased attention to environmental protection requires that wastes be treated with pathogen-eliminating procedures before application to farmland. It is not clear, however, if such procedures affect the plant availability of Cu in the wastes. This 2-year field research investigated the effect of irradiation and composting on Cu availability in sludges and manure using a yield control approach. Four organic wastes [digested and dewatered (DSS), digested and irradiated (DISS), composted (DICSS) sewage sludges and composted livestock manure (CLM)] were applied at four rates (10, 20, 30 and 40 t solid ha^–1 year^–1) with supplemented N and K fertilizers. A control treatment (CT) received N and K fertilizers only. Beans, lettuce and petunias were grown in first year and lettuce were harvested twice in second year. Beans appeared to have a strong ability to absorb Cu compared with the other test crops. In general, crop Cu concentration responses to Cu applied in DSS and DISS were well described by quadratic equations. Tested by a paired t-test, Cu concentration in bean pods was higher in DISS than in DSS treatment, indicating that irradiation increased phytoavailability of Cu. However, the parabolic response of crop Cu to Cu applied in DISS, suggesting that the increases were confined to the lower rates of DISS. Copper applied in DICSS did not increase Cu concentration in any of the test crops. At a given level of applied Cu, crop Cu tended to be lower in DICSS than in DSS or DISS treatment. Sludge composting depressed phytoavailability of Cu. Copper concentration in CLM was much lower than in sludges and sludge composts, but application of CLM increased Cu concentration in bean pods. The pattens of Cu concentration in the two cuts of lettuce in 1991 to Cu applied in CLM were similar, where low rates of CLM application slightly reduced Cu concentration, then the Cu concentration increased with increased rates. The dynamics of available Cu supply were different in the sludge composts and manure composts.     

A New Model for a Carpool Matching Service

Carpooling is an effective means of reducing traffic. A carpool team shares a vehicle for their commute, which reduces the number of vehicles on the road during rush hour periods. Carpooling is officially sanctioned by most governments, and is supported by the construction of high-occupancy vehicle lanes. A number of carpooling services have been designed in order to match commuters into carpool teams, but it known that the determination of optimal carpool teams is a combinatorially complex problem, and therefore technological solutions are difficult to achieve. In this paper, a model for carpool matching services is proposed, and both optimal and heuristic approaches are tested to find solutions for that model. The results show that different solution approaches are preferred over different ranges of problem instances. Most importantly, it is demonstrated that a new formulation and associated solution procedures can permit the determination of optimal carpool teams and routes. An instantiation of the model is presented (using the street network of Guangzhou city, China) to demonstrate how carpool teams can be determined.