A decision support tool for integrated fisheries bycatch management

Reviews in Fish Biology and Fisheries - Participatory decision tools enable stakeholders to reconcile conflicting natural resources management objectives. Fisheries targeting highly productive...     

Increasing Anaerobic Acetate Consumption and Ethanol Yields in Saccharomyces cerevisiae with NADPH-Specific Alcohol Dehydrogenase

Saccharomyces cerevisiae has recently been engineered to use acetate, a primary inhibitor in lignocellulosic hydrolysates, as a cosubstrate during anaerobic ethanolic fermentation. However, the original metabolic pathway devised to convert acetate to ethanol uses NADH-specific acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase and quickly becomes constrained by limited NADH availability, even when glycerol formation is abolished. We present alcohol dehydrogenase as a novel target for anaerobic redox engineering of S. cerevisiae. Introduction of an NADPH-specific alcohol dehydrogenase (NADPH-ADH) not only reduces the NADH demand of the acetate-to-ethanol pathway but also allows the cell to effectively exchange NADPH for NADH during sugar fermentation. Unlike NADH, NADPH can be freely generated under anoxic conditions, via the oxidative pentose phosphate pathway. We show that an industrial bioethanol strain engineered with the original pathway (expressing acetylating acetaldehyde dehydrogenase from Bifidobacterium adolescentis and with deletions of glycerol-3-phosphate dehydrogenase genes GPD1 and GPD2) consumed 1.9 g liter⁻¹ acetate during fermentation of 114 g liter⁻¹ glucose. Combined with a decrease in glycerol production from 4.0 to 0.1 g liter⁻¹, this increased the ethanol yield by 4% over that for the wild type. We provide evidence that acetate consumption in this strain is indeed limited by NADH availability. By introducing an NADPH-ADH from Entamoeba histolytica and with overexpression of ACS2 and ZWF1, we increased acetate consumption to 5.3 g liter⁻¹ and raised the ethanol yield to 7% above the wild-type level.     

Analysis of a spindle pole body mutant reveals a defect in biorientation and illuminates spindle forces

The spindle pole body (SPB) is the microtubule organizing center in Saccharomyces cerevisiae. An essential task of the SPB is to ensure assembly of the bipolar spindle, which requires a proper balancing of forces on the microtubules and chromosomes. The SPB component Spc110p connects the ends of the spindle microtubules to the core of the SPB. We previously reported the isolation of a mutant allele spc110-226 that causes broken spindles and SPB disintegration 30 min after spindle formation. By live cell imaging of mutant cells with green fluorescent protein (GFP)-Tub1p or Spc97p-GFP, we show that spc110-226 mutant cells have early defects in spindle assembly. Short spindles form but do not advance to the 1.5-microm stage and frequently collapse. Kinetochores are not arranged properly in the mutant cells. In 70% of the cells, no stable biorientation occurs and all kinetochores are associated with only one SPB. Examination of the SPB remnants by electron microscopy tomography and fluorescence microscopy revealed that the Spc110-226p/calmodulin complex is stripped off of the central plaque of the SPB and coalesces to from a nucleating structure in the nucleoplasm. The central plaque components Spc42p and Spc29p remain behind in the nuclear envelope. The delamination is likely due to a perturbed interaction between Spc42p and Spc110-226p as detected by fluorescence resonance energy transfer analysis. We suggest that the force exerted on the SPB by biorientation of the chromosomes pulls the Spc110-226p out of the SPB; removal of force exerted by coherence of the sister chromatids reduced fragmentation fourfold. Removal of the forces exerted by the cytoplasmic microtubules had no effect on fragmentation. Our results provide insights into the relative contributions of the kinetochore and cytoplasmic microtubules to the forces involved in formation of a bipolar spindle.     

Vav1 transduces T cell receptor signals to the activation of the Ras/ERK pathway via LAT, Sos, and RasGRP1

Vav1 is a signaling protein required for both positive and negative selection of CD4(+)CD8(+) double positive thymocytes. Activation of the ERK MAPK pathway is also required for positive selection. Previous work has shown that Vav1 transduces T cell receptor (TCR) signals leading to an intracellular calcium flux. We now show that in double positive thymocytes Vav1 is required for TCR-induced activation of the ERK1 and ERK2 kinases via a pathway involving the Ras GTPase, and B-Raf, MEK1, and MEK2 kinases. Furthermore, we show that Vav1 transduces TCR signals to Ras by controlling the membrane recruitment of two guanine nucleotide exchange factors. First, Vav1 transduces signals via phospholipase Cgamma1 leading to the membrane recruitment of RasGRP1. Second, Vav1 is required for recruitment of Sos1 and -2 to the transmembrane adapter protein LAT. Finally, we show that Vav1 is required for TCR-induced LAT phosphorylation, a key event for the activation of both phospholipase Cgamma1 and Sos1/2. We propose that reduced LAT phosphorylation is the key reason for defective TCR-induced calcium flux and ERK activation in Vav1-deficient cells.     

Cooperation of the Dam1 and Ndc80 kinetochore complexes enhances microtubule coupling and is regulated by aurora B

The coupling of kinetochores to dynamic spindle microtubules is crucial for chromosome positioning and segregation, error correction, and cell cycle progression. How these fundamental attachments are made and persist under tensile forces from the spindle remain important questions. As microtubule-binding elements, the budding yeast Ndc80 and Dam1 kinetochore complexes are essential and not redundant, but their distinct contributions are unknown. In this study, we show that the Dam1 complex is a processivity factor for the Ndc80 complex, enhancing the ability of the Ndc80 complex to form load-bearing attachments to and track with dynamic microtubule tips in vitro. Moreover, the interaction between the Ndc80 and Dam1 complexes is abolished when the Dam1 complex is phosphorylated by the yeast aurora B kinase Ipl1. This provides evidence for a mechanism by which aurora B resets aberrant kinetochore–microtubule attachments. We propose that the action of the Dam1 complex as a processivity factor in kinetochore–microtubule attachment is regulated by conserved signals for error correction.     

Protective effect of arginine on oxidative stress in transgenic sickle mouse models

Sickle cell disease (SCD) is characterized by reperfusion injury and chronic oxidative stress. Oxidative stress and hemolysis in SCD result in inactivation of nitric oxide (NO) and depleted arginine levels. We hypothesized that augmenting NO production by arginine supplementation will reduce oxidative stress in SCD. To this end, we measured the effect of arginine (5% in mouse chow) on NO metabolites (NOx), lipid peroxidation (LPO), and selected antioxidants in transgenic sickle mouse models. Untreated transgenic sickle (NY1DD) mice (expressing  75% β^S-globin of all β-globins; mild pathology) and knockout sickle (BERK) mice (expressing exclusively hemoglobin S; severe pathology) showed reduced NOx levels and significant increases in the liver LPO compared with C57BL mice, with BERK mice showing maximal LPO increase in accordance with the disease severity. This was accompanied by reduced activity of antioxidants (glutathione, total superoxide dismutase, catalase, and glutathione peroxidase). However, GSH levels in BERK were higher than in NY1DD mice, indicating a protective response to greater oxidative stress. Importantly, dietary arginine significantly increased NOx levels, reduced LPO, and increased antioxidants in both sickle mouse models. In contrast, nitro-L-arginine methylester, a potent nonselective NOS inhibitor, worsened the oxidative stress in NY1DD mice. Thus, the attenuating effect of arginine on oxidative stress in SCD mice suggests its potential application in the management of this disease.     

Range-wide analysis of eastern massasauga survivorship

Decisions affecting wildlife management and conservation policy of imperiled species are often aided by population models. Reliable population models require accurate estimates of vital rates and an understanding of how vital rates vary geographically. The eastern massasauga (Sistrurus catenatus catenatus) is a rattlesnake species found in the Great Lakes region of North America. Populations of the eastern massasauga are fragmented and only a few areas harbor multiple, sizable populations. Eastern massasauga research has typically focused on single populations or local metapopulations but results suggest that demographic parameters vary geographically. We used 21 radiotelemetry datasets comprising 499 telemetered snakes from 16 distinct locations throughout the range of the eastern massasauga to characterize geographic patterns of adult survival using the known-fate model in Program MARK. Annual adult survival ranged from 0.35 to 0.95 (mean = 0.67) and increased along a southwest to northeast geographic axis. Further analysis of 6 datasets indicated no consistent difference in survival between males and females. Our results provide a better understanding of the relationship between survivorship and geography for the eastern massasauga and suggest that such variation should be incorporated into population models as well as local and regional management plans. © 2012 The Wildlife Society.     

Effects of hydrological forcing on the structure of a tropical estuarine food web

River flow can impact which sources of particulate organic matter (POM) fuel estuarine food webs. Here, we used stable carbon (C) and nitrogen (N) isotope analyses to compare how contributions of different POM sources (terrestrial, estuarine, and marine) to the diets of zooplankton and juvenile fishes differed between low and high river flow conditions, as well as spatially across a tropical estuary, Hilo Bay, Hawaii, USA. Diets of zooplankton and juvenile fishes were affected by river flow conditions, but the magnitude and the change in the basal resources depended on the location of the station in the estuary relative to the ocean and the river mouths. Consumers from the station most isolated from the ocean and with groundwater and overland flow inputs, utilized a combination of estuarine and terrestrial POM during both low and high river flow conditions and exhibited less variability in their basal resources than stations with direct ocean exchange. Consumers from stations in the Bay most affected by ocean exchange and river inputs utilized a combination of estuarine, terrestrial, and marine POM during low flow conditions, but shifted to marine and terrestrial POM during high river flow conditions. This shift to using terrestrial POM during high river flow conditions was substantial and up to 40% higher than values measured in other estuaries. Factors suspected to be affecting which POM source(s) consumers use in Hilo Bay are gross primary production, biological availability of exported terrestrial OM, and estuarine bacteria biomass, all of which are affected by river flow. Overall, our results suggest that Hilo Bay's food web and possibly those from other tropical estuaries are vulnerable to changes in hydrology, which may be further enhanced by global climate change.     

Toxicity testing moves from the legislature to the petri dish-and back

With the growing cost of using animals to test the safety of new chemicals and an increasing backlog of chemicals awaiting testing, the quest for cell-based in vitro alternatives for toxicity testing is gaining momentum.     

Predicting species distributions from herbarium collections: does climate bias in collection sampling influence model outcomes?

Aim Species distribution models and geographical information system (GIS) technologies are becoming increasingly important tools in conservation planning and decision‐making. Often the rich data bases of museums and herbaria serve as the primary data for predicting species distributions. Yet key assumptions about the primary data often are untested, and violation of such assumptions may have consequences for model predictions. For example, users of primary data assume that sampling has been random with respect to geography and environmental gradients. Here we evaluate the assumption that plant voucher specimens adequately sample the climatic gradient and test whether violation of this assumption influences model predictions. Location Bolivia and Ecuador. Methods Using 323,711 georeferenced herbarium collections and nine climatic variables, we predicted the distribution of 76 plant species using maximum entropy models (MAXENT) with training points that sampled the climate environments randomly and training points that reflected the climate bias in the herbarium collections. To estimate the distribution of species, MAXENT finds the distribution of maximum entropy (i.e. closest to uniform) subject to the constraint that the expected value for each environmental variable under the estimated distribution matches its empirical average. The experimental design included species that differed in geographical range and elevation; all species were modelled with 20 and 100 training points. We examined the influence of the number of training points and climate bias in training points, elevation and range size on model performance using analysis of variance models. Results We found that significant parts of the climatic gradient were poorly represented in herbarium collections for both countries. For the most part, existing climatic bias in collections did not greatly affect distribution predictions when compared with an unbiased data set. Although the effects of climate bias on prediction accuracy were found to be greater where geographical ranges were characterized by high spatial variation in the degree of climate bias (i.e. ranges where the bias of the various climates sampled by collections deviated considerably from the mean bias), the greatest influence on model performance was the number of presence points used to train the model. Main conclusions These results demonstrate that predictions of species distributions can be quite good despite existing climatic biases in primary data found in natural history collections, if a sufficiently large number of training points is available. Because of consistent overprediction of models, these results also confirm the importance of validating models with independent data or expert opinion. Failure to include independent model validation, especially in cases where training points are limited, may potentially lead to grave errors in conservation decision‐making and planning.