Impact of PNKP mutations associated with microcephaly, seizures and developmental delay on enzyme activity and DNA strand break repair

Microcephaly with early-onset, intractable seizures and developmental delay (MCSZ) is a hereditary disease caused by mutations in polynucleotide kinase/phosphatase (PNKP), a DNA strand break repair protein with DNA 5'-kinase and DNA 3'-phosphatase activity. To investigate the molecular basis of this disease, we examined the impact of MCSZ mutations on PNKP activity in vitro and in cells. Three of the four mutations currently associated with MCSZ greatly reduce or ablate DNA kinase activity of recombinant PNKP at 30°C (L176F, T424Gfs48X and exon15Δfs4X), but only one of these mutations reduces DNA phosphatase activity under the same conditions (L176F). The fourth mutation (E326K) has little impact on either DNA kinase or DNA phosphatase activity at 30°C, but is less stable than the wild-type enzyme at physiological temperature. Critically, all of the MCSZ mutations identified to date result in ∼10-fold reduced cellular levels of PNKP protein, and reduced rates of chromosomal DNA strand break repair. Together, these data suggest that all four known MCSZ mutations reduce the cellular stability and level of PNKP protein, with three mutations likely ablating cellular DNA 5'-kinase activity and all of the mutations greatly reducing cellular DNA 3'-phosphatase activity

Emergent global patterns of ecosystem structure and function from a mechanistic general ecosystem model

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures

Ingestion of Small-Bodied Zooplankton by Zebra Mussels (Dreissena polymorpha): Can Cannibalism on Larvae Influence Population Dynamics?

The zebra mussel Dreissena polymorpha established populations in western Lake Erie in 1986 and achieved densities exceeding 3.4 × 105 individuals∙m−2 during 1990. We assessed apparently incidental predation on Lake Erie and Erindale Pond zooplankton by adult mussels. Dreissena larvae and small rotifers (Polyarthra spp., Keratella spp., Trichocerca) sustained moderate to high predatory mortality whereas larger taxa (Bosmina, Scapholeberis) were invulnerable to predation. Larval Dreissena almost always sustain \u3e 99% mortality in European lakes. While mortality has been ascribed primarily to lack of suitable settling substrate and unfavourable environmental conditions, it may be confounded by larval predation by adults. We demonstrate using STELLA™-modelling that with a larval mortality rate of 99%, settled mussel densities observed in western Lake Erie during 1990 would not be achieved until at least 1994. A model that combines a lower rate (70%) of abiotic mortality with larval predation by adult mussels c..., Les populations de dreissena polymorphe (Dreissena polymorpha) déjà établies dans la partie ouest du lac Érié en 1986 atteignaient des densités supérieures à 3,4 × 105 individus par mètre carré au cours de 1990. Nous avons évalué Ta prédation du zooplancton du lac Érié et de l\u27étang Erindale par les dreissenas adultes. Les larves des dreissenas et les petits rotifères (Polyarthra spp., Keratella spp., Trichocerca) présentaient une mortalité par prédation variant de moyenne à élevée tandis que les plus gros taxons (Bosmima, Scapholeberis) résistaient à toute prédation. Les larves de Dreissena des lacs européeens présentent presque toujours un taux de mortalité supérieur à 99%. La mortalité a surtout été attribuée à l\u27absence d\u27un substrat de fixation adéquat et à des conditions environnementales défavorables, mais elle peut être confondue avec celle découlant de la prédation des larves par les adultes. Nous avons montré, à l\u27aide d\u27un modèle STELLAmd, que les densités de dreissenas fixées notées en 1990 n\u27..

Sheldon Spectrum and the Plankton Paradox: Two Sides of the Same Coin : A trait-based plankton size-spectrum model

The Sheldon spectrum describes a remarkable regularity in aquatic ecosystems: the biomass density as a function of logarithmic body mass is approximately constant over many orders of magnitude. While size-spectrum models have explained this phenomenon for assemblages of multicellular organisms, this paper introduces a species-resolved size-spectrum model to explain the phenomenon in unicellular plankton. A Sheldon spectrum spanning the cell-size range of unicellular plankton necessarily consists of a large number of coexisting species covering a wide range of characteristic sizes. The coexistence of many phytoplankton species feeding on a small number of resources is known as the Paradox of the Plankton. Our model resolves the paradox by showing that coexistence is facilitated by the allometric scaling of four physiological rates. Two of the allometries have empirical support, the remaining two emerge from predator-prey interactions exactly when the abundances follow a Sheldon spectrum. Our plankton model is a scale-invariant trait-based size-spectrum model: it describes the abundance of phyto- and zooplankton cells as a function of both size and species trait (the maximal size before cell division). It incorporates growth due to resource consumption and predation on smaller cells, death due to predation, and a flexible cell division process. We give analytic solutions at steady state for both the within-species size distributions and the relative abundances across species

The Substrate-Bound Crystal Structure of a Baeyer–Villiger Monooxygenase Exhibits a Criegee-like Conformation

The Baeyer\u2013Villiger monooxygenases (BVMOs) are a family of bacterial flavoproteins that catalyze the synthetically useful Baeyer\u2013Villiger oxidation reaction. This involves the conversion of ketones into esters or cyclic ketones into lactones by introducing an oxygen atom adjacent to the carbonyl group. The BVMOs offer exquisite regio- and enantiospecificity while acting on a wide range of substrates. They use only NADPH and oxygen as cosubstrates, and produce only NADP+ and water as byproducts, making them environmentally attractive for industrial purposes. Here, we report the first crystal structure of a BVMO, cyclohexanone monooxygenase (CHMO) from Rhodococcus sp. HI-31 in complex with its substrate, cyclohexanone, as well as NADP+ and FAD, to 2.4 \uc5 resolution. This structure shows a drastic rotation of the NADP+ cofactor in comparison to previously reported NADP+-bound structures, as the nicotinamide moiety is no longer positioned above the flavin ring. Instead, the substrate, cyclohexanone, is found at this location, in an appropriate position for the formation of the Criegee intermediate. The rotation of NADP+ permits the substrate to gain access to the reactive flavin peroxyanion intermediate while preventing it from diffusing out of the active site. The structure thus reveals the conformation of the enzyme during the key catalytic step. CHMO is proposed to undergo a series of conformational changes to gradually move the substrate from the solvent, via binding in a solvent excluded pocket that dictates the enzyme\u2019s chemospecificity, to a location above the flavin\u2013peroxide adduct where catalysis occurs.Peer reviewed: YesNRC publication: Ye

Efeito das variáveis abióticas e do fitoplâncton sobre a comunidade zooplanctônica em um reservatório do Nordeste brasileiro

O zooplâncton do reservatório de Mundaú, Pernambuco, nordeste do Brasil foi estudado quanto a variabilidade temporal (entre os horários e períodos seco chuvoso) e espacial (nas regiões pelágica e litorânea em diferentes profundidades) correlacionando-as com as variáveis ambientais e com o fitoplâncton. Vinte e três táxons infragenéricos e cinco subgenéricos de zooplâncton foram encontrados. De forma geral, Rotifera foi o grupo dominante em todo o estudo. O fitoplâncton foi dominado pelas cianobactérias. No período seco, as variáveis físicas certamente controlaram o desenvolvimento do zooplâncton, favorecendo o estabelecimento de elevadas densidades algais. No período chuvoso, a correlação do zooplâncton com os níveis de nutrientes do sistema na região pelágica provavelmente conduziu a uma competição de recursos entre o fitoplâncton e o zooplâncton, controlando as densidades algais.Zooplankton from Mundaú reservoir, State of Pernambuco, northeast Brazil was studied concerning temporal (hours and seasonal period) and spatial (pelagic and coastal regions in different depths) variabilities, correlating them to the environmental variables and the phytoplankton. Twenty-three infrageneric and five subgeneric zooplankton taxa were observed. On the whole, Rotifera was the dominant group during this study, especially influenced by the oxygen concentrations. Phytoplankton was dominated by Cyanobacteria. On the dry period, physical variables certainly controlled the zooplankton's development, allowing elevated algal densities. On the rainy period, zooplankton correlation with the system's nutrients levels on pelagic region probably conduced to a resources competition between phytoplankton and zooplankton, controlling algal densities