Screening Human Genes for Small Alterations Performing an Enzymatic Cleavage Mismatched Analysis (ECMA) Protocol

Many human diseases are caused by small alterations in the genes and in the majority of cases sophisticated protocols are required for their detection. In this study we estimated the efficacy of an enzymatic protocol, which using a new mismatch-specific DNA plant endonuclease from celery (CEL family) recognizes and cleaves mismatched alleles between mutant and normal PCR products. The protocol was standardized on a variety of known mutations, in 11 patients with cystic fibrosis (CF), Fabry’s disease (FD), steroid 21-hydroxylase deficiency (21-HD) and Duchenne/Becker muscular dystrophy (DMD/BMD). The method does not require special equipment, labeling or standardization for every PCR product, since conditions of heteroduplex formation and enzyme digestion are universal for all products. The results showed that the method is rapid, effective, safe, reliable, and very simple, as the mutations are visualized on agarose or nusieve/agarose gels. The protocol was furthermore evaluated in three DMD patients with the detection of three alterations which after sequencing, were characterized as disease causative mutations. The proposed assay, which was applied for the first time in a variety of monogenic disorders, indicates that point mutation identification is feasible in any conventional molecular lab even for cases, where other techniques have failed.     

Sclareol induces apoptosis in human HCT116 colon cancer cells <Emphasis Type="Italic">in vitro</Emphasis> and suppression of HCT116 tumor growth in immunodeficient mice

Labd-14-ene-8, 13-diol (sclareol) is a labdane-type diterpene, which has demonstrated significant cytotoxic activity against human leukemic cell lines, but its effect on solid tumor-derived cells is uknown. Here, we demonstrate that addition of sclareol to cultures of human colon cancer HCT116 cells results in inhibition of DNA synthesis, arrest of cells at the G₁ phase of the cell cycle, activation of caspases-8, -9, PARP degradation, and DNA fragmentation, events characteristic of induction of apoptosis. Intraperitoneal (ip) administration of sclareol alone, at the maximum tolerated dose, was unable to induce suppression of growth of HCT116 tumors established as xenografts in immunodeficient SCID mice. In contrast, ip administration of liposome-encapsulated sclareol, following a specific schedule, induced suppression of tumor growth by arresting tumor cell proliferation as assessed by detecting the presence of the cell proliferation-associated nuclear protein, Ki67, in thin tumor sections. These findings suggest that sclareol incorporated into liposomes may possess chemotherapeutic potential for the treatment of colorectal and other types of human cancer.     

Conformational analysis of Epac activation using amide hydrogen/deuterium exchange mass spectrometry

Exchange proteins directly activated by cAMP (Epac) play important roles in mediating the effects of cAMP through the activation of downstream small GTPases, Rap. To delineate the mechanism of Epac activation, we probed the conformation and structural dynamics of Epac using amide hydrogen/deuterium exchange and structural modeling. Our studies show that cAMP induces significant conformational changes that lead to a spatial rearrangement of the regulatory components of Epac and allows the exposure of the catalytic core for effector binding without imposing significant conformational change on the catalytic core. Homology modeling and comparative structural analyses of the cAMP binding domains of Epac and cAMP-dependent protein kinase (PKA) lead to a model of Epac activation, in which Epac and PKA activation by cAMP employs the same underlying principle, although the detailed structural and conformational changes associated with Epac and PKA activation are significantly different.     

Foliar water supply of tall trees: evidence for mucilage-facilitated moisture uptake from the atmosphere and the impact on pressure bomb measurements

The water supply to leaves of 25 to 60 m tall trees (including high-salinity-tolerant ones) was studied. The filling status of the xylem vessels was determined by xylem sap extraction (using jet-discharge, gravity-discharge, and centrifugation) and by (1)H nuclear magnetic resonance imaging of wood pieces. Simultaneously, pressure bomb experiments were performed along the entire trunk of the trees up to a height of 57 m. Clear-cut evidence was found that the balancing pressure (P(b)) values of leafy twigs were dictated by the ambient relative humidity rather than by height. Refilling of xylem vessels of apical leaves (branches) obviously mainly occurred via moisture uptake from the atmosphere. These findings could be traced back to the hydration and rehydration of mucilage layers on the leaf surfaces and/or of epistomatal mucilage plugs. Xylem vessels also contained mucilage. Mucilage formation was apparently enforced by water stress. The observed mucilage-based foliar water uptake and humidity dependency of the P(b) values are at variance with the cohesion-tension theory and with the hypothesis that P(b) measurements yield information about the relationships between xylem pressure gradients and height.     

Methane emissions from contrasting urban freshwaters: Rates,drivers, and a whole‐city footprint

Global urbanization trends impose major alterations on surface waters. This includes impacts on ecosystem functioning that can involve feedbacks on climate through changes in rates of greenhouse gas emissions. The combination of high nutrient supply and shallow depth typical of urban freshwaters is particularly conducive to high rates of methane (CH₄) production and emission, suggesting a potentially important role in the global CH₄ cycle. However, there is a lack of comprehensive flux data from diverse urban water bodies, of information on the underlying drivers, and of estimates for whole cities. Based on measurements over four seasons in a total of 32 water bodies in the city of Berlin, Germany, we calculate the total CH₄ emission from various types of surface waters of a large city in temperate climate at 2.6 ± 1.7 Gg CH₄/year. The average total emission was 219 ± 490 mg CH₄ m^?2 day^?1. Water chemical variables were surprisingly poor predictors of total CH₄ emissions, and proxies of productivity and oxygen conditions had low explanatory power as well, suggesting a complex combination of factors governing CH₄ fluxes from urban surface waters. However, small water bodies (area <1 ha) typically located in urban green spaces were identified as emission hotspots. These results help constrain assessments of CH₄ emissions from freshwaters in the world's growing cities, facilitating extrapolation of urban emissions to large areas, including at the global scale.     

Aerial surveys for Antarctic minke whales (Balaenoptera bonaerensis) reveal sea ice dependent distribution patterns

This study investigates the distribution of Antarctic minke whales (AMW) in relation to sea ice concentration and variations therein. Information on AMW densities in the sea ice‐covered parts of the Southern Ocean is required to contextualize abundance estimates obtained from circumpolar shipboard surveys in open waters, suggesting a 30% decline in AMW abundance. Conventional line‐transect shipboard surveys for density estimation are impossible in ice‐covered regions, therefore we used icebreaker‐supported helicopter surveys to obtain information on AMW densities along gradients of 0%–100% of ice concentration. We conducted five helicopter surveys in the Southern Ocean, between 2006 and 2013. Distance sampling data, satellite‐derived sea‐ice data, and bathymetric parameters were used in generalized additive models (GAMs) to produce predictions on how the density of AMWs varied over space and time, and with environmental covariates. Ice concentration, distance to the ice edge and distance from the shelf break were found to describe the distribution of AMWs. Highest densities were predicted at the ice edge and through to medium ice concentrations. Medium densities were found up to 500 km into the ice edge in all concentrations of ice. Very low numbers of AMWs were found in the ice‐free waters of the West Antarctic Peninsula (WAP). A consistent relationship between AMW distribution and sea ice concentration weakens the support for the hypothesis that varying numbers of AMWs in ice‐covered waters were responsible for observed changes in estimated abundance. The potential decline in AMW abundance stresses the need for conservation measures and further studies into the AMW population status. Very low numbers of AMWs recorded in the ice‐free waters along the WAP support the hypothesis that this species is strongly dependent on sea ice and that forecasted sea ice changes have the potential of heavily impacting AMWs.