Characterization of molecular recognition of Phosphoinositide-3-kinase α inhibitor through molecular dynamics simulation

Phosphatidylinositol 3-kinase α (PI3Kα) is a promising target for anticancer drug discovery due to its overactivation in tumor cells. To systematically investigate the interactions between PI3Kα and PIK75 which is the most selective PI3Kα inhibitor reported to date, molecular docking, molecular dynamics simulation, and ensuing energetic analysis were utilized. The binding free energy between PI3Kα and PIK75 is −10.04 kcal•mol⁻¹ using MMPBSA method, while −13.88 kcal•mol⁻¹ using MMGBSA method, which is beneficial for the binding. The van der Waals/hydrophobic and electrostatic interactions play critical roles for the binding. The binding mode of PIK75 for PI3Kα is predicted. The conserved hydrophobic adenine region of PI3Kα made up of Ile800, Ile848, Val850, Val851, Met922, Phe930, and Ile932 accommodates the flat 6-bromine imidazo[1,2-a]pyridine ring of PIK75. The 2-methyl-5-nitrophenyl group of PIK75 extends to the P-loop region, and has four hydrogen-bond arms with the backbone and side chain of Ser773 and Ser774. And the distinct conformation of the P-loop induced by PIK75 is speculated to be responsible for the selectivity profile of PIK75. The predicted binding mode of PIK75 for PI3Kα presented in this study may help design high affinity and selective compounds to target PI3Kα.     

Rituximab and new regimens for indolent lymphoma: a brief update from 2012 ASCO Annual Meeting

ABSTRACT: Indolent lymphoma (IL), the second most common lymphoma, remains incurable with chemotherapy alone. While R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, prednisone) remains the standard frontline regimen for diffuse Large B --cell lymphoma, the optimal chemotherapy regimen for frontline therapy of advanced IL remains uncertain. FCR (fludarabine, cyclophosphamide, rituximab) has been shown to be better than fludarabine alone and fludarabine plus cyclophosphamide for IL. In FOLL05 trial, R-CHOP was compared with R-CVP (cyclophosphamide, vincristine, prednisone) and R-FM (fludarabine, mitoxantrone). The study showed that R-CHOP appears to have the best risk-benefit ratio for IL. The StiL NHL1 trial showed that BR (bendamustine, rituximab) has longer progression free survival and is better tolerated than R-CHOP. Long-term complications with secondary malignancies between the two regimens appear to be comparable. In this review, new combination regimens reported at 2012 ASCO annual meeting were evaluated for frontline and salvage therapy of indolent lymphoma.     

Modeling spring habitat requirements of the endangered brown eared pheasant Crossoptilon mantchuricum in the Huanglong Mountains, Shaanxi Province, China

A detailed understanding of the habitat needs of brown eared pheasants (Crossoptilon mantchuricum) is essential for conserving the species. We carried out field surveys in the Huanglong Mountains of Shaanxi Province, China, from March to June in 2007 and 2008. We arrayed a total of 206 grid plots (200 × 200 m) along transects in 2007 and 2008 and quantified a suite of environmental variables for each one. In the optimal logistic regression model, the most important variables for brown eared pheasants were slope degree, tree cover, distance to nearest water, cover and depth of fallen leaves. Hosmer and Leweshow goodness-of-fit tests explained that logistic models for the species were good fits. The model suggested that spring habitat selection of the brown eared pheasant was negatively related to distance to nearest water and slope degree, and positively to cover of trees and cover and depth of fallen leaves. In addition, the observed detected and undetected grids in 2007 did not show significant differences with predictions based on the model. These results showed that the model could well predict the habitat selection of brown eared pheasants. Based on these predictive models, we suggest that habitat management plans incorporating this new information can now focus more effectively on restrictions on the number of tourists entering the nature reserve, prohibition of firewood collection, livestock grazing, and medicinal plant harvesting by local residents in the core areas, protection of mixed forest and sources of the permanent water in the reserve, and use of alternatives to firewood.     

Label-free imaging of lipid-droplet intracellular motion in early Drosophila embryos using femtosecond-stimulated Raman loss microscopy

Lipid droplets are complex organelles that exhibit highly dynamic behavior in early Drosophila embryo development. Imaging lipid droplet motion provides a robust platform for the investigation of shuttling by kinesin and dynein motors, but methods for imaging are either destructive or deficient in resolution and penetration to study large populations of droplets in an individual embryo. Here we report real-time imaging and quantification of droplet motion in live embryos using a recently developed technique termed "femtosecond-stimulated Raman loss" microscopy. We captured long-duration time-lapse images of the developing embryo, tracked single droplet motion within large populations of droplets, and measured the velocity and turning frequency of each particle at different apical-to-basal depths and stages of development. To determine whether the quantities for speed and turning rate measured for individual droplets are sufficient to predict the population distributions of droplet density, we simulated droplet motion using a velocity-jump model. This model yielded droplet density distributions that agreed well with experimental observations without any model optimization or unknown parameter estimation, demonstrating the sufficiency of a velocity-jump process for droplet trafficking dynamics in blastoderm embryos.     

What determines "suitable habitat" for metapopulation studies? An analysis of environmental gradients and species assemblages in xeric forest openings

? Premise of the study: For metapopulation and metacommunity studies, "suitable habitat" is an area within an otherwise inhospitable matrix in which a species can potentially or does occur. When examining aquatic habitats, for example, this habitat is much easier to define than in terrestrial regions. We tested the assumption that suitable habitat can be delimited in terrestrial ecosystems. ? Methods: We surveyed vascular plant species found in 38 forest openings (open suitable habitats) within a matrix of dry forest (an inhospitable habitat) at three sites in southern Illinois over two growing seasons. We compared species composition and environmental variables between these two habitats at three sites using non-metric multidimensional scaling (NMDS) and analysis of similarity (ANOSIM). ? Key results: Distinctions such as high canopy openness and high soil temperature were common to all forest openings compared with the forest matrix. Differences in canopy openness and soil temperature were correlated with significantly different vegetation between forest openings and forest matrix at each of the three sites. Among the three sites, 9.3-18.9% were forest opening specialists, consisting of 44 taxa, of which the majority were herbaceous forbs. ? Conclusions: The distinction between suitable and unsuitable habitat for some plant species may depend on a few variables, which may not be consistent between sites. This distinction means that there are potentially more situations than previously thought that metapopulation and metacommunity theory may be capable of explaining, meaning that more systems can be studied using a metapopulation context than previously thought.     

A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions

Differing arresting agents and protocols can be used to synchronize cells in cultures to specific phases of the cell when studying cell-cycle gene expressions. Often, data derived from individual experiments are analyzed separately, since no appropriate statistical methodology is available at the moment to analyze the data from all such experiments simultaneously. The focus of this paper is to determine the association and coherence of the relative activation times of cell-cycling genes under different experimental conditions. Using a circular-circular regression model, we define two parameters, a rotation parameter for the angular difference between cells' arresting times (phases) in two cell-cycle experiments, and an association parameter to describe the correspondence between the cycle times of maximal expression (phase angles) for a set of genes studied in two experiments. Further, we propose a procedure to assess coherence across multiple experiments, i.e. to what extent the circular ordering of the phase angles of genes is maintained across multiple experiments. Coherence of genes across experiments suggests that functionally these genes tend to respond in a stereotypically sequenced way under different experimental conditions. Our proposed methodology is illustrated by applying it to a HeLa cell-cycle gene-expression data.     

Age-related changes in regional brain mitochondria from Fischer 344 rats

Brain mitochondrial function has been posited to decline with aging. In order to test this hypothesis, cortical and striatal mitochondria were isolated from Fischer 344 rats at 2, 5, 11, 24 and 33 months of age. Mitochondrial membrane potential remained stable through 24 months, declining slightly in mitochondria from both brain regions at 33 months. The ability of calcium to induce mitochondrial swelling and depolarization, characteristics of the permeability transition, was remarkably stable through 24 months of age and increased at advanced ages only for cortical, but not striatal, mitochondria. Striatal mitochondria were more sensitive to calcium than were cortical mitochondria throughout the first 2 years of life. A two-fold increased resistance to calcium was observed in striatal mitochondria between 5 and 11 months. Although these measurements do demonstrate changes in mitochondrial function with aging, the changes in polarization are relatively small and the increased cortical susceptibility to the permeability transition only occurred at very advanced ages. Thus mitochondrial decline with advanced age depends upon brain region.     

鸭绿江细鳞鱼的生物学

细鳞鱼是鸭绿江的重要经济鱼类。幽门垂数、鳃耙数及侧线鳞数与国内其他产地相比呈现明显交叉。支流十三道沟河口以上的5公里江段为主要产卵场。产卵期为4—5月,盛期4月末。成熟个体多数4龄,最小成熟雌鱼体长309毫米。体长285—438毫米,体重315—1098克的个体绝对怀卵量1629至3119(平均2194),与体长L的关系式N=9.54924 L-1297.3246,与体重W的关系式N=2.2207W 641.6345。卵径3.5—4.0毫米。水温5.3—9.0℃时,受精后625小时孵出。用鳞片测定年龄及生长。3龄鱼体长可达356毫米,5龄鱼体长一般为389毫米。体长与体重的关系式W_(?)=0.002486L~(2.9146),W_♀=0.004509L~(2.8978)。     

Storage and decomposition of particulate organic matter along the longitudinal gradient of an agriculturally-impacted stream

An agriculturally-impacted stream in northern Idaho was examined over a two-year period to determine seasonal and longitudinal patterns of the storage and decomposition of particulate organic matter. Biomass of benthic organic matter (BOM) was considerably less than values reported in the literature for comparable, undisturbed streams. Coarse, fine, and total benthic particulate organic matter were not correlated with parameters pertaining to stream size (e.g., stream order), but were correlated with sample site and amount of litterfall. The association of BOM with site and litterfall suggests that storage of particulate organic matter is a function of local characteristics rather than stream size. Low biomass of stored organic matter is a response to the low input of terrestrially-derived organic matter resulting from removal of climax vegetation.Leaf packs of alder, Alnus sp., were placed in the stream seasonally for 30 and 60 d. While there were significant differences for months, there was no significant difference among sites for leaf packs exposed for 30 d. Significant differences were observed among both sites and months for leaf packs exposed for 60 d; however, differences among sites accounted for only 5% of the variance. The absence of differences in decomposition of organic matter along the gradient of Lapwai Creek, despite heterogeneity of the drainage basin and availability of organic matter, may be in response to the overall low biomass of stored benthic organic matter. This study demonstrates that agricultural activity can substantially influence instream heterotrophic processes through reduced availability of organic matter and can shape community structure and ecosystem dynamics of streams flowing through agricultural drainage basins.     

Isotopic analysis of three food web theories in constricted and floodplain regions of a large river

Analyses of stable isotope (δ¹³C and δ¹⁵N) and C:N ratios of food webs within a floodplain and a constricted-channel region of the Ohio River during October 1993 and July 1994 indicate that the increasingly influential flood pulse concept (FPC) does not, for either location, adequately address food web structure for this very large river. Furthermore, results of this study suggest that the riverine productivity model (RPM) is more appropriate than the widely known river continuum concept (RCC) for the constricted region of this river. These␣conclusions are based on stable isotope analyses of potential sources of organic matter (riparian C₃ trees, riparian C₄ grasses and agricultural crops, submerged macrophytes, benthic filamentous algae, benthic particulate organic matter, and transported organic matter containing detritus and phytoplankton) and various functional feeding groups of invertebrate and fish consumers. The FPC, which stresses the key contribution of organic matter, particularly terrestrial organic matter, originating from the floodplain to riverine food webs, was judged inappropriate for the floodplain region of the Ohio River for hydrodynamic and biotic reasons. The rising limb and peak period of discharge typically occur in November through March when temperatures are low (generally much less than 10°C) and greater than bank-full conditions are relatively unpredictable and short-lived. The major food potentially available to riverine organisms migrating into the floodplain would be decaying vegetation because autotrophic production is temperature and light limited and terrestrial insect production is minimal at that time. It is clear from our data that terrestrial C₄ plants contribute little, if anything, to the consumer food web (based on δ¹³C values), and δ¹⁵N values for C₃ plants, coarse benthic organic matter, and fine benthic organic matter were too depleted (∼7–12‰ lower than most invertebrate consumer values) for this organic matter to be supporting the food web. The RPM, which emphasizes the primary role of autotrophic production in large rivers, is the most viable of the remaining two ecosystem models for the constricted-channel region of the Ohio based on stable isotope linkage between sources and consumers of organic matter in the food web. The most important form of food web organic matter is apparently transported (suspended) fine (FTOM) and ultra-fine particulate organic matter. We propose that phytoplankton and detritus of an autochthonous origin in the seston would represent a more usable energy source for benthic (bivalve molluscs, hydropsychid caddisflies) and planktonic (microcrustaceans) suspension feeders than the more refractory allochthonous materials derived from upstream processing of terrestrial organic matter. Benthic grazers depend heavily on nonfilamentous benthic algae (based on gut analysis from a separate study), but filamentous benthic algae have no apparent connection to invertebrate consumers (based on δ¹³C values). Amphipod and crayfish show a strong relationship to aquatic macrophytes (possibly through detrital organic matter rather than living plant tissue). These observations contrast with the prediction of the RCC that food webs in large rivers are based principally on refractory FTOM and dissolved organic matter from upstream inefficiencies in organic-matter processing and the bacteria growing upon these suspended or dissolved detrital compounds. The conclusions drawn here for the Ohio River cannot yet be extended to other floodplain and constricted-channel rivers in temperate and tropical latitudes until more comparable data are available on relatively pristine and moderately regulated rivers. Received: 3 January 1997 / Accepted: 28 August 1998