Dealing with Uncertainty in Spatially Explicit Population Models

It has been argued that spatially explicit population models (SEPMs) cannot provide reliable guidance for conservation biology because of the difficulty of obtaining direct estimates for their demographic and dispersal parameters and because of error propagation. We argue that appropriate model calibration procedures can access additional sources of information, compensating the lack of direct parameter estimates. Our objective is to show how model calibration using population-level data can facilitate the construction of SEPMs that produce reliable predictions for conservation even when direct parameter estimates are inadequate. We constructed a spatially explicit and individual-based population model for the dynamics of brown bears (Ursus arctos) after a reintroduction program in Austria. To calibrate the model we developed a procedure that compared the simulated population dynamics with distinct features of the known population dynamics (=patterns). This procedure detected model parameterizations that did not reproduce the known dynamics. Global sensitivity analysis of the uncalibrated model revealed high uncertainty in most model predictions due to large parameter uncertainties (coefficients of variation CV 0.8). However, the calibrated model yielded predictions with considerably reduced uncertainty (CV 0.2). A pattern or a combination of various patterns that embed information on the entire model dynamics can reduce the uncertainty in model predictions, and the application of different patterns with high information content yields the same model predictions. In contrast, a pattern that does not embed information on the entire population dynamics (e.g., bear observations taken from sub-areas of the study area) does not reduce uncertainty in model predictions. Because population-level data for defining (multiple) patterns are often available, our approach could be applied widely.     

Improved Framework for Tractography Reconstruction of the Optic Radiation

The optic radiation (OR) is one of the major components of the visual system and a key structure at risk in white matter diseases such as multiple sclerosis (MS). However, it is challenging to perform track reconstruction of the OR using diffusion MRI due to a sharp change of direction in the Meyer’s loop and the presence of kissing and crossing fibers along the pathway. As such, we aimed to provide a highly precise and reproducible framework for tracking the OR from thalamic and visual cortex masks. The framework combined the generation of probabilistic streamlines by high order fiber orientation distributions estimated with constrained spherical deconvolution and an automatic post-processing based on anatomical exclusion criteria (AEC) to compensate for the presence of anatomically implausible streamlines. Specifically, those ending in the contralateral hemisphere, cerebrospinal fluid or grey matter outside the visual cortex were automatically excluded. We applied the framework to two distinct high angular resolution diffusion-weighted imaging (HARDI) acquisition protocols on one cohort, comprised of ten healthy volunteers and five MS patients. The OR was successfully delineated in both HARDI acquisitions in the healthy volunteers and MS patients. Quantitative evaluation of the OR position was done by comparing the results with histological reference data. Compared with histological mask, the OR reconstruction into a template (OR-TCT) was highly precise (percentage of voxels within the OR-TCT correctly defined as OR), ranging from 0.71 to 0.83. The sensitivity (percentage of voxels in histological reference mask correctly defined as OR in OR-TCT) ranged from 0.65 to 0.81 and the accuracy (measured by F1 score) was 0.73 to 0.77 in healthy volunteers. When AEC was not applied the precision and accuracy decreased. The absolute agreement between both HARDI datasets measured by the intraclass correlation coefficient was 0.73. This improved framework allowed us to reconstruct the OR with high reliability and accuracy independently of the acquisition parameters. Moreover, the reconstruction was possible even in the presence of tissue damage due to MS. This framework could also be applied to other tracts with complex configuration.     

Combined use of 13C chemical shift and 1Hα−13Cα heteronuclear NOE data in monitoring a protein NMR structure refinement

Summary A large portion of the ¹³C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28°C has been determined at natural isotope abundance. Sequence-specific ¹³C assignments are reported for 100% of the assignable C, 96% of the C, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C chemical shifts for regions of regular -sheet structure. These assignments also provide the basis for interpreting ¹H–¹³C heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high internal mobility, indicated by these ¹H–¹³C HNOE measurements, correlate with locations of residues involved in the putative mEGF-receptor binding site. Using four families of mEGF structures obtained over the last few years, we demonstrate that standard deviations between experimental and back-calculated C values can be used to monitor the refinement of this protein's structure, particularly for -sheet regions. Improved agreement between calculated and observed values of C is correlated with other measures of structure quality, including lowered values of residual constraint violations and more negative values of conformational energy. These results support the view that experimental conformation-dependent chemical shifts, C, can provide a reliable source of information for monitoring the process of protein structure refinement and are potentially useful restraints for driving the refinement.Abbreviations HSQC heteronuclear single-quantum coherence spectroscopy - PFG pulsed-field gradient - TOCSY ¹H-¹H total correlation spectroscopy - EGF epidermal growth factor - mEGF murine EGF - hEGF human EGF - hTGF human type- transforming growth factor - DIPSI spm-locking pulse sequence - NOE nuclear Overhauser effect - HNOE heteronuclear Overhauser effect     

Oxygenase domain of Drosophila melanogaster nitric oxide synthase: unique kinetic parameters enable a more efficient NO release

Although nitric oxide (NO) is important for cell signaling and nonspecific immunity in the fruit fly Drosophila melanogaster, little is known about its single NO synthase (dNOS). We expressed the oxygenase domain of dNOS (dNOSoxy), characterized its spectroscopic, kinetic, and catalytic properties, and interpreted them in light of a global kinetic model for NO synthesis. Single turnover reactions with ferrous dNOSoxy showed it could convert Arg to N'omega-hydroxy-l-arginine (NOHA), or NOHA to citrulline and NO, when it was given 6R-tetrahydrobiopterin and O2. The dNOSoxy catalyzed Arg hydroxylation and NOHA oxidation at rates that matched or exceeded the rates catalyzed by the three mammalian NOSoxy enzymes. Consecutive heme-dioxy, ferric heme-NO, and ferric heme species were observed in the NOHA reaction of dNOSoxy, indicating that its catalytic mechanism is the same as in the mammalian NOS. However, NO dissociation from dNOSoxy was 4 to 9 times faster than that from the mammalian NOS enzymes. In contrast, the dNOSoxy ferrous heme-NO complex was relatively unreactive toward O2 and in this way was equivalent to the mammalian neuronal NOS. Our data show that dNOSoxy has unique settings for the kinetic parameters that determine its NO synthesis. Computer simulations reveal that these unique settings should enable dNOS to be a more efficient and active NO synthase than the mammalian NOS enzymes, which may allow it to function more broadly in cell signaling and immune functions in the fruit fly.     

The genes influencing adiponectin levels also influence risk factors for metabolic syndrome and type 2 diabetes

Results from previous studies suggest that adiponectin levels are associated with risk factors for cardiovascular disease and type 2 diabetes mellitus; however, the genetic and/or environmental components of this relationship have not been characterized. The aims of this study were (1) to assess the presence of pleiotropy between adiponectin levels and risk factors for cardiovascular disease and (2) to study the association of circulating levels of adiponectin with risk factors for cardiovascular disease in the absence and presence of obesity in Mexican American adults from the San Antonio Family Heart Study. Body composition and circulating levels of adiponectin, leptin, and lipid subfractions and measurements of glucose metabolism were measured in 898 subjects. The mean and standard error of the circulating levels of adiponectin was 8.7 +/- 3.2 microg/ml. Bivariate quantitative analyses between adiponectin levels and phenotypes related to cardiovascular disease and type 2 diabetes mellitus were conducted using the variance decomposition approach implemented in SOLAR. A second analysis in unrelated subjects compared these risk factors between sex- and age-matched lean and obese subjects with high and low adiponectin levels. We found significant evidence of pleiotropy (i.e., shared genetic effects) between plasma levels of adiponectin and well-established risk factors for cardiovascular disease and type 2 diabetes mellitus. Individuals with low adiponectin levels per body weight had more adverse risk profiles. These findings offer new insights into the genetic connection between increasing adiposity and risk for cardiovascular disease and type 2 diabetes mellitus, and they suggest that adiponectin may be an important risk factor for the development of these conditions.     

Patterns of distribution and abundance of bonefish larvae <Emphasis Type="Italic">Albula</Emphasis> spp. (Albulidae) in the western Caribbean and adjacent areas

Overall patterns of distribution and abundance of Albula spp. leptocephali larvae offshore in the western Caribbean Sea (CAS) and Gulf of Mexico (GOM), and in coastal waters of the Mexican Caribbean (MXC) were analyzed from: (a) cruise data available from the Academy of Natural Sciences of Philadelphia (CAS, GOM) and (b) coastal plankton surveys (1998–2002 and January 2004) (MXC). We found striking inshore-offshore differences in the larval catch and size structure. Offshore cruises yielded 57 leptocephali, mostly determined as early stage I (18.0 ± 8.2 mm SL, mean ± SD). In contrast, coastal samples yielded 2,466 larvae 51.4 ± 3.6 mm SL, mostly late stage I; of these, 2,345 (95%) were caught over 4 nights in January 2004. The relationship between the larval length (mm, SL) and the distance to the coastline (km) was best represented by the regression model with a distinct variance for each locality. To ascertain whether the coastal inflow of leptocephali follows a regular seasonal pattern or depends on episodic events will require further monitoring; available evidence suggests that the southern coast of the MXC offers favorable conditions for the recruitment of Albula spp. larvae.     

β-catenin confers resistance to PI3K and AKT inhibitors and subverts FOXO3a to promote metastasis in colon cancer

The Wnt–β-catenin and PI3K-AKT-FOXO3a pathways have a central role in cancer. AKT phosporylates FOXO3a, relocating it from the cell nucleus to the cytoplasm, an effect that is reversed by PI3K and AKT inhibitors. Simultaneous hyperactivation of the Wnt–β-catenin pathway and inhibition of PI3K-AKT signaling promote nuclear accumulation of β-catenin and FOXO3a, respectively, promoting cell scattering and metastasis by regulating a defined set of target genes. Indeed, the anti-tumoral AKT inhibitor API-2 promotes nuclear FOXO3a accumulation and metastasis of cells with high nuclear β-catenin content. Nuclear β-catenin confers resistance to the FOXO3a-mediated apoptosis induced by PI3K and AKT inhibitors in patient-derived primary cultures and in corresponding xenograft tumors in mice. This resistance is reversed by XAV-939, an inhibitor of Wnt–β-catenin signaling. In the presence of high nuclear β-catenin content, activation of FOXO3a by PI3K or AKT inhibitors makes it behave as a metastasis inductor rather than a proapoptotic tumor suppressor. We show that it is possible to evaluate the β-catenin status of patients' carcinomas and the response of patient-derived cells to target-directed drugs that accumulate FOXO3a in the nucleus before deciding on a course of treatment. We propose that this evaluation could be essential to the provision of a safer and more effective personalized treatment.     

The search for stability on narrow supports: an experimental study in cats and dogs

Kinematic and coordination variables were studied in two carnivorans, one with known locomotor capabilities in arboreal substrates (cat), and the other a completely terrestrial species (dog). Two horizontal substrates were used: a flat trackway on the ground (overground locomotion) and an elevated and narrow runway (narrow-support locomotion). Despite their different degree of familiarity with the ‘arboreal’ situation, both species developed a strategy to adapt to narrow supports. The strategy of cats was based on using slower speeds, coupled with modifications to swing phase duration, to keep balance on narrow supports. The strategy of dogs relied on high speeds to gain in dynamic stability, and they increased cycle frequency by reducing swing phase duration. Furthermore, dogs showed a high variability in limb coordination, although a tendency to canter-like coordination was observed, and also avoided whole-body aerial phases. In different ways, both strategies suggested a reduction of peak vertical forces, and hence a reduction of the vertical oscillations of the centre of mass. Finally, lateral oscillation was reduced by the use of a crouched posture.