Chromosomal position effects on AAV-mediated gene targeting

The effects of chromosomal position and neighboring genomic elements on gene targeting in human cells remain largely unexplored. To study these, we used a shuttle vector system in which murine leukemia virus (MLV)-based proviral targets present at different chromosomal locations and containing mutations in the neomycin phosphotransferase (neo) gene were corrected by adeno-associated virus (AAV)-mediated gene targeting. Sixteen identical target loci present in HT-1080 human sarcoma cells were all successfully corrected by gene targeting. The gene targeting frequencies varied by as much as 10-fold, and there was a clear bias for correction of one of the targets in clones containing two target sites. The targeting frequency at each site was correlated to the proximity and density of various genomic elements, and we found a significant association of higher targeting frequencies at loci near a subset of dinucleotide microsatellite repeats (r = –0.55, P < 0.05), in particular GT repeats (r = –0.87, P < 0.0001). Additionally, there was a correlation between meiotic recombination rates and targeting frequencies at the target loci (r = 0.52, P < 0.05). There was no correlation between surrounding chromosomal transcription units and targeting frequencies. Our results indicate that certain chromosomal positions are preferred sites for gene targeting in human cells

RyR1-targeted drug discovery pipeline integrating FRET-based high-throughput screening and human myofiber dynamic Ca2+ assays.

Elevated cytoplasmic [Ca2+] is characteristic in severe skeletal and cardiac myopathies, diabetes, and neurodegeneration, and partly results from increased Ca2+ leak from sarcoplasmic reticulum stores via dysregulated ryanodine receptor (RyR) channels. Consequently, RyR is recognized as a high-value target for drug discovery to treat such pathologies. Using a FRET-based high-throughput screening assay that we previously reported, we identified small-molecule compounds that modulate the skeletal muscle channel isoform (RyR1) interaction with calmodulin and FK506 binding protein 12.6. Two such compounds, chloroxine and myricetin, increase FRET and inhibit [3H]ryanodine binding to RyR1 at nanomolar Ca2+. Both compounds also decrease RyR1 Ca2+ leak in human skinned skeletal muscle fibers. Furthermore, we identified compound concentrations that reduced leak by &gt; 50% but only slightly affected Ca2+ release in excitation-contraction coupling, which is essential for normal muscle contraction. This report demonstrates a pipeline that effectively filters small-molecule RyR1 modulators towards clinical relevance

White matter microstructural development and cognitive ability in the first 2 years of life

White matter (WM) integrity has been related to cognitive ability in adults and children, but it remains largely unknown how WM maturation in early life supports emergent cognition. The associations between tract-based measures of fractional anisotropy (FA) and axial and radial diffusivity (AD, RD) shortly after birth, at age 1, and at age 2 and cognitive measures at 1 and 2 years were investigated in 447 healthy infants. We found that generally higher FA and lower AD and RD across many WM tracts in the first year of life were associated with better performance on measures of general cognitive ability, motor, language, and visual reception skills at ages 1 and 2, suggesting an important role for the overall organization, myelination, and microstructural properties of fiber pathways in emergent cognition. RD in particular was consistently related to ability, and protracted development of RD from ages 1 to 2 years in several tracts was associated with higher cognitive scores and better language performance, suggesting prolonged plasticity may confer cognitive benefits during the second year of life. However, we also found that cognition at age 2 was weakly associated with WM properties across infancy in comparison to child and demographic factors including gestational age and maternal education. Our findings suggest that early postnatal WM integrity across the brain is important for infant cognition, though its role in cognitive development should be considered alongside child and demographic factors

White matter development in infants at risk for schizophrenia

Background: Schizophrenia is considered a neurodevelopmental disorder with a pathophysiology that likely begins long before the onset of clinical symptoms. White matter abnormalities have been observed in schizophrenia and we hypothesized that the first 2 years of life is a period in which white matter abnormalities associated with schizophrenia risk may emerge. Methods: 38 infants at high risk for schizophrenia and 202 healthy controls underwent diffusion tensor MRIs after birth and at 1 and 2 years of age. Quantitative tractography was used to determine diffusion properties (fractional anisotropy (FA), axial diffusivity (AD), and radial diffusivity (RD)) of 18 white matter tracts and a general linear model was used to analyze group differences at each age. Results: Adjusting gestational age at birth, postnatal age at MRI, gender, MRI scanner type, and maternal education, neonates at high risk had significantly lower FA (p = 0.02) and AD (p = 0.03) in the superior segment of the left cingulate, and higher RD in the hippocampal segment of the left cingulate (p = 0.04). High risk one year olds had significantly lower FA (p < 0.01) and AD (p = 0.02) in the hippocampal segment of the left cingulate. High risk two year olds had significantly lower FA in the left prefrontal cortico-thalamic tract (p = 0.04) and higher RD in the right uncinate fasciculus (p = 0.04). None of the tract differences remained significant after correction for multiple comparisons. Conclusions: There is evidence of abnormal white matter development in young children at risk for schizophrenia, especially in the hippocampal segment of left cingulum. These results support the neurodevelopmental theory of schizophrenia and indicate that impaired white matter may be present in early childhood

CLIMATE CHANGE IMPACTS ON WATER RESOURCES

Climate change impacts on water resources – The most recent scientific assessment by the Intergovernmental Panel on Climate Change (IPCC) [6] concludes that, since the late 19th century, anthropogenic induced emissions of greenhouse gases have contributed to an increase in global surface temperatures of about 0.3 to 0.6o C. Based on the IPCC’s scenario of future greenhouse gas emissions and aerosols a further increase of 2o C is expected by the year 2100. Plants, animals, natural and managed ecosystems, and human settlements are susceptible to variations in the storage, fluxes, and quality of water and sensitive to climate change. From urban and agricultural water supplies to flood management and aquatic ecosystem protection, global warming is affecting all aspects of water resource management. Rising temperatures, loss of snowpack, escalating size and frequency of flood events, and rising sea levels are just some of the impacts of climate change that have broad implications for the management of water resources. With robust scientific evidence showing that human-induced climate change is occurring, it is critical to understand how water quantity and quality might be affected. The purpose of this paper is to highlight the environmental risks caused by climate anomalies on water resources, to examine the negative impacts of a greenhouse warming on the supply and demand for water and the resulting socio-economic implications

3D Geometric Analysis of Tubular Objects based on Surface Normal Accumulation

This paper proposes a simple and efficient method for the reconstruction and extraction of geometric parameters from 3D tubular objects. Our method constructs an image that accumulates surface normal information, then peaks within this image are located by tracking. Finally, the positions of these are optimized to lie precisely on the tubular shape centerline. This method is very versatile, and is able to process various input data types like full or partial mesh acquired from 3D laser scans, 3D height map or discrete volumetric images. The proposed algorithm is simple to implement, contains few parameters and can be computed in linear time with respect to the number of surface faces. Since the extracted tube centerline is accurate, we are able to decompose the tube into rectilinear parts and torus-like parts. This is done with a new linear time 3D torus detection algorithm, which follows the same principle of a previous work on 2D arc circle recognition. Detailed experiments show the versatility, accuracy and robustness of our new method.Comment: in 18th International Conference on Image Analysis and Processing, Sep 2015, Genova, Italy. 201

Pearling: stroke segmentation with crusted pearl strings

We introduce a novel segmentation technique, called Pearling, for the semi-automatic extraction of idealized models of networks of strokes (variable width curves) in images. These networks may for example represent roads in an aerial photograph, vessels in a medical scan, or strokes in a drawing. The operator seeds the process by selecting representative areas of good (stroke interior) and bad colors. Then, the operator may either provide a rough trace through a particular path in the stroke graph or simply pick a starting point (seed) on a stroke and a direction of growth. Pearling computes in realtime the centerlines of the strokes, the bifurcations, and the thickness function along each stroke, hence producing a purified medial axis transform of a desired portion of the stroke graph. No prior segmentation or thresholding is required. Simple gestures may be used to trim or extend the selection or to add branches. The realtime performance and reliability of Pearling results from a novel disk-sampling approach, which traces the strokes by optimizing the positions and radii of a discrete series of disks (pearls) along the stroke. A continuous model is defined through subdivision. By design, the idealized pearl string model is slightly wider than necessary to ensure that it contains the stroke boundary. A narrower core model that fits inside the stroke is computed simultaneously. The difference between the pearl string and its core contains the boundary of the stroke and may be used to capture, compress, visualize, or analyze the raw image data along the stroke boundary