Transfer of LacZ Marker Gene to the Meniscus

Background: Lesions in the avascular two-thirds of the meniscus do not heal well and are of concern clinically. Various growth factors promote the synthesis of matrix by meniscal cells and thus have the potential to augment healing. However, their clinical application is severely hindered by problems with delivery. An attractive approach to overcoming such problems is to transfer genes that encode the growth factors in question to the site of the injury. As a prelude to this, we evaluated methods for delivering genes to the meniscus. Methods: Gene transfer was evaluated in vitro and in vivo with a lacZ marker gene, which expresses the enzyme β-galactosidase. Two types of vectors were tested: an adenovirus and a retrovirus. Monolayers of lapine, canine, and human meniscal cells, as well as intact lapine and human menisci, were used for the in vitro studies. Lesions were created in the menisci of rabbits and dogs for the in vivo studies. Gene transfer to the sites of the experimental meniscal lesions in vivo was accomplished in two ways. In the lapine model, a suspension of adenovirus carrying the lacZ marker gene was mixed with whole blood and the clot was inserted into the lesion. In the canine model, retrovirally transduced allogenic meniscal cells carrying the lacZ marker gene were embedded in collagen gels and transferred to the defects. The animals were killed at various time-points, and gene expression was evaluated by histological examination of sections stained with 5-bromo-4-chloro-indolyl-β-D-galactose (X-gal), from which a blue chromagen is released in the presence of β-galactosidase. Results: Monolayer cultures of lapine, canine, and human meniscal cells were susceptible to genetic transduction by both adenoviral and retroviral vectors. In vitro gene transfer to intact human and lapine menisci proved possible both by direct, adenoviral, delivery and indirect, retroviral, delivery. Gene expression persisted for at least twenty weeks under in vitro conditions. With regard to the in vivo studies, gene expression persisted within the clot and in some of the adjacent meniscal cells for at least three weeks in the lapine defect model. In the canine defect model, gene expression persisted within the transplanted, transduced meniscal cells for at least six weeks. Conclusions: It is possible to transfer genes to sites of meniscal damage and to express them locally within the lesion for several weeks. Clinical Relevance: Healing of the avascular portion of the meniscus may be improved by the transfer of genes encoding the appropriate growth factors. To our knowledge, the present report is the first to describe methods for transferring genes to the meniscus. When used in conjunction with the appropriate growth-factor genes, these techniques should help to provide the basis for potential alternative treatment options for meniscal lesions. Additional studies are needed to determine whether these techniques will lead to improved healing of meniscal defects in vivo

Small Water Bodies in Great Britain and Ireland: Ecosystem function, human-generated degradation, and options for restorative action

© 2018 Small, 1st and 2nd-order, headwater streams and ponds play essential roles in providing natural flood control, trapping sediments and contaminants, retaining nutrients, and maintaining biological diversity, which extend into downstream reaches, lakes and estuaries. However, the large geographic extent and high connectivity of these small water bodies with the surrounding terrestrial ecosystem makes them particularly vulnerable to growing land-use pressures and environmental change. The greatest pressure on the physical processes in these waters has been their extension and modification for agricultural and forestry drainage, resulting in highly modified discharge and temperature regimes that have implications for flood and drought control further downstream. The extensive length of the small stream network exposes rivers to a wide range of inputs, including nutrients, pesticides, heavy metals, sediment and emerging contaminants. Small water bodies have also been affected by invasions of non-native species, which along with the physical and chemical pressures, have affected most groups of organisms with consequent implications for the wider biodiversity within the catchment. Reducing the impacts and restoring the natural ecosystem function of these water bodies requires a three-tiered approach based on: restoration of channel hydromorphological dynamics; restoration and management of the riparian zone; and management of activities in the wider catchment that have both point-source and diffuse impacts. Such activities are expensive and so emphasis must be placed on integrated programmes that provide multiple benefits. Practical options need to be promoted through legislative regulation, financial incentives, markets for resource services and voluntary codes and actions

The use of DNA fingerprinting to study the population dynamics of otters (<i>Lutra lutra</i>) in southern Britain: a feasibility study

Many factors have the potential to limit the recovery of otter (Lutra lutra) populations.including road deaths, resource constraints such as prey, and habitat availability and quality. Current practical conservation measures are based on surveys assessing habitat potential, which is followed up by habitat improvements. There is very little investigation of the requirements of the animals themselves due to lack of suitable survey techniques. The use of DNA fingerprinting of spraint provides a much needed survey tool to address the acknowledged need for research into the conservation needs and population biology of this species. The Report presents the findings of a one-year feasibility study into the use of DNA fingerprinting to study the otter recovery in southern Britain. Four catchments were surveyed, one in Devon, two in Somerset and one in Hampshire. The long-term objective of this study is to characterise the population dynamics underlying the otter recovery in the UK over a period of four years, as a contribution to identifying the factors limiting population expansion, to facilitate a more focused, efficient and effective conservation effort. The objective of the feasibility study was to carry out a field test of the effectiveness of fingerprinting techniques in identifying individual otters and to develop a protocol for applying these techniques to large scale, repeatable projects. The report concludes that the DNA fingerprinting technique applied to otter spraint has great potential for investigation of otter biology but requires development before it can be applied to large-scale projects. Specific recommendations for further development work are made for consideration by the Agency’s Conservation Function and by the UK Biodiversity Action Plan Steering Group

Towards reproducible computational drug discovery

The reproducibility of experiments has been a long standing impediment for further scientific progress. Computational methods have been instrumental in drug discovery efforts owing to its multifaceted utilization for data collection, pre-processing, analysis and inference. This article provides an in-depth coverage on the reproducibility of computational drug discovery. This review explores the following topics: (1) the current state-of-the-art on reproducible research, (2) research documentation (e.g. electronic laboratory notebook, Jupyter notebook, etc.), (3) science of reproducible research (i.e. comparison and contrast with related concepts as replicability, reusability and reliability), (4) model development in computational drug discovery, (5) computational issues on model development and deployment, (6) use case scenarios for streamlining the computational drug discovery protocol. In computational disciplines, it has become common practice to share data and programming codes used for numerical calculations as to not only facilitate reproducibility, but also to foster collaborations (i.e. to drive the project further by introducing new ideas, growing the data, augmenting the code, etc.). It is therefore inevitable that the field of computational drug design would adopt an open approach towards the collection, curation and sharing of data/code.Nalini Schaduangrat, Samuel Lampa and Saw Simeon contributed equally to this work.</p

Mapbook atlas of tamarisk occurrence for 2016 for select Landsat scenes

Models of tamarisk occurrence were created on a Landsat scene by scene basis. There were six scenes modeled in total that included portions of the Dolores, Green, Gila, Verde, and Colorado River. Models were developed using a presence background approach with multi-temporal Landsat imagery and derived indices using the random forest algorithm.Select Landsat scenes in the Colorado River Basin.Users of these maps and other analysis products are solely responsible for interpretations made from these products. The Natural Resource Ecology Laboratory makes every effort to ensure this map is free of errors but does not warrant the map or its features are either spatially or temporally accurate or fit for a particular use. The Natural Resource Ecology Laboratory provides this map without any warranty, either express or implied.An ArcGIS created Mapbook atlas of the results of modeling tamarisk occurrence in select scenes in Colorado River Basin for 2016. The atlas includes an overview of the Colorado River Basin with these model results as well as an indexed tile-by-tile map of the results for a more detailed view.This project was funded by the Walton Family Foundation

Similar estimates of population genetic composition and sex ratio derived from carcasses and faeces of Eurasian otter <i>Lutra lutra</i>

Collecting faeces is viewed as a potentially efficient way to sample elusive animals. Nonetheless, any biases in estimates of population composition associated with such sampling remain uncharacterized. The goal of this study was to compare estimates of genetic composition and sex ratio derived from Eurasian otter Lutra lutra spraints (faeces) with estimates derived from carcasses. Twenty per cent of 426 wild‐collected spraints from SW England yielded composite genotypes for 7–9 microsatellites and the SRY gene. The expected number of incorrect spraint genotypes was negligible, given the proportions of allele dropout and false allele detection estimated using paired blood and spraint samples of three captive otters. Fifty‐two different spraint genotypes were detected and compared with genotypes of 70 otter carcasses from the same area. Carcass and spraint genotypes did not differ significantly in mean number of alleles, mean unbiased heterozygosity or sex ratio, although statistical power to detect all but large differences in sex ratio was low. The genetic compositions of carcass and spraint genotypes were very similar according to confidence intervals of θ and two methods for assigning composite genotypes to groups. A distinct group of approximately 11 carcass and spraint genotypes was detected using the latter methods. The results suggest that spraints can yield unbiased estimates of population genetic composition and sex ratio

2006 riparian vegetation within the Colorado River Basin

A raster that depicts modeled riparian vegetation in 2006. Training data were collected in Google Earth Engine using National Agriculture Imagery Program (NAIP) imagery. Presence and absence riparian vegetation locations were ocularly estimated within Environmental Protection Agency (EPA) ecoregion III boundaries within the Colorado River Basin. Random forests models were then developed at each ecoregion using Landsat composites and associated vegetation indices. Results were mosaicked to create a continuous raster across the Colorado River Basin.GeoTiff 30 meter raster of 2006 riparian vegetation within the Colorado River Basin. This map was created from a random forest model developed in Google Earth Engine.This project was funded by the Walton Family Foundation

Valley bottom extraction tool results for Colorado River Basin

Valley bottoms are representative of the "maximum riparian corridor extent", an area which separates the vegetative, topographic, and environmental characteristics of riparian areas from those of the upland. The Valley Bottom Extraction Tool (V-BET) (Gilbert et al., 2016), a freely available ArcMap Toolbox, was used to map valley bottoms across the Colorado River Basin. The V-BET tool requires two primary data inputs: a high resolution (≤10 m2) digital elevation model and hydrologic flowline data with high cartographic precision. The hydrologic flow line data was obtained from the National Hydrography Dataset and a 10-meter digital elevation model from the National Elevation Dataset. The study area was separated into 149 distinct hydrological unit codes (HUCs) at the HUC-8 level and processed each HUC independently within the V-BET toolbox in ArcMap v10.3. Resulting valley bottom extents, which are output from the tool as polygon files, were qualitatively verified by trained interpreters and edited (mainly streams and rivers equal to Strahler stream order "3") manually in a geographic information system to remove any superfluous channels or over/under estimations of extent using the refinement and editing process detailed in Gilbert et al. (2016). This zip file contains two versions of the Valley bottom extraction tool results for the Colorado River Basin; one as a raster version and another as a polygon shapefile.Valley Bottom Extraction Tool (V-BET) was used to spatially define riparian corridors based on topography and vegetation. The V-BET algorithm was applied to all streams and rivers present within the Colorado River Basin (CRB) that were less than or equal to Strahler stream order "3" (USGS National Hydrologic Database, 2016), thereby capturing the extent of valley bottoms and riparian corridors along the majority of large streams and rivers within the expansive CRB network.This project was funded by the Walton Family Foundation

2016 riparian vegetation within the Colorado River Basin

A raster that depicts modeled riparian vegetation in 2016. Training data were collected in Google Earth Engine using National Agriculture Imagery Program (NAIP) imagery. Presence and absence riparian vegetation locations were ocularly estimated within Environmental Protection Agency (EPA) ecoregion III boundaries within the Colorado River Basin. Random forests models were then developed at each ecoregion using Landsat composites and associated vegetation indices. Results were mosaicked to create a continuous raster across the Colorado River Basin.GeoTiff raster of 2016 riparian vegetation within the Colorado River Basin. This map was created from a random forest model developed in Google Earth Engine.This project was funded by the Walton Family Foundation