Taxonomy based on science is necessary for global conservation

Conservation Biolog

Energetic Path Finding Across Massive Terrain Data

Throughout history, the primary means of transportation for humans has been on foot. We present a software tool which can help visualize and predict where historical trails might lie through the use of a human-centered cost metric, with an emphasis on the ability to generate paths which traverse several thousand kilometers. To accomplish this, various graph simplification and path approximation algorithms are explored. We show that it is possible to restrict the search space for a path finding algorithm while not sacrificing accuracy. Combined with a multi-threaded variant of Dijkstra’s shortest path algorithm, we present a tool capable of computing a path of least caloric cost across the contiguous US, a dataset containing over 19 billion datapoints, in under three hours on a 2.5 Ghz dual core processor. The potential archaeological and historical applications are demonstrated on several examples

COL3A1 2209G>A is a predictor of pelvic organ prolapse.

Contains fulltext : 80499.pdf (publisher's version ) (Closed access)INTRODUCTION AND HYPOTHESIS: A familial tendency has been demonstrated in the etiology of pelvic organ prolapse (POP), but the specific genetic defects have not been identified. Type III collagen is an important factor in the repair of connective tissue, and gene polymorphisms may impair the tensile strength. We hypothesized that polymorphisms in the alpha I chain of the type III collagen protein-encoding gene (COL3A1) pose women at risk for POP. METHODS: In this case-control study, the prevalence of type III collagen polymorphisms was compared in women with and without signs and symptoms of POP. RESULTS: Two hundred and two POP patients and 102 normal parous controls were included. A homozygous single-nucleotide substitution in the coding region of type III collagen (COL3A1 2209G>A, rs1800255) was identified in 27 (13%) POP patients and three (3%) controls (odds ratio, 5.0; 95% confidence interval, 1.4-17.1). CONCLUSIONS: The probability of POP was higher in women with COL3A1 2209G>A. This polymorphism showed to be a relevant risk factor for POP

Collagen type III alpha 1 polymorphism (rs1800255, COL3A1 2209 G>A) assessed with high-resolution melting analysis is not associated with pelvic organ prolapse in the Dutch population

Contains fulltext : 137653.pdf (publisher's version ) (Closed access)INTRODUCTION AND HYPOTHESIS: The rs1800255, COL3A1 2209 G>A polymorphism in the alpha 1 chain of collagen type III has been associated with an increased risk of pelvic organ prolapse (POP). In one of our previous studies however, polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) misdiagnosed rs1800255, COL3A1 2209 G>A in 6 % of cases. The high-resolution melting (HRM) analysis on the contrary obtained a 100 % accordance for this specific polymorphism and was used in the present study to validate this risk factor for POP. METHODS: In this case-control study, women with and without symptoms of POP were included and compared. DNA was extracted from blood samples. HRM analysis was used to assess for the presence of the homozygous rs1800255. Groups were compared using the Pearson chi-square, Mann-Whitney, and t tests. The discrepancy between HRM and PCR-RFLP results was investigated using PCR-RFLP results available from our previous study. RESULTS: The study included 354 women: 272 patients with POP and 82 controls; 18 (7 %) cases versus 3 (4 %) controls had a homozygous rs1800255, COL3A1 2209 G>A polymorphism (odds ratio 1.9, 95 % confidence interval 0.5-6.9, compared to the wild type), and thus no association between POP and the homozygous polymorphism could be demonstrated. A discrepancy between HRM and PCR-RFLP results was found in 8 % of the samples. CONCLUSIONS: The previously found statistically significant association between the rs1800255, COL3A1 2209 G>A polymorphism as measured with PCR-RFLP and POP could no longer be demonstrated. This raises concerns regarding the results of other association studies using PCR-RFLP

Field evaluation of DNA based biodiversity monitoring of caribbean mosquitoes

Mosquito borne diseases pose a threat to human health worldwide. Disease risk is primarily determined by presence and abundance of vector species. A better understanding of mosquito diversity and abundance can direct improved vector control, but this requires a combination of monitoring techniques that yield both rapid and reliable information. Particularly improved larval detection is pivotal to move toward more targeted management with less environmental impact. Current detection methods rely strongly on manual labor and taxonomic expertise, which greatly limits the extent to which these methodologies can be employed. As such, insight in the efficiency of novel, high-throughput vs. traditional sampling techniques is required. We compared the effectiveness of a recently developed environmental DNA (eDNA) approach on water and sediment samples with other commonly used sampling techniques (“dipping” for larvae and adult trapping) in a field study on three Caribbean islands. All sampling methods were employed across a range of ecologically contrasting sites. Species identification was performed both morphologically and molecularly using an in-house developed reference database supplemented with sequences from BOLD and GenBank. Our analysis of water samples from 39 sites shows that eDNA sampling can be more reliable than dipping, yields a higher within-sample richness and produces a subset of the adult community in all sampled water types. Furthermore, for both adults and larvae, our identifications showed complete overlap between morphological and molecular approaches in 133 out of 134 samples. Overall, results from this study provide evidence that both our eDNA-based detection of larvae and our DNA-based identification of larvae and adults present methods that are, although more expensive, as reliable, and for some species even more reliable than the currently used methods. Additionally, our results highlight that a DNA approach can be used to identify larvae of early developmental stages, which generally lack important morphological characteristics. As such it allows for development of efficient disease control strategies, verification of management effectiveness and monitoring of population dynamics.Environmental Biolog

Energetic Path Finding Across Massive Terrain Data

Abstract. Throughout history, the primary means of transportation for humans has been on foot. We present a software tool which can help visualize and predict where historical trails might lie through the use of a human-centered cost metric, with an emphasis on the ability to generate paths which traverse several thousand kilometers. To accomplish this, various graph simplification and path approximation algorithms are explored. We show that it is possible to restrict the search space for a path finding algorithm while not sacrificing accuracy. Combined with a multi-threaded variant of Dijkstra’s shortest path algorithm, we present a tool capable of computing a path of least caloric cost across the contiguous US, a dataset containing over 19 billion datapoints, in under three hours on a 2.5 Ghz dual core processor. The potential archaeological and historical applications are demonstrated on several examples.