Wikipedia as an encyclopaedia of life

In his 2003 essay E O Wilson outlined his vision for an “encyclopaedia of life” comprising “an electronic page for each species of organism on Earth”, each page containing “the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.” Although the “quiet revolution” in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson's essay (e.g., "http://ispecies.org":http://ispecies.org, "http://www.eol.org":http://www.eol.org), we are still some way from the goal of having available online all relevant information about a species, such as its taxonomy, evolutionary history, genomics, morphology, ecology, and behaviour. While the biodiversity community has been developing a plethora of databases, some with overlapping goals and duplicated content, Wikipedia has been slowly growing to the point where it now has over 100,000 pages on biological taxa. My goal in this essay is to explore the idea that, largely independent of the efforts of biodiversity informatics and well-funded international efforts, Wikipedia ("http://en.wikipedia.org/wiki/Main_Page":http://en.wikipedia.org/wiki/Main_Page) has emerged as potentially the best platform for fulfilling E O Wilson’s vision

A baseline survey of potentially toxic elements in the soil of north-west Syria following a decade of conflict

We present the first region-wide chemical survey of soils in NW Syria following more than a decade of ongoing conflict. We sampled topsoil at 66 sites, typically located in marginal agricultural (orchards, arable) or peri-urban settings, grouped around 21 localities covering the whole area of NW Syria currently under Syrian Opposition control. Samples were analysed in the UK using ICP-MS and ICP-OES. Topsoil total concentrations of heavy metals are broadly consistent with pre-war data from Aleppo and recent data from nearby Turkey. Principal Components Analysis (PCA) of associations among the sampling sites identified three groupings. Ni (133.30 ± 72.12 mg/kg) and Cr (122.14 ± 52.25 mg/kg) exist in all samples at levels in excess of typical European guideline thresholds for agricultural soil. Observed Cd (0.57 ± 0.93 mg/kg), Co (23.07 ± 18.48 mg/kg) and As (6.65 ± 4.51 mg/kg) concentrations are up to three times comparable values from nearby agricultural regions in southern Turkey. Maximum observed values for Cd, As, and Co, which exceed EU thresholds, are concentrated in a corridor around Sarmada to the west of Aleppo which has seen some of the most intense conflict-related impacts. Cu (28.33 ± 17.11 mg/kg), Pb (15.65 ± 10.85 mg/kg) and Zn (73.64 ± 40.15 mg/kg) also observe maxima in the Sarmada corridor, but show a more even distribution across the region, widely at values above comparable regional values for agriculture but below EU threshold concentrations. We interpret the occurrence of Ni-Cr as consistent with intensive agriculture using wastewater-contaminated irrigation and fertilisers. Cd-As-Co and Cu-Pb-Zn are likely anthropogenic and reflect intense pressures of conflict, informal settlement, unregulated industry and untreated wastewater irrigation on a historically agricultural region. The sampling method was designed to capture regional variations from a minimal dataset and it is likely that local topsoil concentrations at specific points of impact (proximal to locations of shelling, industry, effluent release or population) will be considerably higher than those reported here. This study establishes an important baseline reference for further targeted studies to identify and mitigate specific pollution hazards in this region of ongoing, extreme humanitarian and ecological threat

Evidence that dorsally mounted satellite transmitters affect migration chronology of Northern Pintails

We compared migration movements and chronology between Northern Pintails (Anas acuta) marked with dorsally mounted satellite transmitters and pintails marked only with tarsus rings. During weekly intervals of spring and autumn migration between their wintering area in Japan and nesting areas in Russia, the mean distance that ringed pintails had migrated was up to 1000 km farther than the mean distance radiomarked pintails migrated. Radiomarked pintails were detected at spring migration sites on average 9.9 days (90 % CI 8.0, 11.8) later than ringed pintails that were recovered within 50 km. Although ringed and radiomarked pintails departed from Japan on similar dates, the disparity in detection of radiomarked versus ringed pintails at shared sites increased 7.7 days (90 % CI 5.2, 10.2) for each 1000 km increase in distance from Japan. Thus, pintails marked with satellite transmitters arrived at nesting areas that were 2500 km from Japan on average 19 days later than ringed birds. Radiomarked pintails were detected at autumn migration stopovers on average 13.1 days (90 % CI 9.8, 16.4) later than ringed birds that were recovered within 50 km. We hypothesize that dorsal attachment of 12?20 g satellite transmitters to Northern Pintails increased the energetic cost of flight, which resulted in more rapid depletion of energetic reserves and shortened the distance pintails could fly without refueling. Radiomarked pintails may have used more stopovers or spent longer periods at stopovers. causing their migration schedule to diverge from ringed pintails. We urge further evaluation of the effects of dorsally mounted transmitters on migration chronology of waterfowl

RNA interference as a key to knockdown overexpressed cyclooxygenase-2 gene in tumour cells

Silencing those genes that are overexpressed in cancer and contribute to the survival and progression of tumour cells is the aim of several researches. Cyclooxygenase-2 (COX-2) is one of the most intensively studied genes since it is overexpressed in most tumours, mainly in colon cancer. The use of specific COX-2 inhibitors to treat colon cancer has generated great enthusiasm. Yet, the side effects of some inhibitors emerging during long-term treatment have caused much concern. Genes silencing by RNA interference (RNAi) has led to new directions in the field of experimental oncology. In this study, we detected sequences directed against COX-2 mRNA, that potently downregulate COX-2 gene expression and inhibit phorbol 12-myristate 13-acetate-induced angiogenesis in vitro in a specific, nontoxic manner. Moreover, we found that the insertion of a specific cassette carrying anti-COX-2 short hairpin RNA sequence into a viral vector (pSUPER.retro) greatly increased silencing potency in a colon cancer cell line (HT29) without activating any interferon response. Phenotypically, COX-2 deficient HT29 cells showed a significant impairment of their in vitro malignant behaviour. Thus, the retroviral approach enhancing COX-2 knockdown, mediated by RNAi, proved to be an useful tool to better understand the role of COX-2 in colon cancer. Furthermore, the higher infection efficiency we observed in tumour cells, if compared to normal endothelial cells, may disclose the possibility to specifically treat tumour cells without impairing endothelial COX-2 activity

Finding Single Copy Genes Out of Sequenced Genomes for Multilocus Phylogenetics in Non-Model Fungi

Historically, fungal multigene phylogenies have been reconstructed based on a small number of commonly used genes. The availability of complete fungal genomes has given rise to a new wave of model organisms that provide large number of genes potentially useful for building robust gene genealogies. Unfortunately, cross-utilization of these resources to study phylogenetic relationships in the vast majority of non-model fungi (i.e. “orphan” species) remains an unexamined question. To address this problem, we developed a method coupled with a program named “PHYLORPH” (PHYLogenetic markers for ORPHans). The method screens fungal genomic databases (107 fungal genomes fully sequenced) for single copy genes that might be easily transferable and well suited for studies at low taxonomic levels (for example, in species complexes) in non-model fungal species. To maximize the chance to target genes with informative regions, PHYLORPH displays a graphical evaluation system based on the estimation of nucleotide divergence relative to substitution type. The usefulness of this approach was tested by developing markers in four non-model groups of fungal pathogens. For each pathogen considered, 7 to 40% of the 10–15 best candidate genes proposed by PHYLORPH yielded sequencing success. Levels of polymorphism of these genes were compared with those obtained for some genes traditionally used to build fungal phylogenies (e.g. nuclear rDNA, β-tubulin, γ-actin, Elongation factor EF-1α). These genes were ranked among the best-performing ones and resolved accurately taxa relationships in each of the four non-model groups of fungi considered. We envision that PHYLORPH will constitute a useful tool for obtaining new and accurate phylogenetic markers to resolve relationships between closely related non-model fungal species