Online identification of Mysida through NeMys

Identification of specimens is a task that every biologist is confronted with. The process of identification in many cases delivers many problems due to unavailability of keys, difficult specialised keys or old keys.Within NeMys (http://intramar.ugent.be/nemys) recently a new identification module has been added. Based upon morphological data derived from published literature, polytomous digital identification keys are made. This kind of keys has the advantage that users are not forced to follow a predefined pathway (as in dichotomous keys), users can choose their best suitable characteristics to work with and the keys can be easily updated with new insights through a fully online key-generation system.By using internet technologies, the identification keys are at any time anywhere available for use. As the data used in the keys is derived from the database system NeMys, it is also possible to check the identification process at any level, with literature sources, images, distribution patterns, … on the website of NeMys.This kind of technology opens new possibilities for biologists to share their taxonomic knowledge with a broader audience without being forced to go through the difficult process of creating dichotomous paper-based keys

Taxonomy and biogeography of the shallow-water Mysidacea of the Western Indian Ocean

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Breed differences in the pharmacokinetics of ivermectin administered subcutaneously to Holstein and Belgian Blue calves

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Biodiversity of Antarctic nematodes: the ‘NEMASLAN’ project

Recent biodiversity research reveals that more than 50% of the free-living marine nematode species found in before unexplored environments, such as Antarctica, are new to science. Too few taxonomists remain to describe them all. Additionally, there are problems with the quality control of the identification of nematode samples since fewer labs possess all the literature (and manpower) required to verify the morphological characteristics of the animals.NEMASLAN, software for a tree-based classification system (Access) is a methodological approach for improving identification, classification and description of specimens in difficult taxonomic groups such as free-living marine nematodes. It seeks to serve as an easy research tool for central management of information of the taxon of the nematodes, and this for people with little training in database technologies.The program consists of four main modules: (see demonstration)1. Module for data- entering: provides possibilities to enter geographic, morphological, ecological, and literature data on species in a record database. An additional connection between these database records and the actual digital sources (e.g. scanned literature from original descriptions and good recent publications) enlarges the scientific value of the system.Personal metadatasets can be created, for example for the use of drawings and/or pictures of undescribed species or not yet published taxonomic papers. 2. Module for document consultation: data sources (PDF documents of original descriptions, text documents, photographs,…) and their references can be consulted. 3. Module for Quick Search: Morphological data from the species identification (e.g. shape and/or position of amphid, cuticle, buccal cavity, tail, oesophagus, caudal glands and spinneret; feeding type; numerical fields of de Man ratios, length, setae, nerve ring, excretory porus, spicule, gubernaculum, male supplements) and other information such as type of biotope and water depth distribution can be consulted; datasheets can be generated.4. Search Module: The output and search within the database can be user configured (i.e. questions like ‘give me all the nematode species so far described from the coastal sites with a spicule longer than 30µm and cuticular punctuations’ get an answer from this database). SQL (Structured Query Language) is the formal language used to query databases. An in-depth knowledge of the fairly complex SQL language is not required.The Windows application functions for multi-users in a local network environment (LAN). The program is distributed free of charge through a website (at present http://allserv.rug.ac.be/~tdeprez: later on through a more specified Antarctic database website) at which demonstration datasets are distributed.NEMASLAN was applied to Antarctic nematodes. The resulting ‘Biodiversity of Antarctic Nematodes’ CD-ROM version includes an archive of all numerical and nominal information for each species ever described in the Southern Ocean. About 350 species have thus been digitized. There is an urgent need to develop appropriate information tools on Antarctic marine biodiversity for scientific, environmental management and conservation purposes. Therefore, the collaboration of three laboratory pioneers in Antarctic biodiversity databases (e.g. Antarctic nematodes, amphipods and echinids, see other presentations) will seek for further developments such as the construction of a common portal, common mapping applications, or links to pertinent information sources of Antarctic benthic biodiversity. The resulting ‘biodiversity information system’ will be made available to the scientific community. This will be done within the framework of the OSTC project on Antarctica - BIANZO (BIodiversity of three representative groups of the ANtarctic ZOobenthos). It will contribute to the DIVERSITAS, SA 2000, CoML-OBIS and GBIF initiatives

Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering

Background: The production of bioethanol from lignocellulose hydrolysates requires a robust, D-xylose-fermenting and inhibitor-tolerant microorganism as catalyst. The purpose of the present work was to develop such a strain from a prime industrial yeast strain, Ethanol Red, used for bioethanol production. Results: An expression cassette containing 13 genes including Clostridium phytofermentans XylA, encoding D-xylose isomerase (XI), and enzymes of the pentose phosphate pathway was inserted in two copies in the genome of Ethanol Red. Subsequent EMS mutagenesis, genome shuffling and selection in D-xylose-enriched lignocellulose hydrolysate, followed by multiple rounds of evolutionary engineering in complex medium with D-xylose, gradually established efficient D-xylose fermentation. The best-performing strain, GS1.11-26, showed a maximum specific D-xylose consumption rate of 1.1 g/g DW/h in synthetic medium, with complete attenuation of 35 g/L D-xylose in about 17 h. In separate hydrolysis and fermentation of lignocellulose hydrolysates of Arundo donax (giant reed), spruce and a wheat straw/hay mixture, the maximum specific D-xylose consumption rate was 0.36, 0.23 and 1.1 g/g DW inoculum/h, and the final ethanol titer was 4.2, 3.9 and 5.8% (v/v), respectively. In simultaneous saccharification and fermentation of Arundo hydrolysate, GS1.11-26 produced 32% more ethanol than the parent strain Ethanol Red, due to efficient D-xylose utilization. The high D-xylose fermentation capacity was stable after extended growth in glucose. Cell extracts of strain GS1.11-26 displayed 17-fold higher XI activity compared to the parent strain, but overexpression of XI alone was not enough to establish D-xylose fermentation. The high D-xylose consumption rate was due to synergistic interaction between the high XI activity and one or more mutations in the genome. The GS1.11-26 had a partial respiratory defect causing a reduced aerobic growth rate. Conclusions: An industrial yeast strain for bioethanol production with lignocellulose hydrolysates has been developed in the genetic background of a strain widely used for commercial bioethanol production. The strain uses glucose and D-xylose with high consumption rates and partial cofermentation in various lignocellulose hydrolysates with very high ethanol yield. The GS1.11-26 strain shows highly promising potential for further development of an all-round robust yeast strain for efficient fermentation of various lignocellulose hydrolysates