http://precedings.nature.com./ The most recent documents on Nature Precedings. Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.4000.1 The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for achievingthe goals. This report builds on the 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems (Boline et al., 2007, Nature Preceedings, doi:10.1038/npre.2007.1046.1) and includes a more detailed analysis of both the current state and desired state of digital atlasing along with specific recommendations for achieving these goals. http://dx.doi.org/10.1038/npre.2009.4000.1 Tue, 24 Nov 2009 09:43:24 UTC The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain doi:10.1038/npre.2009.4000.1 2009-11-24 Nature Precedings 2009-11-24T09:43:24Z Manuscript Neuroscience Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com./documents/3994/version/1 Stereograms mark a threshold in understanding visual perception. Modern study of stereopsis began with Wheatstone’s invention of the stereogram and stereoscope (~ 1832), important tools in vision research and technical imagery ever since. Stereoscopic images formed with frieze and wallpaper patterns in illuminated Insular manuscripts such as the Book of Durrow (~ 680 CE), Lindisfarne Gospels (~ 700-720), and Book of Kells (~ 800) show that, long before spectacle-quality magnifying lenses (~ 1286), illuminators somehow copied multicolored, microscopically detailed designs freehand with an accuracy unsurpassed in scientific instruments until the Renaissance (but well within the power of normally sighted humans’ stereoscopic discrimination). If the artists accomplished this feat by free fusion using the unaided eyes as a magnifying stereocomparator, as suggested, they should have been able to create autostereograms. Did they? Here I report two examples of an apparent stereopair from the Book of Durrow, which gives a sharp, strongly three-dimensional image that includes, among other symbols, an eye-shaped sign identified with mirages (Fig. 1). Apparently, precocious empirical knowledge of stereopsis played more than a technical role in the creation of some of the world’s more famous graphic art. http://precedings.nature.com./documents/3994/version/1 Mon, 23 Nov 2009 15:57:14 UTC An apparent medieval stereogram incorporating a symbol for optical illusion hdl:10101/npre.2009.3994.1 2009-11-23 John L. Cisne Nature Precedings 2009-11-23T15:57:14Z Manuscript Neuroscience http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.4001.1 The syntax of LBFO represents the initial step toward the creation of a rigorously characterized, recursively defined, artificial language for the sole purpose of ontology development. The underlying idea is that maximally fruitful application of ontology requires accurate representation of reality in accordance with current textbook science. Hence, creating a robust, accurate representation of reality is a fundamental concern. An ontology represents general types of entities and relations between them. A domain ontology represents the general types and relations for a given domain of research. A top-level ontology represents the general types of entities in any domain of research. Ontologies serve many purposes in computerized collection, management, and storage of data. These applications include enhancement of storage and retrieval in a data system, integration of diverse systems, integration of semantic content on the web, and annotation of publications in a library setting.Successful application of ontologies has led to the creation of languages with the special purpose of implementing ontologies. A formalized ontology is an ontology expressed in accordance with the grammatical formation rules of an artificial language. Some existing ontology languages have been developed in order to serve specific functions that require expressibility limitations and expression of information in a manner that contributes to human misunderstanding and error. The most potentially detrimental effect is risked when an ontology is constructed in a language designed exclusively for computerized implementation. The result is a skewed representation of salient features of reality. An ontology development language has two purposes: one is to represent reality as accurately and completely as possible, the other is to achieve this in a manner that facilitates computerized implementation: these goals conflict. Validation requires expert human consensus, hence, an ontology should be developed in a language that is understandable to domain experts. However, such a language must be computer tractable, i.e., there must be a correspondence between the information expressed with a sentence and its grammatical structure such that information can be processed on the basis of syntax alone. LBFO will facilitate providing definitions and characterizations of features of reality in a way conformant with Basic Formal Ontology (BFO) thus ensuring maximal rigor and clarity. Since LBFO is a multi-sorted language, LBFO has resources to represent the ontological categories found in BFO and the universals defined in their terms in an economical and at the same time user-friendly way. BFO is a realist ontology in that it recognizes universals as an part of the world. BFO also recognizes the existence of both processes and continuants. A continuant is an individual that exists in full at each point in time in which it exists, a process is an individual that exists in stages and happens through time. Unlike a continuant, a process cannot be identified with any single stage at which it exists at a specific point in time. Capitalized variables range over universals, while lower-case variables range over individuals. Universal constants are upper-case. Individual constants are lower-case. The syntax of LBFO also distinguishes in a straightforward manner between variables for continuants, processes, and times. The syntax of LBFO contains precisely expressed grammatical-formation rules, so that its variables cannot be combined in a manner that results in category errors. The predicates of LBFO are such that the ontological category from which terms representing entities can be taken as arguments is specified in advance. Sentences which express category errors are not grammatically correct in LBFO.Since the demand for implementation often outstrips the demand for accurate representation, stand-alone ontologies are often left by the wayside. LBFO can serve as a bridge between domain experts, knowledge engineers, and implementation languages. The semantic apparatus of an FOL system serves as the basis for the models developed for implementation languages such as OWL and RDF. FOL is also a segregated dialect of Common Logic so there is a link to that international standard; hence, there is potential to develop middle-ware that maps LBFO to the variety of implementation languages that exist both now and in the future. Though there is much work to be done in perfecting LBFO, this first step in the process provides hope for achieving the goal of facilitating maximally accurate, rigorous representations of general features of reality. http://dx.doi.org/10.1038/npre.2009.4001.1 Mon, 23 Nov 2009 15:36:02 UTC LBFO: toward an artificial language for ontology development doi:10.1038/npre.2009.4001.1 2009-11-23 Leonard F. Jacuzzo Nature Precedings 2009-11-23T15:36:02Z Poster Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3984.1 Recently reported, 9aaTAD transcription factors p53, VP16, MLL/ALL, E2A, HSF1, NF-IL6, NFAT1 and NF-kB interact directly with the general coactivator CBP/p300 aside from already referred TAF9. All four domains of CBP/p300 – KIX, TAZ1, TAZ2 and IBiD provide multiple interactions with 9aaTADs, e.g. p53. Annotation of predicted 9aa TAD using Pattern search ScanProsite on ExPASy and relevant experimental data are listed. http://dx.doi.org/10.1038/npre.2009.3984.1 Fri, 20 Nov 2009 13:04:12 UTC 9aaTAD Prediction result (2006) doi:10.1038/npre.2009.3984.1 2009-11-20 Martin Piskacek Nature Precedings 2009-11-20T13:04:12Z Manuscript Genetics & Genomics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com./documents/3988/version/1 Cryptosporidium parvum is a zoonotic apicomplexa-protozoan pathogen that causes gastroenteritis and diarrhoea in mammals worldwide. The organism is transmitted by ingestion of oocysts, which are shed in faeces, and completes its lifecycle in a single host.1 C. parvum is ubiquitous on dairy operations worldwide and is one of the leading causes of diarrhoea in calves on these farms.2,3 Here, for the first time, we describe the antibody response in a large group of cows to a recombinant C. parvum oocyst surface protein (rCP15/60) vaccine and the antibody response in calves fed rCP15/60-immune colostrum produced by these vaccinated cows. Results of recent genotype surveys indicate that calves are the only major reservoir for C. parvum infections in humans.4 Human C. parvum infections are particularly prevalent and often fatal in neonates in developing countries and to immunocompromised people, such as AIDs patients.4 Drug therapy against cryptosporidiosis is limited and not wholly efficacious in either humans or calves5, making development of an effective vaccine of paramount importance. To date, there is no commercially available effective vaccine against C. parvum, although passive immunization utilizing different zoite surface (glyco)proteins has showed promise.6-9 All cows we vaccinated produced an antibody response to the rCP15/60 vaccine and the magnitude of response correlated strongly with the subsequent level of antibody in their colostrum. All calves fed rCP15/60-immune colostrum showed a dose-dependent absorption of antibody. Our results demonstrate that vaccination of cows with rCP15/60 successfully induces antibodies against CP15/60 in their serum and colostrum and that these antibodies are then well absorbed when fed to neonatal calves. With further research, this C. parvum vaccine may well be a practical method of conferring passive protection to calves against cryptosporidiosis. Furthermore, a specifically targeted immune-colostrum may be valuable in protection and treatment of immunocompromised human patients with cryptosporidiosis. http://precedings.nature.com./documents/3988/version/1 Fri, 20 Nov 2009 12:18:51 UTC Antibody responses to a Cryptosporidium parvum rCP15/60 vaccine hdl:10101/npre.2009.3988.1 2009-11-20 Alexandra J. Burton Nature Precedings 2009-11-20T12:18:51Z Manuscript Immunology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3987.1 Synesthesia is a perceptual condition in which normal sensory stimulation can trigger anomalous sensory experiences. For example, synesthetes may experience colors in response to sounds, tastes in response to words, or smells in response to touch. We here focus on colored sequence synesthesia, in which color experiences are triggered by learned ordinal sequences such as letters, numbers, weekdays and months. Although synesthesia has been noted in the scientific literature for over a century, it is understood only at the level of the phenomenology, and not at the molecular and neural levels. We have performed a linkage analysis to identify the first genetic loci responsible for the increased neural crosstalk underlying colored sequence synesthesia. Our analysis has identified a 23 MB region on chromosome 16 as a putative locus for the trait. Our data provide the first step in understanding neural crosstalk from its molecular basis to its behavioral consequences, opening a new inroad into the understanding of the multisensory brain. http://dx.doi.org/10.1038/npre.2009.3987.1 Fri, 20 Nov 2009 07:08:42 UTC The genetics of colored sequence synesthesia: Evidence of linkage to chromosome 16q and genetic heterogeneity for the condition doi:10.1038/npre.2009.3987.1 2009-11-20 Stephanie S. Nelson Nature Precedings 2009-11-20T07:08:42Z Manuscript Genetics & Genomics Neuroscience http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3944.1 In order to study the fossil contents of the Abderaz Formation for biostratigraphical purposes the 300 meters thick section was sampled at type section. The sequence is mainly made up of grey shales and marls with two units of chalky limestone in upper part. The lower contact of the formation with Aitamir Formation is disconform while the upper contact with Abtalkh is continuous. There are huge amounts of inoceramids and ammonite. In the chalk limestone bonds of this formation which is belong to Santonian time planktonic, would exist some foraminifera with a less diversity because during the Santonian, the members of morphotype group three (M3) shows a regression in the above-mentioned section, with association of tegilla shapes decreases in the area and sea water. The study of the planktonic foraminifera in isolated form led to differentiate three morphotype groups. The first group is characterized by trochospiral tests usually indicate shallow waters, the second group contains forms with strong ornamentations and the primary keels representing mid waters and finally compact trochospiral tests with keels known as deep water indices are included in the third group. Studies on the morphotypes showed a regressive cycle for Abderaz Formation. http://dx.doi.org/10.1038/npre.2009.3944.1 Fri, 20 Nov 2009 06:49:53 UTC Lithostratigraphy and study of planktonic foraminifera of the Abderaz Formation at type section, Kopet-Dagh basin, IRAN doi:10.1038/npre.2009.3944.1 2009-11-20 Meysam Shafiee Ardestani Nature Precedings 2009-11-20T06:49:53Z Manuscript Earth & Environment http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com./documents/3982/version/1 Several amyloid-forming proteins and peptides, including insulin1, β-lactoglobulin2 and albumin3, form spherulites in vitro under non-physiological solution conditions. These micrometer-sized, roughly spherical structures are composed of ordered arrays of β sheets of amyloid fibrils in radial arrangements which, characteristically, show a typical Maltese cross pattern of light extinction under the polarizing microscope. The physiological significance, if any, of these amyloid super assemblies is unknown although in Alzheimer’s disease there is the suggestion that senile plaques composed primarily of β sheets of Aβ42 are spherulitic4. Herein we describe the first observation of the formation in vitro of spherulites of Aβ42. They were formed under near-physiological conditions in which the β sheet conformation of pre-formed aggregates of Aβ42 had been abolished following the addition of an excess of copper. Incubation of these preparations at 37oC for up to 9 months resulted in the formation of spherulites. These were globular in appearance, 5 – 20 microns in diameter, and exhibited the typical Maltese cross pattern of light extinction. Similarly to other amyloid spherulites formed in vitro they bound Congo red without giving apple-green birefringence5 while also being thioflavin T-positive when viewed by fluorescence microscopy3. Near-identical spherulitic structures were also observed in abundance in 30 micron thick sections of Alzheimer’s disease brain tissue. Synchrotron x-ray fluorescence showed that the location of these spherulites in AD tissue coincided with locally elevated concentrations of tissue copper. The formation in vitro of spherulites of Aβ42 which morphologically appeared analogous to spherulitic structures observed in vivo strongly supports the hypothesis that spherulites and senile plaques in AD tissue are one and the same structures and that their ultimate formation involves copper. http://precedings.nature.com./documents/3982/version/1 Wed, 18 Nov 2009 20:13:32 UTC Spherulites of Aβ42 in vitro and in Alzheimer’s disease hdl:10101/npre.2009.3982.1 2009-11-18 Christopher Exley Nature Precedings 2009-11-18T20:13:32Z Manuscript Neuroscience http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3981.1 Sir Charles Snow, being a writer and a scientist, felt that he “was moving among two groups – comparable in intelligence, identical in race, not grossly different in social origin, earning about the same incomes, who had ceased to communicate at all”(Snow, 1993 [1959], p.2). He called these two groups, the two cultures, referring to those in the natural sciences and those in the humanities. Many argue that this division is an awful thing. This poster discusses strategies to reacquaint the two cultures in the case of genomics. http://dx.doi.org/10.1038/npre.2009.3981.1 Tue, 17 Nov 2009 11:28:40 UTC Reacquainting two cultures. Preventing a de-elsification of European nutrigenomics? doi:10.1038/npre.2009.3981.1 2009-11-17 Bart Penders Nature Precedings 2009-11-17T11:28:40Z Poster Genetics & Genomics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com./documents/3968/version/1 Nine-amino-acid transactivation domain, 9aaTAD, defines a large superfamily of yeast and mammals transcription factors. The transactivation of the 9aaTAD has been addressed to multiple general co-activators TAF9, MED15, CBP and p300. We demonstrate for the 9aaTAD transcription factors Oaf1 and Gal4 functional and physical interaction with E3-Ubiquitin Ligase Rsp5. The Rsp5-associations with RNA polymerase II and TFIID were reported previously. http://precedings.nature.com./documents/3968/version/1 Mon, 16 Nov 2009 23:52:09 UTC Rsp5 promotes Gene Activation mediated by 9aaTAD Transcription Factors Oaf1 and Gal4 hdl:10101/npre.2009.3968.1 2009-11-16 Joachim Lipp Nature Precedings 2009-11-16T23:52:09Z Manuscript Genetics & Genomics Molecular Cell Biology http://creativecommons.org/licenses/by/3.0/