Using Bayesian multinomial classifier to predict whether a given protein sequence is intrinsically disordered

Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure under physiological conditions. Intrinsic disorder is a common phenomenon, particularly in multicellular eukaryotes, and is responsible for important protein functions including regulation and signaling. Many disease-related proteins are likely to be intrinsically disordered or to have disordered regions. In this paper, a new predictor model based on the Bayesian classification methodology is introduced to predict for a given protein or protein region if it is intrinsically disordered or ordered using only its primary sequence. The method allows to incorporate length-dependent amino acid compositional differences of disordered regions by including separate statistical representations for short, middle and long disordered regions. The predictor was trained on the constructed data set of protein regions with known structural properties. In a Jack-knife test, the predictor achieved the sensitivity of 89.2% for disordered and 81.4% for ordered regions. Our method outperformed several reported predictors when evaluated on the previously published data set of Prilusky et al. [2005. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics 21 (16), 3435-3438]. Further strength of our approach is the ease of implementation.     

Key to the management of the Western Himalayan Hillstreams in relation to

A key to the management of hillstreams in relation to Fish Species Richness (FSR) and Shannon and Weaver Diversity Index (H) (Shannon and Weaver, 1949. The Mathematical Theory of Communications. Urbana, University of Illinois Press, IL, USA) using a multitude of factors such as altitude, water source, bed gradient, dominant channel materials and habitat type has been proposed on the basis of 10 study sites, belonging to three north Indian rivers namely; Ghaggar, Yamuna and Ganga. The selected streams are located between the altitudes ranging from 380 to 1524m. It has been observed that high altitude streams having steep gradient, boulder dominated substrate with rapids as the main habitat type had lower FSR (3–4) and H (0.55–0.99) as compared to hillstreams located in the lower altitudes having gentle gradient, cobble dominated substrate with pools, riffles, runs, rapids and cascades as the main habitats and have high FSR (6–14) and H (1.67–2.35). Types – A, B and F hillstreams were encountered when the hillstreams are classified after Rosgen (Applied River Morphology, Wildland Hydrology, Co, USA).     

Family-group names in Coleoptera (Insecta)

We synthesize data on all known extant and fossil Coleoptera family-group names for the first time. A catalogue of 4887 family-group names (124 fossil, 4763 extant) based on 4707 distinct genera in Coleoptera is given. A total of 4492 names are available, 183 of which are permanently invalid because they are based on a preoccupied or a suppressed type genus. Names are listed in a classification framework. We recognize as valid 24 superfamilies, 211 families, 541 subfamilies, 1663 tribes and 740 subtribes. For each name, the original spelling, author, year of publication, page number, correct stem and type genus are included. The original spelling and availability of each name were checked from primary literature. A list of necessary changes due to Priority and Homonymy problems, and actions taken, is given. Current usage of names was conserved, whenever possible, to promote stability of the classification.New synonymies (family-group names followed by genus-group names): Agronomina Gistel, 1848 syn. nov. of Amarina Zimmermann, 1832 (Carabidae), Hylepnigalioini Gistel, 1856 syn. nov. of Melandryini Leach, 1815 (Melandryidae), Polycystophoridae Gistel, 1856 syn. nov. of Malachiinae Fleming, 1821 (Melyridae), Sclerasteinae Gistel, 1856 syn. nov. of Ptilininae Shuckard, 1839 (Ptinidae), Phloeonomini Ádám, 2001 syn. nov. of Omaliini MacLeay, 1825 (Staphylinidae), Sepedophilini Ádám, 2001 syn. nov. of Tachyporini MacLeay, 1825 (Staphylinidae), Phibalini Gistel, 1856 syn. nov. of Cteniopodini Solier, 1835 (Tenebrionidae); Agronoma Gistel 1848 (type species Carabus familiaris Duftschmid, 1812, designated herein) syn. nov. of Amara Bonelli, 1810 (Carabidae), Hylepnigalio Gistel, 1856 (type species Chrysomela caraboides Linnaeus, 1760, by monotypy) syn. nov. of Melandrya Fabricius, 1801 (Melandryidae), Polycystophorus Gistel, 1856 (type species Cantharis aeneus Linnaeus, 1758, designated herein) syn. nov. of Malachius Fabricius, 1775 (Melyridae), Sclerastes Gistel, 1856 (type species Ptilinus costatus Gyllenhal, 1827, designated herein) syn. nov. of Ptilinus Geoffroy, 1762 (Ptinidae), Paniscus Gistel, 1848 (type species Scarabaeus fasciatus Linnaeus, 1758, designated herein) syn. nov. of Trichius Fabricius, 1775 (Scarabaeidae), Phibalus Gistel, 1856 (type species Chrysomela pubescens Linnaeus, 1758, by monotypy) syn. nov. of Omophlus Dejean, 1834 (Tenebrionidae). The following new replacement name is proposed: Gompeliina Bouchard, 2011 nom. nov. for Olotelina Báguena Corella, 1948 (Aderidae).Reversal of Precedence (Article 23.9) is used to conserve usage of the following names (family-group names followed by genus-group names): Perigonini Horn, 1881 nom. protectum over Trechicini Bates, 1873 nom. oblitum (Carabidae), Anisodactylina Lacordaire, 1854 nom. protectum over Eurytrichina LeConte, 1848 nom. oblitum (Carabidae), Smicronychini Seidlitz, 1891 nom. protectum over Desmorini LeConte, 1876 nom. oblitum (Curculionidae), Bagoinae Thomson, 1859 nom. protectum over Lyprinae Gistel 1848 nom. oblitum (Curculionidae), Aterpina Lacordaire, 1863 nom. protectum over Heliomenina Gistel, 1848 nom. oblitum (Curculionidae), Naupactini Gistel, 1848 nom. protectum over Iphiini Schönherr, 1823 nom. oblitum (Curculionidae), Cleonini Schönherr, 1826 nom. protectum over Geomorini Schönherr, 1823 nom. oblitum (Curculionidae), Magdalidini Pascoe, 1870 nom. protectum over Scardamyctini Gistel, 1848 nom. oblitum (Curculionidae), Agrypninae/-ini Candèze, 1857 nom. protecta over Adelocerinae/-ini Gistel, 1848 nom. oblita and Pangaurinae/-ini Gistel, 1856 nom. oblita (Elateridae), Prosternini Gistel, 1856 nom. protectum over Diacanthini Gistel, 1848 nom. oblitum (Elateridae), Calopodinae Costa, 1852 nom. protectum over Sparedrinae Gistel, 1848 nom. oblitum (Oedemeridae), Adesmiini Lacordaire, 1859 nom. protectum over Macropodini Agassiz, 1846 nom. oblitum (Tenebrionidae), Bolitophagini Kirby, 1837 nom. protectum over Eledonini Billberg, 1820 nom. oblitum (Tenebrionidae), Throscidae Laporte, 1840 nom. protectum over Stereolidae Rafinesque, 1815 nom. oblitum (Throscidae) and Lophocaterini Crowson, 1964 over Lycoptini Casey, 1890 nom. oblitum (Trogossitidae); Monotoma Herbst, 1799 nom. protectum over Monotoma Panzer, 1792 nom. oblitum (Monotomidae); Pediacus Shuckard, 1839 nom. protectum over Biophloeus Dejean, 1835 nom. oblitum (Cucujidae), Pachypus Dejean, 1821 nom. protectum over Pachypus Billberg, 1820 nom. oblitum (Scarabaeidae), Sparrmannia Laporte, 1840 nom. protectum over Leocaeta Dejean, 1833 nom. oblitum and Cephalotrichia Hope, 1837 nom. oblitum (Scarabaeidae).     

Islands and evolution: theory and opinion in Darwin's earlier years

Islands were not of special interest to evolutionists before Darwin. It was he who first appreciated their importance for demonstrating evolution in miniature. They were not of special interest because: (a) their peculiar products seemed no more peculiar than those of continents; (b) there was no special category of oceanic islands, but a continuum from such groups as the Canaries, Madeiras and Galápagos through New Zealand and Madagascar to Australia, Britain, and true continents; and (c) the concept of adaptive radiation, if known at all, was applied only to the higher levels of classification, and then very feebly.
When Darwin was young, classification at the lower levels hardly recognized convergence, and at the higher levels was subject to great changes, while only slowly separating out the major groups. In consequence, many of the facts of geographical distribution were misinterpreted, and numerous theories of the origination of species, groups, and biogeographical provinces were still plausible. It was largely the need for a historical, not ecological, explanation of the distribution of some mammals and plants, plus what he saw for himself in the Galápagos Islands, that convinced Darwin that evolution had occurred. His was a remarkable achievement in recognizing through all this 'noise' the meaning of adaptive radiation.     

Angiosperm classification and phylogeny: a rectifying comment

A commentary is given on the criticism of Dahlgren's recent classification of angiosperms by Corner ( Botanical Journal of the Linnean Society, 82: 81–87 (1981)). In his dissatisfaction with the current, (almost) generally accepted nomenclatural concepts he has chosen to use my classification as a target. It is agreed that nomenclature is not 'fair' to plant groups playing the most important role in building up the biosphere, and that nomenclatural constructions do not reflect the consideration given to various parts of the plant. Corner does not seem to be familiar with the fact that his so-called 'pseudons' are common to all current systems of classification, nor that the termination '-florae' has been used by Thorne (1968) and in a number of publications since. This suffix does not imply that the botanists using it neglect vegetative characters, nor characters from fruits and seeds. Other misunderstandings are also pointed out. In no case has it been satisfactorily demonstrated by Corner that my orders or superorders are unnatural entities (even though a number of them most likely are).     

Systematic classification of Asian colobines

In order to study the differentiation of Asian colobines, fourteen variables were analysed in one way, on 123 skulls, includingRhinopithecus, Presbytis, Presbytiscus, Pygathrix, andNasalis with both cluster and differentiated functions tests. Information on paleoenvironment changes in China and South-East Asia since late Tertiary have been used to examine the influences of migratory habits and the distribution range in Asian colobines. The cladogram among different Asian colobines genera was made from the results of various analysis. Some new points or revisions were suggested: 1. Following the second migratory way, ancient species of Asian colobines perhaps passed through Xizang along the northern bank of Tethis sea and Heng-Duan Shan regions, across Yunnan into Vietnam, since the ancient continent between Yunnan and Xizang was already located in on eastern bank of Tethis sea. Thus, during the evolution, Asian colobines must have had two original centres, i.e. “Sundaland” and Heng-Duan Shan Chinese regions; 2. Pygatrix possesses a lot of cranial features more similar toPresbytiscus than toRhinopithecus. The small difference from the modification combinesPygatrix with other two genera as shown by Groves (1970), but it is better to putPygatrix andPresbytiscus together as one genus; 3.Nasalis (2n=48) may be the most primitive genus within Asian colobines. Some features shared withRhinopithecus, for example body size, terrestrial activities, limb proportion etc. ...seem to be considered as a common inheritance of symlesiomorphus characters; 4.Rhinopithecus, with reference to cranioface and cranium or to its origin, is a special genus of Asian colobine. It may represent the highest level of evolutionary position within various genera (Peng et al., 1985).