scholarly journals Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

2012 ◽  
Vol 40 (20) ◽  
pp. e161-e161 ◽  
Author(s):  
Hiroaki Iwata ◽  
Osamu Gotoh
Keyword(s):  
Extended Version ◽  
Additional Species ◽  
Spliced Alignment ◽  
Species Specific

Morphological and systematic study of the tribe Australiosomatini (Diplopoda:Polydesmida:Paradoxosomatidea:Paradoxosomatidae) and a revision of the genus Australiosoma Brölemann

2006 ◽  
Vol 20 (5) ◽  
pp. 527 ◽  
Author(s):  
Melissah Rowe ◽  
Petra Sierwald
Keyword(s):  
New Species ◽  
Species Level ◽  
Data Matrix ◽  
Adult Males ◽  
Ecological Studies ◽  
Additional Species ◽  
The Family ◽  
Two New Species ◽  
Three New Species ◽  
Species Specific

The collection of several paradoxosomatid species in the context of ecological studies prompted an investigation into the morphology and species-level characteristics of Australian millipedes in the tribe Australiosomatini Brölemann, 1916 (Polydesmida : Paradoxosomatidae). Three new species are described: Akamptogonus caragoon, sp. nov., Australiosoma fulbrighti, sp. nov. and Australiosoma combei, sp. nov. Notes or re-descriptions are provided for nine additional species belonging to the tribe. Scanning electron microscopy was utilised to examine details of the antennal sensory fields, the fifth sternite lamella and associated pores. The presence of the fifth sternite lamella in adult males is considered a synapomorphy for the family Paradoxosomatidae, whereas the prominent tubercle on the first femur in males (adenostyle) represents a synapomorphy of the subfamily Australiosomatinae. With the description of two new species in the genus Australiosoma Brölemann, 1913 a revision of the genus was undertaken with the purpose of constructing a species-level phylogeny. The most commonly described and utilised species-specific characteristics were scored in a data matrix and analysed using PAUP. The analysis resulted in a single, fully resolved tree of the following structure: Hoplatria clavigera ((A. clavigerum, A. inusitatum) (((A. rainbowi, A. nodulosum) A. michelseni) (A. laminatum (A. combei, A. fulbrighti))).

In vitro proteolysis of nematode FMRFamide-like peptides (FLPs) by preparations from a free-living nematode (Panagrellus redivivus) and two plant-parasitic nematodes (Heteroderaglycines and Meloidogyne incognita)

2011 ◽  
Vol 86 (1) ◽  
pp. 77-84 ◽  
Author(s):  
E.P. Masler
Keyword(s):  
Cathepsin L ◽  
Cysteine Proteases ◽  
Developmental Differences ◽  
Parasitic Nematodes ◽  
Free Living ◽  
Additional Species ◽  
Substrate Preferences ◽  
Panagrellus Redivivus ◽  
Species Specific

AbstractProteolytic activities in extracts from three nematodes, the plant parasites Heterodera glycines and Meloidogyneincognita, and the free-living Panagrellus redivivus, were surveyed for substrate preferences using a battery of seven FRET-modified peptide substrates, all derived from members of the large FMRF-amide like peptide (FLP) family in nematodes. Overall protease activity in P. redivivus was four- to fivefold greater than in either of the parasites, a result that might reflect developmental differences. Digestion of the M. incognita FLP KHEFVRFa (substrate Abz-KHEFVRF-Y(3-NO2)a) by M. incognita extract was sevenfold greater than with H. glycines extract and twofold greater than P. redivivus, suggesting species-specific preferences. Additional species differences were revealed upon screening 12 different protease inhibitors. Two substrates were used in the screen, Abz-KHEFVRF-Y(3-NO2)a and Abz-KPSFVRF-Y(3-NO2)a), which was digested equally by all three species. The effects of various inhibitor, substrate and extract source combinations on substrate digestion suggest that M. incognita differs significantly from P. redivivus and H. glycines in its complement of cysteine proteases, particularly cathepsin L-type protease.

scholarly journals Analysis of fish ZP1/ZPB homologous genes--evidence for both genome duplication and species-specific amplification models of evolution

Reproduction ◽  
2003 ◽  
pp. 347-352 ◽  
Author(s):  
SJ Conner ◽  
DC Hughes
Keyword(s):  
Zona Pellucida ◽  
Teleost Fish ◽  
Duplication Event ◽  
Specific Gene ◽  
Additional Species ◽  
Hepatic Expression ◽  
Multiple Copies ◽  
Species Specific ◽  
Related Proteins ◽  
Polyploidization Event

The vertebrate egg envelope is composed of a family of related proteins, the zona pellucida (ZP) proteins, which are characterized by the presence of a conserved zona pellucida domain. Analysis of teleost fish ZP gene sequences has demonstrated that there are no direct orthologues of the mammalian ZPB and ZP1 genes, but that teleost fish contain multiple copies of two classes of genes (ZPXa and ZPXb) that are equally related to ZPB and ZP1. The two classes of genes are further distinguished by expression in liver or ovary, respectively, indicating there was probably an initial duplication event, followed by a switch to hepatic expression of one of the paralogues. This switch was followed in some species by additional amplification of one of the paralogues with the subsequent loss of the other. It is proposed that the expansion of the number of ZPXa and ZPXb genes and the acquisition of dual sites of synthesis are the result of an ancient polyploidization event, followed by additional species-specific gene amplifications.

scholarly journals Immunochemistry of cartilage proteoglycan. Immunodiffusion and gel-electrophoretic studies

1972 ◽  
Vol 126 (1) ◽  
pp. 163-169 ◽  
Author(s):  
H Keiser ◽  
H J. Shulman ◽  
J I. Sandson
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Additional Species ◽  
Link Protein ◽  
Nasal Cartilage ◽  
Caesium Chloride ◽  
Cartilage Proteoglycan ◽  
Core Proteins ◽  
Specific Antigens ◽  
Species Specific

Cartilage proteoglycan is thought to be composed of subunits, core proteins with covalently attached sulphated polysaccharide side chains, which form aggregates by non-covalent association with a link protein. The new technique of non-disruptive extraction followed by fractionation in caesium chloride gradients provides a useful means of preparing relatively pure proteoglycan aggregate, subunit and link fractions. Immunological studies of these fractions led to the identification of an antigen associated with the proteoglycan subunit which was common to several species and to the demonstration of additional species-specific antigens in aggregate and link fractions derived from bovine nasal cartilage. Polyacrylamide-gel electrophoresis with sodium dodecyl sulphate of bovine proteoglycan aggregate and link fractions gave two protein bands in the gels and a protein–polysaccharide band at the origin; subunit fractions gave only the band at the origin. These results are consistent with the current concept of cartilage proteoglycan structure.

scholarly journals Habitat complexity explains species-specific occupancy but not species richness in a Western Australian woodland

2008 ◽  
Vol 56 (2) ◽  
pp. 95 ◽  
Author(s):  
Jarrad A. Cousin ◽  
Ryan D. Phillips
Keyword(s):  
Species Richness ◽  
Western Australia ◽  
Habitat Complexity ◽  
Bird Species ◽  
Ground Vegetation ◽  
Additional Species ◽  
Bird Species Richness ◽  
Litter Cover ◽  
The Individual ◽  
Species Specific

Habitat complexity is an important factor governing species richness and habitat selection in birds. The present study examined this relationship in a large wandoo woodland in Western Australia. Habitat complexity (comprising canopy, shrub, ground vegetation, log and leaf litter cover) and bird species richness was recorded in 48 sites, each ~3 ha in size. We found no significant correlation of habitat complexity with species richness. We propose that the absence of such a relationship results from the resource-poor environment of the woodlands of south-western Australia. The relative scarcity of food resources results in a species richness threshold beyond which there are insufficient niches and resources to support additional species with increasing habitat complexity. Only two species exhibited significant associations with habitat complexity, with the western yellow robin (Eopsaltria griseogularis) occupying sites with higher habitat complexity, and the restless flycatcher (Myiagra inquieta) occupying sites with lower habitat complexity. Although some species may respond specifically to habitat complexity, management of avian biodiversity within Australian woodlands should take into account the potentially greater role that productivity and resource availability play in influencing species richness, rather than habitat complexity per se. Furthermore, the individual components comprising habitat complexity may be of equal importance in assessing relationship of species richness to overall habitat complexity.

ITS-RFLP analysis, an efficient tool for differentiation of Bursaphelenchus species

Nematology ◽  
2009 ◽  
Vol 11 (5) ◽  
pp. 649-668 ◽  
Author(s):  
Wolfgang Burgermeister ◽  
Helen Braasch ◽  
Kai Metge ◽  
Jianfeng Gu ◽  
Thomas Schröder ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Restriction Analysis ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Its Sequence ◽  
Additional Species ◽  
New Information ◽  
Specific Fragment ◽  
Species Specific ◽  
Different Origins

Abstract Restriction analysis of amplified ribosomal ITS sequences has provided species-specific fragment patterns for nematodes of several genera, including Bursaphelenchus. We used restriction enzymes RsaI, HaeIII, MspI, HinfI and AluI to produce ITS-RFLP reference profiles of 44 Bursaphelenchus species, including two intraspecific types in each of B. mucronatus and B. leoni. In addition, reference profiles of Aphelenchoides stammeri and Ruehmaphelenchus asiaticus were produced. Reference profiles of six species are shown here for the first time. Identical ITS-RFLP patterns were usually obtained from different isolates and from individual specimens of the same species. However, in the case of B. 'corneolus', B. lini, B. singaporensis and B. sexdentati, additional bands in the patterns of certain isolates or individual nematodes were observed which may be explained by ITS sequence microheterogeneity, i.e., the presence of ITS sequence variants within the number of rDNA tandem repeats. Since these 'extra' bands appeared only with one out of the five restriction enzymes employed, they did not seriously impair identification of species based on the overall reference patterns. ITS-RFLP analysis has proved valuable for differentiation of the pathogenic pine wood nematode, B. xylophilus, from related species. In many recent descriptions of new Bursaphelenchus species, ITS-RFLP profiles have been used as additional species identification criteria. Comparison of profiles from isolates of many different origins has provided new information on intraspecific types or genetically distinct provenances of several Bursaphelenchus species.

An ancient satellite DNA has maintained repetitive units of the original structure in most species of the living fossil plant genusZamia

Genome ◽  
2014 ◽  
Vol 57 (3) ◽  
pp. 125-135 ◽  
Author(s):  
Donata Cafasso ◽  
Gianni Chinali
Keyword(s):  
Satellite Dna ◽  
Common Ancestor ◽  
Original Structure ◽  
Additional Species ◽  
Living Fossil ◽  
Consensus Sequences ◽  
Specific Amplification ◽  
Species Specific ◽  
Dispersed Repeats ◽  
Common Sequence

ZpS1 satellite DNA is specific to the genus Zamia and presents repetitive units organized as long arrays and also as very short arrays dispersed in the genome. We have characterized the structure of the ZpS1 repeats in 12 species representative of the whole geographic distribution of the genus. In most species, the clone most common sequences (cMCS) were so similar that a general most common sequence (GMCS) of the ZpS1 repetitive unit in the genus could be obtained. The few partial variations from the GMCS found in cMCS of some species correspond to variable positions present in most other species, as indicated by the clone consensus sequences (cCS). Two species have an additional species-specific variety of ZpS1 satellite. The dispersed repeats were found to contain more mutations than repeats from long arrays. Our results indicate that all or most species of Zamia inherited the ZpS1 satellite from a common ancestor in Miocene and have maintained repetitive units of the original structure till present. The features of ZpS1 satellite in the genus Zamia are poorly compatible with the model of concerted evolution, but they are perfectly consistent with a new model of satellite evolution based on experimental evidences indicating that a specific amplification-substitution repair mechanism maintains the homogeneity and stability of the repeats structure in each satellite DNA originally present in a species as long as the species exists.

scholarly journals In Situ Accessibility of Saccharomyces cerevisiae 26S rRNA to Cy3-Labeled Oligonucleotide Probes Comprising the D1 and D2 Domains

2003 ◽  
Vol 69 (5) ◽  
pp. 2899-2905 ◽  
Author(s):  
João Inácio ◽  
Sebastian Behrens ◽  
Bernhard M. Fuchs ◽  
Álvaro Fonseca ◽  
Isabel Spencer-Martins ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Flow Cytometry ◽  
In Situ Hybridization ◽  
Rational Design ◽  
Oligonucleotide Probes ◽  
Yeast Identification ◽  
Additional Species ◽  
Species Specific ◽  
26S Rrna

ABSTRACT Fluorescence in situ hybridization (FISH) has proven to be most useful for the identification of microorganisms. However, species-specific oligonucleotide probes often fail to give satisfactory results. Among the causes leading to low hybridization signals is the reduced accessibility of the targeted rRNA site to the oligonucleotide, mainly for structural reasons. In this study we used flow cytometry to determine whole-cell fluorescence intensities with a set of 32 Cy3-labeled oligonucleotide probes covering the full length of the D1 and D2 domains in the 26S rRNA of Saccharomyces cerevisiae PYCC 4455T. The brightest signal was obtained with a probe complementary to positions 223 to 240. Almost half of the probes conferred a fluorescence intensity above 60% of the maximum, whereas only one probe could hardly detect the cells. The accessibility map based on the results obtained can be extrapolated to other yeasts, as shown experimentally with 27 additional species (14 ascomycetes and 13 basidiomycetes). This work contributes to a more rational design of species-specific probes for yeast identification and monitoring.

scholarly journals Glucose Transporter Isoforms in Brain: Absence of GLUT3 from the Blood—Brain Barrier

1993 ◽  
Vol 13 (2) ◽  
pp. 342-345 ◽  
Author(s):  
Frances Maher ◽  
Susan J. Vannucci ◽  
Ian A. Simpson
Keyword(s):  
Molecular Mass ◽  
Blood Brain Barrier ◽  
Glucose Transporter ◽  
Terminal Sequence ◽  
Additional Species ◽  
Cerebral Microvessels ◽  
Cortical Membranes ◽  
Species Specific ◽  
Specific Sequences ◽  
Isolated Rat

Two glucose transporter (GLUT) isoforms have been identified in brain. The GLUT1 isoform is abundant in cerebral microvessels and may be present in glia and neurons, whereas GLUT3 is probably the major neuronal glucose transporter. This study investigates whether GLUT3 is also present in microvessels from rat, human, and canine brain, by means of antisera directed against the divergent C-terminal sequences of mouse and human GLUT3. GLUT1 was detected in whole brain as two molecular mass forms: 55 kDa in microvessels and 45 kDa in cortical neuronal/glial membranes. With the aid of the appropriate antisera to the species-specific sequences, GLUT3 was detected in rat and human cortical membranes but not in isolated rat or human microvessels. These antisera failed to detect GLUT3 in either canine cortical membranes or canine microvessels, implying additional species specificity in the C-terminal sequence.

scholarly journals Segregation into separate rouleaux of erythrocytes from different species. Evidence against the agglomerin hypothesis of rouleaux formation

1983 ◽  
Vol 214 (1) ◽  
pp. 257-260 ◽  
Author(s):  
D R Forsdyke ◽  
P M Ford
Keyword(s):  
Fluorescence Microscopy ◽  
Specific Surface ◽  
Experimental Approach ◽  
Fluorescein Isothiocyanate ◽  
Additional Species ◽  
Rouleau Formation ◽  
Species Specific ◽  
Rouleaux Formation

Erythrocytes from one species were labelled with fluorescein isothiocyanate and mixed with unlabelled erythrocytes from another species. Albumin polymers were added to generate rouleaux. The species of origin of erythrocytes in rouleaux was determined by fluorescence microscopy. Erythrocytes from different species segregated into independent rouleaux. However, fluorescent and non-fluorescent erythrocytes from one individual were mixed randomly in rouleaux. These results confirm, using a novel experimental approach, previous observations of Sewchand & Canham [(1976) Can. J. Physiol. Pharmacol. 54, 437-442]. Since rouleaugenic agents are not species-specific, under the ‘agglomerin’ hypothesis of rouleau formation they would be expected to form bridges between cells from different species. It follows that either the agglomerin hypothesis is incorrect, or additional species-specific surface components are involved in the aggregation of agglomerin-cross-bridged cells.

Sign in / Sign up

Export Citation Format

Share Document