Home About us Contact
|
Home About us Contact | ||
|
|
||
Extensive Collection (extensive + collection)
Selected AbstractsSympatric spawning of Anguilla marmorata and Anguilla japonica in the western North Pacific OceanJOURNAL OF FISH BIOLOGY, Issue 9 2009M. Kuroki Extensive collections were made of the larvae of the temperate Japanese eel Anguilla japonica and the tropical giant mottled eel Anguilla marmorata in an overlapping area of the North Equatorial Current region of the western North Pacific Ocean. Collections of 189 A. marmorata and > 2500 A. japonica larvae during nine surveys from 1991 to 2007 showed that these two anguillid eels have similar spawning areas just west of the southern West Mariana Ridge. In July to August 2006 and August 2007, morphologically and genetically identified A. marmorata preleptocephali were mainly collected between 14·5,15° N and 142,142·5° E, where A. japonica preleptocephali were also caught in some of the same net tows. Fewer A. marmorata preleptocephali, however, were collected (n = 31) compared to those of A. japonica (n = c. 165), and fewer small larvae of A. marmorata were collected per tow than A. japonica (n = 1,10 and 1,294, respectively), suggesting relatively smaller spawning aggregations of A. marmorata. The distribution of preleptocephali and small larvae was wider in longitude in A. marmorata (131, 143° E) than in A. japonica (137,143° E), while the latitudinal range was almost the same (12,17° N). Although spawning by these two species overlaps both spatially and temporally, the tropical eels of the North Pacific population of A. marmorata probably have a much longer spawning season with fewer spawners, at least in summer, and recruit to a much wider latitudinal range of growth habitats. [source] Generation and analysis of 5318 expressed sequence tags from the filamentous sporophyte of Porphyra haitanensis (Rhodophyta),JOURNAL OF PHYCOLOGY, Issue 6 2007Fan Xiaolei Porphyra haitanensis T. J. Chang et B. F. Zheng (Bangiales, Rhodophyta) is cultivated in China and widely consumed in Asia. To gain more insight into its physiological and biochemical properties, we generated 5318 expressed sequence tags (ESTs) from the sporophyte of P. haitanensis, and upon assembling into a nonredundant set, 2535 sequences were obtained, among which only 32.2% (816) shared certain similarity with published sequences (Nr and KOG). Functional classification of such ESTs revealed that most of the transcripts were related to its conservative biological metabolism, and P. haitanensis most likely possesses cyanide-resistant respiration and a C4-like carbon-fixation pathway, both of which have never been reported in a rhodophyte before. Twenty-eight percent of the nonredundant gene clusters exhibited significant similarity to those from P. yezoensis Ueda sporophytes, and 16 genes up-regulated in P. yezoensis sporophytes were also expressed abundantly in P. haitanensis. Codon usage analysis indicated that exposure to high GC pressure might occur during evolution of P. haitanensis. These findings represent the most extensive collection of ESTs from P. haitanensis to date, and all the ESTs in this study have been submitted to GenBank (accession nos. DN604790,DN608469, EG016226,EG018540). [source] Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment mapsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 6 2010Ruth Isserlin Abstract Global protein expression profiling can potentially uncover perturbations associated with common forms of heart disease. We have used shotgun MS/MS to monitor the state of biological systems in cardiac tissue correlating with disease onset, cardiac insufficiency and progression to heart failure in a time-course mouse model of dilated cardiomyopathy. However, interpreting the functional significance of the hundreds of differentially expressed proteins has been challenging. Here, we utilize improved enrichment statistical methods and an extensive collection of functionally related gene sets, gaining a more comprehensive understanding of the progressive alterations associated with functional decline in dilated cardiomyopathy. We visualize the enrichment results as an Enrichment Map, where significant gene sets are grouped based on annotation similarity. This approach vastly simplifies the interpretation of the large number of enriched gene sets found. For pathways of specific interest, such as Apoptosis and the MAPK (mitogen-activated protein kinase) cascade, we performed a more detailed analysis of the underlying signaling network, including experimental validation of expression patterns. [source] Hair diagnoses and signs: the use of dermatoscopyCLINICAL & EXPERIMENTAL DERMATOLOGY, Issue 1 2010M. P. Wallace Summary Background., Hair-shaft examination is diagnostically useful in a range of adult and paediatric conditions. Objective., To evaluate the usefulness of dermatoscopy in hair-shaft microscopy. Methods., Typical examples of selected conditions from an extensive collection of scalp hair were examined using a dermatoscope and a light microscope with paired cross-polarizing filters. Hair-shaft characteristics were photographed using a digital camera. Results., Dermatoscopy was helpful in detecting tapered hairs, weathering, monilethrix, pediculosis capitis, peripilar casts, ,exclamation-mark' hairs of alopecia areata, bubble hair and pili torti. It was less helpful in pili annulati and unhelpful in detecting ,tiger-tail' banding in trichothiodystrophy. Light microscopy provided greater detail in almost all cases; it was necessary for detection of cuticle changes and added significant information in detecting characteristic features of trichothiodystrophy, pili annulati, bubble hair and pili torti. Conclusions., Dermatoscopy is most revealing in conditions resulting in gross changes in shaft outline and colour, where reflected light is valuable. It is unhelpful for detection of features within the shaft or at higher levels of resolution. When added to its ability to aid evaluation of scalp surface characteristics, dermatoscopy provides an excellent first-line method of assessment in clinics. In vivo it may aid screening and selection of hairs of greatest diagnostic yield for further assessment. In some instances, it may obviate the need for obtaining hair specimens and have implications for public health screening. Where detailed or cortical hair-shaft features need assessment, transmitted light microscopy remains the standard tool. [source] UNEXPLAINED SPLIT SEX RATIOS IN THE NEOTROPICAL PLANT-ANT, ALLOMERUS OCTOARTICULATUS VAR. DEMERARAE (MYRMICINAE): A TEST OF HYPOTHESESEVOLUTION, Issue 1 2010Gabriel D. G. Debout We investigated sex allocation in the Neotropical ant Allomerus octoarticulatus var. demerarae. Because Allomerus is a plant symbiont, we could make geographically extensive collections of complete colonies and of foundresses in saplings, allowing us to estimate not only population- and colony-level sex allocation but also colony resource levels and the relatednesses of competing ant foundresses. This species exhibits a strongly split sex ratio, with 80% of mature colonies producing ,90% of one sex or the other. Our genetic analyses (DNA microsatellites) reveal that Allomerus has a breeding system characterized by almost complete monogyny and a low frequency of polyandry. Contrary to theoretical explanations, we find no difference in worker relatedness asymmetries between female- and male-specialist colonies. Furthermore, no clear link was found between colony sex allocation and life history traits such as the number of mates per queen, or colony size, resource level, or fecundity. We also failed to find significant support for male production by workers, infection by Wolbachia, local resource competition, or local mate competition. We are left with the possibility that Allomerus exhibits split sex ratios because of the evolution of alternative biasing strategies in queens or workers, as recently proposed in the literature. [source] Identifying native-like protein structures using physics-based potentialsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2002Brian N. Dominy Abstract As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's "Decoys ,R' Us" database generated using a sequence homology-based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four-state reduced model also contained in the "Decoys ,R' Us" database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z-scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge-based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics-based force fields in identifying native-like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 147,160, 2002 [source] Revision of the genus Acrochordiceras Hyatt, 1877 (Ammonoidea, Middle Triassic): morphology, biometry, biostratigraphy and intra-specific variabilityPALAEONTOLOGY, Issue 5 2010CLAUDE MONNET Abstract:, The family Acrochordiceratidae Arthaber, 1911 ranges in age from latest Spathian to the middle/late Anisian boundary, and it represents a major component of ammonoid faunas during that time. The middle Anisian genus Acrochordiceras Hyatt, 1877 is the most widespread taxon of the family and occurs abundantly worldwide within the low paleolatitude belt. However, there is a profusion of species names available for Acrochordiceras. This excessive diversity at the species level essentially results from the fact that sufficiently large samples were not available, thus leading to a typological approach to its taxonomy. Based on new extensive collections obtained from the Anisian (Middle Triassic) Fossil Hill Member (Star Peak Group, north-west Nevada) for which a high resolution biostratigraphic frame is available, the taxonomy and biostratigraphy of the genus Acrochordiceras Hyatt, 1877 is herein revised with respect to its intra-specific variation. Morphological and biometric studies (c. 550 bedrock-controlled specimens were measured) show that only one species occurs in each stratigraphic level. Continuous ranges of intra-specific variation of studied specimens enable us to synonymize Haydenites Diener, 1907, Silesiacrochordiceras Diener, 1916 and Epacrochordiceras Spath, 1934 with Acrochordiceras Hyatt, 1877. Three stratigraphically successive species are herein recognized in the low paleolatitude middle Anisian faunas from Nevada: A. hatschekii (Diener, 1907), A. hyatti Meek, 1877 and A. carolinae Mojsisovics, 1882. Moreover, an assessment of intra-specific variation of the adult size range does not support recognition of a dimorphic pair (Acrochordiceras and Epacrochordiceras) as previously suggested by other workers (Epacrochordiceras is the compressed and weakly ornamented end-member variant of Acrochordiceras). The successive middle Anisian species of Acrochordiceras form an anagenetic lineage characterized by increasing involution, adult size and intra-specific variation. This taxonomic revision based on new bedrock-controlled collections is thus an important prerequisite before studying the evolution of the group. [source] | ||||||||||||||||