Phylogenetic Comparisons (phylogenetic + comparison)

Distribution by Scientific Domains
Distribution within Life Sciences


Selected Abstracts


Phylogenetic comparison of spicule networks in cryptobranchiate dorid nudibranchs (Gastropoda, Euthyneura, Nudibranchia, Doridina)

ACTA ZOOLOGICA, Issue 4 2008
Brian K. Penney
Abstract Many dorid nudibranchs possess large numbers of calcareous spicules in their mantle, gill, rhinophores and foot. However, the arrangements of these structures and their differences among taxa are poorly known. Spicule networks were stained with Alizarin red and compared among 12 species of cryptobranchiate dorid nudibranchs and four outgroups. Three general types of networks were found: a cobweb-like, unbraced framework of one or few spicules per side; a ramifying system of thick, spiculated tracts; and a lattice-like arrangement of distinct radial and circumferential tracts. The Discodorididae species investigated shared a cobweb-like network and papillae supported by a ring of spicules, while the Porostomata showed consistent characters leading to a lattice-like network with larger spicules in the central notum. The Dorididae studied were not cohesive, but each species shared characters with the aforementioned groups. Therefore, spicule network form may provide new characters to help resolve the phylogeny of Doridina. [source]


A host species-informative internal control for molecular assessment of African swine fever virus infection rates in the African sylvatic cycle Ornithodoros vector

MEDICAL AND VETERINARY ENTOMOLOGY, Issue 4 2009
A. D. S. BASTOS
Abstract African swine fever virus (ASFV) infection in adult Ornithodoros porcinus (Murry 1877, sensuWalton 1979) ticks collected from warthog burrows in southern and East Africa was assessed using a duplex genomic amplification approach that is informative with respect to the invertebrate host species and infecting sylvatic cycle virus. DNA extracted from individual ticks was used as template for the simultaneous amplification of a C-terminal 478-bp ASFV p72 gene region and a ,313-bp fragment of the tick mitochondrial 16S rRNA gene, under optimized reaction conditions. Within-warthog burrow infection rates ranged from 0% to 43% using this approach, and phylogenetic analysis of 16S gene sequences revealed the presence of three geographically discrete O. porcinus lineages, but no support for subspecies recognition. False negatives are precluded by the inclusion of host species-informative primers that ensure the DNA integrity of cytoplasmically located genome extracts. In addition, infection rate estimates are further improved as false positives arising from carry-over contamination when performing a two-step nested polymerase chain reaction are negated by the one-step approach. Phylogenetic comparison of full-length virus gene sequences with the partial C-terminal p72 gene target confirmed the epidemiological utility of the latter in a sylvatic setting. The method is therefore of particular value in studies assessing the prevalence and diversity of ASFV in relation to the African sylvatic tick vector and holds potential for investigating the role of alternative tick species in virus maintenance and transmission. [source]


ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM THE GREEN ALGA ULVA LINZA (CHLOROPHYTA),

JOURNAL OF PHYCOLOGY, Issue 6 2005
Michele S. Stanley
There is a general lack of genomic information available for chlorophyte seaweed genera such as Ulva, and in particular there is no information concerning the genes that contribute to adhesion and cell wall biosynthesis for this organism. Partial sequencing of cDNA libraries to generate expressed sequence tags (ESTs) is an effective means of gene discovery and characterization of expression patterns. In this study, a cDNA library was created from sporulating tissue of Ulva linza L. Initially, 650 ESTs were randomly selected from a cDNA library and sequenced from their 5, ends to obtain an indication of the level of redundancy of the library (21%). The library was normalized to enrich for rarer sequences, and a further 1920 ESTs were sequenced. These sequences were subjected to contig assembly that resulted in a unigene set of approximately 1104 ESTs. Forty-eight percent of these sequences exhibited significant similarity to sequences in the databases. Phylogenetic comparisons are made between selected sequences with similarity in the databases to proteins involved in aspects of extracellular matrix/cell wall assembly and adhesion. [source]


A gene repertoire for nitrogen transporters in Laccaria bicolor

NEW PHYTOLOGIST, Issue 2 2008
Eva Lucic
Summary ,,Ectomycorrhizal interactions established between the root systems of terrestrial plants and hyphae from soil-borne fungi are the most ecologically widespread plant symbioses. The efficient uptake of a broad range of nitrogen (N) compounds by the fungal symbiont and their further transfer to the host plant is a major feature of this symbiosis. Nevertheless, we far from understand which N form is preferentially transferred and what are the key molecular determinants required for this transfer. ,,Exhaustive in silico analysis of N-compound transporter families were performed within the genome of the ectomycorrhizal model fungus Laccaria bicolor. A broad phylogenetic approach was undertaken for all families and gene regulation was investigated using whole-genome expression arrays. ,,A repertoire of proteins involved in the transport of N compounds in L. bicolor was established that revealed the presence of at least 128 gene models in the genome of L. bicolor. Phylogenetic comparisons with other basidiomycete genomes highlighted the remarkable expansion of some families. Whole-genome expression arrays indicate that 92% of these gene models showed detectable transcript levels. ,,This work represents a major advance in the establishment of a transportome blueprint at a symbiotic interface, which will guide future experiments. [source]


Identification of a defective molecule derived from DNA-A of the bipartite begomovirus of East African cassava mosaic virus

PLANT PATHOLOGY, Issue 1 2006
J. Ndunguru
Geminivirus defective interfering DNAs arise spontaneously in mechanically inoculated test plants, and have previously been found with DNA-B of the bipartite cassava mosaic geminiviruses, but not DNA-A. Reported here for the first time is the cloning and characterization of a naturally occurring truncated form of cassava mosaic geminivirus DNA-A, which at 1525 nt is around half the expected full size. Sequence analysis has shown it to be a defective (df) form of East African cassava mosaic virus (EACMV) DNA-A that has retained its cis elements essential for replication by the helper virus, and it has been termed df DNA-A 15. Phylogenetic comparisons placed the df DNA-A 15 molecule close to mild and severe isolates of EACMV-UG2. Biolistic inoculation of Nicotiana benthamiana with infectious df DNA-A 15 clone and East African cassava mosaic Cameroon virus (EACMCV) resulted in symptom amelioration as compared with EACMCV singly inoculated plants, and there was an accumulation of df DNA-A 15 in systemically infected leaves. In addition, the level of EACMV DNA-B accumulation was reduced in the coinoculated plants compared with those inoculated with EACMCV alone. PCR and sequence analysis confirmed the helper virus as EACMV. [source]


Ribosomal RNA gene fragments from fossilized cyanobacteria identified in primary gypsum from the late Miocene, Italy

GEOBIOLOGY, Issue 2 2010
G. PANIERI
Earth scientists have searched for signs of microscopic life in ancient samples of permafrost, ice, deep-sea sediments, amber, salt and chert. Until now, evidence of cyanobacteria has not been reported in any studies of ancient DNA older than a few thousand years. Here, we investigate morphologically, biochemically and genetically primary evaporites deposited in situ during the late Miocene (Messinian) Salinity Crisis from the north-eastern Apennines of Italy. The evaporites contain fossilized bacterial structures having identical morphological forms as modern microbes. We successfully extracted and amplified genetic material belonging to ancient cyanobacteria from gypsum crystals dating back to 5.910,5.816 Ma, when the Mediterranean became a giant hypersaline brine pool. This finding represents the oldest ancient cyanobacterial DNA to date. Our clone library and its phylogenetic comparison with present cyanobacterial populations point to a marine origin for the depositional basin. This investigation opens the possibility of including fossil cyanobacterial DNA into the palaeo-reconstruction of various environments and could also be used to quantify the ecological importance of cyanobacteria through geological time. These genetic markers serve as biosignatures providing important clues about ancient life and begin a new discussion concerning the debate on the origin of late Miocene evaporites in the Mediterranean. [source]


Amended biochemical characteristics and phylogenetic position of Treponema medium

MOLECULAR ORAL MICROBIOLOGY, Issue 2 2003
F. Nakazawa
Umemoto et al. (1997, Int J Syst Bacteriol 47, pp. 67,72) proposed spirochete strain G7201, isolated from the periodontal pocket of an adult patient, as a new species, Treponema medium. They deposited this strain in the American Type Culture Collection (ATCC) as type strain ATCC 700293T. Recently, ATCC suggested that there is a discrepancy between the previous report and the results obtained by ATCC in biochemical tests on T. medium ATCC 700293T. In this study, we re-examined and verified the biochemical characteristics of T. medium. The fermentation pattern of carbohydrates of T. medium resembled that of Treponema vincentii and Treponema denticola, but T. medium was clearly differentiated from T. vincentii in the production of indole, and from T. denticola in the hydrolysis of esculin. Also, sodium dodecylsulfate,polyacrylamide gel electrophoresis (SDS-PAGE) protein profile analysis and phylogenetic comparison of 16S rDNA sequences revealed that T. medium is clearly differentiated from any established treponemal species, which supports the validity of the proposal of Treponema medium as a new species. [source]


Cryptic variation in butterfly eyespot development: the importance of sample size in gene expression studies

EVOLUTION AND DEVELOPMENT, Issue 1 2007
Robert D. Reed
SUMMARY Previous studies have shown that development can be robust to variation in parameters such as the timing or level of gene expression. This leads to the prediction that natural populations should be able to host developmental variation that has little phenotypic effect. Cryptic variation is of particular interest because it can result in selectable phenotypes when "released" by environmental or genetic factors. Currently, however, we have little idea of how variation is distributed between genes or over time in pattern formation processes. Here we survey expression of Notch (N), Spalt (Sal), and Engrailed (En) during butterfly eyespot determination to better understand how pattern formation may vary within a population. We observed substantial heterochronic variance in the progress of spatial expression patterns for all three proteins, suggesting some degree of developmental buffering in eyespot development. Peak variance for different proteins was found at both early and late stages of development, contrasting with previous models suggesting that the distribution of variance should be more temporally focused during pattern formation. We speculate that our observations are representative of a standing reservoir of cryptic variation that may contribute to phenotypic evolution under certain circumstances. Our results also provide a strong cautionary message that gene expression studies with limited sample sizes can be positively misleading in terms of inferring expression pattern time series, as well as for making cross-species phylogenetic comparisons. [source]


The cis -regulatory sequences required for expression of the Drosophila melanogaster adult cuticle gene ACP65A

INSECT MOLECULAR BIOLOGY, Issue 4 2009
M. Lestradet
Abstract Post-embryonic development in insects requires successive molts. Molts are triggered by ecdysteroids, and the nature of the molt (larval, pupal or adult) is determined by juvenile hormones. The genes encoding cuticle proteins are targets of both classes of hormones, and therefore are interesting models to study hormone action at the molecular level. The Drosophila ACP65A cuticle gene is expressed exclusively during the synthesis of the adult exoskeleton, in epidermal domains synthesising flexible cuticle. We have examined the cis -regulatory sequences of ACP65A using phylogenetic comparisons and functional analysis, and find that only about 180 bp are essential, including an 81 bp intron. The restriction of ACP65A expression appears to depend on a strong repression mechanism. [source]


Raman spectra and structure of a 25mer HCV RNA

JOURNAL OF RAMAN SPECTROSCOPY, Issue 8 2009
Pedro Carmona
Abstract We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1,25 nucleotides) in solution. The principal findings of this study are (1) the A -form secondary structure involving C3,- endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2,- endo/anti and C3,- endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base-paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs. Copyright © 2009 John Wiley & Sons, Ltd. [source]


The influence of floral symmetry and pollination systems on flower size variation

NORDIC JOURNAL OF BOTANY, Issue 5 2004
Atushi Ushimaru
We compared the amount of variation in flower size between autogamous and insect-pollinated species to examine the hypothesis that pollinator-mediated selection stabilizes flower size in plant populations. One would expect the flower size variation to be larger in selfing species that are less affected by pollinator-mediated stabilizing selection than in insect-pollinated species. The results of phylogenetic comparisons between autogamous and insect-pollinated flowers supported the pollinator-mediated stabilizing selection hypothesis, although the non-phylogenetic comparison did not. According to our results, we discuss the factors influencing the flower size variation. [source]