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New Sequences (new + sequence)
Selected AbstractsMultiple origins of symbioses between ascomycetes and bryophytes suggested by a five-gene phylogenyCLADISTICS, Issue 3 2010Soili Stenroos Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit-bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors. ,© The Willi Hennig Society 2009. [source] Cine cardiac imaging using black-blood steady-state free precession (BB-SSFP) at 3TJOURNAL OF MAGNETIC RESONANCE IMAGING, Issue 1 2009Tamer A. Basha MSE Abstract Purpose To propose a new black-blood (BB) pulse sequence that provides BB cine cardiac images with high blood-myocardium contrast. The proposed technique is based on the conventional steady-state free precession (SSFP) sequence. Materials and Methods Numerical simulations of the Bloch equation were conducted to compare the resulting signal-to-noise ratio (SNR) to that of conventional BB imaging, including the effects of changing the imaging flip angle and heart rates. Simulation results were verified using a gel phantom experiment and five normal volunteers were scanned using the proposed technique. Results The new sequence showed higher SNR and contrast-to-noise ratio (CNR) (,100%) compared to the conventional BB imaging. Also, the borders of the left ventricle (LV) and right ventricle (RV) appear more distinguishable than the conventional SSFP. We were also able to cover about 80% of the cardiac cycle with short breath-hold time (,10 cardiac cycles) and with reasonable SNR and CNR. Conclusion Based on an SSFP conventional sequence, the new sequence provides BB cines that cover most of the cardiac cycle and with higher SNR and CNR than the conventional BB sequences. J. Magn. Reson. Imaging 2009;30:94,103. © 2009 Wiley-Liss, Inc. [source] Fast CT-PRESS-based spiral chemical shift imaging at 3 TeslaMAGNETIC RESONANCE IN MEDICINE, Issue 5 2006Dirk Mayer Abstract A new sequence is presented that combines constant-time point-resolved spectroscopy (CT-PRESS) with fast spiral chemical shift imaging. It allows the acquisition of multivoxel spectra without line splitting with a minimum total measurement time of less than 5 min for a field of view of 24 cm and a nominal 1.5 × 1.5-cm2 in-plane resolution. Measurements were performed with 17 CS encoding steps in t1 (,t1 = 12.8 ms) and an average echo time of 151 ms, which was determined by simulating the CT-PRESS experiment for the spin systems of glutamate (Glu) and myo -inositol (mI). Signals from N-acetyl-aspartate, total creatine, choline-containing compounds (Cho), Glu, and mI were detected in a healthy volunteer with no or only minor baseline distortions within 14 min on a 3 T MR scanner. Magn Reson Med, 2006. © 2006 Wiley-Liss, Inc. [source] Establishment of Liebermannia dichroplusae n. comb. on the Basis of Molecular Characterization of Perezia dichroplusae Lange, 1987 (Microsporidia)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2007YULIYA Y. SOKOLOVA ABSTRACT. Perezia dichroplusae Lange, 1987 is a parasite of the Malpighian tubules of an Argentine grasshopper, Dichroplus elongatus (Orthoptera, Acrididae, Melanoplinae). In order to determine relationships of this microsporidium with Perezia nelsoni and with other microsporidia, we sequenced its small subunit ribosomal RNA gene (SSU rDNA) (GenBank Accession No. EF016249) and performed phylogenetic analysis of the novel sequence against 17 microsporidian SSU rDNA sequences from GenBank, using neighbor-joining (NJ), maximum-parsimony (MP), and maximum-likelihood (ML) methods. This analysis revealed the highest similarity (96%) of the new sequence to Liebermannia patagonica, a parasite of gut epithelium cells of another grasshopper from Argentina, versus only 65% similarity to P. nelsoni, a parasite of muscles of paenaeid shrimps. In phylogenetic trees inferred from SSU rDNA sequences, the microsporidium from D. elongatus is sister taxon to L. patagonica and both cluster with Orthosomella operophterae. At the higher hierarchical level, the Liebermania,Orthosomella branch forms a clade with the Endoreticulatus,Cystosporogenus,Vittaforma group and with Enterocytozoon bieneusi. Perezia nelsoni falls into another large clade together with Nosema and Ameson species. We propose transferring P. dichroplusae to the genus Liebermannia and creating a new combination Liebermannia dichroplusae n. comb., based both on SSU rDNA sequence analysis and on common characters between P. dichroplusae and L. patagonica, which include the presence of elongated multinuclear sporonts, sporoblastogenesis by a similar process of sequentially splitting off sporoblasts, ovocylindrical spores of variable size, tissue tropism limited to epithelial cells, Orthoptera as hosts, and geographical distribution of hosts in the southern temperate region of Argentina. We argue that the condition of the nuclei in spores (i.e. diplokaryotic in L. patagonica or monokaryotic in L. dichroplusae) cannot be used to distinguish genera. Therefore, we remove the statement about the presence of diplokaryotic spores from the revised diagnosis of the genus Liebermannia. [source] Identification and characterization of multiple Spidroin 1 genes encoding major ampullate silk proteins in Nephila clavipesINSECT MOLECULAR BIOLOGY, Issue 5 2008W. A. Gaines IV Abstract Spider dragline silk is primarily composed of proteins called major ampullate spidroins (MaSps) that consist of a large repeat array flanked by nonrepetitive N- and C-terminal domains. Until recently, there has been little evidence for more than one gene encoding each of the two major spidroin silk proteins, MaSp1 and MaSp2. Here, we report the deduced N-terminal domain sequences for two distinct MaSp1 genes from Nephila clavipes (MaSp1A and MaSp1B) and for MaSp2. All three MaSp genes are co-expressed in the major ampullate gland. A search of the GenBank database also revealed two distinct MaSp1 C-terminal domain sequences. Sequencing confirmed that both MaSp1 genes are present in all seven Nephila clavipes spiders examined. The presence of nucleotide polymorphisms in these genes confirmed that MaSp1A and MaSp1B are distinct genetic loci and not merely alleles of the same gene. We experimentally determined the transcription start sites for all three MaSp genes and established preliminary pairing between the two MaSp1 N- and C-terminal domains. Phylogenetic analysis of these new sequences and other published MaSp N- and C-terminal domain sequences illustrated that duplications of MaSp genes may be widespread among spider species. [source] Methods and applications of diffusion imaging of vertebral bone marrowJOURNAL OF MAGNETIC RESONANCE IMAGING, Issue 6 2006José G. Raya MSc Abstract Diffusion-weighted imaging (DWI) is an MRI technique that is sensitive to random water movements at spatial scales far below typical MRI voxel dimensions. DWI is a valuable tool for the diagnoses of diseases that involve alterations in water mobility. In the spine, DWI has proven to be a highly useful method for the differential diagnosis of benign and malignant compression fractures. In these pathologies, the microscopic structure of bone marrow is altered in a very different ways, leading to different water mobility, which can be depicted by DWI. Most of the pulse sequences developed for MRI can be adapted for DWI. However, these DWI-adapted sequences are frequently affected by artifacts, mostly caused by physiological motion. Therefore, the introduction of additional correction techniques, or even the development of new sequences is necessary. The first part of this article describes the principles of DWI and the sequences used for DWI of the spine: spin echo (SE), turbo spin echo (TSE), single-shot echo planar imaging (EPI), and steady-state free precession (SSFP) sequences. In the second part, clinical applications of DWI of the spinal bone marrow are extensively discussed. J. Magn. Reson. Imaging 2006. © 2006 Wiley-Liss, Inc. [source] Comparison of new sequences for high-resolution cartilage imagingMAGNETIC RESONANCE IN MEDICINE, Issue 4 2003Brian A. Hargreaves Abstract The high prevalence of osteoarthritis continues to demand improved accuracy in detecting cartilage injury and monitoring its response to different treatments. MRI is the most accurate noninvasive method of diagnosing cartilage lesions. However, MR imaging of cartilage is limited by scan time, signal-to-noise ratio (SNR), and image contrast. Recently, there has been renewed interest in SNR-efficient imaging sequences for imaging cartilage, including various forms of steady-state free-precession as well as driven-equilibrium imaging. This work compares several of these sequences with existing methods, both theoretically and in normal volunteers. Results show that the new steady-state methods increase SNR-efficiency by as much as 30% and improve cartilage-synovial fluid contrast by a factor of three. Additionally, these methods markedly decrease minimum scan times, while providing 3D coverage without the characteristic blurring seen in fast spin-echo images. Magn Reson Med 49:700,709, 2003. © 2003 Wiley-Liss, Inc. [source] Phylogenetic analyses of Caulerpa taxifolia (Chlorophyta) and of its associated bacterial microflora provide clues to the origin of the Mediterranean introductionMOLECULAR ECOLOGY, Issue 4 2001I. Meusnier Abstract The accidental introduction of Caulerpa taxifolia into the Mediterranean is no longer under dispute. What has eluded researchers until now, is definitive evidence for the original, biogeographical source population. Here we present two independent lines of evidence that support an Australian origin for the Mediterranean populations of C. taxifolia. First, we reanalysed algal rDNA-internal transcribed spacer (rDNA-ITS) sequences, combining previously published sequences from different studies with 22 new sequences. The ITS sequence comparison showed that the Australian sample is the sister group of the Mediterranean,aquarium clade. Second, cloned bacterial 16S rDNA gene sequences were analysed from the associated microflora of C. taxifolia collected from Australia, Tahiti, the Philippines and the Mediterranean. Five bacterial lineages were identified, of which three were dominant. Alpha Proteobacteria were the most abundant and were found in all samples. In contrast, members of the beta Proteobacterial line and Cytophaga-Flexibacter-Bacteroides line (CFB) were mainly associated with Mediterranean and Australian samples. Frequency distributions of the five bacterial lineages were significantly different among biogeographical locations. Phylogenetic analyses of the 54 bacterial sequences derived from the four C. taxifolia individuals resulted in a well-resolved tree with high bootstrap support. The topologies of the beta Proteobacteria and CFB mirror the geographical sources of their algal hosts. Bacterial,algal associations provide an identification tool that may have wide application for the detection of marine invasions. [source] A Molecular Phylogenetic Investigation of Opisthonecta and Related Genera (Ciliophora, Peritrichia, Sessilida)THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2007DANIEL WILLIAMS ABSTRACT. The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs. [source] The Cyclotide Fingerprint in Oldenlandia affinis: Elucidation of Chemically Modified, Linear and Novel Macrocyclic PeptidesCHEMBIOCHEM, Issue 9 2007Manuel Rey R. Plan Dr. Abstract The complete suite of cyclotides present in Oldenlandia affinis (Rubiaceae), the plant that was originally found to contain this unique family of circular proteins, has been characterised. This study expands the number of known cyclotides in this plant to 17, of which nine new sequences (kalata B9,B17) were characterised in this work. In addition, five derivatives that contain oxidation products of the conserved tryptophan were identified, and it was shown that the formation of these derivatives is catalysed by exposure to sunlight. Furthermore, we describe two "linear" cyclotide analogues. These acyclic peptides have three intact disulfide bonds, and their N and C termini coincide with the hypothesised cleavage sites from the precursor protein. This work increases our knowledge about the sequence variation that is accommodated by the cyclic cystine knot scaffold, confirms its applicability as a template for drug design, and also shows the first natural degradation pathways for cyclotides. These pathways have important implications for the persistence and environmental fate of the cyclotides if used as crop-protection agents. [source] | |||||||||||||