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Banding Patterns (banding + pattern)
Selected AbstractsShort-term dynamics of bacterial communities in a tidally affected coastal ecosystemFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Beate Rink Abstract Tidal effects on the composition of free-living (FL) and particle-associated (PA) bacterial communities were studied in a tidal flat ecosystem in the southern North Sea. Denaturing gradient gel electrophoresis targeting the 16S rRNA gene and the 16S rRNA of Bacteria, Bacteroidetes, Alphaproteobacteria and the Roseobacter clade was applied. Despite strong tidal variations in the quantity and, depending on the season, also the quality of suspended matter as well as variations in bacterial activity, the bacterial community composition remained rather stable. FISH showed some variations of the community composition, but these were not related to typical tidal situations. Variations were higher during tidal cycles in May and July compared with November. Bacteroidetes, Alpha - and Gammaproteobacteria constituted the majority of the bacterial communities but relative proportions of the different groups varied considerably. On particles, Betaproteobacteria were also detected to substantial proportions. The Roseobacter clade constituted up to 90% of FL but only 30% of PA Alphaproteobacteria. Banding patterns of the Bacteroidetes -specific amplicons, and in particular those targeting the 16S rRNA, revealed tidally induced effects, as several bands appeared or disappeared at distinct events such as slack water or resuspension. Sequencing of prominent bands revealed predominantly phylotypes reported previously from this ecosystem. [source] Characterisation of symbionts of entomopathogenic nematodes by universally primed-PCR (UP-PCR) and UP-PCR product cross-hybridisationFEMS MICROBIOLOGY LETTERS, Issue 1 2002O. Nielsen Abstract This work introduces and demonstrates the applicability of universally primed-PCR (UP-PCR) for differentiating bacterial symbionts of entomopathogenic nematodes. Furthermore, typing by UP-PCR product cross-hybridisation was successfully introduced to cluster the bacterial strains. The work was initiated by isolating 10 isolates of Photorhabdus temperata (S172) from the nematode host Heterorhabditis sp. (DK172) and 12 isolates of Xenorhabdus bovienii (S1) from the nematode Steinernema feltiae (DK1). The isolates were compared by UP-PCR using different primers. The two bacterial species (P. temperata and X. bovienii) could be distinguished on the basis of the banding pattern whereas isolates isolated from the same nematode host had identical banding patterns. Three isolates obtained from DK172 and DK1, respectively, were then selected along with a number of reference strains (Hb, HP88, C1, K122, HSH2, HL81, T228, 61, AN6, Q58) and further characterised by UP-PCR product cross-hybridisation. The Xenorhabdus strains (Q58, AN6, 61, T228, S1) represented three species and these species were separated by the hybridisation technique. The Photorhabdus strains (Hb, HP88, C1, K122, HSH2, HL81, S172) represented two species and were also separated according to this in the cross-hybridisation. Within each species of Photorhabdus, two subgroups were formed as a result of intensity of the hybridisation signals. This grouping was in agreement with previous studies in other laboratories. [source] Strength of two structured soils in triaxial compressionINTERNATIONAL JOURNAL FOR NUMERICAL AND ANALYTICAL METHODS IN GEOMECHANICS, Issue 2 2001Ron C. K. Wong Abstract Oil sands are dense granular materials with interlocked structure and clay shales are heavily overconsolidated clays. They are classified as structured soil or weak rock, exhibiting high peak strength with severe softening and dilation, particularly at low confining stress. The triaxial compression test results indicate that both materials yield linear Mohr,Coulomb envelopes with an apparent cohesion for peak and residual strengths. However, the strength components mobilized from these two materials are very different. This paper investigates if these strength parameters are intrinsic properties or responses derived in triaxial compression conditions. Computer tomography scanning technique is used to aid in examining the micro-structural features of the sheared specimens such as shear banding pattern, shear band thickness, spatial porosity distributions inside and outside shear bands. These micro-structural features are used to explain the macro-deformation response observed in the triaxial compression tests. Mobilization of strength components derived from interlocked structure, cementation, dilation, rolling and critical state are analysed for pre-, post-peak softening and residual stages. It is found that the empirical correlation such as Mohr,Coulomb failure criterion based on triaxial compression test results does not necessarily reflect the intrinsic properties of the test materials. Testing conditions are embedded in the empirical correlation. Copyright © 2001 John Wiley & Sons, Ltd. [source] SYNTHESIS OF MOLECULAR RESEARCH ON BATRACHOSPERMUM HELMINTHOSUM (RHODOPHYTA) FROM STREAM REACHES IN EASTERN NORTH AMERICAJOURNAL OF PHYCOLOGY, Issue 2001Article first published online: 24 SEP 200 Vis, M. L., Hall, M. M., Machesky, N. J. & Miller, E. J. Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701 USA The freshwater red alga Batrachospermum helminthosum was collected from eleven streams throughout the species range in eastern North America as follows: three stream reaches from Ohio, and one each from Michigan, Indiana, Tennessee, Louisiana, North Carolina, Connecticut, Rhode Island and Massachusetts. The molecular marker technique of inter-simple sequence repeats (ISSR) and sequence data from the plastid encoded rubisco large subunit gene (rbcL), the mitochondrial COX2-COX3 gene spacer region, and the nuclear region of ITS1-5.8S rDNA-ITS2 were employed to examine biogeographic trends in this alga. Analysis of the rbcL sequence revealed 5 genotypes with one genotype representing individuals from seven stream reaches. Data from the ISSR molecular markers gave a distinct banding pattern for each of 165 individuals examined. ISSR results showed all individuals within a reach clustered together but did not provide well-defined groupings based on stream reach. The sequence data for the COX2-COX3 gene spacer was invariant among individuals from a stream reach. The individuals from Connecticut, Rhode Island and 2 Ohio stream reaches were identical and similarly the individuals from the North Carolina and another Ohio location did not vary in sequence so that seven genotypes were recorded among the individuals from the eleven stream reaches. Analysis of the ITS1-5.8S rDNA-ITS2 region showed sequence variation not only among individuals from different streams but also among individuals from the same reach. The utility and congruency of these data sets to answer biogeographic questions will be discussed. [source] Analysis of Pathotypic and Genotypic Diversity of Xanthomonas oryzae pv. oryzae in ChinaJOURNAL OF PHYTOPATHOLOGY, Issue 4 2009Gang Li Abstract Virulence analysis and restriction fragment length polymorphism (RFLP) were used to evaluated the population structure of Xanthomonas oryzae pv. oryzae (Xoo) from the main rice-growing region in China. The pathotype of Xoo was determined for 103 strains by inoculating 13 near-isogenic rice lines using IR24 as the recurrent parent. Sixty-one pathotypes was shared by these strains, on the basis of the consensus of three clustering statistics, and four clusters for pathotype were formed. Cluster 2 consists of strains with high molecular polymorphorism and many pathotypes that are either virulent to a majority of the 13 major resistance (R) genes or avirulent only to Xa21, and is geographically dispersed. The resistance gene Xa21 has broader resistance than others to the strains tested. A probe from a member of the avrBs3/pthA type III effector family, 1376 bp SphI-digested fragment, was used to screen the genomes of 52 strains tested. Four common bands were found in the DNA fingerprint pattern of Xoo, suggesting basic patterns of evolutionary relationship for members of avrBs3/pthA family and/or the pathogen. Each distinct RFLP banding pattern of each strain was considered as a haplotype; 42 haplotypes were revealed by the probe and divided into four lineages by the same statistics method. It was observed that some isolates with different pathotypes shared the same haplotype and others with different haplotypes harboured identical pathotype. There was a weak correlation between virulent pathotypes and molecular haplotypes. [source] A genomic walking method for screening sequence length polymorphismMOLECULAR ECOLOGY RESOURCES, Issue 2 2006JEAN-CLAUDE WALSER Abstract We adapted a recently developed nonrestrictional, nonligational genome walking method, Universal Fast Walking (UFW), for detection of length polymorphism in the proximal promoter region of genes. We demonstrate its efficacy at discovering naturally occurring transposition into heat-shock genes of wild Drosophila and show that it surmounts limitations of simple polymerase chain reaction (PCR) approaches. We further present modifications to the standard UFW protocol and provide some guidelines to improve specificity. Although the resultant banding pattern of a standard UFW can be regarded as a DNA fingerprint, many amplicons result from false priming and not real polymorphisms. We describe ways to distinguish between UFW amplicons and false priming products in a high-throughput assay. [source] Investigation of bacterial communities associated with asymptomatic and symptomatic endodontic infections by denaturing gradient gel electrophoresis fingerprinting approachMOLECULAR ORAL MICROBIOLOGY, Issue 6 2004J. F. Siqueira Jr The purpose of the present study was to investigate the bacterial communities associated with asymptomatic and symptomatic endodontic infections and to compare denaturing gradient gel electrophoresis (DGGE) fingerprinting patterns of these two clinical conditions. The root canal microbiota of teeth associated with asymptomatic or symptomatic periradicular lesions was profiled by the PCR-DGGE method and then compared, taking into consideration the banding patterns. Bacteria were present in all examined cases. Comparative analysis of the two clinical conditions revealed bands that were common to both symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique for each clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles were 12.1 ± 9.4 (range 2,29) for symptomatic samples and 6.7 ± 2.7 (range 2,11) for asymptomatic ones. Clustering methods and principal component analysis of DGGE banding pattern placed the samples according to the presence or absence of symptoms. Four intense bands that were excised from the gel and sequenced showed similarities to species of the Campylobacter genus (found in 5/12 asymptomatic and in 3/11 symptomatic cases), Fusobacterium genus (4/11 symptomatic cases), Acinetobacter genus (5/12 asymptomatic cases), and Enterobacteriaceae family (11/12 asymptomatic and 2/11 symptomatic cases). The profiles of the predominant bacterial community appeared to be unique for each individual. These findings confirm that endodontic infections are polymicrobial and showed that there are significant differences in the predominant bacterial composition between asymptomatic and symptomatic cases. [source] Vibration Causes Acute Vascular Injury in a Two-Step Process: Vasoconstriction and Vacuole DisruptionTHE ANATOMICAL RECORD : ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY, Issue 8 2008Sandya R. Govindaraju Abstract Hand,arm vibration syndrome is a vasospastic and neurodegenerative occupational disease. In the current study, the mechanism of vibration-induced vascular smooth muscle cell (SMC) injury was examined in a rat-tail vibration model. Tails of male Sprague Dawley rats were vibrated continuously for 4 hr at 60 Hz, 49 m/s2 with or without general anesthesia. Ventral tail arteries were aldehyde fixed and embedded in epoxy resin to enable morphological analysis. Vibration without anesthesia caused vasoconstriction and vacuoles in the SMC. Anesthetizing rats during vibration prevented vasoconstriction and vacuole formation. Exposing tail arteries in situ to 1 mM norepinephrine (NE) for 15 min induced the greatest vasoconstriction and vacuolation. NE induced vacuoles were twice as large as those formed during vibration. When vibrated 4 hr under anesthesia after pretreatment with NE for 15 min, the SMC lacked vacuoles and exhibited a longitudinal banding pattern of dark and light staining. The extracellular matrix was filled with particulates, which were confirmed by electron microscopy to be cellular debris. The present findings demonstrate that vibration-induced vasoconstriction (SMC contraction) requires functioning central nervous system reflexes, and the physical stress of vibration damages the contracted SMC by dislodging and fragmenting SMC vacuoles. Anat Rec, 291:999,1006, 2008. © 2008 Wiley-Liss, Inc. [source] The Absence of Phosphorylated Tyrosine Hydroxylase Expression in the Purkinje Cells of the Ataxic Mutant Pogo MouseANATOMIA, HISTOLOGIA, EMBRYOLOGIA, Issue 3 2006N. S. Lee Summary The pogo mouse is a new ataxic autosomal recessive mutant that arose in Korean wild mice (KJR/Mskist). Its ataxic phenotype includes difficulty in maintaining a normal posture and the inability to walk in a straight line. Several studies have reported that tyrosine hydroxylase (TH) is persistently ectopically expressed in particular subsets of Purkinje cells in a parasagittal banding pattern in several ataxic mutant mice, e.g. tottering alleles and pogo mice. In this present study, we examined the expression of an enzymatically active form of TH and phosphorylated TH at Ser40 (phospho-TH) by using immunohistochemistry and double immunofluorescence in the cerebellum of pogo mice. TH immunostaining appeared in some Purkinje cells in pogo, but in only a few of Purkinje cells of their heterozygous littermate controls. In all groups of mice, no phospho-TH immunoreactive Purkinje cells were observed in the cerebellum, although subsets of TH immunoreactive Purkinje cells were found in adjacent sections. This study suggests that TH expression in the Purkinje cells of pogo abnormally increases without activation of this enzyme by phosphorylation. This may mean that TH in the Purkinje cells of these mutants does not catalyse the conversion of tyrosine to l -DOPA, and is not related to catecholamine synthesis. [source] Effect of environmental variables on eukaryotic microbial community structure of land-fast Arctic sea iceENVIRONMENTAL MICROBIOLOGY, Issue 3 2010Brian Eddie Summary Sea ice microbial community structure affects carbon and nutrient cycling in polar seas, but its susceptibility to changing environmental conditions is not well understood. We studied the eukaryotic microbial community in sea ice cores recovered near Point Barrow, AK in May 2006 by documenting the composition of the community in relation to vertical depth within the cores, as well as light availability (mainly as variable snow cover) and nutrient concentrations. We applied a combination of epifluorescence microscopy, denaturing gradient gel electrophoresis and clone libraries of a section of the 18S rRNA gene in order to compare the community structure of the major eukaryotic microbial phylotypes in the ice. We find that the community composition of the sea ice is more affected by the depth horizon in the ice than by light availability, although there are significant differences in the abundance of some groups between light regimes. Epifluorescence microscopy shows a shift from predominantly heterotrophic life styles in the upper ice to autotrophy prevailing in the bottom ice. This is supported by the statistical analysis of the similarity between the samples based on the denaturing gradient gel electrophoresis banding patterns, which shows a clear difference between upper and lower ice sections with respect to phylotypes and their proportional abundance. Clone libraries constructed using diatom-specific primers confirm the high diversity of diatoms in the sea ice, and support the microscopic counts. Evidence of protistan grazing upon diatoms was also found in lower sections of the core, with implications for carbon and nutrient recycling in the ice. [source] Biogeography of bacteria associated with the marine sponge Cymbastela concentricaENVIRONMENTAL MICROBIOLOGY, Issue 3 2005Michael W. Taylor Summary Recent debate regarding microbial biogeography has focused largely on free-living microbes, yet those microbes associated with host organisms are also of interest from a biogeographical perspective. Marine eukaryotes and associated bacteria should provide ideal systems in which to consider microbial biogeography, as (i) bacteria in seawater should be able to disperse among individuals of the same host species, yet (ii) potential for adaptation to particular hosts (and thus speciation) also exists. We used 16S rDNA-DGGE (denaturing gradient gel electrophoresis) to examine geographic variability in bacterial community composition in the marine sponge Cymbastela concentrica. Denaturing gradient gel electrophoresis banding patterns (and phylogenetic analysis of excised DGGE bands) indicated different communities in Cymbastela concentrica from tropical versus temperate Australia. In contrast, communities were very similar over a 500-km portion of the sponge's temperate range. Variation in bacterial community composition was also considered with respect to ocean current patterns. We speculate that the divergent communities in different parts of the sponge's range provide evidence of endemism attributed to host association, although variation in environmental factors such as light and temperature could also explain the observed results. Interestingly, bacterial communities in seawater varied much less between tropical and temperate locations than did those in C. concentrica, supporting the concept of widespread dispersal among these free-living microbes. [source] Heteroduplex mobility assay for the identification of Listeria sp. and Listeria monocytogenes strains: application to characterisation of strains from sludge and food samplesFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 3 2003N Garrec Abstract One hundred and ten Listeria sp. isolates from sewage sludge were identified according to phenotypic and genotypic methods. The Listeria sp. strains isolated from five types of sludge from three sewage treatment plants in Angers (France) and the surrounding area included L. monocytogenes (55.5%), L. innocua (29.1%), L. seeligeri (13.6%) and L. welshimeri (1.8%). The majority of L. monocytogenes strains belonged to serotypes 4b, 1/2b and 1/2a. Moreover, a heteroduplex mobility assay based on the 16S rRNA sequences was tested for its ability to identify the six species of the genus Listeria. This study, performed on 283 Listeria sp. strains from human, food and sewage sludge samples, showed that all the species were distinguishable from one another. L. innocua and L. seeligeri showed respectively three and two distinct banding patterns. Within L. monocytogenes, four groups (I,IV) were defined. The majority of food and environmental isolates were clustered in group I and it is noteworthy that group IV clustered epidemiologic isolates and strains belonging to serotypes 4b, 1/2a and 1/2b. [source] High vertical and low horizontal diversity of Prochlorococcus ecotypes in the Mediterranean Sea in summerFEMS MICROBIOLOGY ECOLOGY, Issue 2 2007Laurence Garczarek Abstract Natural populations of the marine cyanobacterium Prochlorococcus exist as two main ecotypes, inhabiting different layers of the ocean's photic zone. These so-called high light- (HL-) and low light (LL-) adapted ecotypes are both physiologically and genetically distinct. HL strains can be separated into two major clades (HLI and HLII), whereas LL strains are more diverse. Here, we used several molecular techniques to study the genetic diversity of natural Prochlorococcus populations during the Prosope cruise in the Mediterranean Sea in the summer of 1999. Using a dot blot hybridization technique, we found that HLI was the dominant HL group and was confined to the upper mixed layer. In contrast, LL ecotypes were only found below the thermocline. Secondly, a restriction fragment length polymorphism analysis of PCR-amplified pcb genes (encoding the major light-harvesting proteins of Prochlorococcus) suggested that there were at least four genetically different ecotypes, occupying distinct but overlapping light niches in the photic zone. At comparable depths, similar banding patterns were observed throughout the sampled area, suggesting a horizontal homogenization of ecotypes. Nevertheless, environmental pcb gene sequences retrieved from different depths at two stations proved all different at the nucleotide level, suggesting a large genetic microdiversity within those ecotypes. [source] Characterisation of symbionts of entomopathogenic nematodes by universally primed-PCR (UP-PCR) and UP-PCR product cross-hybridisationFEMS MICROBIOLOGY LETTERS, Issue 1 2002O. Nielsen Abstract This work introduces and demonstrates the applicability of universally primed-PCR (UP-PCR) for differentiating bacterial symbionts of entomopathogenic nematodes. Furthermore, typing by UP-PCR product cross-hybridisation was successfully introduced to cluster the bacterial strains. The work was initiated by isolating 10 isolates of Photorhabdus temperata (S172) from the nematode host Heterorhabditis sp. (DK172) and 12 isolates of Xenorhabdus bovienii (S1) from the nematode Steinernema feltiae (DK1). The isolates were compared by UP-PCR using different primers. The two bacterial species (P. temperata and X. bovienii) could be distinguished on the basis of the banding pattern whereas isolates isolated from the same nematode host had identical banding patterns. Three isolates obtained from DK172 and DK1, respectively, were then selected along with a number of reference strains (Hb, HP88, C1, K122, HSH2, HL81, T228, 61, AN6, Q58) and further characterised by UP-PCR product cross-hybridisation. The Xenorhabdus strains (Q58, AN6, 61, T228, S1) represented three species and these species were separated by the hybridisation technique. The Photorhabdus strains (Hb, HP88, C1, K122, HSH2, HL81, S172) represented two species and were also separated according to this in the cross-hybridisation. Within each species of Photorhabdus, two subgroups were formed as a result of intensity of the hybridisation signals. This grouping was in agreement with previous studies in other laboratories. [source] Digital cementum luminance analysis (DCLA): a tool for the analysis of climatic and seasonal signals in dental cementumINTERNATIONAL JOURNAL OF OSTEOARCHAEOLOGY, Issue 1 2008C. M. Wall-Scheffler Abstract Cementum banding patterns have been used by archaeozoologists and wildlife managers for a number of decades to assess the season and age at death of mammalian populations. However, the observation and measurement of the nature of cementum banding, especially that of the final band, has proved to be difficult except under conditions of excellent preservation and advanced microscopy. The research presented here details a method for extracting luminance data from the banding patterns of cementum in order to quantify the optical properties of cementum tissue. By doing so, analysis of the relationship between cementum deposition and environmental variables is achieved. We present the results of a digital cementum luminance analysis (DCLA) on a sample of first molars from two species, Ovis aries, Soay and Capra ibex. The results indicate that significant relationships occur between seasonal temperature changes and cementum histology. Furthermore, we show that luminance values can be used to assess the geographical range of genetically similar populations. Our results demonstrate that the study of luminance is a vital tool for the quantitative study of dental cementum for both archaeological and ecological studies. Copyright © 2007 John Wiley & Sons, Ltd. [source] Temporal Dynamics of River Biofilm in Constant Flows: A Case Study in a Riverside Laboratory FlumeINTERNATIONAL REVIEW OF HYDROBIOLOGY, Issue 2 2010Stéphanie Boulêtreau Abstract A 15-week experiment was performed in a riverside laboratory flume (with diverted river water) to check variations of river biofilm structure (biomass, algal and bacterial compositions) and function (community gross primary production GPP and respiration) under constant flow while water quality went through natural temporal variations. One major suspended matter pulse coinciding with one river flood was recorded after 10 weeks of experiment. Epilithic biofilm first exhibited a 10-week typical pattern of biomass accrual reaching 33 g ash-free dry matter (AFDM) m,2 and 487 mg chlorophyll- a m,2 and then, experienced a shift to dominance of loss processes (loss of 60% AFDM and 80% chlorophyll- a) coinciding with the main suspended matter pulse. Algal diversity remained low and constant during the experiment: Fragilaria capucina and Encyonema minutum always contribute over 80% of cell counts. DGGE banding patterns discriminated between two groups that corresponded to samples before and after biomass loss, indicating major changes in the bacterial community composition. GPP/R remained high during the experiment, suggesting that photoautotrophic metabolism prevailed and detachment was not autogenic (i.e., due to algal senescence or driven by heterotrophic processes within the biofilm). Observational results suggested that silt deposition into the biofilm matrix could have triggered biomass loss. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Porcine ESTs detected by differential display representing possible candidates for the trait ,eye muscle area'JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 1 2000By S. Ponsuksili In order to identify ESTs which represent possible candidates for carcass traits in pigs, the differential display approach was used. F2 animals of a resource population and pure-bred German Landrace (DL) pigs were selected for the trait ,eye muscle area' in order to build up groups of three high and three low performing individuals within each population. To increase the probability that differentially expressed DNA fragments were not found due to the genetic background but due to differences in a few genes affecting the trait of interest, siblings were included in the high and in the low performing groups. RNA was isolated from M. longissimus dorsi and four ,intra-litter constrasting pools' were prepared: high performing F2, low performing F2, high performing DL and low performing DL. Differential display banding patterns were produced using (d)T11VA (V:A,C,G) and 20 arbitrary primers. Comparing the banding patterns of the four RNA pools revealed 27 nonshared bands. Here we report on the analysis of seven of these bands, including sequencing, search for homology and mapping using a somatic cell hybrid panel. Two clones showed high homology to known genes, two were homologous to an EST and a SINE sequence. Three clones did not show any homology. Differential expression was tested by semiquantitative reverse transcription,polymerase chain reaction (RT,PCR) and could be confirmed for six clones. [source] Comprehensive analysis of 112 melanocytic skin lesions demonstrates microsatellite instability in melanomas and dysplastic nevi, but not in benign neviJOURNAL OF CUTANEOUS PATHOLOGY, Issue 7 2001Mahmoud R. Hussein Introduction: Alterations in the length of DNA repetitive sequences (microsatellite instability (MSI)) represent distinct tumorigenic pathways associated with several familial and sporadic tumors. Material and methods: To investigate the prevalence and frequency of MSI in melanocytic lesions, the polymerase chain reaction (PCR)-based microsatellite assay was used to examine formalin-fixed, paraffin-embedded tissues of 30 benign melanocytic nevi, 60 melanocytic dysplastic nevi (MDN), and 22 primary vertical growth phase cutaneous malignant melanomas (CMM). Twenty-four microsatellite markers at the 1p, 2p, 3p, 4q and 9p chromosomal regions were used. Results: MSI was found at 1p and 9p in MDN and CMM but not in benign melanocytic nevi. The overall prevalence of MSI was17/60 (28%) in MDN and 7/22 (31%) in CMM. The frequency of MSI ranged from 2/24 (9%) to 4/24 (17%) and was most commonly found at D9S162. There was a statistically significant correlation between degree of atypia and frequency of MSI (p<0.001) in MDN. There were two MSI banding patterns: band shifts and additional bands. Conclusions: The data presented revealed the presence of low-frequency MSI (MSI-L) at the 1p and 9p regions in both MDN and CMM. Whether the MSI-L pattern reflects a defect in mismatch repair genes is still to be determined. [source] Morphology of the prometamorphic larva of the spadefoot toad, Scaphiopus intermontanus (Anura: Pelobatidae), with an emphasis on the lateral line system and mouthpartsJOURNAL OF MORPHOLOGY, Issue 2 2002John A. Hall Abstract We provide a detailed description of the larval morphology of the Great Basin spadefoot toad (Scaphiopus intermontanus), a species with documented morphological variability in larval structures associated with feeding. We based our findings on laboratory-raised individuals fed a herbivorous diet. We characterized the morphology of the prometamorphic larva (limited to developmental stages 37 and 38) and then related our findings to the larval ecology of the species. Based on its morphology, such as slightly depressed body, dorsally positioned eyes, anteroventrally oriented oral disc, intermediate tail fin height and slightly attenuated tail tip, relative lack of ventral neuromasts (compared to Xenopus laevis), and pigmentation banding patterns, and habits, such as selection of breeding sites by adults and larval foraging behavior, S. intermontanus can be characterized best as belonging to a (lentic-) benthic guild of anuran larvae. Nevertheless, the larvae are capable of occupying a broader array of ecological niches. Because we characterized individuals raised on a herbivorous diet, our morphological descriptions apply only to the herbivorous S. intermontanus larva (and perhaps to those larvae that are dietary generalists and may feed carnivorously only infrequently). Our findings can serve as a baseline for future morphological and developmental comparisons with the carnivorous morphological variant of this species. J. Morphol. 252:114,130, 2002. © 2002 Wiley-Liss, Inc. [source] Genetic Diversity of Cryphonectria hypovirus 1 in China, Japan and ItalyJOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2007F.-X. Liu Abstract The aim of this study was to examine the origin of Cryphonectria hypovirus 1 (CHV1) which infects chestnut blight fungus, Cryphonectria parasitica. The genetic diversity of 39 CHV1 isolates from China, Japan and Italy was assessed by combining sequencing and restriction fragment length polymorphic (RFLP) experiments. Based on their partial sequences, 26 CHV1 isolates within 26 haplotypes were grouped into three subtypes. The 17 viruses from China were distributed between subtypes I and III, while all four of the isolates from Japan were subtype II. Of the five isolates from Italy, four were subtype I, and one (IT 192) was subtype III. Our analysis of the geographic distribution of the isolates indicated that all but one of the Chinese subtype III CHV1s are present in northern China; meanwhile all but three of the Chinese subtype I CHV1s are present in South China. Unlike in Europe where there is one predominant CHV1 subtype, our distribution analysis indicates that there has been gene flow between the populations in Asia. Cluster analysis based on the RFLP banding patterns showed that the viral isolates could be separated into four clusters. Most of the viral isolates (29 of 39, 74.4%) were grouped into one large cluster. Greater genetic diversity was observed among the CHV1s from China than among those from Japan and Italy. The Italian isolates were genetically more similar to the Japanese and South Chinese isolates than to the North Chinese isolates, indicating that CHV1 in Italy may have originated from Japan and/or South China. [source] Characterization and Identification of Asexual Strains of Pythium Associated with Root Rot of Rose in JapanJOURNAL OF PHYTOPATHOLOGY, Issue 9 2003K. Kageyama Abstract This study was conducted to survey the distribution of asexual isolates of Pythium in rose production and to characterize and identify them. Asexual isolates with proliferating globose sporangia belong to group P according to the key of van der Plaats-Niterink (1981; Monograph of the genus Pythium. Studies in Mycology, Vol. 21, Centraalbueau Voor Schimmelcultures, Baarn, The Netherlands). Group P isolates were recovered from rotted roots of both cutting and miniature roses cultured in rock wool and ebb-and-flow culture systems, respectively, throughout the main rose production area of Japan. The typical feature of the P group isolates was that they could grow fast at high temperature, at least 30 mm per 24 h at 35°C. There was no difference between the P group isolates and P. helicoides in morphology and size of sporangia and sporangial germination mode. The symptoms caused by the group P isolates were root rot, followed by leaf blight and plant death in severe cases. In restriction fragment length polymorphism analysis of the rDNA-ITS region, the banding patterns with five of six enzymes were identical between group P and P. helicoides, the only difference being seen with HhaI. In direct amplification analysis of minisatellite-region DNA with M13 primer, group P and P. helicoides shared three of five distinct bands. In contrast, P. oedochilum and P. ostracodes showed different banding patterns except for each one band. The results suggest that the group P isolates obtained from rose root rot may be asexual strains of P. helicoides. [source] Physiological and Biochemical Characteristics of Iranian Strains of Xanthomonas axonopodis pv. citri, the Causal Agent of Citrus bacterial Canker DiseaseJOURNAL OF PHYTOPATHOLOGY, Issue 2 2001M. Mohammadi Twenty-four strains of Xanthomonas axonopodis pv. citri (Xac), the causal agent of bacterial canker of citrus, isolated from Mexican lime (Citrus aurantifolia) and lemon (Citrus limon) in southern Iran, were characterized phenotypically. Strains were all pathogenic on C. aurantifolia. Sodium dodecyl sulphate-polyacrylamide gel electrophoresis analysis revealed slight differences in soluble protein profiles among the strains. Based on host range specificity and phenotypic characteristics, representative strains were differentiated into two groups of Asiatic (A) and atypical Asiatic (aA) forms. DNA fingerprinting analysis using EcoRI as the restriction endonuclease showed a negligible difference in restriction pattern between the two groups. On the basis of isozymic analysis, the two groups were distinct with respect to superoxide dismutase (SOD) and esterase (EST) banding patterns. Plasmid DNA profile analysis showed that the bacterial strains were different from each other in terms of plasmid number and molecular weight. Phage typing study revealed that most of group A strains were susceptible to Cp1 and/or Cp2 and some were resistant to both phage types including the strain in aA group. Bacteriocin production test indicated that there was a variation among Xac strains using different indicators for each bacteriocin producer. It is concluded that the Iranian strains of Xac are heterogeneous and constitute a subgroup(s) within the pathotype A. Physiologische und biochemische Merkmale iranischer Stämme von Xanthomonas axonopodis pv. citri, dem Erreger des bakteriellen Zitruskrebses Vierundzwanzig Stämme von Xanthomonas axonopodis pv. citri, dem Erreger des bakteriellen Zitruskrebses, wurden von mexikanischen Sauren Limetten (Citrus aurantifolia) und Zitronen (Citrus limon) im Südiran isoliert und phänotypisch charakterisiert. Alle Stämme waren für C. aurantifolia pathogen. Eine SDS-PAGE-Analyse zeigte, daß zwischen den Stämmen geringfügige Unterschiede bei den Profilen der löslichen Proteine bestanden. Auf Grundlage der Spezifität des Wirtsspektrums und phänotypischer Merkmale wurden repräsentative Stämme in die zwei Gruppen asiatische (A) und atypische asiatische (aA) Formen eingeteilt. Eine Analyse mit DNA-Fingerabdrücken, wobei EcoRI als Restriktionsendonuclease diente, zeigte einen vernachlässigbar kleinen Unterschied bei den Restriktionsmustern der beiden Gruppen. Die Isoenzymanalyse ergab Unterschiede zwischen beiden Gruppen bezüglich der Bandenmuster von Superoxiddismutase (SOD) und Esterase (EST). Eine Analyse der Plasmid-DNA-Profile zeigte, daß die Bakterienstämme unterschiedliche Plasmidzahlen und verschiedene Molekülmassen aufwiesen. Eine Phagentypisierung ergab, daß die meisten Stämme der Gruppe A anfällig für Cp1 und/oder Cp2 waren; einige waren resistent gegen beide Phagentypen, darunter der Stamm in der aA-Gruppe. Ein Test der Bacteriocinproduktion ergab, daß die Xac -Stämme variierten; hier wurden verschiedene Indikatoren für jeden Bakteriocinbildner verwendet. Es wird gefolgert, daß die iranischen Stämme von Xac heterogen sind und eine oder mehrere Untergruppen innerhalb des Pathotyps A bilden. [source] The Effects of Dietary Yeast Culture or Short-chain Fructo-oligosaccharides on the Intestinal Autochthonous Bacterial Communities in Juvenile Hybrid Tilapia, Oreochromis niloticus,×Oreochromis aureus,JOURNAL OF THE WORLD AQUACULTURE SOCIETY, Issue 4 2009Zhi-Gang Zhou The effects of dietary yeast culture (YC) or short-chain fructo-oligosaccharides (FOS) on intestinal autochthonous bacterial communities in juvenile hybrid tilapia, Oreochromis niloticus,×Oreochromis aureus, were studied by 16S rDNA denaturing gradient gel electrophoresis (DGGE). Ninety Tilapias in tanks (10 fish per tank) were randomly and equally divided into three groups. At the end of an 8-wk feeding period of CK (the control treatment), YC (3 g/kg), or FOS (1 g/kg), autochthonous gut bacteria were analyzed in intestinal samples of all fish in each tank of a recirculating aquaculture system. The clear differences in the banding patterns indicated the obvious effects of dietary prebiotics on intestinal communities in hybrid tilapia. Higher variation was detected within the dietary YC group. This difference might be due to the effects of certain immune-stimulating agents in YC on the immunity response of hybrid tilapia. It was concluded that dietary prebiotics, YC, and FOS obviously affected the intestinal bacterial community in hybrid tilapia with different patterns for different kinds. [source] Phylogeography of the invasive cyanobacterium Cylindrospermopsis raciborskiiMOLECULAR ECOLOGY, Issue 1 2003B. A. Neilan Abstract Cylindrospermopsis raciborskii is a planktonic freshwater cyanobacterium that has become increasingly prevalent in tropical and temperate water bodies world-wide. This species is of concern from a water-quality perspective because of its known ability to produce toxins that can affect the health of humans and other animals. This study investigates genetic vari-ation between strains of C. raciborskii isolated from freshwater rivers and reservoirs in Australia, Brazil, Germany, Hungary, Portugal and the USA. Strains were first characterized by analysis of their 16S rRNA gene nucleotide sequences and were found to have a sequence divergence of 99.1%. A phylogenetic tree, constructed using the 16S rRNA gene sequences showed that strains grouped into Australian, European and North/South American phylotypes. To investigate further the observed separation of strains into geographically distinct groups, we applied a cyanobacterium-specific short tandem repeat sequence technique, HIP1. An electrophoretic comparison of the HIP1 polymerase chain reaction products showed clear distinctions between the C. raciborskii strains. A phylogenetic tree, based on the repeat element banding patterns, also revealed three distinct groups of C. raciborskii strains. The first group consisted of strains from the USA and Brazil; the second comprised European strains from Germany, Hungary and Portugal; and the third were strains from Australia. In general, between-country variation was greater than within-country variation, indicating that this fingerprinting technique can successfully distinguish C. raciborskii strains taken from different global locations. The relationship between toxicity and the observed HIP1 polymerase chain reaction fingerprint profiles was less clear, although it is interesting to note that of the strains analysed in this study, only Australian strains are known to produce cylindrospermopsin and only Brazilian strains have been reported to produce paralytic shellfish poisoning toxins. [source] Individual female clutch identification through yolk protein electrophoresis in the communally breeding guira cuckoo (Guira guira)MOLECULAR ECOLOGY, Issue 11 2002Mariana O. Cariello Abstract Avian communal breeding systems generate alternative behavioural strategies for females, resulting in differences in reproductive success. Identifying eggs of different females in such systems is problematic, however, due to egg destruction before incubation, difficulty of capturing adults, and/or inaccuracy of egg identification based on egg morphometry. Here, we describe a technique that uses electrophoresis of yolk proteins to determine egg ownership, which we applied to communally breeding guira cuckoos (Guira guira). Validation of the method included identical yolk protein banding patterns in all eggs of the same female, but different patterns in eggs of different females in budgerigars (Melopsittacus undulatus), and identical patterns in yolk follicles of the same females in guira cuckoos. We applied the protocol to 195 guira cuckoo eggs from 34 joint nests in 2 years. All multiple guira cuckoo eggs laid on the same day in single nests had distinct banding patterns of yolk proteins, practically eliminating the possibility of more than one female being represented by the same pattern. Some identical banding patterns were repeated in different days within a nesting bout, indicating that some females laid several eggs in shared nests. Identical patterns occasionally occurred in renestings of groups, indicating that some females lay eggs in consecutive nestings. Yolk protein electrophoresis is a useful tool to identify egg maternity in other circumstances, such as polygynous mating systems with joint nests and intraspecific parasitism. Additionally, it is an alternative method for species where electrophoresis of egg white proteins does not show sufficient polymorphism. [source] Isolation, characterization, and cross-amplification of polymorphic microsatellite loci in Guaiacum coulteri (Zygophyllaceae)MOLECULAR ECOLOGY RESOURCES, Issue 3 2008ROSS A. MCCAULEY Abstract Guaiacum coulteri is a dry forest hardwood species of conservation concern endemic to the Pacific coast of Mexico. Fifteen microsatellite markers were developed which show high levels of polymorphism across two populations with the number of alleles ranging from four to 21. Most loci additionally exhibited consistent multiple banding patterns, indicating the likely polyploidy of this species. All loci were tested for cross-amplification with most found to amplify well across the genus Guaiacum, although amplification in other related genera of the Zygophyllaceae was limited. [source] Isolation and characterization of novel microsatellite markers from the Australian water skink Eulamprus kosciuskoi and cross-species amplification in other members of the species-groupMOLECULAR ECOLOGY RESOURCES, Issue 1-2 2001Ian A. W. Scott Abstract A panel of six samples from three Eulamprus species was used to screen 24 primer pairs developed from the Australian water skink Eulamprus kosciuskoi. We provide details of 10 microsatellite loci that exhibited the cleanest and strongest banding patterns. We also screened six of these microsatellite loci against 118 individuals from a population of E. heatwolei. These microsatellites exhibited large numbers of alleles per locus (4,19) and high heterozygosity (0.271,0.898) in this population. This suggests that they will be extremely useful for investigating mating systems and other facets of population biology in these lizards. [source] Isolation and characterization of novel microsatellite markers from the Australian tiger snakes (Elapidae: Notechis) and amplification in the closely related genus HoplocephalusMOLECULAR ECOLOGY RESOURCES, Issue 3 2001Ian A. W. Scott Abstract We provide details of seven microsatellite loci (out of 20 primer pairs designed) that exhibited the cleanest and strongest banding patterns for the Eastern tiger snake Notechis scutatus. These loci were used to screen 76 individuals from across the geographical range of N. scutatus and a further 14 individuals of the closely related and endangered broadheaded snake Hoplocephalus bungaroides. We observed large numbers of alleles per locus (14,52) and relatively high levels of heterozygosity (0.270,0.696) within the N. scutatus sample. These markers are also likely to be informative for work on H. bungaroides. [source] Bacterial community profiles of endodontic abscesses from Brazilian and USA subjects as compared by denaturing gradient gel electrophoresis analysisMOLECULAR ORAL MICROBIOLOGY, Issue 1 2007J. C. Machado de Oliveira This study compared the bacterial community profiles of the microbiota associated with acute apical abscesses from Brazilian and USA patients using denaturing gradient gel electrophoresis (DGGE). DNA was extracted from purulent exudate aspirates and part of the 16S rRNA gene was amplified by polymerase chain reaction and separated by DGGE. The resulting banding patterns, which were representative of the bacterial community structures in samples from the two locations, were then compared. Distinct DGGE banding patterns were observed from different samples. Ninety-nine bands with distinct positions in the gels were detected, of which 27 were found only in the USA samples and 13 were exclusive to Brazilian samples. Four of the 59 shared bands showed very discrepant findings with regard to prevalence in the two locations. Cluster analysis of DGGE banding profiles showed a great variability in the bacterial populations associated with teeth with abscesses regardless of the geographical location. Two big clusters, one for each location, were observed. Other clusters contained a mixture of samples from the two locations. The results of the present study demonstrated a great variability in the bacterial community profiles among samples. This indicates that the bacterial communities of abscesses are unique for each individual in terms of diversity. The composition of the microbiota in some samples showed a geography-related pattern. Furthermore, several bands were exclusive for each location and others were shared by the two locations and showed great differences in prevalence. [source] Investigation of bacterial communities associated with asymptomatic and symptomatic endodontic infections by denaturing gradient gel electrophoresis fingerprinting approachMOLECULAR ORAL MICROBIOLOGY, Issue 6 2004J. F. Siqueira Jr The purpose of the present study was to investigate the bacterial communities associated with asymptomatic and symptomatic endodontic infections and to compare denaturing gradient gel electrophoresis (DGGE) fingerprinting patterns of these two clinical conditions. The root canal microbiota of teeth associated with asymptomatic or symptomatic periradicular lesions was profiled by the PCR-DGGE method and then compared, taking into consideration the banding patterns. Bacteria were present in all examined cases. Comparative analysis of the two clinical conditions revealed bands that were common to both symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique for each clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles were 12.1 ± 9.4 (range 2,29) for symptomatic samples and 6.7 ± 2.7 (range 2,11) for asymptomatic ones. Clustering methods and principal component analysis of DGGE banding pattern placed the samples according to the presence or absence of symptoms. Four intense bands that were excised from the gel and sequenced showed similarities to species of the Campylobacter genus (found in 5/12 asymptomatic and in 3/11 symptomatic cases), Fusobacterium genus (4/11 symptomatic cases), Acinetobacter genus (5/12 asymptomatic cases), and Enterobacteriaceae family (11/12 asymptomatic and 2/11 symptomatic cases). The profiles of the predominant bacterial community appeared to be unique for each individual. These findings confirm that endodontic infections are polymicrobial and showed that there are significant differences in the predominant bacterial composition between asymptomatic and symptomatic cases. [source] | |||||||||||||||||||||||||||||||