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Results for “Copy Number Variations”

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PubMed2005

Preservation and high sequence conservation of satellite DNAs suggest functional constraints.

Due to a high evolutionary turnover many satellite DNAs are restricted to a group of closely related species. Here we demonstrate that the satellite DNA family PSUB, abundant in the beetle Palorus subdepressus, is distributed in a low number of copies among diverse taxa of Coleoptera (Insecta), some of them separated for an evolutionary period of up to 60 Myr. Comparison of PSUB cloned from the species Tribolium brevicornis with the PSUB family previously characterized in Palorus subdepressus revealed high sequence conservation and absence of fixed species-specific mutations. The most polymorphic sites are those with ancestral mutations shared among clones of both species. Since the ancestral mutations contribute significantly to overall diversity, it could be proposed that a similar mutational profile already existed in an ancestral species. The pattern of variability along the satellite monomer is characterized by the presence of conserved and variable regions. The nonrandom pattern of variability as well as the absence of sequence divergence is also discerned for PRAT satellite DNA, cloned previously from two Palorus species and a distantly related Pimelia elevata. Since PRAT and PSUB are present in parallel in diverse taxa of Coleoptera, we propose that their long evolutionary preservation suggests a possible functional significance. This indication is additionally supported not only by the high evolutionary conservation of the sequences, but also by the presence of significantly conserved and variable regions along the monomers.

Animals↗

PubMed1992

A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere.

Fission yeast centromeres vary in size but are organized in a similar fashion. Each consists of two distinct domains, namely, the approximately 15-kilobase (kb) central region (cnt+imr), containing chromosome-specific low copy number sequences, and 20- to 100-kb outer surrounding sequences (otr) with highly repetitive motifs common to all centromeres. The central region consists of an inner asymmetric sequence flanked by inverted repeats that exhibit strict identity with each other. Nucleotide changes in the left repeat are always accompanied with the same changes in the right. The chromatin structure of the central region is unusual. A nucleosomal nuclease digestion pattern formed on unstable plasmids but not on stable chromosome. DNase I hypersensitive sites correlate with the location of tRNA genes in the central region. Autonomously replicating sequences are also present in the central region. The behavior of truncated minichromosomes suggested that the central region is essential, but not sufficient, to confer transmission stability. A portion of the outer repetitive region is also required. A larger outer region is necessary to ensure correct meiotic behavior. Fluorescence in situ hybridization identified individual cens. In the interphase, they cluster near the nuclear periphery. The central sequence (cnt+imr) may play a role in positioning individual chromosomes within the nucleus, whereas the outer regions (otr) may interact with each other to form the higher-order complex structure.

Base Sequence↗

PubMed1990

Somatic diversification of chicken immunoglobulin light chains by point mutations.

The light-chain locus of chicken has 1 functional V lambda 1 gene, 1 J gene, and 25 pseudo-V lambda-genes (where V = variable and J = joining). A major problem is which somatic mechanisms expand this extremely limited germ-line information to generate many different antibodies. Weill's group [Reynaud, C. A., Anquez, V., Grimal, H. & Weill, J. C. (1987) Cell 48, 379-388] has shown that the pseudo-V lambda-genes diversify the rearranged V lambda 1 by gene conversion. Here we demonstrate that chicken light chains are further diversified by somatic point mutations and by V lambda 1-J flexible joining. Somatic point mutations were identified in the J and 3' noncoding DNA of rearranged light-chain genes of chicken. These regions were analyzed because point mutations in V lambda 1 are obscured by gene conversion; the J and 3' noncoding DNA are presented in one copy per haploid genome and are not subject to gene conversion. In rodents point mutations occur as frequently in the V-J coding regions as in the adjacent flanking DNA. Therefore, we conclude that somatic point mutations diversify the V lambda 1 of chicken. The frequency (0-1%) and distribution of the mutations (decreasing in number with increased distance from the V lambda 1 segment) in chicken were as observed in rodents. Sequence variability at the V lambda 1-J junctions could be attributed to imprecise joining of the V lambda 1 and J genes. The modification by gene conversion of rearranged V lambda 1 genes in the bursa was similar in chicken aged 3 months (9.5%) or 3 weeks (9.1%)--i.e., gene conversion that generates the preimmune repertoire in the bursa seems to level off around 3 weeks of age. This preimmune repertoire can be further diversified by somatic point mutations that presumably lead to the formation of antibodies with increased affinity. A segment with structural features of a matrix association region [(A + T)-rich and four topoisomerase II binding sites] was identified in the middle of the J-C lambda intron (where C = constant).

Animals↗

PubMed1994

Analysis of the VPE sequences in the Caenorhabditis elegans vit-2 promoter with extrachromosomal tandem array-containing transgenic strains.

The Caenorhabditis elegans vit genes, encoding vitellogenins, are abundantly expressed in the adult hermaphrodite intestine. Two repeated elements, vit promoter element 1 (VPE1 [TGTCAAT]) and VPE2 (CTGATAA), have been identified in the 5' flanking DNA of each of the vit genes of C. elegans and Caenorhabditis briggsae. These elements have previously been shown to be needed for correctly regulated expression of a vit-2/vit-6 fusion gene in low-copy-number, integrated transgenes. Here we extend the analysis of the function of VPE1 and VPE2 by using transgenic lines carrying large, extrachromosomal arrays of the test genes. The results validate the use of such arrays for transgenic analysis of gene regulation in C. elegans, by confirming previous findings showing that the VPE1 at -45 and both VPE2s are sites of activation. Additional experiments now indicate that when the -45 VPE1 is inverted or replaced by a VPE2, nearly total loss of promoter function results, suggesting that the highly conserved -45 VPE1 plays a unique role in vit-2 promoter function. In contrast, single mutations eliminating the three upstream VPE1s are without effect. However, in combination in double and triple mutants, these upstream VPE1 mutations cause drastic reductions in expression levels. The -150 VPE2 can be replaced by a XhoI site (CTCGAG), and the -90 VPE2 can be eliminated, as long as the overlapping VPE1 is left intact, but when these two replacements are combined, activity is lost. Thus, the promoter must have at least one VPE2 and it must have at least two VPE1s, one at -45 and one additional upstream element.

Animals↗

PubMed2006

Full-field digital mammography on LCD versus CRT monitors.

OBJECTIVE: Our purpose was to determine if the display of full-field digital mammograms on a 5-megapixel liquid crystal display (LCD) monitor is at least equivalent to the display of the same on a 5-megapixel cathode ray tube (CRT) monitor. MATERIALS AND METHODS: Five radiologists evaluated normal anatomy and features of 61 abnormalities in 48 full-field digital mammograms. A 9-point Likert scale was used to compare images on two identical soft-copy review workstations, one equipped with two 5-megapixel CRTs and the other with two 5-megapixel LCDs. Outcomes were evaluated using a random-effects analysis of variance model. Means and SEs were reported. Ninety-five percent confidence intervals and p values were calculated. RESULTS: The two systems were equivalent for most features. The LCDs were rated better for the sharpness of mass margins (p = 0.011) and mass conspicuity (p = 0.050). For calcium features, the LCDs were rated better than the CRTs for lesion conspicuity (p = 0.010) and number of calcifications (p = 0.043). For architectural distortions, there was no statistically significant difference between the monitors in any of the features evaluated. For display characteristics, the LCDs were better for luminance (p = 0.021). The CRTs were significantly better for image noise (p = 0.001). In the overall ratings, there was no statistically significant difference between the two displays. CONCLUSION: The 5-megapixel monochrome active-matrix LCD is equivalent to and in some respects better than the 5-megapixel CRT display for full-field digital mammograms over a range of normal and abnormal findings.

Breast Neoplasms↗

PubMed2003

Assessing the 'cyclodiode G-probe' using a grey scale test: reproducibility and differences between probes.

AIMS: 1. To determine the number of clinicians performing cyclodiode therapy who reuse the 'G-probe' used for the delivery of cyclodiode therapy. 2. To show a simple method to assess the output of the 'G-probe' that can be used in the clinical setting. METHODS: A total of 71 questionnaires were sent to ophthalmologists who have an Oculight SLx Iris Medical Diode Laser. Ophthalmologists were asked as to whether they performed cycloablative therapy using the 'G-probe' and whether they reused the G-probe. They were also asked as to the frequency of any reuse of probes. To determine the output of the 'G-probe', paper copies of a custom-made grey scale chart containing graded blocks of increasing shades of grey densities were produced. A special probe holder was made so that the G-probe tip could be held at a fixed distance from the grey scale chart. Laser burns were made on the grey scale using this arrangement and measurements of the burn size were made. After using 'standard settings' of 2000 ms and 2000 mW, 'threshold' burns were defined. Five new probes (with two different operators) were tested to assess the interprobe, interoperator, and intersheet variability of test. Probes were then tested for the burn size produced between 1000 and 3000 mW, and 1000 and 3000 ms. RESULTS: Results from the questionnaire showed that of the 44 respondents (62.0% response), 93.2% performed cyclodiode therapy with 58.5% reusing the G-probe. Among them, 56.1% reused probes on more than one occasion. Results from testing a new G-probe on the grey scale chart showed that with 'standard settings', highly reproducible burns at grey density 8 could be produced. No significant interprobe, interoperator, and intersheet variations were noted. Above 3 J of laser energy, the test could detect a 20% increase in energy settings and it was found that at levels of 4 J or above, alterations to the power setting had a greater influence on burn production than alterations to the time setting. CONCLUSIONS: This study demonstrates 1. that many clinicians in the UK reuse G-probes, 2. a simple, quick, and highly reproducible method to assess the laser output from the G-probe used for cyclodiode therapy. The method can help the ophthalmic surgeon to test the G-probe prior to commencement of therapy and with a standard treatment protocol, may produce a more predictable intraocular pressure reduction.

Ciliary Body↗

PubMed1996

A single gene copy merozoite surface antigen and immune evasion?

During the course of chronic malaria infection antigenic variants of a parasite antigen are expressed and exposed on the surface of infected erythrocyte membranes. There also exists a number of apparently invariant single gene copy blood-stage antigens, exposed or non-exposed, which have been shown to afford immunity under experimental conditions. To determine why the host, presented with invariant 'protective' antigens, is unable to control infections effectively, immunity to a representative single gene copy antigen, the merozoite surface protein 1 (MSP1) was investigated in Plasmodium chabaudi chabaudi AS, a murine model of chronic malaria. Immunization with monoclonal antibody affinity purified native MSP1 resulted in enhanced control of parasitaemia on challenge, irrespective of the parasite inoculum size; challenge with a single parasite, however, suggested that expansion of resistant parasite subpopulations was not occurring. Challenge of mice immunized with recombinant fusion proteins encoding N- or C-terminal regions of the P.c. chabaudi AS MSP1 produced inconsistent effects, often parasitaemias were indistinguishable from controls despite significant anti-MSP1 antibody responses. The not unlikely contamination of MSP1 native preparations with erythrocyte (E) components was considered. Immunization with a mixture of the MSP1 C-terminus recombinant polypeptide and a Triton X-100 solubilized lysate of normal E resulted in enhanced control of parasitaemia, however, no effect was seen after administration of either component on its own. Co-immunization of E with the N-terminus polypeptide reversed the inhibition seen, on this occasion with this construct alone.

Animals↗

PubMed1992

The insertion sequence IS200 fingerprints chromosomal genotypes and epidemiological relationships in Salmonella heidelberg.

In Salmonella heidelberg the copy number of the Salmonella-specific insertion element IS200 was found to vary from four to six. All strains tested contained at least one common insertion site which was serovar specific, and most strains contained three common sites. Concurrent analysis of plasmids indicated that all insertion sequence copies were chromosomally located, and also supported the equivalence of an IS200 fingerprint and clonality. Seven intra-serovar clonal lines were thereby identified. One of these was associated with human infections, including septicaemias. Another was associated with chicken as a host: all these strains also carried a unique plasmid of 23 MDa, which was typed as a member of the IncX group. The chromosomal fingerprint of a third clone showed it to be a descendant of the chicken line marked by a single IS200 transposition. One or two representatives of four other clonal lines were identified. These lines of S. heidelberg could be related by divergent evolution, and the most recent relatives conformed to a continuous branching process model of IS200 transposition. This insertion sequence provided a highly discriminatory molecular marker of the S. heidelberg chromosome, and two of the seven clonal lines so identified were associated with distinct clinical/epidemiological contexts.

Animals↗

PubMed2006

Outliers in RhD membrane integration are explained by variant RH haplotypes.

BACKGROUND: Variations in a multipass transmembrane protein may affect its membrane integration. To study this effect, the systematic molecular characterization of variant D antigen density is a suitable model. Unlike most other membrane proteins, the expression of the D antigen is often determined by a single allele, because it occurs frequently in hemizygous form. STUDY DESIGN AND METHODS: The D antigen density distribution of 530 CcDee, 475 ccDEe, and 514 ccDee random samples was established by flow cytometry. The molecular bases of samples with D antigen densities outside a bell-shaped peak was investigated. RESULTS: The antigen densities of 499 CcDee, 437 ccDEe, and 480 ccDee samples formed bell-shaped peaks. Three, 10, and 12 samples, respectively, had decreased antigen densities and carried variant RHD alleles. Weak D type 19, RHD(I204T); weak D type 20, RHD(F417S); and the partial D DYU (also known as DQC), RHD(R234W) were new RHD alleles. Twenty-eight CcDee, 28 ccDEe, and 22 ccDee samples had increased antigen densities; 53 of them lacked a hybrid Rhesus box and were thus predicted to be RHD homozygous. Eight ccDee samples were predicted to be heterozygous despite a large relative dose of RHD to RHCE alleles in quantitative polymerase chain reaction. One of these samples was further investigated and carried an RHD-CE hybrid transcript characteristic for a -D- haplotype. CONCLUSIONS: Unusual little and large RhD protein integration into the membrane could be traced to a host of distinct protein variants. Weak expression of D antigen was invariably associated with variant RHD alleles. Larger than normal D antigen density may often be caused by the presence of two D encoding alleles, which may be located in cis, and confounding zygosity testing that is solely based on gene copy number.

Alleles↗

PubMed2001

Amyloid angiopathy and variability in amyloid beta deposition is determined by mutation position in presenilin-1-linked Alzheimer's disease.

The presenilins (PSs) are components of large molecular complexes that contain beta-catenin and function as gamma-secretase. We report here a striking correlation between amyloid angiopathy and the location of mutation in PS-1 linked Alzheimer's disease. The amount of amyloid beta protein, Abeta(42(43)), but not Abeta(40,) deposited in the frontal cortex of the brain is increased in 54 cases of early-onset familial Alzheimer's disease, encompassing 25 mutations in the presenilin-1 (PS-1) gene, compared to sporadic Alzheimer's disease. The amount of Abeta(40) in PS-1 Alzheimer's disease varied according to the copy number of epsilon4 alleles of the Apolipoprotein E gene. Although the amounts of Abeta(40) and Abeta(42(43)) deposited did not correlate with the genetic location of the mutation in a strict linear sense, the histological profile did so vary. Cases with mutations between codon 1 and 200 showed, in frontal cortex, many diffuse plaques, few cored plaques, and mild or moderate amyloid angiopathy. Cases with mutations occurring after codon 200 also showed many diffuse plaques, but the number and size of cored plaques were increased (even when epsilon4 allele was not present) and these were often clustered around blood vessels severely affected by amyloid angiopathy. Similarly, diverging histological profiles, mainly according to the degree of amyloid angiopathy, were seen in the cerebellum. Mutations in the PS-1 gene may therefore alter the topology of the PS-1 protein so as to favor Abeta formation and deposition, generally, but also to facilitate amyloid angiopathy particularly in cases in which the mutation lies beyond codon 200. Finally we report that the amount of Abeta(42(43)) deposited in the brain correlated with the amount of this produced in culture by cells bearing the equivalent mutations.

Adult↗

PubMed1999

Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene.

The single-copy RAG-1 gene is found throughout higher vertebrates and consists of a single 3.1-kb exon without intervening introns. A 2.9-kb region of the RAG-1 locus was sequenced for 14 basal taxa of birds plus the crocodylian outgroups Alligator and Gavialis. Phylogenetic analysis of the sequences supported the hypothesis that the deepest evolutionary split in extant birds separates paleognaths from neognaths. A deep division among neognaths separates the chicken- and duck-like birds ("galloanserines") from a clade consisting of all other birds ("plethornithines"). The relationships of these three basal clades in Aves were supported by high bootstrap (98 to 100%) and large decay index values (above 14). Additionally, the plethornithine clade is characterized by a 15-bp (five-codon) synapomorphic deletion relative to all other birds. RAG-1 evolves slowly, with a number of properties favoring its phylogenetic utility, including rarity of indels, minimal saturation of transition changes at 3rd positions of codons, nearly constant base composition across taxa, and no asymmetry in directional patterns of reconstructed change. However, RAG-1 does not evolve in a clocklike manner, suggesting that this gene cannot easily be used for estimating ages of ancient lineages.

Alleles↗

PubMed2005

Structural basis for segmental gene conversion in generation of Anaplasma marginale outer membrane protein variants.

Bacterial pathogens in the genus Anaplasma generate surface coat variants by gene conversion of chromosomal pseudogenes into single-expression sites. These pseudogenes encode unique surface-exposed hypervariable regions flanked by conserved domains, which are identical to the expression site flanking domains. In addition, Anaplasma marginale generates variants by recombination of oligonucleotide segments derived from the pseudogenes into the existing expression site copy, resulting in a combinatorial increase in variant diversity. Using the A. marginale genome sequence to track the origin of sequences recombined into the msp2 expression site, we demonstrated that the complexity of the expressed msp2 increases during infection, reflecting a shift from recombination of the complete hypervariable region of a given pseudogene to complex mosaics with segments derived from hypervariable regions of different pseudogenes. Examination of the complete set of 1183 variants with segmental changes revealed that 99% could be explained by one of the recombination sites occurring in the conserved flanking domains and the other within the hypervariable region. Consequently, we propose an 'anchoring' model for segmental gene conversion whereby the conserved flanking sequences tightly align and anchor the expression site sequence to the pseudogene. Associated with the recombination sites were deletions, insertions and substitutions; however, these are a relatively minor contribution to variant generation as these occurred in less than 2% of the variants. Importantly, the anchoring model, which can account for more variants than a strict segmental sequence identity mechanism, is consistent with the number of msp2 variants predicted and empirically identified during persistent infection.

Amino Acid Sequence↗

PubMed2006

Detection of divergent genes in microbial aCGH experiments.

BACKGROUND: Array-based comparative genome hybridization (aCGH) is a tool for rapid comparison of genomes from different bacterial strains. The purpose of such analysis is to detect highly divergent or absent genes in a sample strain compared to an index strain. Development of methods for analyzing aCGH data has primarily focused on copy number abberations in cancer research. In microbial aCGH analyses, genes are typically ranked by log-ratios, and classification into divergent or present is done by choosing a cutoff log-ratio, either manually or by statistics calculated from the log-ratio distribution. As experimental settings vary considerably, it is not possible to develop a classical discriminant or statistical learning approach. METHODS: We introduce a more efficient method for analyzing microbial aCGH data using a finite mixture model and a data rotation scheme. Using the average posterior probabilities from the model fitted to log-ratios before and after rotation, we get a score for each gene, and demonstrate its advantages for ranking and detecting divergent genes with enlarged specificity and sensitivity. RESULTS: The procedure is tested and compared to other approaches on simulated data sets, as well as on four experimental validation data sets for aCGH analysis on fully sequenced strains of Staphylococcus aureus and Streptococcus pneumoniae. CONCLUSION: When tested on simulated data as well as on four different experimental validation data sets from experiments with only fully sequenced strains, our procedure out-competes the standard procedures of using a simple log-ratio cutoff for classification into present and divergent genes.

Computational Biology↗

PubMed2005

The effects of nuclear DNA content (C-value) on the quality and utility of AFLP fingerprints.

BACKGROUND AND AIMS: Nuclear DNA content (C-value) varies approximately 1000-fold across the angiosperms, and this variation has been reported to have an effect on the quality of AFLP fingerprints. Various methods have been proposed for circumventing the problems associated with small and large genomes. Here we investigate the range of nuclear DNA contents across which the standard AFLP protocol can be used. METHODS: AFLP fingerprinting was conducted on an automated platform using the standard protocol (with 3 + 3 selective bases) in which DNA fragments are visualized as bands. Species with nuclear DNA contents ranging from 1C = 0.2 to 32.35 pg were included, and the total number of bands and the number of polymorphic bands were counted. For the species with the smallest C-value (Bixa orellana) and for one of the species with a large C-value (Damasonium alisma), alternative protocols using 2 + 3 and 3 + 4 selective bases, respectively, were also used. KEY RESULTS: Acceptable AFLP traces were obtained using the standard protocol with 1C-values of 0.30-8.43 pg. Below this range, the quality was improved by using 2 + 3 selective bases. Above this range, the traces were generally characterized by a few strongly amplifying bands and noisy baselines. Damasonium alisma, however, gave more even traces, probably due to it being a tetraploid. CONCLUSIONS: We propose that for known polyploids, genome size is a more useful indicator than the 1C-value in deciding which AFLP protocol to use. Thus, knowledge of ploidy (allowing estimation of genome size) and C-value are both important. For small genomes, the number of interpretable bands can be increased by decreasing the number of selective bases. For larger genomes, increasing the number of bases does not necessarily decrease the number of bands as predicted. The presence of a small number of strongly amplifying bands is likely to be linked to the presence of repetitive DNA sequences in high copy number in taxa with large genomes.

Cell Nucleus↗

PubMed2002

Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria.

Denaturing gradient gel electrophoresis (DGGE) of PCR amplicons of the ammonia monooxygenase gene (amoA) was developed and employed to investigate the diversity of ammonia-oxidizing bacteria (AOB) in four different habitats. The results were compared to DGGE of PCR-amplified partial 16S rDNA sequences made with primers specific for ammonia-oxidizing bacteria. Potential problems, such as primer degeneracy and multiple gene copies of the amoA gene, were investigated to evaluate and minimize their possible impact on the outcome of a DGGE analysis. amoA and 16S rDNA amplicons were cloned, and a number of clones screened by DGGE to determine the abundance of different motility types in the clone library. The abundance of clones was compared to the relative intensity of bands emerging in the band pattern produced by direct amplification of the genes from the environmental sample. Selected clones were sequenced to evaluate the specificity of the respective primers. The 16S rDNA primer pair, reported to be specific for ammonia-oxidizing bacteria (AOB), generated several sequences that were not related to the known Nitrosospira-Nitrosomonas group and, thus, not likely to be ammonia oxidizers. However, no false positives were found among the sequences retrieved with the modified amoA primers. Some phylogenetic information could be deduced from the position of amoA bands in DGGE gels. The Nitrosomonas-like sequences were found within a denaturant range from 30% to 46%, whereas the Nitrosospira-like sequences migrated to 50% to 60% denaturant. The majority of retrieved sequences from all four habitats with high ammonia loads were Nitrosomonas-like and only few Nitrosospira-like sequences were detected.

Ammonia↗

PubMed1999

Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts.

dUTPase is a ubiquitous and essential enzyme responsible for regulating cellular levels of dUTP. The dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. Crystallized single-copy dUTPases have been shown to assemble as homotrimers. dUTPase is encoded as an auxiliary gene in a number of virus genomes. The origin of viral dut genes has remained unresolved since their initial discovery. A comprehensive analysis of dUTPase amino acid sequence relationships was performed to explore the evolutionary dynamics of dut in viruses and their hosts. Our data set, comprised of 24 host and 51 viral sequences, includes representative sequences from available eukaryotes, archaea, eubacteria cells, and viruses, including herpesviruses. These amino acid sequences were aligned by using a hidden Markov model approach developed to align divergent data. Known secondary structures from single-copy crystals were mapped onto the aligned duplicate and triplicate sequences. We show how duplicated dUTPases might fold into a monomer, and we hypothesize that triplicated dUTPases also assemble as monomers. Phylogenetic analysis revealed at least five viral dUTPase sequence lineages in well-supported monophyletic clusters with eukaryotic, eubacterial, and archaeal hosts. We have identified all five as strong examples of horizontal transfer as well as additional potential transfer of dut genes among eubacteria, between eubacteria and viruses, and between retroviruses. The evidence for horizontal transfers is particularly interesting since eukaryotic dut genes have introns, while DNA virus dut genes do not. This implies that an intermediary retroid agent facilitated the horizontal transfer process between host mRNA and DNA viruses.

Amino Acid Sequence↗

PubMed1992

Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker.

The first tandemly repeated sequence examined in a passerine bird, a 431-bp PstI fragment named pMAT1, has been cloned from the genome of the brown-headed cowbird (Molothrus ater). The sequence represents about 5-10% of the genome (about 4 x 10(5) copies) and yields prominent ethidium bromide stained bands when genomic DNA cut with a variety of restriction enzymes is electrophoresed in agarose gels. A particularly striking ladder of fragments is apparent when the DNA is cut with HinfI, indicative of a tandem arrangement of the monomer. The cloned PstI monomer has been sequenced, revealing no internal repeated structure. There are sequences that hybridize with pMAT1 found in related nine-primaried oscines but not in more distantly related oscines, suboscines, or nonpasserine species. Little sequence similarity to tandemly repeated PstI cut sequences from the merlin (Falco columbarius), saurus crane (Grus antigone), or Puerto Rican parrot (Amazona vittata) or to HinfI digested sequence from the Toulouse goose (Anser anser) was detected. The isolated sequence was used as a probe to examine DNA samples of eight members of the tribe Icterini. This examination revealed phylogenetically informative characters. The repeat contains cutting sites from a number of restriction enzymes, which, if sufficiently polymorphic, would provide new phylogenetic characters. Sequences like these, conserved within a species, but variable between closely related species, may be very useful for phylogenetic studies of closely related taxa.

Animals↗

PubMed2001

Digital chest radiography with a solid-state flat-panel x-ray detector: contrast-detail evaluation with processed images printed on film hard copy.

PURPOSE: To evaluate and compare human observer performance in a contrast-detail test by using postprocessed hard-copy images from a digital chest radiography system and conventional screen-film radiographs. MATERIALS AND METHODS: The digital radiography system is based on a large-area flat-panel x-ray detector with a structured cesium iodide scintillator layer and an amorphous silicon thin-film transistor array for image readout. Images of a contrast-detail phantom were acquired at two exposure levels by using two standard thoracic screen-film systems and the digital system at matched dose. By using images of the phantom processed with standard chest image postprocessing techniques, a four-alternative forced-choice observer perception study was performed, and the number of detectable test signals (disk-shaped objects 0.3-4.0 mm in diameter) was determined for each image type. RESULTS: On average, observers detected more test signals on digital images than on screen-film radiographs at all diameters up to 2.0 mm and an equivalent number at larger diameters. Test signals with lower inherent subject contrast were detected more readily on digital images than on screen-film images, even when x-ray exposure levels for the digital system were reduced by 20%. CONCLUSION: Observer performance in a contrast-detail detection task can be improved by using images acquired with the flat-panel digital chest radiography system as compared with those acquired with state-of-the-art screen-film combinations.

Humans↗