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PubMed1988

Gene sequence and mapping data from Marek's disease virus and herpesvirus of turkeys: implications for herpesvirus classification.

Purified DNAs from Marek's disease virus (MDV) and the herpesvirus of turkeys (HVT) were randomly sheared and cloned into the M13 bacteriophage. Two-hundred and ten MDV and 130 HVT clones were sequenced to give representative samples of the genome sequences. The predicted amino acid sequences from these gammaherpes-viruses were compared to known sequences from other herpesviruses using computer analysis. Thirty-five MDV and 24 HVT genes were identified by comparison with varicella-zoster virus (VZV), an alphaherpesvirus. However, only 14 MDV and seven HVT genes, giving generally lower homology scores, were found by comparison with Epstein-Barr virus (EBV), a gammaherpesvirus, indicating that MDV and HVT sequences bear greater similarity to VZV than to EBV sequences. A number of sequences were mapped by hybridizing labelled M13 clones to Southern blots of restriction fragments of MDV or HVT DNA. The results were consistent with the MDV and HVT genomes being collinear with VZV.

Amino Acid Sequence↗

PubMed2006

The enduracidin biosynthetic gene cluster from Streptomyces fungicidicus.

The biosynthetic gene cluster for the 17 aa peptide antibiotic enduracidin has been cloned and sequenced from Streptomyces fungicidicus ATCC 21013. The 84 kb gene cluster contains 25 ORFs and is located within a 116 kb genetic locus that was fully sequenced. Targeted disruption of non-ribosomal peptide synthetase (NRPS) genes in the cluster abolished enduracidin production and confirmed function. The cluster includes four genes, endA-D, encoding two-, seven-, eight- and one-module NRPSs, respectively, and includes unique modules for the incorporation of citrulline and enduracididine. The NRPS organization generally follows the collinearity principle, and starts with a condensation domain (C domain) similar to those found in other lipopeptide systems for the coupling of an acyl group to the starting amino acid. The sixth module of EndB, corresponding to Thr(8), is missing an adenylation domain (A domain) and this module is presumed to be loaded in trans by the single module protein EndD. The most striking feature of the NRPS organization is the lack of epimerization domains (E domains) in light of the fact that the product has seven d-amino acid residues. Sequence analysis reveals that C domains following modules corresponding to d-amino acids belong to a unique subset of C domains able to catalyse both epimerization and condensation reactions. Other genes directing lipid modification and activation, and formation of the non-proteinogenic amino acids 4-hydroxyphenylglycine and enduracididine are readily identified, as are genes possibly involved in regulation of antibiotic biosynthesis and export. These findings provide the basis to further genetically manipulate and improve lipodepsipeptide antibiotics via combinatorial and chemical methods.

Cloning, Molecular↗

PubMed1995

Organization, inheritance and expression of acetohydroxyacid synthase genes in the cotton allotetraploid Gossypium hirsutum.

The acetohydroxyacid synthase (AHAS) gene family of the cotton AD allotetraploid Gossypium hirsutum has been cloned and characterized. We have identified six different AHAS genes from an analysis of genomic clones and Southern blots of genomic DNA. Four of the six genes are organized as tandem pairs, in which the genes are separated by only 2-3 kb. Conservation of restriction fragment length polymorphisms between G. hirsutum and A-genome and D-genome-containing diploid cottons was sufficient to assign the single genes in clones A5 and A19 to the A and D subgenomes, respectively. Each diploid genome has one tandem pair, but in these cases we could not make specific subgenomic assignments. DNA and deduced amino acid sequences were determined for the A5 and A19 genes, and an AHAS cDNA clone isolated from a leaf library. The sequence of the A19 gene matches that of the cDNA clone, while the A5 gene is 97.8% similar. The four genes comprising the tandem pairs are much less similar to the cDNA clone. The deduced amino acid sequences of the mature polypeptides encoded by the A5 and A19 genes are collinear with the housekeeping forms of AHAS from Arabidopsis thaliana, Nicotiana tabacum and Brassica napus. The constitutive expression of A5 and A19 was confirmed with RNase protection assays and northern blots. We conclude that these genes encode the main housekeeping forms of AHAS in G. hirsutum. Among the four AHAS genes comprising the two tandem pairs, at least two are functional. These genes exhibit either low-level constitutive expression (one or both of the 'downstream' genes of each pair), or highly specific expression in reproductive tissue (one or both of the 'upstream' genes of each pair). The AHAS gene family of G. hirsutum is more complex than that of other plants so far examined.

Acetolactate Synthase↗

PubMed2006

A windowless flow cell-based miniaturized fluorescence detector for capillary flow systems.

A miniaturized fluorescence detector utilizing a three-dimensional windowless flow cell has been constructed and evaluated. The inlet and outlet liquid channels are collinear and are located in the same plane as the excitation paths, while the optical fiber used to collect the emission light is perpendicular to this plane. The straightforward arrangement of the flow path minimizes band dispersion and eliminates bubble formation or accumulation inside the cell. The use of high-brightness light-emitting diodes (LEDs) as the excitation source and a miniaturized metal package photomultiplier tube (PMT) results in a compact and sensitive fluorescence detector. The detection limit obtained from the system for fluorescein isothiocyanate (FITC) in flow injection mode is 2.6 nmol/L. The analysis of riboflavin and FITC by packed capillary liquid chromatography is demonstrated.

Journal Article↗

PubMed2004

Measuring inequalities in the distribution of dental caries.

OBJECTIVES: To evaluate different measurements of prevalence and inequality in the distribution of dental caries as to their partial collinearity, and ability in expressing associations with the supply of fluoridated tap water, indices of socioeconomic status and provision of dental services. METHODS: The DMFT, the Significant Caries (SiC) Index, the proportions of children with high- (DMFT > or = 4) and rampant- (DMFT > or = 7) caries experience, caries-free children (DMFT = 0), the Gini coefficient and the Dental Health Inequality Index (DHII) were the dental outcomes appraised in a sample comprising 18 718 oral examination records for 11- and 12-year-old schoolchildren in 131 towns of the state of São Paulo, Brazil. Spatial data analysis assessed the association between aggregate figures of dental indices and several covariates. RESULTS: The DMFT, the SiC Index and the proportions of children with high- and rampant-caries experience presented strong linear associations (Pearson r near or higher than 0.95), and an analogous profile of correlation with indicators of socioeconomic status, dental services and access to fluoride tap water. The same was observed for the DHII, the Gini coefficient and the proportion of caries-free children. These observations involve the perception of variables in each set as interchangeable tools for ecological studies assessing factors influencing, respectively, prevalence levels and inequality in the distribution of dental disease. CONCLUSION: An improved characterization of the skewed distribution of caries experience demands the concurrent estimation of figures of prevalence and inequality in dental outcomes. This strategy may contribute to the design of socially appropriate programmes of oral health promotion.

Brazil↗

PubMed1994

Selected micronutrient intake and the risk of colorectal cancer.

The relationship between estimated intake of selected micronutrients and the risk of colorectal cancer was analysed using data from a case-control study conducted in northern Italy. The study was based on 828 patients with colon cancer, 498 with rectal cancer and 2,024 controls in hospital for acute, non-neoplastic, non-digestive tract diseases. Relative risks (RRs) of intake quintiles were computed after allowance for age, sex and other major potential confounding factors, including an estimate of total energy intake. No apparent trend in risk across intake quintiles was evident for retinol, vitamin D, methionine and calcium. For beta-carotene, ascorbic acid, vitamin E and folate there was a trend of a protective effect with increasing consumption: the RR for the highest versus the lowest quintile was 0.32 for beta-carotene, 0.40 for ascorbic acid, 0.60 for vitamin E and 0.52 for folate. These inverse associations were similar for colon and rectal cancer, and consistent across strata of sex and age. When simultaneous allowance was made for all these micronutrients, besides other covariates, the only persistent protective effects were for beta-carotene (RR = 0.38 for the highest quintile) and ascorbic acid (RR = 0.52). Whether this reflects a specific, or stronger, effect of these micronutrients, rather than problems of collinearity between micronutrients or other limitations of the data, remains open to discussion. Still, this study suggests that specific micronutrients may exert an independent protective effect against colorectal carcinogenesis.

Adult↗

PubMedDate not supplied

A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP, RFLP and SSR markers.

Using AFLP technology and a recombinant inbred line population derived from the sorghum cross of BTx623 x IS3620C, a high-density genetic map of the sorghum genome was constructed. The 1713 cM map encompassed 2926 loci distributed on ten linkage groups; 2454 of those loci are AFLP products generated from either the EcoRI/MseI or PstI/MseI enzyme combinations. Among the non-AFLP markers, 136 are SSRs previously mapped in sorghum, and 203 are cDNA and genomic clones from rice, barley, oat, and maize. This latter group of markers has been mapped in various grass species and, as such, can serve as reference markers in comparative mapping. Of the nearly 3000 markers mapped, 692 comprised a LOD >3.0 framework map on which the remaining markers were placed with lower resolution (LOD <3.0). By comparing the map positions of the common grass markers in all sorghum maps reported to date, it was determined that these reference markers were essentially collinear in all published maps. Some clustering of the EcoRI/MseI AFLP markers was observed, possibly in centromeric regions. In general, however, the AFLP markers filled most of the gaps left by the RFLP/SSR markers demonstrating that AFLP technology is effective in providing excellent genome coverage. A web site, http://SorghumGenome.tamu.edu, has been created to provide all the necessary information to facilitate the use of this map and the 2590 PCR-based markers. Finally, we discuss how the information contained in this map is being integrated into a sorghum physical map for map-based gene isolation, comparative genome analysis, and as a source of sequence-ready clones for genome sequencing projects.

Chromosome Mapping↗

PubMed1999

Characterization of two human beta1-adrenergic receptor transcripts: cloning and alterations in the failing heart.

Two human beta1-adrenergic receptor cDNAs, approximately 2.75 kb and approximately 3 kb in length, were isolated from a placenta phage library. Both transcripts are collinear with the previously isolated genomic sequence. Additionally, all clones begin between -274 and -236 bp relative to the translational start site, which is consistent with the previously identified transcriptional start site at -263. Furthermore, the 2.75 and 3 kb transcripts utilize conserved polyadenylation consensus sites at +2469 and +2751, respectively. Thus, this is the first report of the identification of full-length human beta1-AR cDNA clones. Both transcripts are expressed in placenta, heart, cerebral cortex, and lung with the 3 kb transcript more highly expressed than the 2.75 kb transcript in all tissues. RNase protection analysis utilizing left ventricular heart RNA isolated from patients with idiopathic dilated cardiomyopathy demonstrates 2.1-fold and 2.7-fold decreases of the 2. 75 and 3 kb transcripts, respectively, as compared with nonfailing controls. Thus, in heart failure patients the 3 kb transcript decreases to a significantly greater extent than the 2.75 kb transcript. This preferential reduction may be the result of differences in mRNA stability mediated by putative AU-rich elements specific to the 3'-untranslated region of the larger transcript.

Base Sequence↗

PubMed1991

DNA sequence and organization of genes in a 5.5 kbp EcoRI fragment mapping in the short unique segment of Marek's disease virus (strain RB1B).

The DNA sequence of a 5.5 kbp EcoRI fragment located in the short unique region (US) of the 'highly oncogenic' strain RB1B of Marek's disease virus (MDV) was determined. The sequence contained six open reading frames (ORFs), four of which were homologous to proteins mapping in the US region of herpes simplex virus type 1 (HSV-1). These include the homologues of HSV-1 protein kinase, glycoprotein D (gD), glycoprotein I (gI) and US2 which is of unknown function. The MDV ORFs had a marked bias for A or T in the third codon position and analysis of the dinucleotide frequencies showed a marginal deficit in ApG/CpT but no overall deviation of CpG from random expectations. Comparison of genes in the US region of MDV to herpesvirus proteins confirmed and extended our previous observation that MDV is more closely related to alphaherpesviruses than to gamma-herpesviruses. We also showed that MDV possessed a homologue of HSV-1 gD which is lacking in varicella-zoster virus (VZV) but that MDV probably lacked homologues of US4 and US5 of HSV-1. These results show that in contrast to the genes in the long unique region which were grossly collinear in HSV, VZV and MDV, those mapping in US show greater diversity.

Amino Acid Sequence↗

PubMed2002

Mechanical characterization of a novel cell stimulating system (CSS) to apply dynamic, uniform and isotropic biaxial strains to cells in vitro.

Mechanical loading alters cellular responses. While in vitro mechanical stimulation is a powerful tool for exploration of mechanotransduction, very little has been published documenting techniques for validation of such devices. We have developed an in vitro experimental system that imposes well-defined temporal and spatial strain profiles using a pressure-actuated, tethered diaphragm substrate (Bioflex dishes). More importantly we have accurately characterized the strain and strain rate performance of this system and herein describe that methodology. The prototype CSS deflected cell substrates over cylindrical platens, producing dynamic biaxial strains. Dynamic studies at 1 Hz were conducted at 8.0, 9.0, 10.0 and 13.0 kPa peak transmural pressures for a total of 1000 loading cycles. To study the effects of frequency, experiments were also run at 0.5 and 1.5 Hz at 8 and 13 kPa. A series of 33 dots were placed collinearly in rings on the membrane. Dot motions were monitored via a CCD video camera and acquisition was performed using an 8-bit gray-scale video board and N1H Image software. Strain fields and rates were subsequently calculated using Mathematica software. Results confirmed that the strains were biaxially uniform over the frequencies and pressures examined: e.g., at 9.0 KPa, max radial & circumferential strain = 0.009 +/- 0.001. It was also shown that, as transmural pressure was increased, both membrane strains and strain rates increased; however biaxial strain isotropy was preserved. While we cannot measure out-of-plane deflections, video-based image analysis is a very useful technique for validation of dynamic planar biaxial strains in cell stimulation systems.

Anisotropy↗

PubMed1991

Solution structure of the luzopeptin-DNA complex.

The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. One equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. We have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The molecular dynamics calculations were guided by 140 intramolecular nucleic acid distance constraints, 74 intramolecular luzopeptin distance constraints, and 96 intermolecular distance constraints between luzopeptin and the nucleic acid protons in the complex. The quinoline rings of luzopeptin bisintercalate at d(C-A).d(T-G) steps in the d(C-A-T-G) duplex and sandwich two Watson-Crick A.T base pairs between the bisintercalation site. The long axis of the quinoline rings are collinear with the long axis of the flanking Watson-Crick C1.G4 and A2.T3 base pairs such that the OCH3-6 group is directed toward the C1-A2 step and the OH-3 group is directed toward the T3-G4 step in the complex. The quinoline chromophore stacks with purines on both strands, with the quinoline A ring stacked on A2 and the quinoline B ring stacked on G4 in the complex. The C1.G4 and A2.T3 base pairs that flank the intercalation sites are parallel to each other with partial overlap of T3 and G4 in the T3-G4 step but no overlap of C1 and A2 in the C1-A2 step in the complex. The cyclic depsipeptide ring of luzopeptin is positioned in the minor groove of the d(C-A-T-G) duplex with the oligopeptide and oligonucleotide chains running antiparallel to each other. The cyclic depsipeptide backbone of luzopeptin exhibits cis peptide bonds at Pyr-Gly and Gly-Sar steps in the luzopeptin-d(C-A-T-G) complex in solution, in contrast to all trans peptide bonds for free luzopeptin in the crystalline state.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed2000

Is high peritoneal transport rate an independent risk factor for CAPD mortality?

UNLABELLED: Is high peritoneal transport rate an independent risk factor for CAPD mortality? BACKGROUND: Patients with high peritoneal transport display the lowest serum albumin (SAlb) and the highest peritoneal protein loss. An association between high peritoneal membrane permeability and diabetes mellitus (DM) has been suggested. As malnutrition, hypoalbuminemia, and DM cause high mortality, it is probable that a high peritoneal transport rate is associated with high mortality on continuous ambulatory peritoneal dialysis (CAPD). The aim of the study was to identify whether a high peritoneal transport rate is an independent risk factor for mortality on CAPD. METHODS: We included 167 patients with a peritoneal equilibration test that was performed between January 1994 and July 1997. The endpoint was the patient's status (alive, dead, or lost) in December 1997. Survival analysis was done by the Kaplan-Meier method and multivariate Cox proportional-hazard model. RESULTS: DM was significantly more frequent in the high (H) peritoneal transport type (20 out of 33) and was less frequent in the low (L) transport group (3 out of 18). SAlb (g/dL) was significantly lower as the peritoneal transport type was higher [H 2.7 +/- 0.5, high average (HA) 2.9 +/- 0.7, low average (LA) 3.2 +/- 0.6, and L 3.6 +/- 0.5]. Serum creatinine (SCr) was significantly higher in the L transport type (12.0 +/- 4.3 mg/dL) than in the other transport groups (H 8.7 +/- 3.1, HA 8.6 +/- 3.7, and LA 9.6 +/- 4.5). No other differences were found between peritoneal transport types. In the univariate analysis, high peritoneal transport rate, DM, low SCr, low SAlb, and older age significantly predicted mortality. However, in the multivariate analysis (chi2 = 40.55, P < 0.0001), only DM (b = 1.34, P = 0.0001), low SCr (b = -0.11, P = 0.02), and high peritoneal transport rate (b = 2.6, P = 0.06) were shown as mortality risk factors. CONCLUSIONS: DM was the most important risk factor for mortality on CAPD. A high peritoneal transport rate also predicted mortality, yet its role seems to be related to the presence of DM. The role of higher SCr predicting a better survival might have been associated with a better nutritional status. Hypoalbuminemia, previously shown as risk factor for mortality, did not play an important role in this study, probably because of its collinearity with DM.

Adult↗

PubMed1997

Evaluating the decay gradient for collinearity bias with lateral displacement from the axis of induction.

The misperception of alignment which is found in many geometric illusions can be quantified using relatively simple stimulus configurations. Perceived collinearity of one segment (designated as the test segment) is biased by a second segment (designated as the induction segment), with the size of effect being a function of the relative angle between the two segments. The process can be described as angular induction. The strength of bias is greatest when the induction segment is centered at the tip of the test segment. Tong and Weintraub have reported that lateral displacement from the tip, i.e., at right angles to the axis of the induction segment, produces a sharp drop in the strength of effect. This decline is described as a "decay gradient" for the angular induction. One experiment replicates and provides better quantification of this "decay gradient". Two other experiments examine the decay gradient using a pair of induction segments, one on each side of the tip of the test segment. Displacement of the segments (either in the same direction or in opposite directions) produces substantially the same gradient of effect. Therefore, previous evidence of "tandem boosting" of effect for segment pairs does not depend on collinearity among the stimulus components. Finally, a fourth experiment finds that an induction segment which is at a fixed position and orientation differentially affects the influence of a variable induction segment. At some angles the influence of the variable segment is augmented, and at others it is suppressed. These findings are discussed in a neuroreductionist context, and a simple model for angular induction is presented.

Analysis of Variance↗

PubMed2004

GRIL: genome rearrangement and inversion locator.

UNLABELLED: GRIL is a tool to automatically identify collinear regions in a set of bacterial-size genome sequences. GRIL uses three basic steps. First, regions of high sequence identity are located. Second, some of these regions are filtered based on user-specified criteria. Finally, the remaining regions of sequence identity are used to define significant collinear regions among the sequences. By locating collinear regions of sequence, GRIL provides a basis for multiple genome alignment using current alignment systems. GRIL also provides a basis for using current inversion distance tools to infer phylogeny. AVAILABILITY: GRIL is implemented in C++ and runs on any x86-based Linux or Windows platform. It is available from http://asap.ahabs.wisc.edu/gril

Chromosome Inversion↗

PubMed2003

In-depth view of structure, activity, and evolution of rice chromosome 10.

Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.

Chromosomes, Plant↗

PubMed2004

A review of two journals found that articles using multivariable logistic regression frequently did not report commonly recommended assumptions.

BACKGROUND AND OBJECTIVE: To examine if commonly recommended assumptions for multivariable logistic regression are addressed in two major epidemiological journals. METHODS: Ninety-nine articles from the Journal of Clinical Epidemiology and the American Journal of Epidemiology were surveyed for 10 criteria: six dealing with computation and four with reporting multivariable logistic regression results. RESULTS: Three of the 10 criteria were addressed in 50% or more of the articles. Statistical significance testing or confidence intervals were reported in all articles. Methods for selecting independent variables were described in 82%, and specific procedures used to generate the models were discussed in 65%. Fewer than 50% of the articles indicated if interactions were tested or met the recommended events per independent variable ratio of 10:1. Fewer than 20% of the articles described conformity to a linear gradient, examined collinearity, reported information on validation procedures, goodness-of-fit, discrimination statistics, or provided complete information on variable coding. There was no significant difference (P>.05) in the proportion of articles meeting the criteria across the two journals. CONCLUSION: Articles reviewed frequently did not report commonly recommended assumptions for using multivariable logistic regression.

Epidemiologic Methods↗

PubMed2000

Occlusion, symmetry, and object-based attention: reply to Saiki (2000).

J. Saiki (2000) argued that, because the stimuli used by M. Behrmann, R. S. Zemel, and M. C. Mozer (1998) were confounded by symmetry, conclusions about whether amodally completed objects can benefit from object-based attention are unwarranted. Here, the authors examine J. Saiki's claim further and expand on their view of the mechanisms underlying object-based attention, suggesting that perceptual organization is the process whereby features from a single object are selectively attended. In light of this, they claim that heuristics such as symmetry and collinearity play an important role in the facilitation of features from a single object. In support of this claim, they present data from a further experiment using displays that exploit common fate, another grouping heuristic, and show that, under these conditions, the hallmark of object-based attention, a single-object advantage, is obtained for the occluded (amodally completed) shapes.

Adult↗

PubMed2003

Femtosecond phase-coherent two-dimensional spectroscopy.

Femtosecond phase-coherent two-dimensional (2D) spectroscopy has been experimentally demonstrated as the direct optical analog of 2D nuclear magnetic resonance. An acousto-optic pulse shaper created a collinear three-pulse sequence with well-controlled and variable interpulse delays and phases,which interacted with a model atomic system of rubidium vapor. The desired nonlinear polarization was selected by phase cycling (coadding experimental results obtained with different interpulse phases). This method may enhance our ability to probe the femtosecond structural dynamics of macromolecules.

Chemical Phenomena↗