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PubMed2002

Assessing the level of collinearity between Arabidopsis thaliana and Brassica napus for A. thaliana chromosome 5.

This study describes a comprehensive comparison of chromosome 5 of the model crucifer Arabidopsis with the genome of its amphidiploid crop relative Brassica napus and introduces the use of in silico sequence homology to identify conserved loci between the two species. A region of chromosome 5, spanning 8 Mb, was found in six highly conserved copies in the B. napus genome. A single inversion appeared to be the predominant rearrangement that had separated the two lineages leading to the formation of Arabidopsis chromosome 5 and its homologues in B. napus. The observed results could be explained by the fusion of three ancestral genomes with strong similarities to modern-day Arabidopsis to generate the constituent diploid genomes of B. napus. This supports the hypothesis that the diploid Brassica genomes evolved from a common hexaploid ancestor. Alignment of the genetic linkage map of B. napus with the genomic sequence of Arabidopsis indicated that for specific regions a genetic distance of 1 cM in B. napus was equivalent to 285 Kb of Arabidopsis DNA sequence. This analysis strongly supports the application of Arabidopsis as a tool in marker development, map-based gene cloning, and candidate gene identification for the larger genomes of Brassica crop species.

Arabidopsis↗

PubMed1997

Perceptual organization in schizophrenia: utilization of the Gestalt principles.

In 2 experiments, the authors investigated perceptual organization in schizophrenia to determine whether patients with schizophrenia used the Gestalt principles. In the visual embedded figures task (Experiment 1), the authors examined the principles of proximity and collinearity, whereas in the similarity task (Experiment 2), the authors examined similarity. Forty-three people participated in the study: patients diagnosed with schizophrenia (14) or with bipolar disorder (15), and "normal" participants (14). All 3 groups of participants showed performance superiority in the condition that was facilitated by the use of the Gestalt principles in both tasks. This study supports the hypothesis that visual perceptual organization, in terms of utilizing the Gestalt principles, is relatively intact in people with schizophrenia.

Adult↗

PubMed2002

OWEN: aligning long collinear regions of genomes.

OWEN is an interactive tool for aligning two long DNA sequences that represents similarity between them by a chain of collinear local similarities. OWEN employs several methods for constructing and editing local similarities and for resolving conflicts between them. Alignments of sequences of lengths over 10(6) can often be produced in minutes. OWEN requires memory below 20 L, where L is the sum of lengths of the compared sequences.

Algorithms↗

PubMed2006

High-sensitivity vibrational imaging with frequency modulation coherent anti-Stokes Raman scattering (FM CARS) microscopy.

We demonstrate a new approach to coherent anti-Stokes Raman scattering (CARS) microscopy that significantly increases the detection sensitivity. CARS signals are generated by collinearly overlapped, tightly focused, and raster scanned pump and Stokes laser beams, whose difference frequency is rapidly modulated. The resulting amplitude modulation of the CARS signal is detected through a lock-in amplifier. This scheme efficiently suppresses the nonresonant background and allows for the detection of far fewer vibrational oscillators than possible through existing CARS microscopy methods.

Image Enhancement↗

PubMed2002

Prevalence and correlates of elder abuse and neglect in a geriatric psychiatry service.

OBJECTIVE: To determine the prevalence and correlates of 4 types of elder abuse and neglect in a geriatric psychiatry service. METHOD: We conducted a cross-sectional retrospective chart review of new in- and outpatients seen by the Montreal General Hospital Division of Geriatric Psychiatry in one calendar year. RESULTS: Abuse or neglect was suspected or confirmed in 20 (16%) of 126 patients, comprising financial abuse in 16 (13%), neglect in 7 (6%), emotional abuse in 5 (4%), physical abuse in 3 (2%), and multiple abuse in 7 (6%). On bivariate analysis, patients living with nonspouse family, friends, or other persons were significantly more likely to have suffered abuse than were those living with their spouse or in a supervised setting (OR 10.5; 95%CI, 2.3 to 47.8); widowed, divorced, or separated patients were significantly more likely to have suffered abuse than were married patients (OR 4.7; 95%CI, 1.02 to 22.0). Nonsignificant trends included female sex (OR 4.1; 95%CI, 0.89 to 18.6); alcohol abuse (OR 2.1; 95%CI, 0.71 to 6.2); behaviour problems (OR 1.9; 95%CI, 0.71 to 5.2); and chronic cognitive impairment (OR 1.4; 95%CI, 0.55 to 3.8). Although living situation with nonspouse family, friends, or others and marital status of widowed, divorced, or separated were significantly associated with abuse when examined in separate logistic regression models, both were nonsignificant when examined together, suggesting collinearity. Both were retained in the model because they probably represent different aspects of vulnerability. The final model included living situation with nonspouse family, friends, or others (OR 6.1; 95%CI, 0.75 to 49.5) and widowed, divorced, or separated marital status (OR 2.4; 95%CI, 0.21 to 26.8). Nonsignificant trends included female sex (OR 2.6; 95%CI, 0.45 to 14.4); alcohol abuse (OR 2.2; 95%CI, 0.59 to 7.9); and lowest quartile on the Global Assessment of Functioning (GAF) scale (GAF < 35; OR 2.0; 95%CI, 0.64 to 6.0). CONCLUSIONS: The practical implications of our study are that elder abuse and neglect are common among patients referred to geriatric psychiatry services, that such services should have access to multidisciplinary expertise and resources to deal with abuse, and that certain situations may signal higher risk. In our setting, the situation of living with nonspouse family, friends, or other persons in a nonsupervised setting and a history of family disruption by widowhood, divorce, or separation were significant correlates of abuse. Suggestive but nonsignificant trends of potential importance (OR > or = 2.0) included female sex, alcohol abuse, and lowest quartile of functional status. Study limitations include a cross-sectional retrospective chart review design, a clinically derived sample, a small sample size, and a lack of structured instruments for several variables.

Aged↗

PubMed2005

Complexities of chromosome landing in a highly duplicated genome: toward map-based cloning of a gene controlling blackleg resistance in Brassica napus.

The LmR1 locus, which controls seedling resistance to the blackleg fungus Leptosphaeria maculans in the Brassica napus cultivar Shiralee, was positioned on linkage group N7. Fine genetic mapping in a population of 2500 backcross lines identified three molecular markers that cosegregated with LmR1. Additional linkage mapping in a second population colocalized a seedling resistance gene, ClmR1, from the cultivar Cresor to the same genetic interval on N7 as LmR1. Both genes were located in a region that showed extensive inter- and intragenomic duplications as well as intrachromosomal tandem duplications. The tandem duplications seem to have occurred in the Brassica lineage before the divergence of B. rapa and B. oleracea but after the separation of Brassica and Arabidopsis from a common ancestor. Microsynteny was found between the region on N7 carrying the resistance gene and the end of Arabidopsis chromosome 1, interrupted by a single inversion close to the resistance locus. The collinear region in Arabidopsis was assayed for the presence of possible candidate genes for blackleg resistance. These data provided novel insights into the genomic structure and evolution of plant resistance loci and an evaluation of the candidate gene approach using comparative mapping with a model organism.

Ascomycota↗

PubMed1990

Equine herpesvirus type 1 unique short fragment encodes glycoproteins with homology to herpes simplex virus type 1 gD, gI and gE.

The nucleotide sequence of a 6.4 kbp portion of the 10.6 kbp BamHI fragment D contained in the unique short region of the equine herpesvirus type 1 (EHV-1) genome has been determined. Analysis of this sequence revealed five open reading frames (ORFs), four complete and one incomplete, which were encoded by the same sense strand. Comparison of the EHV-1 DNA sequence with that encoding glycoproteins of other alphaherpesviruses has revealed no significant homologies. Comparison at the amino acid level, however, has demonstrated regions of significant sequence similarity between the three complete EHV-1 ORFs 2, 3 and 4, and the herpes simplex virus type 1 (HSV-1) glycoprotein gD encoded by the US6 gene, the HSV-1 glycoprotein gI encoded by the US7 gene and the HSV-1 glycoprotein gE encoded by the US8 gene, respectively. The interrupted ORF 5 was found to display partial homology with the HSV-1 US9-encoded protein, but no homology was found between the protein encoded by ORF 1 and other proteins. The three collinear EHV-1 ORFs encoding putative glycoproteins with homology to the HSV-1 glycoproteins were therefore designated EHV-1 gD, gI and gE, respectively. Moreover, further similarities were found between EHV-1 gD and pseudorabies virus (PRV) gp50, between EHV-1 gI and PRV gp63 and varicellazoster virus (VZV) gpIV, and between EHV-1 gE and PRV gI and VZV gpI. It is concluded that EHV-1, PRV, HSV-1 and VZV encode homologous glycoprotein genes in the small unique components of their genomes and that the genetic organization of these regions is conserved.

Amino Acid Sequence↗

PubMed2005

Evaluating the MSCEIT V2.0 via CFA: comment on Mayer et al. (2003).

This investigation uncovered several substantial errors in the confirmatory factor analysis results reported by J. D. Mayer, P. Salovey, D. R. Caruso, and G. Sitarenios (see record 2003-02341-015). Specifically, the values associated with the close-fit indices (normed fit index, Tucker-Lewis Index, and root-mean-square error of approximation) are inaccurate. A reanalysis of the Mayer et al. subscale intercorrelation matrix provided accurate values of the close-fit indices, which resulted in different evaluations of the models tested by J. D. Mayer et al. Contrary to J. D. Mayer et al., the 1-factor model and the 2-factor model did not provide good fit. Although the 4-factor model was still considered good fitting, the non-constrained 4-factor model yielded a non-positive definite matrix, which was interpreted to be due to the fact that two of the branch-level factors (Perceiving and Facilitating) were collinear, suggesting that a model with 4 factors was implausible.

Data Interpretation, Statistical↗

PubMed2006

On the formation of amelogenin microribbons.

We recently reported the remarkable spontaneous self-assembly and hierarchical organization of amelogenin 'microribbons' and their ability to facilitate oriented growth of apatite crystals in vitro. In a letter of correction we communicated the finding that the X-ray diffraction pattern reported in our original report was that of cellulose contaminant and not amelogenin microribbon. We have re-evaluated our data and confirmed the protein nature of the microribbons using Fourier transform infrared and Raman microspectroscopy. Some microribbons were remarkably similar in their morphology to that of cellulose fibers. The size distribution of amelogenin microribbons was wider, particularly in width and length, and generally smaller than those originally reported. Here we present additional detailed information on the formation of a series of intermediate hierarchical structures of amelogenin assemblies prior to the formation of microribbon. The most significant finding was that full-length amelogenin nanospheres had a tendency to assemble into collinear arrays whose function is assumed to be critical at the initial stage of enamel mineral deposition. The present data gives an insight into the step-by-step assembly process of amelogenin from nanometer scale molecules to micrometer scale organized structures that can be used as templates for controlled and oriented growth of apatite mineralization in vitro.

Amelogenesis↗

PubMed1997

Social support deficits, loneliness and life events as risk factors for depression in old age. The Gospel Oak Project VI.

BACKGROUND: A companion paper reported a very strong cross-sectional association between handicap and late-life depression. Adjusting for handicap weakened associations between sociodemographic variables and depression. It was unclear whether handicap was a confounder, or a useful summary variable, mediating the effect of a range of sociodemographic disadvantages. This paper focuses on the cross-sectional relationship between depression and demographic variables, social support, and life events. METHOD: A community survey of all residents over the age of 65 years of an electoral district in London, UK. RESULTS: There was a moderate association between SHORT-CARE pervasive depression and the number of life events experienced over the previous year. Personal illness, bereavement and theft were the most salient events. There was a stronger, graded, relationship between the number of social support deficits (SSDs) and depression. Number of SSDs also related to age, handicap, loneliness and use of homecare services. Loneliness was itself strongly associated with depression; odds ratio 12.4 (7.6-20.0). CONCLUSIONS: Problems of collinearity, and the cross-sectional design of the study limited interpretation of the exact nature of the relationship between social support, loneliness, handicap and depression. However, the clustering of these four factors can be used to define a large part of the elderly population with a poor quality of life. An important avenue for future research will be the development and implementation of population intervention strategies designed to address some or all of these problems among older people in general.

Aged↗

PubMed1998

Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome.

The genome organization of the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus (BusuNPV) was largely elucidated and compared to those of other baculoviruses. A detailed physical map was constructed for the restriction enzymes BamHI, BglI, BglII, EcoRI, HindIII, KpnI, PstI, XbaI and XhoI. The 120.9 kbp viral genome was cloned as restriction fragments into a plasmid library from which about 43.5 kbp of dispersed sequence information was generated. Fifty-two putative open reading frames homologous to those of other baculoviruses were identified and their location in the genome of BusuNPV was determined. Although the gene content of BusuNPV is similar to that of Autographa californica multiple-nucleocapsid nucleopolyhedrovirus, Bombyx mori nucleopolyhedrovirus and Orgyia pseudotsugata multiple-nucleocapsid nucleopolyhedrovirus, the gene order is, however, significantly different from that observed in the other viruses, which have a high degree of collinearity. A new approach (GeneParityPlot) was developed to represent the differences in gene order among baculoviruses when limited sequence information is available and to take advantage of the high degree of gene conservation. The data obtained show that BusuNPV is a distinct baculovirus species and the analyses suggest that gene distribution along baculovirus genomes may be used as a phylogenetic marker.

Animals↗

PubMed1997

A 3' remote control region is a candidate to modulate Hoxb-8 expression boundaries.

Hox genes have been shown to play a key role in the acquisition of positional identity by precursors of embryonic axial, paraxial and limb structures. This function is thought to depend on the sequential, concerted expression of these genes in time and space. However the underlying molecular mechanisms of this collinear expression are still largely unknown. So far we had identified proximal regulatory elements driving expression of Hoxb-8/LacZ transgenes in Hox-like expression patterns with rostral boundaries more posterior than those of the endogenous gene. In this work we have analyzed 30 kb of 3' genomic sequences for Hoxb-8 regulatory activity in transgenic mice. We have identified a control region in the Hoxb-5/b-4 intergenic region that rostrally extends the Hoxb-8/LacZ expression domain into the posterior hindbrain. In combination with the Hoxb-8 minimal promoter, the 3' control region drives transgene expression with boundaries more anterior than those of Hoxb-8 in the neural tube. When combined with a 4.5 kb Hoxb-8 upstream sequence, where essential proximal regulatory sequences are located, the 3' control region drives transgene expression in a domain which seems to correspond to that of the endogenous Hoxb-8. By deletion analysis we have narrowed down to 550bp the regulatory activity interacting with the Hoxb-8 minimal promoter. We discuss the possibility that this remote 3' enhancer, which is the closest regulatory region found in the cluster to rostrally extend Hoxb-8/LacZ expression, could be involved in the regulation of Hoxb-8 and interact with the proximal control elements.

Animals↗

PubMed2006

Subtractive hybridization and optical mapping of the enterotoxigenic Escherichia coli H10407 chromosome: isolation of unique sequences and demonstration of significant similarity to the chromosome of E. coli K-12.

Enterotoxigenic Escherichia coli (ETEC) is a primary cause of diarrhoea in infants in developing countries and in travellers to endemic regions. While several virulence genes have been identified on ETEC plasmids, little is known about the ETEC chromosome, although it is expected to share significant homology in backbone sequences with E. coli K-12. In the absence of genomic sequence information, the subtractive hybridization method and the more recently described optical mapping technique were carried out to determine the degree of genomic variation between virulent ETEC strain H10407 and the non-pathogenic E. coli K-12 strain MG1655. In one round of PCR-based suppression subtractive hybridization, 153 fragments representing sequences unique to strain H10407 were identified. blast searches indicated that few unique sequences showed homology to known pathogenicity island genes identified in related E. coli pathogens. A total of 65 fragments contained sequences that were either linked to hypothetical proteins or showed no homology to any known sequence in the database. The remaining sequences were either phage or prophage related or displayed homology to classifiable genes that function in various aspects of bacterial metabolism. The 153 unique sequences showed variable distribution across different ETEC strains including ETEC strain B7A, which is attenuated in virulence and lacked several H10407-specific sequences. Restriction-enzyme-based optical maps of strain H10407 were compared to in silico restriction maps of strain MG1655 and related E. coli pathogens. The 5.1 Mb ETEC chromosome was approximately 500 kb greater in length than the chromosome of E. coli K-12, collinear with it and indicated several discrete regions where insertions and/or deletions had occurred relative to the chromosome of strain MG1655. No major inversions, transpositions or gross rearrangements were observed on the ETEC chromosome. Based on comparisons with known genomic sequences and related optical-map-based restriction site similarity, the sequence of the H10407 chromosome is expected to demonstrate approximately 96 % identity with that of E. coli K-12.

Bacteriophages↗

PubMed2002

New perspectives on taste and primate evolution: the dichotomy in gustatory coding for perception of beneficent versus noxious substances as supported by correlations among human thresholds.

In various environments where primates are presently observed, as well as in forests and savannas which have been inhabited by australopithecines and early hominids, there are (or there have been presumably) categories of substances eliciting taste signals associated with stereotyped responses. Such is the case for various soluble sugars of fruits and nectars, attracting consumers, and for several plant compounds in which bitter or strongly astringent properties have a repulsive effect. The occurrence of such classes of tasty substances among natural products appears to be related to the evolutionary trends that shaped primate sensory perception (for detecting either beneficent or potentially noxious substances) in the context of a long history of coevolution between animals and plants. Here, we present original psychophysical data on humans (412 individuals aged 17-59 years) as an analogy with which to test recent evidence from electrophysiology in nonhuman primates (Hellekant et al. [1997] J. Neurophysiol. 77:978-993; Danilova et al. [1998] Ann. N.Y. Acad. Sci. 855:160-164) that taste fibers can be grouped into clusters of "best-responding fibers" with two more specific clusters, one for sugars and one for quinine and tannins. The collinearity found between human taste responses (recognition thresholds) for fructose and sucrose, as well as for quinine and tannins, is presented and discussed as another evidence of the two-direction evolutionary trend determining taste sensitivity. Salt perception appears to be totally independent of these trends. Accordingly, the appreciation of a salty taste seems to be a recent culturally learned response, and not a primary taste perception. The very existence of primary tastes is discussed in the context of evolutionary trends, past and present.

Adolescent↗

PubMed1997

Cloning and characterization of the Bg/II restriction-modification system reveals a possible evolutionary footprint.

Bg/II, a type II restriction-modification (R-M) system from Bacillus globigii, recognizes the sequence 5'-AGATCT-3'. The system has been cloned into E. coli in multiple steps: first the methyltransferase (MTase) gene, bglIIM, was cloned from B. globigii RUB561, a variant containing an inactivated endonuclease (ENase) gene (bglIIR). Next the ENase protein (R.BglII) was purified to homogeneity from RUB562, a strain expressing the complete R-M system. Oligonucleotide probes specific for the 5' end of the gene were then synthesized and used to locate bglIIR, and the gene was isolated and cloned in a subsequent step. The nucleotide sequence of the system has been determined, and several interesting features have been found. The genes are tandemly arranged, with bglIIR preceding bglIIM. The amino acid sequence of M.BglII is compared to those of other known MTases. A third gene encoding a protein with sequence similarity to known C elements of other R-M systems is found upstream of bglIIR. This is the first instance of a C gene being associated with an R-M system where the R and M genes are collinear. In addition, open reading frames (ORFs) resembling genes involved with DNA mobility are found in close association with BglII. These may shed light on the evolution of the R-M system.

Amino Acid Sequence↗

PubMed2006

Survival predictability of time-varying indicators of bone disease in maintenance hemodialysis patients.

Although renal osteodystrophy and vitamin D analogs may be related to survival in maintenance hemodialysis (MHD) patients, most studies have examined associations between baseline values and survival without accounting for variations in clinical and laboratory measures over time. We examined associations between survival and quarterly laboratory values and administered paricalcitol in a 2-year (July 2001-June 2003) cohort of 58,058 MHD patients from all DaVita dialysis clinics in USA using both time-dependent Cox models with repeated measures and fixed-covariate Cox models with only baseline values. Whereas hypercalcemia and hyperphosphatemia were robust predictors of higher death risk in all models, the association between serum calcium and mortality was different in time-varying models. Changes in baseline calcium and phosphorus values beyond the Kidney Disease Outcome Quality Initiative recommended targets were associated with increased mortality. Associations between high serum parathyroid hormone and increased death risk were masked by case-mix characteristics of MHD patients. Time-varying serum alkaline phosphatase had an incremental association with mortality. Administration of any dose of paricalcitol was associated with improved survival in time-varying models. Controlling for nutritional markers may introduce overadjustment bias owing to their strong collinearity with osteodystrophy surrogates. Whereas both time-dependent and fixed-covariate Cox models result in similar associations between osteodystrophy indicators and survival, subtle but potentially clinically relevant differences between the two models exist, probably because fixed models do not account for variations of osteodystrophy indices and changes in medication dose over time.

Aged↗

PubMed2004

Risk factors for the presence of Campylobacter spp. in Dutch broiler flocks.

The campylobacter status of 495 broiler flocks sampled in The Netherlands between April 1997 and December 2000 was related to farm- and flock-specific information obtained from questionnaires to identify potential risk factors for campylobacter presence. Approximately 30% of the flocks tested positive for Campylobacter spp. in at least one pooled faecal sample. Multivariable logistic regression showed significant risk increments for: ages 29-35 days (OR = 2.34) and 36-42 days (OR = 3.96) compared to 22-28 days; > or =5 broiler houses on the premises (OR = 3.02); the presence of other farm animals on the farm (OR = 1.88); the presence of animals on farms within 1 km (OR = 9.56); and summer (OR = 3.48) and fall (OR = 2.59) compared to winter. Furthermore, hatcheries differed (ORs from 5.42 to 20.2), although this variable showed strong collinearity with the variables explaining feed mill and integrated poultry operations. We also identified interaction in which an increased risk from children entering the broiler house (OR = 28.0) was diminished by the use of broiler-specific workclothes. Population attributable fractions (PAFs) suggested that animals on farms within 1 km (PAF = 0.76) and hatchery (PAF = 0.67) had the highest impacts on campylobacter presence in Dutch broiler flocks. These factors, however, lack an easy interpretation of the mechanism behind the suggested effect.

Age Factors↗

PubMed2005

RSIR: regularized sliced inverse regression for motif discovery.

MOTIVATION: Identification of transcription factor binding motifs (TFBMs) is a crucial first step towards the understanding of regulatory circuitries controlling the expression of genes. In this paper, we propose a novel procedure called regularized sliced inverse regression (RSIR) for identifying TFBMs. RSIR follows a recent trend to combine information contained in both gene expression measurements and genes' promoter sequences. Compared with existing methods, RSIR is efficient in computation, very stable for data with high dimensionality and high collinearity, and improves motif detection sensitivities and specificities by avoiding inappropriate model specification. RESULTS: We compare RSIR with SIR and stepwise regression based on simulated data and find that RSIR has a lower false positive rate. We also demonstrate an excellent performance of RSIR by applying it to the yeast amino acid starvation data and cell cycle data. AVAILABILITY: Matlab programs are available upon request from the authors.

Algorithms↗