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Results for “collinearity analysis”

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PubMed2006

High-density mapping and comparative analysis of agronomically important traits on wheat chromosome 3A.

Bread wheat chromosome 3A has been shown to contain genes/QTLs controlling grain yield and other agronomic traits. The objectives of this study were to generate high-density physical and genetic-linkage maps of wheat homoeologous group 3 chromosomes and reveal the physical locations of genes/QTLs controlling yield and its component traits, as well as agronomic traits, to obtain a precise estimate of recombination for the corresponding regions and to enrich the QTL-containing regions with markers. Physical mapping was accomplished by 179 DNA markers mostly representing expressed genes using 41 single-break deletion lines. Polymorphism survey of cultivars Cheyenne (CNN) and Wichita (WI), and a substitution line of CNN carrying chromosome 3A from WI [CNN(WI3A)], with 142 RFLP probes and 55 SSR markers revealed that the extent of polymorphism is different among various group 3 chromosomal regions as well as among the homoeologs. A genetic-linkage map for chromosome 3A was developed by mapping 17 QTLs for seven agronomic traits relative to 26 RFLP and 15 SSR chromosome 3A-specific markers on 95 single-chromosome recombinant inbred lines. Comparison of the physical maps with the 3A genetic-linkage map localized the QTLs to gene-containing regions and accounted for only about 36% of the chromosome. Two chromosomal regions containing 9 of the 17 QTLs encompassed less than 10% of chromosome 3A but accounted for almost all of the arm recombination. To identify rice chromosomal regions corresponding to the particular QTL-containing wheat regions, 650 physically mapped wheat group 3 sequences were compared with rice genomic sequences. At an E value of E < or = 10(-5), 82% of the wheat group 3 sequences identified rice homologs, of which 54% were on rice chromosome 1. The rice chromosome 1 region collinear with the two wheat regions that contained 9 QTLs was about 6.5 Mb.

Chromosome Mapping↗

PubMed2003

Crossed two-beam coherent anti-stokes Raman spectroscopy in dispersive media.

Coherent anti-Stokes Raman spectroscopy (CARS) is a nonlinear optical wave mixing process that is used in gas-phase systems to determine the energy distribution of the probed species (usually N2) and, through a fitting procedure, the temperature giving rise to it. CARS signal strengths are maximized when the phase matching condition is met. Because gases are generally non-dispersive, this phase matching condition can be found geometrically as a function of the crossing angles between the CARS beams and their wavelengths. In addition, perfect phase matching in non-dispersive media occurs automatically for collinear beams. To improve spatial resolution, however, intersecting the laser beams is desirable. Being a third-order process, phase matching for CARS in gases typically requires three input laser beams. This paper discusses and demonstrates the issues of phase matching for CARS when the medium is dispersive, and the ability for CARS phase matching to occur with only two crossed laser beams (one pump and one probe). This two-beam X-CARS in dispersive media can be used as an alignment tool for gas-phase CARS and may be relevant as a simpler diagnostic in high-pressure environments. The paper also discusses the effects of non-ideal phase matching in dispersive and non-dispersive media.

Computer Simulation↗

PubMed2006

Interactions between attention and perceptual grouping in human visual cortex.

Freeman et al. demonstrated that detection sensitivity for a low contrast Gabor stimulus improved in the presence of flanking, collinearly oriented grating stimuli, but only when observers attended to them. By recording visual event-related potentials (ERPs) elicited by a Gabor stimulus, we investigated whether this contextual cueing effect involves changes in the short-latency afferent visual signal from V1 that have a stimulus onset latency between 60 and 80 ms and/or longer-latency changes from visual cortex. Under dual-task conditions, the subjects performed contrast discrimination for a central Gabor and an orientation judgment for a pre-specified subset of the flanking Gabors. On random trials, the central Gabor could be collinearly or orthogonally oriented with respect to the attended flankers. Subjects showed improvements in discriminating the contrast of the central grating when it was oriented collinearly with the attended flankers. The ERP difference between attending to collinear versus orthogonal flankers manifested as a positive polarity response at occipital electrodes with a latency of 180-250 ms after stimulus onset. No shorter-latency contextual cueing differences were observed in the ERPs. The ERP latency profile of the contextual cueing effect argues against the hypothesis that short-latency afferent activity from V1 is the stage of processing at which attention can influence neuronal lateral interactions. However, the scalp voltage distribution of the longer-latency contextual cueing effect is similar to the one generated by the early phasic stimulus onset activity from V1. These findings leave open the possibility that V1 is involved in the attentional modulation of lateral interactions but that this has a longer time course, likely being mediated by re-afferent inputs from later stages of the visual pathway.

Adolescent↗

PubMed2002

Penalized partial likelihood regression for right-censored data with bootstrap selection of the penalty parameter.

The Cox proportional hazards model is often used for estimating the association between covariates and a potentially censored failure time, and the corresponding partial likelihood estimators are used for the estimation and prediction of relative risk of failure. However, partial likelihood estimators are unstable and have large variance when collinearity exists among the explanatory variables or when the number of failures is not much greater than the number of covariates of interest. A penalized (log) partial likelihood is proposed to give more accurate relative risk estimators. We show that asymptotically there always exists a penalty parameter for the penalized partial likelihood that reduces mean squared estimation error for log relative risk, and we propose a resampling method to choose the penalty parameter. Simulations and an example show that the bootstrap-selected penalized partial likelihood estimators can, in some instances, have smaller bias than the partial likelihood estimators and have smaller mean squared estimation and prediction errors of log relative risk. These methods are illustrated with a data set in multiple myeloma from the Eastern Cooperative Oncology Group.

Antineoplastic Agents↗

PubMed1997

Mortality in the elderly and ambient ozone concentration during the hot summer, 1994, in Belgium.

Extensive investigations were carried out to study the relationship between daily mortality in the elderly, outdoor air temperature, and ozone concentration observed in Belgium during the hot summer, 1994. The two environmental variables were assessed through mean daily temperature and 24-hr ozone concentration, both measured the day before and averaged over the country. Data were stratified by terciles of mean daily temperature in order to reduce the degree of collinearity between the investigated environmental variables. In the first stratum, which ranged from 9.9 to 15.4 degrees C (41 days), mean daily temperature and 24-hr ozone concentration were not correlated while the mean number of daily deaths was higher when 24-hr ozone concentration increased from 45 to 55 micrograms/m3 (P < 0.05). In the second stratum, which ranged from 15.6 to 20.3 degrees C (42 days), mean daily temperature and 24-hr ozone concentration were strongly correlated (r = 0.54, P < 0.0001). In this stratum, the number of daily deaths did not depend on the mean daily temperature but increased linearly with 24-hr ozone concentration within the range 25 to 85.5 micrograms/m3 (P < 0.001). After having examined the possible confounding effect of sulfur dioxide, nitrogen dioxide, fine particulates, and humidity, ozone was found to be the only investigated variable contributing to the increased daily mortality. In the third stratum, which ranged from 20.4 to 27.6 degrees C (40 days), mean daily temperature and 24-hr ozone concentration were also strongly correlated (r = 0.71, P < 0.0001). Daily mortality, in this stratum, was correlated more with mean daily temperature (r = 0.68, P < 0.001) than with 24-hr ozone concentration (r = 0.55, P < 0.001). Nonparametric regression analyses were performed to model the number of daily deaths in the whole range of temperatures. These analyses confirmed the effect of 24-hr ozone concentration on daily mortality already uncovered by the least-squares regression analysis in the second stratum of mean daily temperature. In addition, at levels exceeding 20 degrees C, the effect of ozone concentration on daily mortality was enhanced by temperature owing to a positive interaction between these two variables. The present study thus demonstrated a statistical association between daily mortality, observed in the elderly during the hot summer, 1994, in Belgium, and ambient ozone concentration. This relationship was dependent on the range of temperatures.

Aged↗

PubMed2001

Effect of organic solvents in the on-line thermal lens spectrometric detection of chromium(III) and chromium(VI) after ion chromatographic separation.

The effect of methanol, acetone and acetonitrile on the sensitivity, selectivity and the detection limits (LODs) of the determination of chromium species by ion chromatography was investigated. A collinear dual-beam thermal lens spectrometer was used for the direct detection of chromium complexes [pre-column derivatized Cr(III)-pyridine-2,6-dicarboxylic acid, and post-column derivatized Cr(VI)-1,5-diphenylcarbazide] following the ion chromatographic separation on a Dionex HPIC-CS5A solvent compatible column. Different amounts of organic solvents were added directly to the eluent (up to 30%) and to the post-column reagent (up to 60%) to improve the thermooptical properties of the solvents. Consequently, the sensitivity of the technique was increased by a factor of 2-3 and LODs of 0.1 and 10 microg dm(-3) were achieved for Cr(VI) and Cr(III), respectively, when the eluent reaching the detector contained 30% of acetonitrile. The addition of organic solvents also resulted in significant changes in retention times, which improved the Cr(III)/Cr(VI) separation.

Chromatography, Liquid↗

PubMed2002

A hierarchical approach to aligning collinear regions of genomes.

MOTIVATION: As a first approximation, similarity between two long orthologous regions of genomes can be represented by a chain of local similarities. Within such a chain, pairs of successive similarities are collinear (non-conflicting), i.e. segments involved in the nth similarity precede in both sequences segments involved in the (n+1)th similarity. However, when all similarities between two long sequences are considered, usually there are many conflicts between them. Although some conflicts can be avoided by masking transposons or low-complexity sequences, selecting only those similarities that reflect orthology and, thus, belong to the evolutionarily true chain is not trivial. RESULTS: We propose a simple, hierarchical algorithm of finding the true chain of local similarities. Starting from similarities with low P-values, we resolve each pairwise conflict by deleting a similarity with a higher P-value. This greedy approach constructs a chain of similarities faster than when a chain optimal with respect to some global criterion is sought, and makes more sense biologically.

Algorithms↗

PubMed2005

Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data.

DNA microarray technology provides a promising approach to the diagnosis and prognosis of tumors on a genome-wide scale by monitoring the expression levels of thousands of genes simultaneously. One problem arising from the use of microarray data is the difficulty to analyze the high-dimensional gene expression data, typically with thousands of variables (genes) and much fewer observations (samples), in which severe collinearity is often observed. This makes it difficult to apply directly the classical statistical methods to investigate microarray data. In this paper, total principal component regression (TPCR) was proposed to classify human tumors by extracting the latent variable structure underlying microarray data from the augmented subspace of both independent variables and dependent variables. One of the salient features of our method is that it takes into account not only the latent variable structure but also the errors in the microarray gene expression profiles (independent variables). The prediction performance of TPCR was evaluated by both leave-one-out and leave-half-out cross-validation using four well-known microarray datasets. The stabilities and reliabilities of the classification models were further assessed by re-randomization and permutation studies. A fast kernel algorithm was applied to decrease the computation time dramatically. (MATLAB source code is available upon request.).

Acute Disease↗

PubMed2026

TL-HDMR: a transfer learning framework for advancing equitable causal inference reveals metabolic signatures of stroke across multiple ancestries.

The limited genetic diversity in genome-wide association studies (GWAS) poses a significant challenge to the generalizability and equity of biomedical discoveries. Most causal inferences, particularly from high-dimensional phenomes (e.g. metabolomics), are primarily based on European populations, and their applicability to other ancestries remains uncertain. Traditional multivariable Mendelian randomization (MVMR) methods further struggle in high-dimensional and correlated settings due to collinearity and model instability. To bridge this gap, we present a two-step transfer learning framework for high-dimensional MR (TL-HDMR), designed to enhance causal exposure detection in understudied populations. Our approach leverages the Minimax Concave Penalty for asymptotically unbiased estimation amidst exposure correlations. Crucially, we introduce two novel pre-transfer procedures-HDMR.TSD for sourcing beneficial data and HDMR.PRESSO for filtering pleiotropic instruments-to ensure robust knowledge transfer. Extensive simulations demonstrated TL-HDMR's superior performance in ROC curves and mean absolute error over alternative methods. When applied to identify causal metabolites for stroke across multi-ancestry cohorts (European, East Asian, South Asian, and African), TL-HDMR successfully pinpointed both shared and ethnic-specific causal biomarkers, showcasing its unique capability for equitable causal inference. This work provides a powerful statistical tool that not only addresses critical methodological challenges but also promotes inclusivity and fairness in human health research.

Humans↗

PubMed2003

A large rearrangement involving genes and low-copy DNA interrupts the microcollinearity between rice and barley at the Rph7 locus.

Grass genomes differ greatly in chromosome number, ploidy level, and size. Despite these differences, very good conservation of the marker order (collinearity) was found at the genetic map level between the different grass genomes. Collinearity is particularly good between rice chromosome 1 and the group 3 chromosomes in the Triticeae. We have used this collinearity to saturate the leaf rust resistance locus Rph7 on chromosome 3HS in barley with ESTs originating from rice chromosome 1S. Chromosome walking allowed the establishment of a contig of 212 kb spanning the Rph7 resistance gene. Sequencing of the contig showed an average gene density of one gene/20 kb with islands of higher density. Comparison with the orthologous rice sequence revealed the complete conservation of five members of the HGA gene family whereas intergenic regions differ greatly in size and composition. In rice, the five genes are closely associated whereas in barley intergenic regions are >38-fold larger. The size difference is due mainly to the presence of six additional genes as well as noncoding low-copy sequences. Our data suggest that a major rearrangement occurred in this region since the Triticeae and rice lineage diverged.

Chromosome Mapping↗

PubMed2004

Diuretics and mortality in acute renal failure.

OBJECTIVE: According to recent research, diuretics may increase mortality in acute renal failure patients. The administration of diuretics in such patients has been discouraged. Our objective was to determine the impact of diuretics on the mortality rate of critically ill patients with acute renal failure. DESIGN: Prospective, multiple-center, multinational epidemiologic study. SETTING: Intensive care units from 54 centers and 23 countries. PATIENTS: Patients were 1,743 consecutive patients who either were treated with renal replacement therapy or fulfilled predefined criteria for acute renal failure. INTERVENTIONS: Three distinct multivariate models were developed to assess the relationship between diuretic use and subsequent mortality: a) a propensity score adjusted multivariate model containing terms previously identified to be important predictors of outcome; b) a new propensity score adjusted multivariate model; and c) a multivariate model developed using standard methods, compensating for collinearity. MEASUREMENTS AND MAIN RESULTS: Approximately 70% of patients were treated with diuretics at study inclusion. Mean age was 68 and mean Simplified Acute Physiology Score II was 47. Severe sepsis/septic shock (43.8%), major surgery (39.1), low cardiac output (29.7), and hypovolemia (28.2%) were the most common conditions associated with the development of acute renal failure. Furosemide was the most common diuretic used (98.3%). Combination therapy was used in 98 patients only. In all three models, diuretic use was not associated with a significantly increased risk of mortality. CONCLUSIONS: Diuretics are commonly prescribed in critically ill patients with acute renal failure, and their use is not associated with higher mortality. There is full equipoise for a randomized controlled trial of diuretics in critically ill patients with renal dysfunction.

Acute Kidney Injury↗

PubMed2002

Temporal and spatial relations between age specific mortality and ambient air quality in the United States: regression results for counties, 1960-97.

OBJECTIVE: To investigate longitudinal and spatial relations between air pollution and age specific mortality for United States counties (except Alaska) from 1960 to the end of 1997. METHODS: Cross sectional regressions for five specific periods using published data on mortality, air quality, demography, climate, socioeconomic status, lifestyle, and diet. Outcome measures are statistical relations between air quality and county mortalities by age group for all causes of death, other than AIDS and trauma. RESULTS: A specific regression model was developed for each period and age group, using variables that were significant (p<0.05), not substantially collinear (variance inflation factor <2), and had the expected algebraic sign. Models were initially developed without the air pollution variables, which varied in spatial coverage. Residuals were then regressed in turn against current and previous air quality, and dose-response plots were constructed. The validity of this two stage procedure was shown by comparing a subset of results with those obtained with single stage models that included air quality (correlation=0.88). On the basis of attributable risks computed for overall mean concentrations, the strongest associations were found in the earlier periods, with attributable risks usually less than 5%. Stronger relations were found when mortality and air quality were measured in the same period and when the locations considered were limited to those of previous cohort studies (for PM(2.5) and SO(4)(2-)). Thresholds were suggested at 100-130 microg/m(3) for mean total suspended particulate (TSP), 7-10 microg/m(3) for mean sulfate, 10-15 ppm for peak (95th percentile) CO, 20-40 ppb for mean SO(2.) Contrary to expectations, associations were often stronger for the younger age groups (<65 y). Responses to PM, CO, and SO(2) declined over time; responses in elderly people to peak O(3) increased over time as did responses to NO(2) for the younger age groups. These results generally agreed with previous prospective cohort and ecological studies for comparable periods, age groups, and pollutants, but they also suggest that the results of those previous studies may no longer be applicable. CONCLUSIONS: Spatially derived relations between air quality and mortality vary significantly by age group and period and may be sensitive to the locations included in the analysis.

Adolescent↗

PubMed1992

Analysis of nucleotide sequence of the rightmost 43 kbp of herpesvirus saimiri (HVS) L-DNA: general conservation of genetic organization between HVS and Epstein-Barr virus.

We present an analysis of 43,658 bp of contiguous nucleotide sequence comprising the right terminal region (conventional orientation) of the unique protein-coding component (L-DNA) of the herpesvirus saimiri (HVS) genome. Within this region lie the genes encoding the 160-kDa virion protein, which is homologous to the 140-kDa membrane antigen of Epstein-Barr virus (EBV), thymidylate synthase (TS), and the immediate-early (IE) 52-kDa protein which is homologous to the EBV BMLF1 product. The 160-kDa gene of HVS lies at the right terminus of HVS L-DNA, its homologue in EBV occurring at the left terminus of the EBV genome (conventional orientation). The TS gene of HVS occurs within a group of 5 genes that have no homologues in EBV. The translation product of one of these genes, ECRF3, shows amino acid sequence and hydrophobicity pattern similarities to the HCMV and cellular G-protein-coupled receptor family of proteins. Another, ECLF2, is homologous to the cyclin family of cellular proteins. The 5 nonconserved genes lie adjacent to the 160-kDa gene. In EBV, the region to the right of the 140-kDa gene (BNRF1) contains the latent replication origin (OriP) and the open reading frames BCRF1, BWRF1 (repeated 12 times), BYRF1, BHLF1, and BHRF1, counterparts of which are not present in this position in HVS. The subsequent 18 genes in EBV (BFLF2 to BLRF2, approximate positions 56,000-89,500) are represented in HVS, and the relative positions and orientations of these genes are directly comparable between the two viruses. There then occurs a nonhomologous gene in HVS, and genes BLLF2 to BZLF1 (positions 89,500 to 103,200) in EBV which are not present in this region of HVS, before collinearity resumes. Thus, the HVS sequence presented here shows general collinearity between conserved genes in the right terminal region of HVS and the left terminal region of EBV and reveals the presence of two sets of unique genes which occur in exactly analogous positions in HVS and EBV.

Amino Acid Sequence↗

PubMed2005

Lateral interactions in the visual cortex of patients with schizophrenia and bipolar disorder.

BACKGROUND: Schizophrenia is associated with perceptual organization deficits and abnormal neuronal connectivity has been described in early visual areas. The purpose of this study was to investigate the functional integrity of lateral connections in early visual areas of patients with schizophrenia and type I bipolar disorder with a history of psychosis. METHOD: Twenty-four out-patients with schizophrenia, 22 out-patients with bipolar disorder, and 20 healthy control subjects participated in the study. Using a computer-assisted psychophysical test, contrast thresholds were measured for centrally presented target stimuli (Gabor patches), which were surrounded by two collinear flankers. Target-to-flanker distances were 0, 1, 2, 3, 4, 6, 9 and 122. Psychophysical measures were contrast threshold changes at each target-to-flanker distance compared with baseline thresholds determined for isolated targets with no flankers. Clinical measures included IQ, positive, negative, and depressive symptoms. Results. In patients with schizophrenia, flankers did not facilitate contrast detection for target stimuli at 2-6 lambda distances compared to controls [effect size (Cohen's d): 1.25-1.42]. The inhibitory effect of flankers (0 and 1lambda) and contrast thresholds in the absence of flankers were spared. Patients with bipolar disorder did not differ from the controls. Medicated and non-medicated patients displayed similar performances. Positive and negative symptoms and depression did not correlate with contrast threshold values. CONCLUSIONS: Excitatory lateral connections in early visual cortex are specifically impaired in patients with schizophrenia, which may contribute to perceptual disorders such as unclear seeing, partial or skewed sight, disrupted rectilinearity, and abnormal figure-ground segregation.

Adult↗

PubMed2004

Inexpensive system for real-time 3-dimensional video-oculography using a fluorescent marker array.

We describe a novel, inexpensive method for real-time measurement of binocular three-dimensional eye position. The method employs consumer-grade digital video cameras ("webcams") to track an array of three fluorescent non-collinear markers affixed to each eye. The instantaneous position of the marker array relative to a reference position is used to construct a rotation matrix describing the eye rotation. The mathematical computation used to determine the rotation matrix is conceptually simpler and computationally more efficient than methods previously described, allowing generation of binocular three-dimensional eye position in real-time during image acquisition. The fluorescent marker is illuminated using a UV-A light source. The light source and reflective artifacts are filtered out to improve the signal to noise ratio. In addition, we present a method to align the camera with the center of eye rotation. When tested in vitro, the video-oculography (VOG) method had a <2.9% positional error (in each component of 3-D eye position) for eye positions within 20 degrees of center. We directly compared this method of VOG to the search coil technique by measuring three-dimensional eye position simultaneously using search coils and VOG in a chinchilla (C. laniger). The in vivo positional difference between the two methods was <3.1% for each component of 3-D eye position.

Algorithms↗

PubMed1999

Brain SPECT imaging and left hemispatial neglect covaried using partial least squares: the Sunnybrook Stroke study.

Hemispatial neglect, characterized as failure to attend to contralesional space, is hypothesized by current neuroanatomical models to result from damage to a network involving the frontal, parietal, and cingulate cortices, basal ganglia, and thalamus. This study investigated this model of neglect in 81 right hemisphere-damaged acute stroke patients using 99mTc-HMPAO single photon emission-computed tomography (SPECT). In order to exploit the inherent collinearity of SPECT regional brain ratios, a novel statistical technique, partial least squares (PLS), was utilized. It makes use of high correlations to identify biologically relevant patterns of brain activity. Averaged ipsilesional cerebellar ratios from 152 brain segments were covaried with performance on subtests of the Sunnybrook Neglect Battery. In this patient sample, the most influential region identified by PLS corresponded to the area surrounding the right temporal-parietal-occipital (TPO) junction that included the right lateral occipital, temporal, and inferior parietal lobes. Hypoperfusion in the medial frontal cortex, including the anterior cingulate, also emerged as significantly associated with more severe neglect. Thus, hypoperfusion in only two of the five hypothesized network regions emerged as significantly associated with hemispatial neglect on SPECT imaging. This work converges with structural imaging studies to suggest that damage to the TPO junction, not just the parietal lobe, may be the critical region for hemispatial neglect. Our study demonstrated the utility of PLS for analyzing functional imaging and behavioral data sets in a clinical population in relation to current neuroanatomical models of neglect.

Aged↗

PubMed2006

Understanding community structure: a data-driven multivariate approach.

Habitat is known to influence community structure yet, because these effects are complex, elucidating these relationships has proven difficult. Multiple aspects of vegetation architecture or plant species composition, for example, may simultaneously affect animal communities and their constituent species. Many traditional statistical approaches (e.g., regression) have difficulty in handling large numbers of collinear variables. On the other hand, multivariate methods, such as ordination, are well suited to handle these large datasets, but they have primarily been used in ecology as descriptive techniques, and less frequently as a data reduction tool for predictor variables in regression. Here, I employ a multivariate approach for variable reduction of both the predictor and response variables to investigate the influences of vegetation architecture and plant species on community composition in spiders using multiple regression. This allows retention of the information in the original dataset while producing statistically tractable variables for use in further analyses. I used nonmetric multidimensional scaling to reduce the number of variables for predictor (habitat architecture and plant species) and response (spider species) data matrices, and used these new variables in multiple regression analyses. These axes can be interpreted based on their correlations with the original variables, allowing for recovery of biologically meaningful information from regressions. Consequently, the important variables are determined by the data themselves, rather than by a priori assumptions of the researcher. Contrary to expectations based on previous work in spiders and other animals, plant species composition explained more variation in spider communities than did habitat architecture, and was also a stronger predictor of other community structure variables (overall abundance, species richness, and species diversity). I discuss possible ecological explanations for these results, and the advantages of the proposed method.

Animals↗

PubMed1997

Identification and characterization of a G protein-coupled receptor homolog encoded by murine cytomegalovirus.

This report describes the identification of a murine cytomegalovirus (MCMV) G protein-coupled receptor (GCR) homolog. This open reading frame (M33) is most closely related to, and collinear with, human cytomegalovirus UL33, and homologs are also present in human herpesvirus 6 and 7 (U12 for both viruses). Conserved counterparts in the sequenced alpha- or gammaherpesviruses have not been identified to date, suggesting that these genes encode proteins which are important for the biological characteristics of betaherpesviruses. We have detected transcripts for both UL33 and M33 as early as 3 or 4 h postinfection, and these reappear at late times. In addition, we have identified N-terminal splicing for both the UL33 and M33 RNA transcripts. For both open reading frames, splicing results in the introduction of amino acids which are highly conserved among known GCRs. To characterise the function of the M33 in the natural host, two independent MCMV recombinant viruses were prepared, each of which possesses an M33 open reading frame which has been disrupted with the beta-galactosidase gene. While the recombinant M33 null viruses showed no phenotypic differences in replication from wild-type MCMV in primary mouse embryo fibroblasts in vitro, they showed severely restricted growth in the salivary glands of infected mice. These data suggest that M33 plays an important role in vivo, in particular in the dissemination to or replication in the salivary gland, and provide the first evidence for the function of a viral GCR homolog in vivo.

Amino Acid Sequence↗