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PubMed2000

Li2VO(Si,Ge)O4, a prototype of a two-dimensional frustrated quantum heisenberg antiferromagnet

NMR and magnetization measurements in Li2VOSiO4 and Li2VOGeO4 are reported. The analysis of the susceptibility shows that both compounds are two-dimensional S = 1/2 Heisenberg antiferromagnets on a square lattice with a sizable frustration induced by the competition between the superexchange couplings J1 along the sides of the square and J2 along the diagonal. Li2VOSiO4 undergoes a low-temperature phase transition to a collinear order, as theoretically predicted for J2/J1>0.5. Just above the magnetic transition the degeneracy between the two collinear ground states is lifted by the onset of a structural distortion.

Journal Article↗

PubMed2004

Peculiarities of herpes simplex virus (HSV) transcription: an overview.

The herpes simplex virus (HSV) has a 152 kbp dsDNA encoding probably 84 proteins. The approximate number of ORFs is 94, from which seven are doubled. The most probable number of single copy ORFs is 84 after omitting the two latency associated transcripts (LAT)/ORFs and the putative UL27.5 ORF. The high gene number creates a "crowded" genome with several overlapping transcripts. The unique long (U(L)) segment has at least 10 interposed ORFs, the existence of which was not obvious at first sequence analysis, while the unique short (U(S)) segment has two such genes. The surplus of ORFs causes complex transcription patterns: (1) Transcripts with common initiation signals but different termination; (2) Transcripts with different initiation sites but co-terminal ends; (3) "Nested" transcripts differing at both, the initiation as well as termination signals, having partially collinear sequences. At least three or possibly four ORF (gene) pairs (UL9.5/UL10; UL27/UL27.5; UL43/UL43.5; ICP34.5/ORF P and O) occupy both DNA strands at complementary positions rising anti-sense transcripts expressed by an antagonistic mechanism of mutual exclusion. The anti-sense mRNA mechanism might also operate when either LAT or ICP0 ORFs are expressed during latency assuring the absence of lytic virus replication. In contrast, during productive replication the cascade regulation of gene expression predominates, based on stepwise activation of immediate early (IE), early (E), early late (EL) and late (L) promoters. The promoters of different expression kinetic classes (alpha, beta, gamma-1 and gamma-2) are equipped with different number of cellular transcription factor binding and/or enhancer motifs. Surprisingly, only a few HSV mRNAs are being spliced (ICP0, UL15, US1, US12/ICP47). As reviewed here, the transcription pattern of the great majority of overlapping ORFs within the HSV-1 was quite convincingly elucidated, with exception of the putative UL27.5 gene. The UL27.5 transcript was not identified yet. Since the existence of the UL27.5 gene was based on indirect rather than direct evidence, it needs final confirmation.

Base Sequence↗

PubMed2003

What does visual agnosia tell us about perceptual organization and its relationship to object perception?

The authors studied 2 patients, S.M. and R.N., to examine perceptual organization and its relationship to object recognition. Both patients had normal, low-level vision and performed simple grouping operations normally but were unable to apprehend a multielement stimulus as a whole. R.N. failed to derive global structure even under optimal stimulus conditions, was less sensitive to grouping by closure, and was more impaired in object recognition than S.M. These findings suggest that perceptual organization involves a multiplicity of processes, some of which are simpler and are instantiated in lower order areas of visual cortex (e.g., collinearity). Other processes are more complex and rely on higher order visual areas (e.g., closure and shape formation). The failure to exploit these latter configural processes adversely affects object recognition.

Adolescent↗

PubMed2005

Visual analysis of changes of motion in reaction-time tasks.

Subjects observed a random-dot pattern moving uniformly in the vertical direction (vector V1). The motion vector abruptly changed to V2, both in speed and direction simultaneously. It was found that the time of simple reaction to such changes V1 --> V2 can be described by a function of a single variable, [w(V1 - V2c) + (1 - w) V2N], 0 < w < 0.5, where V2c and V2N are the components of V2 collinear with and normal to V1. The choice-reaction time for changes in direction that are accompanied by changes in speed can be described by a function solely of the absolute value of V2N. Unlike the simple-reaction time, the choice-reaction time was independent of the initial speed of motion. The processes that may be engaged in simple and choice reactions to motion are discussed.

Adult↗

PubMed2000

Hierarchical motion organization in random dot configurations.

Motion organization has 2 aspects: the extraction of a (moving) frame of reference and the hierarchical organization of moving elements within the reference frame. Using a discrimination of relative motions task, the authors found large differences between different types of motion (translation, divergence, and rotation) in the degree to which each can serve as a moving frame of reference. Translation and divergence are superior to rotation. There are, however, situations in which rotation can serve as a reference frame. This is due to the presence of a second factor, structural invariants (SIs). SIs are spatial relationships persisting among the elements within a configuration such as a collinearity among points or one point coinciding with the center of rotation for another (invariant radius). The combined effect of these 2 factors--motion type and SIs-influences perceptual motion organization.

Adult↗

PubMed2006

Genomic comparison of Neodiprion sertifer and Neodiprion lecontei nucleopolyhedroviruses and identification of potential hymenopteran baculovirus-specific open reading frames.

Genomic comparison of Neodiprion sertifer nucleopolyhedrovirus (NeseNPV) and Neodiprion lecontei nucleopolyhedrovirus (NeleNPV) showed that the hymenopteran baculoviruses had features in common and were distinct from other, fully sequenced lepidopteran and dipteran baculoviruses. Their genomes were small in size (86,462 and 81,755 bp, respectively), had low G+C contents (33.8 and 33.3 mol%, respectively) and contained fewer open reading frames (ORFs) (90 and 89, respectively) than other baculoviruses. They shared 69 ORFs (48.6% mean amino acid identity overall), 43 of which were previously identified baculovirus homologues. The remaining shared ORFs could be common to other baculoviruses, but low amino acid identities precluded identifying them as such. Some may also be unique to hymenopteran baculoviruses. These included a trypsin-like protease, a zinc-finger protein, regulator of chromosome condensation proteins, a densovirus capsid-like protein and a phosphotransferase. Structural analysis, the presence of conserved domains and phylogenetic studies suggested that some of these ORFs may be functional and could have been transferred horizontally from an insect host. ORFs found only in NeseNPV and NeleNPV may play a role in host specificity and/or tissue tropism, as hymenopteran baculoviruses are restricted to the midgut. The genomes were basically collinear, but contained non-syntenic regions (NSRs) with large numbers of repeats between their polyhedrin and dbp genes. They differed from each other in the number of ORFs and the G+C content of their NSRs and the presence of homologous regions in the NeseNPV genome. NeleNPV also had a short inversion relative to NeseNPV. NeseNPV contained 21 ORFs not found in NeleNPV and NeleNPV had 20 ORFs not found in NeseNPV.

Amino Acid Sequence↗

PubMed2026

Chromosome-Scale Genome of Zoonotic Eyeworm Thelazia callipaeda from China.

Thelazia callipaeda is a vector-borne zoonotic eyeworm infecting companion animals, wildlife, and humans, but chromosome-scale genomic resources from Chinese clinical material remain limited. We generated a genome supported by Pacific Biosciences (PacBio) high-fidelity (HiFi) sequencing and high-throughput chromosome conformation capture (Hi-C) from 100 adult worms recovered from naturally infected dogs in Beijing and compared its chromosome-scale organization with Portuguese assembly GCA_965194785.1. The final assembly spans 119.53 megabases (Mb) and comprises 115 top-level sequences, including four pseudomolecules totaling 91.26 Mb (76.34%) and 111 unanchored sequences. Genome-mode Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis recovered 98.5% complete chromadorean orthologues, and the representative 11,788-protein gene set recovered 92.6%. Sequence-level alignment resolved Chinese chromosomes 1-4 (chr1-chr4) to Portuguese chr1, chrX, chr3, and chr2, respectively, with retained alignments covering 95.9-99.2% of each Chinese pseudomolecule and estimated sequence identities of 99.75-99.91%. Strong chromosome-scale collinearity was accompanied by localized reverse-collinear regions, including 0.243 Mb and 0.115 Mb intervals on chr2-chrX and chr3-chr3. The anchored sequences contained 96.7% of predicted genes and were substantially more gene-dense than the unanchored sequences. These results establish a clinically sourced Chinese chromosome-scale reference and provide a validated framework for future individual-worm, population-genomic, structural-variation, and comparative genomic studies of this parasite.

Hi-C↗

PubMed2005

A major gene mapped on chromosome XII is the main factor of a quantitatively inherited resistance to Meloidogyne fallax in Solanum sparsipilum.

Meloidogyne fallax is an emerging pest in Europe and represents a threat for potato production. We report the mapping of genetic factors controlling a quantitative resistance against M. fallax identified in the Solanum sparsipilum genotype 88S.329.15. When infected, this genotype develops a necrotic reaction at the feeding site of the juveniles and totally prevents their development to the female stage. A "F1" diploid progeny consisting of 128 individuals was obtained using the potato (S. tuberosum) dihaploid genotype BF15 H1 as female progenitor. Sixty-eight hybrid genotypes displayed necrosis at the feeding site of the juveniles and 60 other genotypes showed no defence reaction. This suggested a monogenic control of the resistance. However, when considering the number of nematode females developed in their roots, a continuous distribution was observed for both "necrotic" and "non-necrotic" hybrid genotypes, indicating a polygenic control of the resistance. A linkage map of each parental genotype was constructed using AFLP markers. The necrotic reaction (NR) was mapped as a qualitative trait on chromosome XII of the resistant genotype 88S.329.15. Quantitative trait locus (QTL) analysis for the number of nematode females developed per "F1" plant genotype was performed using the QTL cartographer software. No QTL was detected on the linkage map of the susceptible parent. A QTL explaining 94.5% of the phenotypic variation was mapped on chromosome XII of the resistant progenitor. This QTL, named MfaXIIspl, was mapped in a genomic region collinear to the map position of the Mi-3 gene conferring resistance to Meloidogyne incognita in tomato. It corresponds to the NR locus.

Animals↗

PubMed1993

Nucleotide sequence and transcriptional analysis of the p10 gene of Spodoptera exigua nuclear polyhedrosis virus.

The p10 gene of Spodoptera exigua multiple nuclear polyhedrosis virus (SeMNPV) was localized on the XbaI fragment H (5.1 kb) of the physical map of the viral genome. The coding sequence of the SeMNPV p10 gene is 264 nucleotides (nt) long corresponding to a predicted protein of 88 amino acids with an MHF of 9607. The SeMNPV p10 protein showed only limited amino acid identity (39% and 26%, respectively) to those of Orgyia pseudotsugata MNPV (OpMNPV) and Autographa californica MNPV (AcMNPV) and thus appears less conserved than other viral proteins. The SeMNPV p10 gene was expressed by a transcript of approximately 450 nt, which started in the conserved baculovirus late gene promoter motif TAAG. The leader of the SeMNPV p10 transcript was AT-rich (92%) and at 36 nt was the shortest leader of all baculovirus major late genes reported so far. The SeMPNV p10 transcript terminated 6 nt downstream from a putative poly(A) signal sequence (AATAAA); the latter was 61 nt downstream of the translational stop codon TAA. Upstream and downstream of the p10 gene, partial putative ORFs were found that showed significant amino acid sequence identity to the baculovirus p26 and p74 proteins. It is concluded that the region of SeMNPV DNA containing the p10 gene is collinear with the corresponding regions in the AcMNPV and OpMNPV genomes.

Amino Acid Sequence↗

PubMed2003

Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement.

The completed rice genome sequence will accelerate progress on the identification and functional classification of biologically important genes and serve as an invaluable resource for the comparative analysis of grass genomes. In this study, methods were developed for sequence-based alignment of sorghum and rice chromosomes and for refining the sorghum genetic/physical map based on the rice genome sequence. A framework of 135 BAC contigs spanning approximately 33 Mbp was anchored to sorghum chromosome 3. A limited number of sequences were collected from 118 of the BACs and subjected to BLASTX analysis to identify putative genes and BLASTN analysis to identify sequence matches to the rice genome. Extensive conservation of gene content and order between sorghum chromosome 3 and the homeologous rice chromosome 1 was observed. One large-scale rearrangement was detected involving the inversion of an approximately 59 cM block of the short arm of sorghum chromosome 3. Several small-scale changes in gene collinearity were detected, indicating that single genes and/or small clusters of genes have moved since the divergence of sorghum and rice. Additionally, the alignment of the sorghum physical map to the rice genome sequence allowed sequence-assisted assembly of an approximately 1.6 Mbp sorghum BAC contig. This streamlined approach to high-resolution genome alignment and map building will yield important information about the relationships between rice and sorghum genes and genomic segments and ultimately enhance our understanding of cereal genome structure and evolution.

Base Sequence↗

PubMed2000

Daily mortality and fine and ultrafine particles in Erfurt, Germany part I: role of particle number and particle mass.

Increases in morbidity and mortality have been observed consistently and coherently in association with ambient air pollution. A number of studies on short-term effects have identified ambient particles as a major pollutant in urban air. This study, conducted in Erfurt, Germany, investigated the association of mortality not only with ambient particles but also with gaseous pollutants and indicators of sources. Part I of this study concentrates on particles. Data were collected prospectively over a 3.5-year period from September 1995 to December 1998. Death certificates were obtained from the local authorities and aggregated to daily time series of total counts and counts for subgroups. In addition to standard data for particle mass with diameters < or = 2.5 microm (PM2.5)* or < or = 10 microm (PM10) from impactors, a mobile aerosol spectrometer (MAS) was used to obtain size-specific number and mass concentration data in six size classes between 0.01 microm and 2.5 microm. Particles smaller than 0.1 microm were labeled ultrafine particles (three size classes), and particles between 0.1 and 2.5 microm were termed fine particles (three size classes). Concentrations of the gases sulfur dioxide (SO2), nitrogen dioxide (NO2), and carbon monoxide (CO) were also measured. The daily average total number concentration was 18,000 particles/cm3 with 88% of particles below 0.1 pm and 58% below 0.03 microm in diameter. The average mass concentration (PM2.5) was 26 microg/m3; of this, 75% of particles were between 0.1 and 0.5 microm in diameter. Other average concentrations were 38 microg/m3 for PM10, 17 microg/m3 for SO2, 36 microg/m3 for NO2, and 600 microg/m3 for CO. Ambient air pollution demonstrated a strong seasonality with maximum concentrations in winter. Across the study period, fine particle mass decreased, whereas ultrafine particle number was unchanged. The proportion of ultrafine particles below 0.03 microm diameter increased compared with the proportion of other particles. During the study, concentrations of SO2 and CO also decreased, whereas the concentration of NO2 remained unchanged. The data were analyzed using Poisson regression techniques with generalized additive modeling (GAM) to allow nonparametric adjustment for the confounders. Both the best single-day lag and the overall association of multiple days fitted by a polynomial distributed lag model were used to assess the lag structure between air pollution and death. Mortality increased in association with level of ambient air pollution after adjustment for season, influenza epidemics, day of week, and weather. In the sensitivity analyses, the results proved stable against changes of the confounder model. We saw comparable associations for ultrafine and fine particles in a distributed lag model where the contribution of the previous 4 to 5 days was considered. Furthermore, the data suggest a somewhat more delayed association of ultrafine particles than of fine particles if single-day lags are considered. The associations tended to be stronger in winter than in summer and at ages below 70 years compared to ages above 70 years. Analysis of the prevalent diseases mentioned on death certificates revealed that the overall association for respiratory diseases was slightly stronger than for cardiovascular diseases. In two-pollutant models, associations of ultrafine and fine particles seemed to be largely independent of each other, and the risk was enhanced if both were considered at the same time. Furthermore, when the associations were summed for the six size classes between 0.01 and 2.5 microm, the overall association was clearly stronger than the associations of the individual size classes alone. Associations were observed for SO2, NO2, and CO with mortality despite low concentrations of these gases. These associations disappeared in two-pollutant models for NO2 and CO, but they remained stable for SO2. The persistence of the SO2 effect was interpreted as artifact, however, because the SO2 concentration was much below levels at which effects are usually expected. Furthermore, the results for SO2 were inconsistent with those from earlier studies conducted in Erfurt. We conclude that both fine particles (represented by particle mass) and ultrafine particles (represented by particle number) showed independent effects on mortality at ambient concentrations. Comparable associations for gaseous pollutants were interpreted as artifacts of collinearity with particles from the same sources.

Adolescent↗

PubMed1986

A comparison of Nd:YAG laser damage thresholds for PMMA and silicone intraocular lenses.

Power density producing damage at a probability of 0.5 (ie, damage threshold, DT-50) was determined for PMMA (with/without UV absorber) and Silicone intraocular lenses. Scattered light from a collinear diagnostic He:Ne beam was one of four damage monitors deployed to enhance the sensitivity of the system. In order of increasing laser resistance the following results were obtained: injection molded PMMA (1.9/GW/cm2) Silicone (2.63 GW/cm2) Lathe-cut PMMA (4.47 GW/cm2), Lathe-cut PMMA with UV absorber (8.32 GW/cm2), Cast-molded PMMA (12.30 GW/cm2). An analysis of variance revealed interclass differences significant at the .01 level. Cast-molded PMMA was the most laser-resistant IOL material.

Lasers↗

PubMed1990

Variation in vital rates by age, period, and cohort.

"The analysis of age-specific vital rates is studied, and special attention is given to the problem of decomposing an array of rates into factors related to age, period, and cohort.... The paper focuses on the age and period dimensions and derives an initial description of the matrix's structure with regard to changes only in those two directions. This two-dimensional description is then augmented by a consideration of residual patterns that seem clearly linked to cohorts. The use of a model that is asymmetric in age, period, and cohort is justified by a detailed discussion of the problems of identification in models involving perfectly collinear independent variables. An important conclusion is that traditional modeling approaches that treat age, period, and cohort in a symmetric fashion are fundamentally flawed." Some of these concepts are illustrated using mortality data from France. This is a revised version of a paper originally presented at the 1989 Annual Meeting of the Population Association of America (see Population Index, Vol. 55, No. 3, Fall 1989, pp. 375-6).

Age Factors↗

PubMed2004

Reduced facilitation effect of collinear flankers on contrast detection reveals impaired lateral connectivity in the visual cortex of schizophrenia patients.

The aim of this study was to investigate lateral connectivity in early visual cortex of schizophrenia patients. Contrast thresholds were measured for centrally presented Gabor patches which were surrounded by two collinear or orthogonal flankers. The healthy subjects (n = 15) showed lower contrast thresholds for central Gabor patches when collinear flankers were presented. This effect was significantly reduced in unmedicated highly functioning schizophrenia patients (n = 20) who performed normally on the continuous performance test. The performance of the patients did not correlate with the positive and negative symptoms. The facilitation effect of collinear flankers is believed to reflect lateral interactions between feature-specific units in early visual cortex (V1). Our results therefore suggest abnormal lateral interactions in early visual cortex of schizophrenia patients.

Adult↗

PubMed1993

African swine fever virus thymidylate kinase gene: sequence and transcriptional mapping.

A putative thymidylate kinase gene of African swine fever virus has been identified at the left end of the SalI I' fragment of the virus genome. The gene, designated A240L, has the potential to encode a protein of 240 amino acids with an M(r) of 27,754 and is transcribed early after infection. Primer extension analysis indicates that transcription is initiated a short distance from the first ATG codon of open reading frame A240L. The deduced amino acid sequence of this open reading frame shows significant similarity with the human, yeast and vaccinia virus thymidylate kinases, the degree of identity being 23.7, 25 and 23.5%, respectively. The putative African swine fever virus thymidylate kinase sequence is essentially collinear with the other thymidylate kinase sequences, but contains a carboxy-terminal extension of 37 amino acids rich in glutamic and aspartic acids. The A240L protein conserves the ATP-binding and nucleotide/nucleoside-binding domains characteristic of thymidylate kinases.

African Swine Fever Virus↗

PubMed2026

First genomic insights into the introgression of almond PPV-Marcus resistance into peach.

AIM: Sharka, caused by Plum pox virus (PPV), is one of the most damaging viral diseases of stone fruit crops, with peach among the most susceptible cultivated Prunus species. Almond is a promising source of resistance, but its genetic architecture and expression in a peach genetic background remain largely unknown. This study aimed to construct parental genetic linkage maps and identify genomic regions associated with PPV response in almond × peach interspecific populations. METHODS: Progenies derived from the almond cultivars 'Del Cid', 'Garrigues', and 'Mono' were evaluated by RT-PCR after graft inoculation with the PPV-Marcus (PPV-M) strain over consecutive infection cycles. Phenotypic data were summarized for each genotype using best linear unbiased estimates (BLUEs). High-density SNP almond and peach arrays were used to construct parental maps for 'Garrigues' and 'Mono' and perform quantitative trait locus (QTL) analysis. RESULTS: Phenotypic variation was observed among and within families. 'Del Cid'-derived progenies showed the greatest resistance, 'Garrigues'-derived progenies displayed intermediate responses, and 'Mono'-derived progenies showed greater susceptibility and variability. The parental maps covered 546.69 cM in 'Mono' and 521.72 cM in 'Garrigues', with average intervals of 0.61 and 1.26 cM per unique marker position, respectively, and showed strong collinearity with the reference genome. QTL associated with PPV-M response were detected on linkage groups (LG) 1 and 6 in 'Garrigues' and LG2 in 'Mono'. The main QTL in 'Garrigues' peaked near 22.39 Mb on LG1, whereas the 'Mono' QTL was located at 22.27-22.62 Mb on LG2; a weaker QTL was detected near 25.38 Mb on LG6 in 'Garrigues'. The results support a quantitative and genetic-background-dependent architecture of PPV resistance. CONCLUSION: This study provides the first evidence of genomic regions associated with PPV-Marcus response in almond × peach populations. The detected QTLs provide an initial basis to support the introgression of almond-derived resistance into peach breeding material.

Prunus↗

PubMed2003

The complete sequence of the Adoxophyes orana granulovirus genome.

The nucleotide sequence of the Adoxophyes orana granulovirus (AdorGV) DNA genome was determined and analysed. The genome contains 99,657 bp and has an A + T content of 65.5%. The analysis predicted 119 ORFs of 150 nucleotides or larger that showed minimal overlap. Of these putative genes, 104 (87%) were homologous to genes identified previously in other baculoviruses. The mean overall amino acid identity of AdorGV ORFs was highest with CpGV ORFs at 48%. Sixty-three ORFs were conserved among all lepidopteran baculoviruses and are considered to be common baculoviral genes. Several genes reported to have major roles in baculovirus biology were not found in the AdorGV genome. These included chitinase and cathepsin, which are involved in the liquefaction of the host, which explains why AdorGV-infected insects do not degrade in a typical manner. The AdorGV genome encoded two inhibitor of apoptosis (iap) genes iap-3 and iap-5. Among all of the granuloviruses genomes there was a very high level of gene collinearity. The genes shared by AdorGV and CpGV had exactly the same order along the genome with the exception of one gene, iap-3. The AdorGV genome did not contain typical homologous region (hr) sequences. However, it contained nine repetitive regions in the genome.

Animals↗

PubMed2003

Genetic analysis and genome mapping in Raphanus.

The first genetic map of the Raphanus genome was developed based on meiosis in a hybrid between Raphanus sativus (cultivated radish) and Raphanus raphanistrum (wild radish). This hybrid was used to produce a BC1 population of 54 individuals and an F2 population of 85 individuals. A total of 236 marker loci were assayed in these populations using a set of 144 informative Brassica RFLP probes previously used for genetic mapping in other crucifer species. The genetic maps derived from the BC1 and F2 populations were perfectly collinear and were integrated to produce a robust Raphanus map. Cytological observations demonstrated strict bivalent pairing in the R. sativus x R. raphanistrum hybrids. Productive pairing along the length of each chromosome was confirmed by the identification of nine extensive linkage groups and the lack of clustering of marker loci. Indeed, the distributions of both marker loci and crossovers was more random than those reported for other crop species. The genetic markers and the reference map of Raphanus will be of considerable value for future trait mapping and marker-assisted breeding in this crop, as well as in the intergenomic transfer of Raphanus genes into Brassica crops. The future benefits of comparative mapping with Arabidopsis and Brassica species are also discussed.

Chromosome Mapping↗