104,691 research outputs found
Marthinius A. Strand
No full textBlack and white photograph of Marthinius A. Strand in his Utah Ski Club sweater on the out run of a jumping hill
Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis
No full textIn all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.
Application of Pulsed Field Gel Electrophoresis to Determine γ-ray-induced Double-strand Breaks in Yeast Chromosomal Molecules
No full textThe frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb
Replication data for: Playing with fire compounds
No full textThe dataset contains:
Praat scripts for extracting and annotating relevant utterances from larger sound files, and extracting data (F0) from shorter sound files for further analysis.
Sound files (.wav) containing single utterances
Praat Pitch files with F0 contours of pitch accent tones
Praat TextGrid Files
R script for smoothing F0 contours using functional data analysis (fda), and making plots from and calculating correlation coefficients on the contours.
All material from a corpus of 7 children engaging in free peer interaction and self recording of 5 adults for baseline data.
Publication abstract:
Prosodic features are some of the most salient features of dialect variation in Norway. It is therefore no wonder that the switch in prosodic systems is what is first recognized by caretakers and scholars when Norwegian children code-switch to something resembling the dialect of the capital (henceforth Urban East Norwegian, UEN) in role play. With focus on the Scandinavian system of lexical accent tones, this paper investigates the spontaneous speech of North Norwegian children engaging in peer social role play. The paper makes the case that children fail to apply the target accent tone in compounds in consistency with UEN in role play, although the production of accent tones otherwise seems to be phonetically target like UEN. Put in other words, they perform in accordance with UEN phonetics, but not UEN morpho-phonology.</p
Strand-specific RNA-seq data.
No full text(A) Heat map showing strand-specific expression data from all 7G8 var gene loci in Sanaria cell bank ring stage parasites (aliquot B, 8. Generation). Strand-specific mapping of RNA-seq reads to the 7G8 reference genome (version 59). Scale bar indicates strand-specific bam file read coverage over 50 bp bins normalized to RPKM. Group affiliation of var genes is indicated by the color code: A-type var genes in red, the subfamily var1 in dark red, B-type genes in blue, group C genes in green, and the var2csa gene (group E) in yellow. On PlasmoDB annotated pseudogenes are marked with asterisk. The orientation of each gene is indicated in brackets after the accession number. (B) Forward and reverse strand profiles of transcribed var genes in cell bank A parasites (IGV). Scales were adjusted to depict low level antisense lncRNA transcripts. (PDF)</p
Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
No full textOne of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information
Strand-specific affinity of host factor hnRNP C1/C2 guides positive to negative-strand ratio in Coxsackievirus B3 infection
No full textCoxsackievirus B3 is an enterovirus, with positive-sense single-stranded RNA genome containing ‘Internal Ribosome Entry Site’ (IRES) in the 5ʹUTR. Once sufficient viral proteins are synthesized in the cell from the input RNA, viral template switches from translation to replication to synthesize negative-strand RNA. Inhibition of translation is a key step in regulating this switch as the positive-strand RNA template should be free of ribosomes to enable polymerase movement. In this study, we show how a host protein hnRNP C1/C2 inhibits viral RNA translation. hnRNP C1/C2 interacts with stem-loop V in the IRES and displaces poly-pyrimidine tract binding protein, a positive regulator of translation. We further demonstrate that hnRNP C1/C2 induces translation to replication switch, independently from the already known role of the ternary complex (PCBP2-3CD-cloverleaf RNA). These results suggest a novel function of hnRNP C1/C2 in template switching of positive-strand from translation to replication by a new mechanism. Using mathematical modelling, we show that the differential affinity of hnRNP C1/C2 for positive and negative-strand RNAs guides the final ± RNA ratio, providing first insight in the regulation of the positive to negative-strand RNA ratio in enteroviruses.</p
Sex differences in Cognitive Abilities Test scores: a UK national picture
No full textBackground and aims. There is uncertainty about the extent or even existence of sex differences in the mean and variability of reasoning test scores ( Jensen, 1998; Lynn, 1994, ; Mackintosh, 1996). This paper analyses the Cognitive Abilities Test (CAT) scores of a large and representative sample of UK pupils to determine the extent of any sex differences.
Sample. A nationally representative UK sample of over 320,000 school pupils aged 11-12 years was assessed on the CAT (third edition) between September 2001 and August 2003. The CAT includes separate nationally standardized tests for verbal, quantitative, and non-verbal reasoning. The size and recency of the sample is unprecedented in research on this issue.
Methods. The sheer size of the sample ensures that any sex difference will achieve statistical significance. Therefore, effect sizes (d) and variance ratios (VR) are employed to evaluate the magnitude of sex differences in mean scores and in score variability, respectively.
Results. The mean verbal reasoning score for girls was 2.2 standard score points higher than the mean for boys, but only 0.3 standard points in favour of girls for non-verbal reasoning (NVR), and 0.7 points in favour of boys for quantitative reasoning (QR). However, for all three tests there were substantial sex differences in the standard deviation of scores, with greater variance among boys. Boys were over represented relative to girls at both the top and the bottom extremes for all tests, with the exception of the top 10% in verbal reasoning.
Conclusions. Given the small differences in means, explanations for sex differences in wider domains such examination attainment at age 16 need to look beyond conceptions of `ability'. Boys tend to be both the lowest and the highest performers in terms of their reasoning abilities, which warns against the danger of stereotyping boys as low achievers
Strand-seq of the proximal inversion at 15q25.
No full textOn the left, ideograms of expected Strand-seq results for each possible inversion genotype are shown. On the right, a UCSC Genome Browser view (coordinates lifted to GRCh37/hg19) of Strand-seq data, BED-formatted and uploaded as custom tracks, of the three libraries is shown. For each cell, aligned reads are indicated as individual lines in Crick (teal) or Watson (orange) state. In the library on the top (HsSs_0256) mixed Watson and Crick reads at the proximal inversion (black arrow) indicate the heterozygosity of the region while in the others a direct orientation of the region is shown.</p
Strand-specific deep sequencing of the transcriptome
No full textSeveral studies support that antisense-mediated regulation may affect a large proportion of genes. Using the Illumina next-generation sequencing platform, we developed DSSS (direct strand specific sequencing), a strand-specific protocol for transcriptome sequencing. We tested DSSS with RNA from two samples, prokaryotic (Mycoplasma pneumoniae) as well as eukaryotic (Mus musculus), and obtained data containing strand-specific information, using single-read and paired-end sequencing. We validated our results by comparison with a strand-specific tiling array data set for strain M129 of the simple prokaryote M. pneumoniae, and by quantitative PCR (qPCR). The results of DSSS were very well supported by the results from tiling arrays and qPCR. Moreover, DSSS provided higher dynamic range and single-base resolution, thus enabling efficient antisense detection and the precise mapping of transcription start sites and untranslated regions. DSSS data for mouse confirmed strand specificity of the protocol and the general applicability of the approach to studying eukaryotic transcription. We propose DSSS as a simple and efficient strategy for strand-specific transcriptome sequencing and as a tool for genome annotation exploiting the increased read lengths that next-generation sequencing technology now is capable to deliver.</jats:p
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