110,240 research outputs found
Joshua Davis: Author of Spare Parts
No full textCitation: K-State First (2016). Joshua Davis: Author of Spare Parts [Flier]. Manhattan, Kansas: K-State First.Flyer advertising Joshua Davis's author talk at Kansas State University
Steven Johnson Author Talk Poster
No full textK-State Book NetworkA poster advertising an author talk by Steven Johnson at Kansas State University on September 3, 2014. Steven Johnson's book "The Ghost Map" was the 2014-2015 common book
Strand-specific expression data reveal novel transcript features.
No full textTop row: Novel transcripts observed antisense to HAH_2649 (arCOG11826) and HAH_0885 (SOS response associated peptidase). Bottom row: Targets predicted to encode small proteins appear to have extended 3’ UTRs. Green tracks show the per base coverage of transcripts originating from the top strand for representative sample. Blue histograms show transcripts originating from the bottom strand. (EPS)</p
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
K-ras and p53 mutations in colonic lavage fluid of patients with colorectal neoplasias
No full textBackground: The adenoma-carcinoma sequence has its molecular basis in several gene mutations of which K-ras and p53 are of paramount importance. The aims of this study were to evaluate whether these genetic alterations can be detected in colonic lavage fluid from patients with colorectal adenomas and carcinomas. Methods: In 45 patients with adenomas, 20 patients with colorectal carcinomas and 38 patients with non-neoplastic and noninflammatory diseases of the colon p53 and K-ras mutations were evaluated in colonic lavage fluid employing single-strand confirmation polymorphism analysis and dot-blot hybridization, respectively. Results: Mutations of the K-ras and the p53 gene were found in 15.6% (p = 0.065) of patients with adenomas, in 25.0% (p = 0.016) of patients with carcinomas and in 2.6% in the control group. Conclusion: Genetic alterations in the colonic lavage fluid could be an additional diagnostic tool for the surveillance of patients with colorectal neoplasias. Copyright (C) 2001 S. Karger AG, Basel
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.
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
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
Smoothed particle hydrodynamics modelling for failure in metals
No full textIt is generally regarded to be a difficult task to model multiple fractures leading to
fragmentation in metals subjected to high strain rates using numerical methods.
Meshless methods such as Smoothed Particle Hydrodynamics (SPH) are well suited to
the application of fracture mechanics, since they are not prone to the problems
associated with mesh tangling.
This research demonstrates and validates a numerical inter-particle fracture model for
the initiation, growth and subsequent failure in metals at high strain rate, applicable
within a Total Lagrangian SPH scheme. Total Lagrangian SPH performs calculations in
the reference state of a material and therefore the neighbourhoods remain fixed
throughout the computation; this allows the inter-particle bonds to be stored and tracked
as material history parameters. Swegle (2000) showed that the SPH momentum
equation can be rearranged in terms of a particle-particle interaction area. By reducing
this area to zero via an inter-particle damage parameter, the principles of continuum
damage mechanics can be observed without the need for an effective stress term, held at
the individual particles.
This research makes use of the Cochran-Banner damage growth model which has been
updated for 3D damage and makes the appropriate modifications for inter-particle
damage growth. The fracture model was tested on simulations of a 1D flyer plate impact
test and the results were compared to experimental data. The test showed that the model
can recreate the phenomena associated with uniaxial spall to a high degree of accuracy.
Some limited modelling was also conducted in 2 and 3 dimensions and promising
results were observed.
Research was also performed into the mesh sensitivity of the explosively driven Mock-
Holt experiment. 3D simulations using the Eulerian SPH formulation were conducted
and the best results were observed with a radial packing arrangement.
An in-depth assessment of the Monaghan repulsive force correction was also conducted
in attempt to eliminate the presence of the SPH tensile instability and stabilise the
available Eulerian SPH code. Successful results were observed in 1D, although the
results could not be replicated consistently in 2D. A further study was also conducted
into an approach that makes use of a partition of unity weighting to two different SPH
approximations of the same flow-field; one local and one non-local (or extended).
Unfortunately this approach could not be made to stabilise the code
Strand-specific cDNA and RT-PCR analysis of the mouse GnRH-E1 RNA variants.
No full text(A) Schematic diagram of the sense GnRH-E1 RNA variant, with a 3’ polyA site located downstream of GnRH-E1 as predicted by RACE. PCR primers in reverse direction at -1128 bp or -1271 bp (reverse arrows) were used for strand-specific cDNA synthesis to capture the sense GnRH-E1 RNA. PCR analysis was performed using -1271 bp or -1128 bp reverse primer paired with the forward primers at -3560 bp, -3606 bp, -3779 bp, and -3746 bp (forward arrows) from the mouse Gnrh1 TSS. Primer positions are aligned to the mouse conserved regulatory elements and coordinates diagrammed above. (B) Strand-specific cDNA synthesized using the -1271 bp reverse primer was subject to PCR analysis using the following primer pairs: -3560F/-1271R, -3606F/-1271R, -3779F/-1271R, -3746F/-1271R. Strand-specific cDNA synthesized using -1128 bp reverse primer was subject to PCR analysis using the primer pair -3560F/-1128R. (C) Schematic diagram of the mouse antisense GnRH-E1 RNA variant, with a 3’ polyA site predicted upstream of GnRH-E2 by RACE. PCR primers in the forward direction at -3560 bp or -3371 bp (forward arrows) was used for strand-specific cDNA synthesis to capture the antisense GnRH-E1 RNA variant. PCR analysis was performed using -3371 bp or -3560 bp forward primer paired with the reverse primers at -1443 bp, -1271 bp, -1128 bp from the Gnrh1 TSS. D) Strand-specific cDNA synthesized using the -3371 bp forward primer was subject to PCR analysis using the following PCR primer pairs -3371F/-1443R, -3371F/-1271R, and -3371F/-1128R. Strand-specific cDNA synthesized using the -3560 bp forward primer was subject to PCR analysis using the primer pair at -3560F/-1443R. All reverse transcription reactions were performed on total RNA samples with (+) and without (-) reverse transcriptase and were amplified by PCR in parallel with GT1-7 genomic DNA control and no-template water control (NTC). The size of PCR amplicons was marked by 1 kbp DNA ladder.</p
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