171 research outputs found
Destruction Prediction of a Rubble Mound Weir Using VOF-DEM Coupled Model
Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchiv
Logic Ciucuits Using Solution-processed Single-walled Carbon Nanotue Transistors
This letter reports on the realization of logic circuits employing
solution-processed networks of single-walled carbon nanotubes. We constructed
basic logic gates (inverter, NAND and NOR) with n- and p-type field-effect
transistors fabricated by solution-based chemical doping. Complementary
metal-oxide-semiconductor inverters exhibited voltage gains of up to 20, which
illustrates the great potential of carbon nanotube networks for printable
flexible electronics.Comment: 12 PAGES, 3 FIGURE
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes
<p>Abstract</p> <p>Background</p> <p>A theoretical model of genetic redundancy has proposed that the fates of redundant genes depend on the degree of functional redundancy, and that functionally redundant genes will not be inherited together. However, no example of actual gene evolution has been reported that can be used to test this model. Here, we analyzed the molecular evolution of the ribonuclease H (RNase H) family in prokaryotes and used the results to examine the implications of functional redundancy for gene evolution.</p> <p>Results</p> <p>In prokaryotes, RNase H has been classified into RNase HI, HII, and HIII on the basis of amino acid sequences. Using 353 prokaryotic genomes, we identified the genes encoding the RNase H group and examined combinations of these genes in individual genomes. We found that the RNase H group may have evolved in such a way that the RNase HI and HIII genes will not coexist within a single genome – in other words, these genes are inherited in a mutually exclusive manner. Avoiding the simultaneous inheritance of the RNase HI and HIII genes is remarkable when RNase HI contains an additional non-RNase H domain, double-stranded RNA, and an RNA-DNA hybrid-binding domain, which is often observed in eukaryotic RNase H1. This evolutionary process may have resulted from functional redundancy of these genes, because the substrate preferences of RNase HI and RNase HIII are similar.</p> <p>Conclusion</p> <p>We provide two possible evolutionary models for RNase H genes in which functional redundancy contributes to the exclusion of redundant genes from the genome of a species. This is the first empirical study to show the effect of functional redundancy on changes in gene constitution during the course of evolution.</p
Uso da matriz de regeneração dérmica no tratamento cirúrgico de queimaduras em crianças
Trabalho de Conclusão de Curso - Universidade Federal de Santa Catarina. Curso de Medicina. Departamento de Pediatria
Transcription-Associated Mutagenesis Increases Protein Sequence Diversity More Effectively than Does Random Mutagenesis in Escherichia coli
BACKGROUND: During transcription, the nontranscribed DNA strand becomes single-stranded DNA (ssDNA), which can form secondary structures. Unpaired bases in the ssDNA are less protected from mutagens and hence experience more mutations than do paired bases. These mutations are called transcription-associated mutations. Transcription-associated mutagenesis is increased under stress and depends on the DNA sequence. Therefore, selection might significantly influence protein-coding sequences in terms of the transcription-associated mutability per transcription event under stress to improve the survival of Escherichia coli. METHODOLOGY/PRINCIPAL FINDINGS: The mutability index (MI) was developed by Wright et al. to estimate the relative transcription-associated mutability of bases per transcription event. Using the most stable fold of each ssDNA that have an average length n, MI was defined as (the number of folds in which the base is unpaired)/nx(highest -DeltaG of all n folds in which the base is unpaired), where DeltaG is the free energy. The MI values show a significant correlation with mutation data under stress but not with spontaneous mutations in E. coli. Protein sequence diversity is preferred under stress but not under favorable conditions. Therefore, we evaluated the selection pressure on MI in terms of the protein sequence diversity for all the protein-coding sequences in E. coli. The distributions of the MI values were lower at bases that could be substituted with each of the other three bases without affecting the amino acid sequence than at bases that could not be so substituted. Start codons had lower distributions of MI values than did nonstart codons. CONCLUSIONS/SIGNIFICANCE: Our results suggest that the majority of protein-coding sequences have evolved to promote protein sequence diversity and to reduce gene knockout under stress. Consequently, transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis under stress. Nonrandom transcription-associated mutagenesis under stress should improve the survival of E. coli
Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
The discovery of separate 5′ and 3′ halves of transfer RNA (tRNA) molecules—so-called split tRNA—in the archaeal parasite Nanoarchaeum equitans made us wonder whether ancestral tRNA was encoded on 1 or 2 genes. We performed a comprehensive phylogenetic analysis of tRNAs in 45 archaeal species to explore the relationship between the three types of tRNAs (nonintronic, intronic and split). We classified 1953 mature tRNA sequences into 22 clusters. All split tRNAs have shown phylogenetic relationships with other tRNAs possessing the same anticodon. We also mimicked split tRNA by artificially separating the tRNA sequences of 7 primitive archaeal species at the anticodon and analyzed the sequence similarity and diversity of the 5′ and 3′ tRNA halves. Network analysis revealed specific characteristics of and topological differences between the 5′ and 3′ tRNA halves: the 5′ half sequences were categorized into 6 distinct groups with a sequence similarity of >80%, while the 3′ half sequences were categorized into 9 groups with a higher sequence similarity of >88%, suggesting different evolutionary backgrounds of the 2 halves. Furthermore, the combinations of 5′ and 3′ halves corresponded with the variation of amino acids in the codon table. We found not only universally conserved combinations of 5′–3′ tRNA halves in tRNAiMet, tRNAThr, tRNAIle, tRNAGly, tRNAGln, tRNAGlu, tRNAAsp, tRNALys, tRNAArg and tRNALeu but also phylum-specific combinations in tRNAPro, tRNAAla, and tRNATrp. Our results support the idea that tRNA emerged through the combination of separate genes and explain the sequence diversity that arose during archaeal tRNA evolution
Quantum key distribution with an efficient countermeasure against correlated intensity fluctuations in optical pulses
Quantum key distribution (QKD) allows two distant parties to share secret
keys with the proven security even in the presence of an eavesdropper with
unbounded computational power. Recently, GHz-clock decoy QKD systems have been
realized by employing ultrafast optical communication devices. However,
security loopholes of high-speed systems have not been fully explored yet. Here
we point out a security loophole at the transmitter of the GHz-clock QKD, which
is a common problem in high-speed QKD systems using practical band-width
limited devices. We experimentally observe the inter-pulse intensity
correlation and modulation-pattern dependent intensity deviation in a practical
high-speed QKD system. Such correlation violates the assumption of most
security theories. We also provide its countermeasure which does not require
significant changes of hardware and can generate keys secure over 100 km fiber
transmission. Our countermeasure is simple, effective and applicable to wide
range of high-speed QKD systems, and thus paves the way to realize ultrafast
and security-certified commercial QKD systems
Renormalization Group Approach to Einstein Equation in Cosmology
The renormalization group method has been adapted to the analysis of the
long-time behavior of non-linear partial differential equation and has
demonstrated its power in the study of critical phenomena of gravitational
collapse. In the present work we apply the renormalization group to the
Einstein equation in cosmology and carry out detailed analysis of
renormalization group flow in the vicinity of the scale invariant fixed point
in the spherically symmetric and inhomogeneous dust filled universe model.Comment: 16 pages including 2 eps figures, RevTe
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals
<p>Abstract</p> <p>Background</p> <p>In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. We sought to elucidate a set of conserved miRNA/target-gene pairs and to analyse the mechanism underlying miRNA-mediated gene regulation in the early stage of bilaterian evolution.</p> <p>Results</p> <p>Initially, we extracted five evolutionarily conserved miRNAs (<it>let-7</it>, <it>miR-1</it>, <it>miR-124</it>, <it>miR-125/lin-4</it>, and <it>miR-34</it>) among five diverse bilaterian animals. Subsequently, we designed a procedure to predict evolutionarily conserved miRNA/target-gene pairs by introducing orthologous gene information. As a result, we extracted 31 orthologous miRNA/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous miRNA/target-gene pairs that were verified experimentally. Approximately 84% of the target genes were regulated by three miRNAs (<it>let-7, miR-1</it>, and <it>miR-124</it>) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. We used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in HeLa cells.</p> <p>Conclusions</p> <p>The application of our new method enables the identification of 31 miRNA/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. The downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by miRNAs; it was also an efficient tool for the elimination of false positives from the predicted candidates. In conclusion, our study identified potentially important miRNA-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage miRNA functions.</p
Star Formation Efficiency in the Central 1 kpc Region of Early-Type Spiral Galaxies
It has been reported recently that there are some early-type spiral (Sa--Sab)
galaxies having evident star-forming regions which concentrate in their own
central 1-kpc. In such central region, is the mechanism of the star formation
distinct from that in disks of spiral galaxies? To reveal this, we estimate the
star formation efficiency (SFE) in this central 1-kpc star-forming region of
some early-type spiral galaxies, taking account of the condition for this 1-kpc
region to be self-gravitating. Using two indicators of present star formation
rate (H and infrared luminosity), we estimate the SFE to be a few
percents. This is equivalent to the observational SFE in the disks of late-type
spiral (Sb--) galaxies. This coincidence may support the universality of the
mean SFE of spiral galaxies reported in the recent studies. That is, we find no
evidence of distinct mechanism of the star formation in the central 1-kpc
region of early-type galaxies. Also, we examine the structure of the central
star-forming region, and discuss a method for estimating the mass of
star-forming regions.Comment: accepted by A
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