5,133 research outputs found
Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome
LINE-1 elements (L1s) are a family of highly successful retrotransposons comprising ∼ 17% of the human genome, the majority of which have inserted through an endonuclease-dependent mechanism termed target-primed reverse transcription. Recent in vitro analyses suggest that in the absence of non-homologous end joining proteins, L1 elements may utilize an alternative, endonuclease-independent pathway for insertion. However, it remains unknown whether this pathway operates in vivo or in cell lines where all DNA repair mechanisms are functional. Here, we have analyzed the human genome to demonstrate that this alternative pathway for L1 insertion has been active in recent human evolution and characterized 21 loci where L1 elements have integrated without signs of endonuclease-related activity. The structural features of these loci suggest a role for this process in DNA double-strand break repair. We show that endonuclease-independent L1 insertions are structurally distinguishable from classical L1 insertion loci, and that they are associated with inter-chromosomal translocations and deletions of target genomic DNA. © 2007 The Author(s)
Endophytes: A Treasure House of Bioactive Compounds of Medicinal Importance
Endophytes are an endosymbiotic group of microorganisms that colonize in plants and microbes that can be readily isolated from any microbial or plant growth medium. They act as reservoirs of novel bioactive secondary metabolites, such as alkaloids, phenolic acids, quinones, steroids, saponins, tannins, and terpenoids that serve as a potential candidate for antimicrobial, anti-insect, anticancer and many more properties. While plant sources are being extensively explored for new chemical entities for therapeutic purposes, endophytic microbes also constitute an important source for drug discovery. This review aims to comprehend the contribution and uses of endophytes as an impending source of drugs against various forms of diseases and other possible medicinal use
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages
Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of ∼18 kb of sequence from the human genome and ∼15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1-mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions
Label-free biophysical markers from whole blood microfluidic immune profiling reveals severe immune response signatures
10.1002/smll.202006123SMALL171
Matter-gravity interaction in a multiply warped braneworld,
The role of a bulk graviton in predicting the signature of extra dimensions
through collider-based experiments is explored in the context of a multiply
warped spacetime. In particular it is shown that in a doubly warped braneworld
model, the presence of the sixth dimension, results in enhanced concentration
of graviton Kaluza Klein (KK) modes compared to that obtained in the usual
5-dimensional Randall-Sundrum model. Also, the couplings of these massive
graviton KK modes with the matter fields on the visible brane turn out to be
appreciably larger than that in the corresponding 5- dimensional model. The
significance of these results are discussed in the context of KK graviton
search at the Large Hadron Collider (LHC).Comment: 13 pages, 2 table
Human genomic deletions mediated by recombination between Alu elements
Recombination between Alu elements results in genomic deletions associated with many human genetic disorders. Here, we compare the reference human and chimpanzee genomes to determine the magnitude of this recombination process in the human lineage since the human-chimpanzee divergence ∼6 million years ago. Combining computational data mining and wet-bench experimental verification, we identified 492 human-specific deletions (for a total of ∼400 kb) attributable to this process, a significant component of the insertion/deletion spectrum of the human genome. The majority of the deletions (295 of 492) coincide with known or predicted genes (including 3 that deleted functional exons, as compared with orthologous chimpanzee genes), which implicates this process in creating a substantial portion of the genomic differences between humans and chimpanzees. Overall, we found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome. © 2006 by The American Society of Human Genetics. All rights reserved
Anchoring Bias in Online Voting
Voting online with explicit ratings could largely reflect people's
preferences and objects' qualities, but ratings are always irrational, because
they may be affected by many unpredictable factors like mood, weather, as well
as other people's votes. By analyzing two real systems, this paper reveals a
systematic bias embedding in the individual decision-making processes, namely
people tend to give a low rating after a low rating, as well as a high rating
following a high rating. This so-called \emph{anchoring bias} is validated via
extensive comparisons with null models, and numerically speaking, the extent of
bias decays with interval voting number in a logarithmic form. Our findings
could be applied in the design of recommender systems and considered as
important complementary materials to previous knowledge about anchoring effects
on financial trades, performance judgements, auctions, and so on.Comment: 5 pages, 4 tables, 5 figure
Alu Recombination-Mediated Structural Deletions in the Chimpanzee Genome
With more than 1.2 million copies, Alu elements are one of the most important sources of structural variation in primate genomes. Here, we compare the chimpanzee and human genomes to determine the extent of Alu recombination-mediated deletion (ARMD) in the chimpanzee genome since the divergence of the chimpanzee and human lineages (∼6 million y ago). Combining computational data analysis and experimental verification, we have identified 663 chimpanzee lineage-specific deletions (involving a total of ∼771 kb of genomic sequence) attributable to this process. The ARMD events essentially counteract the genomic expansion caused by chimpanzee-specific Alu inserts. The RefSeq databases indicate that 13 exons in six genes, annotated as either demonstrably or putatively functional in the human genome, and 299 intronic regions have been deleted through ARMDs in the chimpanzee lineage. Therefore, our data suggest that this process may contribute to the genomic and phenotypic diversity between chimpanzees and humans. In addition, we found four independent ARMD events at orthologous loci in the gorilla or orangutan genomes. This suggests that human orthologs of loci at which ARMD events have already occurred in other nonhuman primate genomes may be “at-risk” motifs for future deletions, which may subsequently contribute to human lineage-specific genetic rearrangements and disorders
Stochastic Heterostructures in B/N-Doped Carbon Nanotubes
Carbon nanotubes are one-dimensional and very narrow. These obvious facts
imply that under doping with boron and nitrogen, microscopic doping
inhomogeneity is much more important than for bulk semiconductors. We consider
the possibility of exploiting such fluctuations to create interesting devices.
Using self-consistent tight-binding (SCTB), we study heavily doped highly
compensated nanotubes, revealing the spontaneous formation of structures
resembling chains of random quantum dots, or nano-scale diode-like elements in
series. We also consider truly isolated impurities, revealing simple scaling
properties of bound state sizes and energies.Comment: 4 pages RevTeX, 4 PostScript figure
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