156 research outputs found
Boron and Nitrogen Doped Single walled Carbon Nanotubes as Possible Dilute Magnetic Semiconductors
The structure of single walled armchair and zig-zag carbon nanotubes having 70 atoms and two carbons replaced by boron or nitrogen is obtained at minium energy using HF/6-31G* molecular orbital theory. The calculations show that the ground state of the zig-zag tubes is a triplet state while for the armchair tubes it is a singlet. In the zig-zag tubes the density of states at the Fermi level is greater for the spin down states compared to the spin up state indicating that the doped tubes could be ferromagnetic
The DLV System for Knowledge Representation and Reasoning
This paper presents the DLV system, which is widely considered the
state-of-the-art implementation of disjunctive logic programming, and addresses
several aspects. As for problem solving, we provide a formal definition of its
kernel language, function-free disjunctive logic programs (also known as
disjunctive datalog), extended by weak constraints, which are a powerful tool
to express optimization problems. We then illustrate the usage of DLV as a tool
for knowledge representation and reasoning, describing a new declarative
programming methodology which allows one to encode complex problems (up to
-complete problems) in a declarative fashion. On the foundational
side, we provide a detailed analysis of the computational complexity of the
language of DLV, and by deriving new complexity results we chart a complete
picture of the complexity of this language and important fragments thereof.
Furthermore, we illustrate the general architecture of the DLV system which
has been influenced by these results. As for applications, we overview
application front-ends which have been developed on top of DLV to solve
specific knowledge representation tasks, and we briefly describe the main
international projects investigating the potential of the system for industrial
exploitation. Finally, we report about thorough experimentation and
benchmarking, which has been carried out to assess the efficiency of the
system. The experimental results confirm the solidity of DLV and highlight its
potential for emerging application areas like knowledge management and
information integration.Comment: 56 pages, 9 figures, 6 table
Transphyletic conservation of developmental regulatory state in animal evolution
Specific regulatory states, i.e., sets of expressed transcription factors, define the gene expression capabilities of cells in animal development. Here we explore the functional significance of an unprecedented example of regulatory state conservation from the cnidarian Nematostella to Drosophila, sea urchin, fish, and mammals. Our probe is a deeply conserved cis-regulatory DNA module of the SRY-box B2 (soxB2), recognizable at the sequence level across many phyla. Transphyletic cis-regulatory DNA transfer experiments reveal that the plesiomorphic control function of this module may have been to respond to a regulatory state associated with neuronal differentiation. By introducing expression constructs driven by this module from any phyletic source into the genomes of diverse developing animals, we discover that the regulatory state to which it responds is used at different levels of the neurogenic developmental process, including patterning and development of the vertebrate forebrain and neurogenesis in the Drosophila optic lobe and brain. The regulatory state recognized by the conserved DNA sequence may have been redeployed to different levels of the developmental regulatory program during evolution of complex central nervous systems
Since 2015 the SinoGerman research project SIGN supports water quality improvement in the Taihu region, China
Internationalization and diversification strategies of agricultural cooperatives: a quantitative study of the agricultural cooperatives in the state of Parana
Tailor-Made Zinc-Finger Transcription Factors Activate FLO11 Gene Expression with Phenotypic Consequences in the Yeast Saccharomyces cerevisiae
Cys2His2 zinc fingers are eukaryotic DNA-binding motifs, capable of distinguishing different DNA sequences, and are suitable for engineering artificial transcription factors. In this work, we used the budding yeast Saccharomyces cerevisiae to study the ability of tailor-made zinc finger proteins to activate the expression of the FLO11 gene, with phenotypic consequences. Two three-finger peptides were identified, recognizing sites from the 5β² UTR of the FLO11 gene with nanomolar DNA-binding affinity. The three-finger domains and their combined six-finger motif, recognizing an 18-bp site, were fused to the activation domain of VP16 or VP64. These transcription factor constructs retained their DNA-binding ability, with the six-finger ones being the highest in affinity. However, when expressed in haploid yeast cells, only one three-finger recombinant transcription factor was able to activate the expression of FLO11 efficiently. Unlike in the wild-type, cells with such transcriptional activation displayed invasive growth and biofilm formation, without any requirement for glucose depletion. The VP16 and VP64 domains appeared to act equally well in the activation of FLO11 expression, with comparable effects in phenotypic alteration. We conclude that the functional activity of tailor-made transcription factors in cells is not easily predicted by the in vitro DNA-binding activity
Cytoskeletal protein kinases: titin and its relations in mechanosensing
Titin, the giant elastic ruler protein of striated muscle sarcomeres, contains a catalytic kinase domain related to a family of intrasterically regulated protein kinases. The most extensively studied member of this branch of the human kinome is the Ca2+βcalmodulin (CaM)-regulated myosin light-chain kinases (MLCK). However, not all kinases of the MLCK branch are functional MLCKs, and about half lack a CaM binding site in their C-terminal autoinhibitory tail (AI). A unifying feature is their association with the cytoskeleton, mostly via actin and myosin filaments. Titin kinase, similar to its invertebrate analogue twitchin kinase and likely other βMLCKsβ, is not Ca2+βcalmodulin-activated. Recently, local protein unfolding of the C-terminal AI has emerged as a common mechanism in the activation of CaM kinases. Single-molecule data suggested that opening of the TK active site could also be achieved by mechanical unfolding of the AI. Mechanical modulation of catalytic activity might thus allow cytoskeletal signalling proteins to act as mechanosensors, creating feedback mechanisms between cytoskeletal tension and tension generation or cellular remodelling. Similar to other MLCK-like kinases like DRAK2 and DAPK1, TK is linked to protein turnover regulation via the autophagy/lysosomal system, suggesting the MLCK-like kinases have common functions beyond contraction regulation
The HLH-6 Transcription Factor Regulates C. elegans Pharyngeal Gland Development and Function
The Caenorhabditis elegans pharynx (or foregut) functions as a pump that draws in food (bacteria) from the environment. While the βorgan identity factorβ PHA-4 is critical for formation of the C. elegans pharynx as a whole, little is known about the specification of distinct cell types within the pharynx. Here, we use a combination of bioinformatics, molecular biology, and genetics to identify a helix-loop-helix transcription factor (HLH-6) as a critical regulator of pharyngeal gland development. HLH-6 is required for expression of a number of gland-specific genes, acting through a discrete cis-regulatory element named PGM1 (Pharyngeal Gland Motif 1). hlh-6 mutants exhibit a frequent loss of a subset of glands, while the remaining glands have impaired activity, indicating a role for hlh-6 in both gland development and function. Interestingly, hlh-6 mutants are also feeding defective, ascribing a biological function for the glands. Pharyngeal pumping in hlh-6 mutants is normal, but hlh-6 mutants lack expression of a class of mucin-related proteins that are normally secreted by pharyngeal glands and line the pharyngeal cuticle. An interesting possibility is that one function of pharyngeal glands is to secrete a pharyngeal lining that ensures efficient transport of food along the pharyngeal lumen
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