542 research outputs found
Pairwise alignment incorporating dipeptide covariation
Motivation: Standard algorithms for pairwise protein sequence alignment make
the simplifying assumption that amino acid substitutions at neighboring sites
are uncorrelated. This assumption allows implementation of fast algorithms for
pairwise sequence alignment, but it ignores information that could conceivably
increase the power of remote homolog detection. We examine the validity of this
assumption by constructing extended substitution matrixes that encapsulate the
observed correlations between neighboring sites, by developing an efficient and
rigorous algorithm for pairwise protein sequence alignment that incorporates
these local substitution correlations, and by assessing the ability of this
algorithm to detect remote homologies. Results: Our analysis indicates that
local correlations between substitutions are not strong on the average.
Furthermore, incorporating local substitution correlations into pairwise
alignment did not lead to a statistically significant improvement in remote
homology detection. Therefore, the standard assumption that individual residues
within protein sequences evolve independently of neighboring positions appears
to be an efficient and appropriate approximation
CMOS + stochastic nanomagnets: heterogeneous computers for probabilistic inference and learning
Extending Moore's law by augmenting complementary-metal-oxide semiconductor
(CMOS) transistors with emerging nanotechnologies (X) has become increasingly
important. Accelerating Monte Carlo algorithms that rely on random sampling
with such CMOS+X technologies could have significant impact on a large number
of fields from probabilistic machine learning, optimization to quantum
simulation. In this paper, we show the combination of stochastic magnetic
tunnel junction (sMTJ)-based probabilistic bits (p-bits) with versatile Field
Programmable Gate Arrays (FPGA) to design a CMOS + X (X = sMTJ) prototype. Our
approach enables high-quality true randomness that is essential for Monte Carlo
based probabilistic sampling and learning. Our heterogeneous computer
successfully performs probabilistic inference and asynchronous Boltzmann
learning, despite device-to-device variations in sMTJs. A comprehensive
comparison using a CMOS predictive process design kit (PDK) reveals that
compact sMTJ-based p-bits replace 10,000 transistors while dissipating two
orders of magnitude of less energy (2 fJ per random bit), compared to digital
CMOS p-bits. Scaled and integrated versions of our CMOS + stochastic nanomagnet
approach can significantly advance probabilistic computing and its applications
in various domains by providing massively parallel and truly random numbers
with extremely high throughput and energy-efficiency
An ATP-binding cassette-type cysteine transporter in Campylobacter jejuni inferred from the structure of an extracytoplasmic solute receptor protein
Campylobacter jejuni is a Gram-negative food-borne pathogen associated with gastroenteritis in humans as well as cases of the autoimmune disease Guillain Barre syndrome. C. jejuni is asaccharolytic because it lacks an active glycolytic pathway for the use of sugars as a carbon source. This suggests an increased reliance on amino acids as nutrients and indeed the genome sequence of this organism indicates the presence of a number of amino acid uptake systems. Cj0982, also known as CjaA, is a putative extracytoplasmic solute receptor for one such uptake system as well as a major surface antigen and vaccine candidate. The crystal structure of Cj0982 reveals a two-domain protein with density in the enclosed cavity between the domains that clearly defines the presence of a bound cysteine ligand. Fluorescence titration experiments were used to demonstrate that Cj0982 binds cysteine tightly and specifically with a K-d of similar to 10(-7) M consistent with a role as a receptor for a high- affinity transporter. These data imply that Cj0982 is the binding protein component of an ABC-type cysteine transporter system and that cysteine uptake is important in the physiology of C. jejuni
Development of Full-Length cDNAs from Chinese Cabbage (Brassica rapa Subsp. pekinensis) and Identification of Marker Genes for Defence Response
Arabidopsis belongs to the Brassicaceae family and plays an important role as a model plant for which researchers have developed fine-tuned genome resources. Genome sequencing projects have been initiated for other members of the Brassicaceae family. Among these projects, research on Chinese cabbage (Brassica rapa subsp. pekinensis) started early because of strong interest in this species. Here, we report the development of a library of Chinese cabbage full-length cDNA clones, the RIKEN BRC B. rapa full-length cDNA (BBRAF) resource, to accelerate research on Brassica species. We sequenced 10 000 BBRAF clones and confirmed 5476 independent clones. Most of these cDNAs showed high homology to Arabidopsis genes, but we also obtained more than 200 cDNA clones that lacked any sequence homology to Arabidopsis genes. We also successfully identified several possible candidate marker genes for plant defence responses from our analysis of the expression of the Brassica counterparts of Arabidopsis marker genes in response to salicylic acid and jasmonic acid. We compared gene expression of these markers in several Chinese cabbage cultivars. Our BBRAF cDNA resource will be publicly available from the RIKEN Bioresource Center and will help researchers to transfer Arabidopsis-related knowledge to Brassica crops
Quasi-radial growth of metal tube on si nanowires template
It is reported in this article that Si nanowires can be employed as a positive template for the controllable electrochemical deposition of noble metal tube. The deposited tube exhibits good crystallinity. Scanning electron microscope and transmission electron microscope characterizations are conducted to reveal the growth process of metal tube, showing that the metal tube grows quasi-radially on the wall of Si nanowire. The quasi-radial growth of metal enables the fabrication of thickness-defined metal tube via changing deposition time. Inner-diameter-defined metal tube is achieved by choosing Si nanowires with desired diameter as a template. Metal tubes with inner diameters ranging from 1 μm to sub-50 nm are fabricated
NBRP databases: databases of biological resources in Japan
The National BioResource Project (NBRP) is a Japanese project that aims to establish a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is promoted by 27 core resource facilities, each concerned with a particular group of organisms, and by one information center. The NBRP database is a product of this project. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created and made available through the NBRP home page (http://www.nbrp.jp). The 30 independent databases have individual features which directly reflect the data maintained by each resource facility. The BRW is designed for users who need to search across several resources without moving from one database to another. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones and so on. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials. A circulation system allows users to submit details of papers published on research conducted using NBRP resources
Models of natural mutations including site heterogeneity
New computational models of natural site mutations are developed that account for the different selective pressures acting on different locations in the protein. The number of adjustable parameters is greatly reduced by basing the models on the underlying physical-chemical properties of the amino acids. This allows us to use our method on small data sets built of specific protein types. We demonstrate that with this approach we can represent the evolutionary patterns in HIV envelope proteins far better than with more traditional methods. Proteins 32:289–295, 1998. © 1998 Wiley-Liss, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/38528/1/4_ftp.pd
Microscopic approach to current-driven domain wall dynamics
This review describes in detail the essential techniques used in microscopic
theories on spintronics. We have investigated the domain wall dynamics induced
by electric current based on the - exchange model. The domain wall is
treated as rigid and planar and is described by two collective coordinates: the
position and angle of wall magnetization. The effect of conduction electrons on
the domain wall dynamics is calculated in the case of slowly varying spin
structure (close to the adiabatic limit) by use of a gauge transformation. The
spin-transfer torque and force on the wall are expressed by Feynman diagrams
and calculated systematically using non-equilibrium Green's functions, treating
electrons fully quantum mechanically. The wall dynamics is discussed based on
two coupled equations of motion derived for two collective coordinates. The
force is related to electron transport properties, resistivity, and the Hall
effect. Effect of conduction electron spin relaxation on the torque and wall
dynamics is also studied.Comment: manucript accepted to Phys. Re
- …