335 research outputs found
Efficient Seeds Computation Revisited
The notion of the cover is a generalization of a period of a string, and
there are linear time algorithms for finding the shortest cover. The seed is a
more complicated generalization of periodicity, it is a cover of a superstring
of a given string, and the shortest seed problem is of much higher algorithmic
difficulty. The problem is not well understood, no linear time algorithm is
known. In the paper we give linear time algorithms for some of its versions ---
computing shortest left-seed array, longest left-seed array and checking for
seeds of a given length. The algorithm for the last problem is used to compute
the seed array of a string (i.e., the shortest seeds for all the prefixes of
the string) in time. We describe also a simpler alternative algorithm
computing efficiently the shortest seeds. As a by-product we obtain an
time algorithm checking if the shortest seed has length at
least and finding the corresponding seed. We also correct some important
details missing in the previously known shortest-seed algorithm (Iliopoulos et
al., 1996).Comment: 14 pages, accepted to CPM 201
Sequence context and crosslinking mechanism affect the efficiency of in vivo capture of a proteinâprotein interaction
Proteinâprotein interactions (PPIs) are essential for implementing cellular processes and thus methods for the discovery and study of PPIs are highly desirable. An emerging method for capturing PPIs in their native cellular environment is in vivo covalent chemical capture, a method that uses nonsense suppression to site specifically incorporate photoactivable unnatural amino acids (UAAs) in living cells. However, in one study we found that this method did not capture a PPI for which there was abundant functional evidence, a complex formed between the transcriptional activator Gal4 and its repressor protein Gal80. Here we describe the factors that influence the success of covalent chemical capture and show that the innate reactivity of the two UAAs utilized, ( pâ benzoylphenylalanine (pBpa) and p âazidophenylalanine (pAzpa)), plays a profound role in the capture of Gal80 by Gal4. Based upon these data, guidelines are outlined for the successful use of in vivo photoâcrosslinking to capture novel PPIs and to characterize the interfaces. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 391â397, 2014.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102672/1/bip22395.pd
Unzipping Kinetics of Double-Stranded DNA in a Nanopore
We studied the unzipping kinetics of single molecules of double-stranded DNA
by pulling one of their two strands through a narrow protein pore. PCR analysis
yielded the first direct proof of DNA unzipping in such a system. The time to
unzip each molecule was inferred from the ionic current signature of DNA
traversal. The distribution of times to unzip under various experimental
conditions fit a simple kinetic model. Using this model, we estimated the
enthalpy barriers to unzipping and the effective charge of a nucleotide in the
pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter
Technical assistance, neo-colonialism or mutual trade? The experience of an Anglo/Ukrainian/Russian social work practice learning project
Since the collapse of the Soviet Union there has been a steady stream of Western consultants ready to work in Eastern Europe and Russia and share professional and academic expertise and experience. Social work, unknown as a discrete discipline or profession in the Soviet Union, has been a growth area with funding from a variety of sources to help promote East-West partnerships.Social work theory and practice emphasises critical appraisal of policy and embraces issues of power, discrimination and oppression. Social work educators should therefore be especially alert to the complex ethical questions which these kinds of collaborations raise, and adept at finding practical solutions or workable compromises. This article explores these ethical and political issues with reference to a project to develop social work practice learning in a Russian oblast' (region). The project was an ambitious partnership of British, Ukrainian and Russian educators, involving numerous Russian social work and related agencies, and four Russian universities and colleges in one oblast'. The authors use a series of vignettes to help the reader achieve insights into these East-West transactions. The article concludes with a discussion of different interpretations of these dealings, using three prisms: technical assistance, neo-colonialism and mutual trade
Single Molecule Statistics and the Polynucleotide Unzipping Transition
We present an extensive theoretical investigation of the mechanical unzipping
of double-stranded DNA under the influence of an applied force. In the limit of
long polymers, there is a thermodynamic unzipping transition at a critical
force value of order 10 pN, with different critical behavior for homopolymers
and for random heteropolymers. We extend results on the disorder-averaged
behavior of DNA's with random sequences to the more experimentally accessible
problem of unzipping a single DNA molecule. As the applied force approaches the
critical value, the double-stranded DNA unravels in a series of discrete,
sequence-dependent steps that allow it to reach successively deeper energy
minima. Plots of extension versus force thus take the striking form of a series
of plateaus separated by sharp jumps. Similar qualitative features should
reappear in micromanipulation experiments on proteins and on folded RNA
molecules. Despite their unusual form, the extension versus force curves for
single molecules still reveal remnants of the disorder-averaged critical
behavior. Above the transition, the dynamics of the unzipping fork is related
to that of a particle diffusing in a random force field; anomalous,
disorder-dominated behavior is expected until the applied force exceeds the
critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure
Promoter prediction using physico-chemical properties of DNA
The ability to locate promoters within a section of DNA is known to be a very difficult and very important task in DNA analysis. We document an approach that incorporates the concept of DNA as a complex molecule using several models of its physico-chemical properties. A support vector machine is trained to recognise promoters by their distinctive physical and chemical properties. We demonstrate that by combining models, we can improve upon the classification accuracy obtained with a single model. We also show that by examining how the predictive accuracy of these properties varies over the promoter, we can reduce the number of attributes needed. Finally, we apply this method to a real-world problem. The results demonstrate that such an approach has significant merit in its own right. Furthermore, they suggest better results from a planned combined approach to promoter prediction using both physicochemical and sequence based techniques
Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts
A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/ Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts
The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs
We describe the design and performance of the near-infrared (1.51--1.70
micron), fiber-fed, multi-object (300 fibers), high resolution (R =
lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point
Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~
10^5 red giant stars that systematically sampled all Milky Way populations
(bulge, disk, and halo) to study the Galaxy's chemical and kinematical history.
It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014
using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New
Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV,
as well as a second spectrograph, a close copy of the first, operating at the
2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several
fiber-fed, multi-object, high resolution spectrographs have been built for
visual wavelength spectroscopy, the APOGEE spectrograph is one of the first
such instruments built for observations in the near-infrared. The instrument's
successful development was enabled by several key innovations, including a
"gang connector" to allow simultaneous connections of 300 fibers; hermetically
sealed feedthroughs to allow fibers to pass through the cryostat wall
continuously; the first cryogenically deployed mosaic volume phase holographic
grating; and a large refractive camera that includes mono-crystalline silicon
and fused silica elements with diameters as large as ~ 400 mm. This paper
contains a comprehensive description of all aspects of the instrument including
the fiber system, optics and opto-mechanics, detector arrays, mechanics and
cryogenics, instrument control, calibration system, optical performance and
stability, lessons learned, and design changes for the second instrument.Comment: 81 pages, 67 figures, PASP, accepte
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