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LEAping to conclusions: a computational reanalysis of late embryogenesis abundant proteins and their possible roles.
RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: The late embryogenesis abundant (LEA) proteins cover a number of loosely related groups of proteins, originally found in plants but now being found in non-plant species. Their precise function is unknown, though considerable evidence suggests that LEA proteins are involved in desiccation resistance. Using a number of statistically-based bioinformatics tools the classification of a large set of LEA proteins, covering all Groups, is reexamined together with some previous findings. Searches based on peptide composition return proteins with similar composition to different LEA Groups; keyword clustering is then applied to reveal keywords and phrases suggestive of the Groups' properties. RESULTS: Previous research has suggested that glycine is characteristic of LEA proteins, but it is only highly over-represented in Groups 1 and 2, while alanine, thought characteristic of Group 2, is over-represented in Group 3, 4 and 6 but under-represented in Groups 1 and 2. However, for LEA Groups 1 2 and 3 it is shown that glutamine is very significantly over-represented, while cysteine, phenylalanine, isoleucine, leucine and tryptophan are significantly under-represented. There is also evidence that the Group 4 LEA proteins are more appropriately redistributed to Group 2 and Group 3. Similarly, Group 5 is better found among the Group 3 LEA proteins. CONCLUSIONS: There is evidence that Group 2 and Group 3 LEA proteins, though distinct, might be related. This relationship is also evident in the overlapping sets of keywords for the two Groups, emphasising alpha-helical structure and, at a larger scale, filaments, all of which fits well with experimental evidence that proteins from both Groups are natively unstructured, but become structured under stress conditions. The keywords support localisation of LEA proteins both in the nucleus and associated with the cytoskeleton, and a mode of action similar to chaperones, perhaps the cold shock chaperones, via a role in DNA-binding. In general, non-globular and low-complexity proteins, such as the LEA proteins, pose particular challenges in determining their functions and modes of action. Rather than masking off and ignoring low-complexity domains, novel tools and tool combinations are needed which are capable of analysing such proteins in their entirety
Court Disregards Legislative History of the Civil Rights Act of 1991 and Bucks Current Trends Regarding Punitive Damages
Kolstad v. American Dental Ass\u27n, 108 F.3d 1431 (D.C. Cir. 1996)
Minimal Extension of the Standard Model Scalar Sector
The minimal extension of the scalar sector of the standard model contains an
additional real scalar field with no gauge quantum numbers. Such a field does
not couple to the quarks and leptons directly but rather through its mixing
with the standard model Higgs field. We examine the phenomenology of this model
focusing on the region of parameter space where the new scalar particle is
significantly lighter than the usual Higgs scalar and has small mixing with it.
In this region of parameter space most of the properties of the additional
scalar particle are independent of the details of the scalar potential.
Furthermore the properties of the scalar that is mostly the standard model
Higgs can be drastically modified since its dominant branching ratio may be to
a pair of the new lighter scalars.Comment: 4 pages, 2 figure
Welcome to Microbial Informatics and Experimentation
Microbial Informatics and Experimentation (MIE) is a journal about computers and microbes. We created a new journal to fill a gap for which there is no publication avenue that is particularly geared to computationally-oriented, strongly biologically motivated, pragmatic articles focused on microbes. On the one hand, the bioinformatics journals are generally very computer technical and unlikely to be read by the diverse community of microbiologists. There is also a strong emphasis in bioinformatics literature on human/mammalian systems, though this is a secondary issue. On the other hand, microbial informatics work has appeared in a variety of microbiological publications, but it is seldom a good fit there either, and methods that span diverse microbes have no obvious home
How Magnetic is the Dirac Neutrino?
We derive model-independent, "naturalness" upper bounds on the magnetic
moments \mu_\nu of Dirac neutrinos generated by physics above the scale of
electroweak symmetry breaking. In the absence of fine-tuning of effective
operator coefficients, we find that current information on neutrino mass
implies that |\mu_\nu | < 10^(-14) Bohr magnetons. This bound is several orders
of magnitude stronger than those obtained from analyses of solar and reactor
neutrino data and astrophysical observations.Comment: 4 pages, 3 figures, Majorana case discussion corrected. References
updated; replaced to match published versio
Towards a High Energy Theory for the Higgs Phase of Gravity
Spontaneous Lorentz violation due to a time-dependent expectation value for a
massless scalar has been suggested as a method for dynamically generating dark
energy. A natural candidate for the scalar is a Goldstone boson arising from
the spontaneous breaking of a U(1) symmetry. We investigate the low-energy
effective action for such a Goldstone boson in a general class of models
involving only scalars, proving that if the scalars have standard kinetic terms
then at the {\em classical} level the effective action does not have the
required features for spontaneous Lorentz violation to occur asymptotically in an expanding FRW universe. Then we study the large limit of
a renormalizable field theory with a complex scalar coupled to massive
fermions. In this model an effective action for the Goldstone boson with the
properties required for spontaneous Lorentz violation can be generated.
Although the model has shortcomings, we feel it represents progress towards
finding a high energy completion for the Higgs phase of gravity.Comment: 20 pages, 5 figures;fixed typos and added reference
Resistant Somatoform Symptoms: Try CBT and Antidepressants. Preferred Strategy for ‘Mismatched’ Category of Illnesses.
This articles describes: debate about how to categorize somatoform disorders--as psychological or physiologic evidence supporting psychotherapy and antidepressants to help patients with treatment-resistant somatoform disorders
Heavy Quark Fragmentation to Baryons Containing Two Heavy Quarks
We discuss the fragmentation of a heavy quark to a baryon containing two
heavy quarks of mass . In this limit the heavy quarks
first combine perturbatively into a compact diquark with a radius small
compared to , which interacts with the light hadronic
degrees of freedom exactly as does a heavy antiquark. The subsequent evolution
of this diquark to a baryon is identical to the fragmentation of a
heavy antiquark to a meson. We apply this analysis to the production of baryons
of the form , , and .Comment: 9 pages, 1 figure included, uses harvmac.tex and epsf.tex, UCSD/PTH
93-11, CALT-68-1868, SLAC-PUB-622
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