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51.
Jonathan D. Nickels Joseph E. Curtis Hugh O’Neill Alexei P. Sokolov 《Journal of biological physics》2012,38(3):497-505
Recent studies have discovered strong differences between the dynamics of nucleic acids (RNA and DNA) and proteins, especially at low hydration and low temperatures. This difference is caused primarily by dynamics of methyl groups that are abundant in proteins, but are absent or very rare in RNA and DNA. In this paper, we present a hypothesis regarding the role of methyl groups as intrinsic plasticizers in proteins and their evolutionary selection to facilitate protein dynamics and activity. We demonstrate the profound effect methyl groups have on protein dynamics relative to nucleic acid dynamics, and note the apparent correlation of methyl group content in protein classes and their need for molecular flexibility. Moreover, we note the fastest methyl groups of some enzymes appear around dynamical centers such as hinges or active sites. Methyl groups are also of tremendous importance from a hydrophobicity/folding/entropy perspective. These significant roles, however, complement our hypothesis rather than preclude the recognition of methyl groups in the dynamics and evolution of biomolecules. 相似文献
52.
Hiroyuki Kozu Isao Kobayashi Mitsutoshi Nakajima Kunihiko Uemura Seigo Sato Sosaku Ichikawa 《Food biophysics》2010,5(4):330-336
This paper uses computational fluid dynamics to simulate and analyze intragastric fluid motions induced by human peristalsis.
We created a two-dimensional computational domain of the distal stomach where peristalsis occurs. The motion of the gastric
walls induced by an antral contraction wave (ACW) on the wall of the computational domain was well simulated using a function
defined in this study. Retropulsive flow caused by ACW was observed near the occluded region, reaching its highest velocity
of approximately 12 mm/s in the narrowest region. The viscosity of the model gastric contents applied in this study hardly
affected the highest velocity, but greatly affected the velocity profile in the computational domain. The shear rate due to
gastric fluid motion was calculated using the numerical output data. The shear rate reached relatively high values of approximately
20 s−1 in the most occluded region. The shear rate profile was almost independent of the fluid viscosity. We also simulated mass
transfer of a gastric digestive enzyme (pepsin) in model gastric content when peristalsis occurs on the gastric walls. The
visualized simulation results suggest that gastric peristalsis is capable of efficiently mixing pepsin secreted from the gastric
walls with an intragastric fluid. 相似文献
53.
Patrizia Vaccino Heinz-Albert Becker Andrea Brandolini Francesco Salamini Benjamin Kilian 《Molecular genetics and genomics : MGG》2009,281(3):289-300
The celiac disease (CD) is an inflammatory condition characterized by injury to the lining of the small-intestine on exposure
to the gluten of wheat, barley and rye. The involvement of gluten in the CD syndrome has been studied in detail in bread wheat,
where a set of “toxic” and “immunogenic” peptides has been defined. For wheat diploid species, information on CD epitopes
is poor. In the present paper, we have adopted a genomic approach in order to understand the potential CD danger represented
by storage proteins in diploid wheat and sequenced a sufficiently large number of cDNA clones related to storage protein genes
of Triticum monococcum. Four bona fide toxic peptides and 13 immunogenic peptides were found. All the classes of storage proteins were shown to contain harmful
sequences. The major conclusion is that einkorn has the full potential to induce the CD syndrome, as already evident for polyploid
wheats. In addition, a complete overview of the storage protein gene arsenal in T. monococcum is provided, including a full-length HMW x-type sequence and two partial HMW y-type sequences.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
54.
Background
Radial chromosome positioning in interphase nuclei is nonrandom and can alter according to developmental, differentiation, proliferation, or disease status. However, it is not yet clear when and how chromosome repositioning is elicited. 相似文献55.
Background
In heterogeneous environments, sex-biased dispersal could lead to environmental adaptive parental effects, with offspring selected to perform in the same way as the parent dispersing least, because this parent is more likely to be locally adapted. We investigate this hypothesis by simulating varying levels of sex-biased dispersal in a patchy environment. The relative advantage of a strategy involving pure maternal (or paternal) inheritance is then compared with a strategy involving classical biparental inheritance in plants and in animals. 相似文献56.
TNF inhibitors are currently considered both effective and cost-effective in patients with active rheumatoid arthritis (RA),
particularly in patients who have not responded fully to methotrexate. There is substantial doubt about the cost-effectiveness
of TNF inhibitors as initial treatment for active RA. New data from the National Data Bank for Rheumatic Diseases now question
the current consensus in methotrexate failures. The data suggest that in routine clinical practice TNF inhibitors provide
only modest incremental benefits over best conventional therapy. If confirmed, these observational studies suggest that the
economic argument underpinning the widespread use of TNF inhibitors in established RA is unsustainable. 相似文献
57.
Background
DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. 相似文献58.
59.
Emin Oguzhan Oguz Hayati Yuksel Yasar Enli A. Cevik Tufan Gunfer Turgut 《Biological trace element research》2010,133(3):335-341
Copper is an essential trace element that is extremely toxic to organisms and organs at high doses. We have investigated the
histological and biochemical effects of a toxic dose of copper sulfate on the liver of term Ross broiler chicks. Fertilized
eggs were divided into three groups: experimental, injected with 50 mcg/0.1 ml copper sulfate in the air chambers on day 1;
sham, injected with 0.1 ml saline; and control, no injection. Term chicks were killed and their livers investigated histologically,
with hematoxylin–eosin-stained sections examined under light microscopy, and biochemically, for malondialdehyde and glutathione
levels. Histological examinations showed copper-treated samples with granular degeneration and necrosis of hepatocytes and
impairment to the cell lining of the remark cords. The samples had a congestive appearance, with blood in the vena centralis
and sinusoids, slight connective tissue increase, and lymphocyte infiltration. Control and sham group sections had normal
appearances. As oxidative damage parameters, in the copper-treated group, malondialdehyde levels were increased and glutathione
levels decreased. In the sham and control groups, there were no significant differences. At this toxic dose, copper sulfate
shows oxidative damage according to the histology of term chick liver that are confirmed biochemically by the changes in malondialdehyde
and glutathione levels. 相似文献
60.
The seminal receptacle or spermatheca of Portunus sanguinolentus consists of two parts--an anterior glandular and a posterior chitinous part. The chitinous part continues as the oviduct, which opens on the sternite of the sixth thoracic segment. Significant morphological and histological differences were observed between the spermatheca, as well as the oviduct, of mated and unmated crabs. In mated crabs the spermatheca is much more bulging, owing to receipt of a copious supply of seminal products, and its cells are hyperactive. Further stages of ovarian development were observed as indicators of sequential changes in the spermatheca. The secretory cells gradually disintegrate by way of holocrine secretion; this results in cellular stratification and the formation of distinct furrows in the chitinous posterior part. 相似文献