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31.
Cebrià F Nakazawa M Mineta K Ikeo K Gojobori T Agata K 《Development, growth & differentiation》2002,44(2):135-146
The planarian central nervous system (CNS) can be used as a model for studying neural regeneration in higher organisms. Despite its simple structure, recent studies have shown that the planarian CNS can be divided into several molecular and functional domains defined by the expression of different neural genes. Remarkably, a whole animal, including the molecularly complex CNS, can regenerate from a small piece of the planarian body. In this study, a collection of neural markers has been used to characterize at the molecular level how the planarian CNS is rebuilt. Planarian CNS is composed of an anterior brain and a pair of ventral nerve cords that are distinct and overlapping structures in the head region. During regeneration, 12 neural markers have been classified as early, mid-regeneration and late expression genes depending on when they are upregulated in the regenerative blastema. Interestingly, the results from this study show that the comparison of the expression patterns of different neural genes supports the view that at day one of regeneration, the new brain appears within the blastema, whereas the pre-existing ventral nerve cords remain in the old tissues. Three stages in planarian CNS regeneration are suggested. 相似文献
32.
Ernest D Benavente Francesc Coll Nick Furnham Ruth McNerney Judith R Glynn Susana Campino Arnab Pain Fady R Mohareb Taane G Clark 《BMC bioinformatics》2015,16(1)
Background
Phylogenetic-based classification of M. tuberculosis and other bacterial genomes is a core analysis for studying evolutionary hypotheses, disease outbreaks and transmission events. Whole genome sequencing is providing new insights into the genomic variation underlying intra- and inter-strain diversity, thereby assisting with the classification and molecular barcoding of the bacteria. One roadblock to strain investigation is the lack of user-interactive solutions to interrogate and visualise variation within a phylogenetic tree setting.Results
We have developed a web-based tool called PhyTB (http://pathogenseq.lshtm.ac.uk/phytblive/index.php) to assist phylogenetic tree visualisation and identification of M. tuberculosis clade-informative polymorphism. Variant Call Format files can be uploaded to determine a sample position within the tree. A map view summarises the geographical distribution of alleles and strain-types. The utility of the PhyTB is demonstrated on sequence data from 1,601 M. tuberculosis isolates.Conclusion
PhyTB contextualises M. tuberculosis genomic variation within epidemiological, geographical and phylogenic settings. Further tool utility is possible by incorporating large variants and phenotypic data (e.g. drug-resistance profiles), and an assessment of genotype-phenotype associations. Source code is available to develop similar websites for other organisms (http://sourceforge.net/projects/phylotrack). 相似文献33.
Longitudinal patterns of dissolved organic carbon concentration and suspended bacterial density along a blackwater river 总被引:2,自引:0,他引:2
Dissolved organic carbon (DOC) is the dominant form of carbon in transport in blackwater rivers, and bacteria are the major
biological agents of its utilization. This study describes longitudinal patterns in DOC concentration and relates them to
suspended bacterial populations in the channel. Concentrations of total DOC, three molecular weight fractions, and bacterial
numbers were determined at 12 sites along the Ogeechee River in 1985–1986 and 1989 during periods of low and high discharge.
Suspended bacterial populations were compared with DOC concentrations to determine if differences in bacterial abundance were
related to longitudinal patterns of DOC concentration. Three distinct longitudinal patterns were observed: (1) The longitudinal
pattern followed by both total and intermediate molecular weight DOC concentrations was a linear function of the geographic
distance along the river. (2) During low flow conditions, there was a high degree of correspondence between patterns of bacterial
numbers and low MW DOC (< 1000 apparent MW). (3) During periods of high discharge, the proportion of high (> 10,000) and intermediate
(1000–10,000) MW fractions increased, and there was no longer a clear relationship between bacterial cells and low MW DOC. 相似文献
34.
Gemma Fabris M. Pilar Marco Francisco Camps 《Archives of insect biochemistry and physiology》1994,27(2):77-87
The control of Spodoptera littoralis sex pheromone biosynthesis has been investigated with synthetic pheromone biosynthesis activating neuropeptide (PBAN) and different labeled tracers using an in vitro isolated gland system. Responsiveness of the glands to PBAN stimulation was impaired by careless tissue manipulation. The fact that PBAN is active in the isolated gland system suggests that this might be a target organ for this peptide in S. littoralis. As reported previously with Br-SOG extracts and intact females, label incorporation into the pheromone increased in glands treated with PBAN from all the precursors tested. However, the formation of labeled intermediates from d5E11–14:Acid also occurred in glands incubated in the absence of the peptide, but the amounts of d5Z9, E11–14:Acid were lower in PBAN treated glands than in controls. These results indicate that PBAN controls pheromone biosynthesis in S. littoralis by regulating the reduction of acyl moieties. © 1994 Wiley-Liss, Inc. 相似文献
35.
Isolation and re-association of the subunits from the pro-(carboxypeptidase A)–pro-(proteinase E) binary complex from pig pancreas 下载免费PDF全文
Josep Vendrell Francesc X. Aviles Blanca San Segundo Claudi M. Cuchillo 《The Biochemical journal》1982,205(2):449-452
The component subunits of the pro-(carboxypeptidase A)–pro-(proteinase E) binary complex from pig pancreas were separated with a high recovery (80–95%) of their original potential activity. The isolated subunits and the reconstituted complex have properties similar to those of the corresponding natural species. The tryptic activation course of the pro-(carboxypeptidase A) subunit is substantially modified when bound to pro-(proteinase E), whereas the activation of pro-(proteinase E) is not dependent on this association. 相似文献
36.
Noggin genes are mainly known as inhibitors of the Bone Morphogenetic Protein (BMP) signalling pathway. Noggin genes play an important role in various developmental processes such as axis formation and neural differentiation. In vertebrates, inhibition of the BMP pathway is usually carried out together with other inhibitory molecules: chordin and follistatin. Recently, it has been shown in planarians that the BMP pathway has a conserved function in the maintenance and re-establishment of the dorsoventral axis during homeostasis and regeneration. In an attempt to further characterize the BMP pathway in this model we have undertaken an in silico search of noggin genes in the genome of Schmidtea mediterranea. In contrast to other systems in which between one and four noggin genes have been reported, ten genes containing a noggin domain are present in S. mediterranea. These genes have been classified into two groups: noggin genes (two genes) and noggin-like genes (eight genes). Noggin-like genes are characterized by the presence of an insertion of 50–60 amino acids in the middle of the noggin domain. Here, we report the characterization of this expanded family of noggin genes in planarians as well as their expression patterns in both intact and regenerating animals. In situ hybridizations show that planarian noggin genes are expressed in a variety of cell types located in different regions of the planarian body. 相似文献
37.
Marsillach J Ferré N Camps J Rull A Beltran R Joven J 《Molecular and cellular biochemistry》2008,308(1-2):101-109
Chronic liver diseases are accompanied by changes in the biochemical pathways related to the regulation of apoptosis and extra-cellular
matrix deposition. The present study was designed to investigate, using low density arrays, changes in the hepatic gene expression
together with hepatic biochemical and histological alterations in rats that had liver impairment induced by chronic exposure
to CCl4. Further, we examined the possible recovery of genetic and pathological changes following the cessation of the hepatotoxic
injury. Experimental fibrosis was induced in male Wistar rats by CCl4 administration. Animals were subdivided into two groups. One group was given CCl4 and animals were killed at 8 and 12 weeks of treatment. The other group was treated with CCl4 for 6 weeks, the CCl4 was then stopped and, subsequently, subgroups of animals were killed after 1 and 2 weeks of recovery. CCl4 administration over 12 weeks was associated with significant changes in B-cell leukemia/lymphoma 2, procollagen type I α
2, matrix metalloproteinases 3 and 8, tissue inhibitors of metalloproteinases 1, 2, and 3 and the inhibitor of apoptosis 4
gene expressions. Recovery after CCl4 cessation was associated with changes in procollagen type I α 2, matrix metalloproteinase 7, tissue inhibitors of metalloproteinases
1 and 2, inhibitor of apoptosis 4, and survivin gene expressions. This study shows an association between changes in the expression
of several genes regulating hepatic cell apoptosis, the fibrosis process, and the recovery of the hepatic function after removal
of the toxic injury. 相似文献
38.
Despite being a paradigm of quantitative linguistics, Zipf’s law for words suffers from three main problems: its formulation is ambiguous, its validity has not been tested rigorously from a statistical point of view, and it has not been confronted to a representatively large number of texts. So, we can summarize the current support of Zipf’s law in texts as anecdotic. We try to solve these issues by studying three different versions of Zipf’s law and fitting them to all available English texts in the Project Gutenberg database (consisting of more than 30 000 texts). To do so we use state-of-the art tools in fitting and goodness-of-fit tests, carefully tailored to the peculiarities of text statistics. Remarkably, one of the three versions of Zipf’s law, consisting of a pure power-law form in the complementary cumulative distribution function of word frequencies, is able to fit more than 40% of the texts in the database (at the 0.05 significance level), for the whole domain of frequencies (from 1 to the maximum value), and with only one free parameter (the exponent). 相似文献
39.
Ada Pastor Zacchaeus G. Compson Paul Dijkstra Joan L. Riera Eugènia Martí Francesc Sabater Bruce A. Hungate Jane C. Marks 《Oecologia》2014,176(4):1111-1121
Leaf litter decomposition plays a major role in nutrient dynamics in forested streams. The chemical composition of litter affects its processing by microorganisms, which obtain nutrients from litter and from the water column. The balance of these fluxes is not well known, because they occur simultaneously and thus are difficult to quantify separately. Here, we examined C and N flow from streamwater and leaf litter to microbial biofilms during decomposition. We used isotopically enriched leaves (13C and 15N) from two riparian foundation tree species: fast-decomposing Populus fremontii and slow-decomposing Populus angustifolia, which differed in their concentration of recalcitrant compounds. We adapted the isotope pool dilution method to estimate gross elemental fluxes into litter microbes. Three key findings emerged: litter type strongly affected biomass and stoichiometry of microbial assemblages growing on litter; the proportion of C and N in microorganisms derived from the streamwater, as opposed to the litter, did not differ between litter types, but increased throughout decomposition; gross immobilization of N from the streamwater was higher for P. fremontii compared to P. angustifolia, probably as a consequence of the higher microbial biomass on P. fremontii. In contrast, gross immobilization of C from the streamwater was higher for P. angustifolia, suggesting that dissolved organic C in streamwater was used as an additional energy source by microbial assemblages growing on slow-decomposing litter. These results indicate that biofilms on decomposing litter have specific element requirements driven by litter characteristics, which might have implications for whole-stream nutrient retention. 相似文献
40.
Villanueva J Fernández-Ballester G Querol E Aviles FX Serrano L 《Journal of molecular biology》2003,330(5):1039-1048
Here, we present a new approach for protein ligand screening based on the use of limited exoproteolysis coupled to MALDI-TOF mass spectrometry, combined with computational modelling and prediction of binding energies. As a test for this combined approach, we have screened a combinatorial library containing 8000 peptides (organized in 60 peptide samples) based on positional scanning format. This library is attached to a poly-Pro framework, and screened against the Abl-SH3 domain. The results obtained demonstrated the validity of the experimental and theoretical approaches in identifying better ligands and in rationalizing the changes in affinity. Exoproteolysis coupled to MALDI-TOF mass spectrometry could be used to screen complex libraries in a fast and efficient way. 相似文献