mRNA选择性剪接的分子机制

真核细胞mRNA前体经过剪接成为成熟的mRNA,而mRNA前体的选择性剪接极大地增加了蛋白质的多样性和基因表达的复杂程度,剪接位点的识别可以以跨越内含子的机制(内含子限定)或跨越外显子的机制(外显子限定)进行。选择性剪接有多种剪接形式：选择不同的剪接位点,选择不同的剪接末端,外显子的不同组合及内含子的剪接与否等。选择性剪接过程受到许多顺式元件和反式因子的调控,并与基本剪接过程紧密联系,剪接体中的一些剪接因子也参与了对选择性剪接的调控。选择性剪接也是1个伴随转录发生的过程,不同的启动子可调控产生不同的剪接产物。mRNA的选择性剪接机制多种多样,已发现RNA编辑和反式剪接也可参与选择性剪接过程。     

稻田蜘蛛混合种群空间分布模式动态分析(英文)

结果表明,在东方红农场稻田中总共有11科29属43种蜘蛛,其中早稻田中有8科19属43种,晚稻田中有10科27属36种。在水稻的不同发育阶段蜘蛛混合种群的空间分布模式存在差异。在早稻发育的前期、中期和后期,稻田蜘蛛混合种群的空间分布模式分别是聚集的、随机的和聚集的;在晚稻发育的前期、中期和后期,其空间分布模式依次是均匀的、聚集的和均匀的。同时,对其空间分布模式动态进行了初步分析。     

Activities of fructan- and sucrose-metabolizing enzymes in wheat stems subjected to water stress during grain filling

This study investigated if a controlled water deficit during grain filling of wheat (Triticum aestivum L.) could accelerate grain filling by facilitating the remobilization of carbon reserves in the stem through regulating the enzymes involved in fructan and sucrose metabolism. Two high lodging-resistant wheat cultivars were grown in pots and treated with either a normal (NN) or high amount of nitrogen (HN) at heading time. Plants were either well-watered (WW) or water-stressed (WS) from 9 days post anthesis until maturity. Leaf water potentials markedly decreased at midday as a result of water stress but completely recovered by early morning. Photosynthetic rate and zeatin + zeatin riboside concentrations in the flag leaves declined faster in WS plants than in WW plants, and they decreased more slowly with HN than with NN when soil water potential was the same, indicating that the water deficit enhanced, whereas HN delayed, senescence. Water stress, both at NN and HN, facilitated the reduction in concentration of total nonstructural carbohydrates (NSC) and fructans in the stems but increased the sucrose level there, promoted the re-allocation of pre-fixed ¹⁴C from the stems to grains, shortened the grain-filling period, and accelerated the grain-filling rate. Grain weight and grain yield were increased under the controlled water deficit when HN was applied. Fructan exohydrolase (FEH; EC 3.2.1.80) and sucrose phosphate synthase (SPS; EC 2.4.1.14) activities were substantially enhanced by water stress and positively correlated with the total NSC and fructan remobilization from the stems. Acid invertase (EC 3.2.1.26) activity was also enhanced by the water stress and associated with the change in fructan concentration, but not correlated with the total NSC remobilization and ¹⁴C increase in the grains. Sucrose:sucrose fructosyltransferase (EC 2.4.1.99) activity was inhibited by the water stress and negatively correlated with the remobilization of carbon reserves. Sucrose synthase (EC 2.4.1.13) activity in the stems decreased sharply during grain filling and showed no significant difference between WW and WS treatments. Abscisic acid (ABA) concentration in the stem was remarkably enhanced by water stress and significantly correlated with SPS and FEH activities. Application of ABA to WW plants yielded similar results to those for WS plants. The results suggest that the increased remobilization of carbon reserves by water stress is attributable to the enhanced FEH and SPS activities in wheat stems, and that ABA plays a vital role in the regulation of the key enzymes involved in fructan and sucrose metabolism.Abbreviations ABA Abscisic acid - DAS Days after sowing - DPA Days post anthesis - ESC Ethanol-soluble carbohydrate - FEH Fructan exohydrolase - HN High amount of nitrogen - INV Invertase - NN Normal amount of nitrogen - NSC Nonstructural carbohydrate - _leaf Leaf water potential - _soil Soil water potential - Pr Photosynthetic rate - SPS Sucrose phosphate synthase - SS Sucrose synthase - SST Sucrose:sucrose fructosyltransferase - V_limit Limiting substrate - V_max Saturated substrate - WS Water stressed - WSC Water-soluble carbohydrate - WW Well watered - Z Zeatin - ZR Zeatin riboside     

Proline fed to intact soybean plants influences acetylene reducing activity and content and metabolism of proline in bacteroids

Supplying l-proline to the root system of intact soybean (Glycine max [L.] Merr.) plants stimulated acetylene reducing activity to the same extent as did supplying succinate. Feeding l-proline also caused an increase in bacteroid proline dehydrogenase activity that was highly correlated with the increase in acetylene-reducing activity. Twenty-four hours after irrigating with l-proline, endogenous proline content had increased in host cell cytoplasm and bacteroids, about three- and eightfold, respectively. In bacteroids, proline concentration was calculated to be at least 3.5 millimolar. In experiments in which [U-¹⁴C]l-proline was supplied to uprooted, intact plants incubated in aerated solution, ¹⁴C-labeled products of proline metabolism, as well as [¹⁴C]proline itself, accumulated in both host cells and bacteroids. When plants were incubated in aerated solutions containing [5-³H]l-proline, ³H-labeled proline was found in host cells and bacteroids. [³H] Pyrroline-5-carboxylate was found in bacteroids, but not host cells, after a 2-hour incubation in [5-³H]l-proline. When [U-¹⁴C]l-proline was supplied for 24 hours, a significant amount of [¹⁴C] pyrroline-5-carboxylate was found in the host cells, in contrast with the results from the shorter incubation in [5-³H]proline, although the amount in the host cells was only about half the quantity found in the bacteroids. Taken as a whole, these results indicate that proline crosses both plant and bacterial membranes under the in vivo experimental conditions utilized and are consistent with a significant role for proline as an energy source in support of bacteroid functioning. In spite of the increase in acetylene-reducing activity when proline was supplied to the root system of intact plants, proline application did not rescue stemgirdled plants from loss of acetylene-reducing activity, although succinate application did. This suggests a nonphloem route for succinate, but not proline, from roots to nodules.     

Nudel and FAK as Antagonizing Strength Modulators of Nascent Adhesions through Paxillin

Adhesion and detachment are coordinated critical steps during cell migration. Conceptually, efficient migration requires both effective stabilization of membrane protrusions at the leading edge via nascent adhesions and their successful persistence during retraction of the trailing side via disruption of focal adhesions. As nascent adhesions are much smaller in size than focal adhesions, they are expected to exhibit a stronger adhesivity in order to achieve the coordination between cell front and back. Here, we show that Nudel knockdown by interference RNA (RNAi) resulted in cell edge shrinkage due to poor adhesions of membrane protrusions. Nudel bound to paxillin, a scaffold protein of focal contacts, and colocalized with it in areas of active membrane protrusions, presumably at nascent adhesions. The Nudel-paxillin interaction was disrupted by focal adhesion kinase (FAK) in a paxillin-binding–dependent manner. Forced localization of Nudel in all focal contacts by fusing it to paxillin markedly strengthened their adhesivity, whereas overexpression of structurally activated FAK or any paxillin-binding FAK mutant lacking the N-terminal autoinhibitory domain caused cell edge shrinkage. These results suggest a novel mechanism for selective reinforcement of nascent adhesions via interplays of Nudel and FAK with paxillin to facilitate cell migration.     

Characterization of S-Triazine Herbicide Metabolism by a Nocardioides sp. Isolated from Agricultural Soils

Atrazine, a herbicide widely used in corn production, is a frequently detected groundwater contaminant. Nine gram-positive bacterial strains able to use this herbicide as a sole source of nitrogen were isolated from four farms in central Canada. The strains were divided into two groups based on repetitive extragenic palindromic (rep)-PCR genomic fingerprinting with ERIC and BOXA1R primers. Based on 16S ribosomal DNA sequence analysis, both groups were identified as Nocardioides sp. strains. None of the isolates mineralized [ring-U-¹⁴C]atrazine. There was no hybridization to genomic DNA from these strains using atzABC cloned from Pseudomonas sp. strain ADP or trzA cloned from Rhodococcus corallinus. S-Triazine degradation was studied in detail in Nocardioides sp. strain C190. Oxygen was not required for atrazine degradation by whole cells or cell extracts. Based on high-pressure liquid chromatography and mass spectrometric analyses of products formed from atrazine in incubations of whole cells with H₂¹⁸O, sequential hydrolytic reactions converted atrazine to hydroxyatrazine and then to the end product N-ethylammelide. Isopropylamine, the putative product of the second hydrolytic reaction, supported growth as the sole carbon and nitrogen source. The triazine hydrolase from strain C190 was isolated and purified and found to have a K_m for atrazine of 25 μM and a V_max of 31 μmol/min/mg of protein. The subunit molecular mass of the protein was 52 kDa. Atrazine hydrolysis was not inhibited by 500 μM EDTA but was inhibited by 100 μM Mg, Cu, Co, or Zn. Whole cells and purified triazine hydrolase converted a range of chlorine or methylthio-substituted herbicides to the corresponding hydroxy derivatives. In summary, an atrazine-metabolizing Nocardioides sp. widely distributed in agricultural soils degrades a range of s-triazine herbicides by means of a novel s-triazine hydrolase.     

The institute for genomic research Osa1 rice genome annotation database

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 non-transposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.     

Increases in tumor necrosis factor-alpha following transient global cerebral ischemia do not contribute to neuron death in mouse hippocampus

The actions of tumor necrosis factor-alpha (TNF-alpha) produced by resident brain cells and bone marrow-derived cells in brain following a transient global ischemia were evaluated. In wild-type mice (C57Bl/6J) following 20 min ischemia with bilateral common carotid artery occlusion (BCCAo), TNF-alpha mRNA expression levels in the hippocampus were significantly increased at 3 h and 36 h and exhibited a biphasic expression pattern. There were no hippocampal TNF-alpha mRNA expression levels at early time points in either wild-type mice bone marrow transplanted (BMT)-chimeric-TNF-alpha gene-deficient (T/W) or TNF-alpha gene-deficient mice BMT-TNF-alpha gene-deficient mice (T/T), although TNF-alpha mRNA levels were detectable in T/W BMT mice at 36 h. Histopathological findings showed no intergroup differences between wild-type and TNF-alpha gene-deficient mice at 4 and 7 days after transient ischemia. In addition, nuclear factor-kappaB (NF-kappaB) was activated within 12 h after global cerebral ischemia, but electrophoretic mobility shift assays (EMSA) showed no intergroup differences between wild type and TNF-alpha gene-deficient mice. In summary, early hippocampal TNF-alpha mRNA expression may not be related to bone marrow-derived cells, and secondary TNF-alpha expression as early as 36 h after ischemia probably resulted mainly from endogenous brain cells and possibly a few bone marrow-derived cells. Although we cannot exclude the possibility of the TNF-alpha contribution to the physiologic changes of hippocampus after transient global ischemia, these results indicate that TNF-alpha does not influence the morphological changes of the hippocampal neurons under our study condition.     

Isolation of a triazophos-degrading strain Klebsiella sp. E6 effectively utilizing triazophos as sole nitrogen source

A triazophos-degrading strain, Klebsiella sp. E6, was isolated by enrichment technology from soil that had been exposed long-term to triazophos. The strain grew well at pH 7.0-8.0 with a broad temperature profile ranging from 32 to 37 degrees C. It could keep good growth on methanol as carbon source and TAP as additional carbon source or nitrogen source. The experiment on the degradation activities of strain E6 showed that it utilized TAP more effectively when TAP was supplied as the sole nitrogen source, as opposed to additional carbon source. The intermediates of triazophos metabolism indicated that degradation occurred through a hydrolysis mechanism, one of the products of which, 1-phenyl-3-hydroxy-1,2,4-triazole, was also mineralized by strain E6.     

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005)

The spring workshop of the HUPO-PSI convened in Siena to further progress the data standards which are already making an impact on data exchange and deposition in the field of proteomics. Separate work groups pushed forward existing XML standards for the exchange of Molecular Interaction data (PSI-MI, MIF) and Mass Spectrometry data (PSI-MS, mzData) whilst significant progress was made on PSI-MS' mzIdent, which will allow the capture of data from analytical tools such as peak list search engines. A new focus for PSI (GPS, gel electrophoresis) was explored; as was the need for a common representation of protein modifications by all workers in the field of proteomics and beyond. All these efforts are contextualised by the work of the General Proteomics Standards workgroup; which in addition to the MIAPE reporting guidelines, is continually evolving an object model (PSI-OM) from which will be derived the general standard XML format for exchanging data between researchers, and for submission to repositories or journals.