Purification and Partial Characterization of an Antibacterial Protein Tz1

A strain (T3) of Bacillus has been screened from paddy field. It secretes large amount of antibacterialproteins which show a strong inhibiting activity against several pathogens of rice. This paper presentsa systematic study of the inhibition spectrum and characteristics of T3 proteins. Total proteins wereprecipitated with ammonium sulfate at 70% saturation from cell-free culture. One of the proteins(Tzl) was purified from the crude extracts with Sephadex G-100, DEAE52 and FPLC Superose 12columns. A single band was demonstrated in both 15% SDS-PAGE and IEF, with an apparent MWof 6,9 kd and a pI of 7.8. Its amino acid composition was analyzed and part of its sequence,determined.

A Simple and Reliable Assay for Detecting Specifi c Nucleotide Sequences in Plants Using Optical Thin-fi lm Biosensor Chips

Here we report the adaptation and optimization of an effi cient, accurate and inexpensive assay that employs custom-designed silicon-based optical thin-fi lm biosensor chips to detect unique transgenes in genetically modi-

Transcriptome Profiling and Biochemical Studies Reveal New Mechanisms for Cotton Fiber Cell Elongation

Cotton is the world's most important natural textile fi ber, and is practiced on about 2.5% of arable land that supported the life of about 100 million family units. Each cotton fi ber, about 25 000 per seed, is a single, phe-

Molecular evolution of the exon 2 of CHS genes and the possibility of its application to plant phylogenetic analysis

The exon 2 of chalcone synthase (CHS) gene is relatively conserved during evolution. In this study, three exon 2 fragments from two species in gymnosperm (Cycas panzhihuaensis, Ginkgo biloba ) and seven from four species in angiosperm (Magnolia denudata, Salix babylonica, Nymphaea tetragona, Camellia japonica) have been amplified by PCR from genomic DNA and sequenced. Together with other 73 sequences of CHS collected from EMBL database and literature, these sequences, which embrace 19 families of gymnosperm and angiosperm, have been analyzed for their phylogenetic relations by parsimony method. The result indicated that sequences from the same systematic family usually grouped together except those from Theaceae, Magnoliaceae and Nymphaeaceae. The relative rate test revealed the rate heterogeneity of CHS genes among the families. For the nucleotide substitution the sequences from Asteraceae and Solanaceae evolve faster than those from the other families analyzed while the sequences from Poaceae,

MEF2C mediates the activation induced cell death(AICD)of macrophages

有免疫力的房间的导致激活的房间死亡(AICD ) 广泛地被相信为有免疫力的回答的规定关键。尽管巨噬细胞 apoptosis 在许多病理学的条件下面被观察了，是否并且怎么有巨噬细胞的 AICD 的问题巨噬细胞寿命被调整很好没被探讨。在巨噬细胞的 AICD 要求二个信号。一个人是 LPS 或另外的细菌的部件触发的房间激活。其它是存在在的一个事件 AICD 易受影响(告知) 然而并非 unsusceptible (休息) 巨噬细胞。这里，我们证明当它与沙门氏菌 typhimurium，类型 5 侵入人体气管粘膜的病菌(Ad5 ) 或 IFN-gamma 被告知时，那个 RAW264.7 房间产生 LPS 刺激。我们发现抄写因素 MEF2C 的稳定性在告知的 RAW264.7 房间被增加。MEF2C 的一种主导的否定形式的 Transfection 保护告知的巨噬细胞免受 LPS 触发的房间死亡的伤害。我们的数据证明 MEF2C 蛋白质稳定性的增加是在巨噬细胞的 AICD 的一个关键因素。

SAD phasing by OASIS at different resolutions down to 0.30 nm and below

Single-wavelength anomalous diffraction （SAD） phasing is increasingly important in solving de novo protein structures. Direct methods have been proved very efficient in SAD phasing. This paper aims at probing the low-resolution limit of direct-method SAD phasing. Two known proteins TT0570 and Tom70p were used as test samples. Sulfur-SAD data of the protein TT0570 were collected with conventional Cu-Kα source at 0.18 nm resolution. Its truncated subsets respectively at 0.21, 0.30, 0.35 and 0.40 nm resolutions were used in the test. TT0570 Cu-Kα sulfur-SAD data have an expected Bijvoet ratio 〈 ｜△F｜ 〉 / 〈 F 〉 ～ 0.55%. In the 0.21 nm case, a single run of OASIS-DM-ARP/wARP led automatically to a model containing 1178 of the total 1206 residues all docked into the sequence. In 0.30 and 0.35 nm cases, SAD phasing by OASIS-DM led to traceable electron density maps. In the 0.40 nm case, SAD phasing by OASIS-DM resulted in a degraded electron density map, which may be difficult to trace but still contains useful secondary-structure information. Test on real 0.33 nm selenium-SAD data of the protein Tom70p showed that even automatic model building was not successful, the combination of manual tracing and direct-method fragment extension was capable of significantly improving the electron-density map. This provides the possibility of effectively improving the manually built model before structure refinement is performed.

Differences in action potential propagation speed and axon initial segment plasticity between neurons from Sprague-Dawley rats and C57BL/6 mice

Action potentials(APs)in neurons are generated at the axon initial segment(AIS).AP dynamics,including initiation and propagation,are intimately associated with neuronal excitability and neurotransmitter release kinetics.Most learning and memory studies at the single-neuron level have relied on the use of animal models,most notably rodents.Here,we studied AP initiation and propagation in cultured hippocampal neurons from Sprague-Dawley(SD)rats and C57BL/6(C57)mice with genetically encoded voltage indicator(GEVI)-based voltage imaging.Our data showed that APs traveled bidirectionally in neurons from both species;forward-propagating APs(fpAPs)had a different speed than backpropagating APs(bpAPs).Additionally,we observed distinct AP propagation characteristics in AISs emerging from the somatic envelope compared to those originating from dendrites.Compared with rat neurons,mouse neurons exhibited higher bpAP speed and lower fpAP speed,more distally located ankyrin G(AnkG)in AISs,and longer Nav1.2 lengths in AISs.Moreover,during AIS plasticity,AnkG and Nav1.2 showed distal shifts in location and shorter lengths of labeled AISs in rat neurons;in mouse neurons,however,they showed a longer AnkG-labeled length and more distal Nav1.2 location.Our findings suggest that hippocampal neurons in SD rats and C57 mice may have different AP propagation speeds,different AnkG and Nav1.2 patterns in the AIS,and different AIS plasticity properties,indicating that comparisons between these species must be carefully considered.

Structural Insight into the Binding of Hypoxanthine with Purine Nucleoside Phosphorylase from Streptococcus mutants

Purine nucleoside phosphorylase is a key enzyme in the purine-salvage pathway and an attractive target for drug design. The crystal structure of Streptococcus mutants purine nucleoside phosphorylase（Smu PNP） has been solved by molecular replacement at 1.80 resolution and refined to R factors of 19.9%/23.7%（Rcryst/Rfree） . Sequence alignment and structural comparison show that Smu PNP has more similarity with PNPs isolated from human and malarial sources than the bacterial PNPs. The structure complexed with hypoxanthine（HPA） and sulfate ion was solved at 2.24A resolution and refined to R factors of 21.6%/24.1%（Rcryst/Rfree） . It is interesting to note that the resulting electron density indicated the product,HPA,presents in the active site although inosine was included in the crystallization mixture with Smu PNP. Asn233 and Glu191 are the important residues for ligand binding and recognition. Comparison with PNPs from different species gives detailed information about binding of small molecules on the active site,which is important for the studies of enzymatic mechanism and rational design of specific inhibitors for PNPs.

Genetic Basis of Ethylene Perception and Signal Transduction in Arabidopsis

Ethylene is a simple gaseous hormone in plants. It plays important roles in plant development and stress tolerance. In the presence of ethylene treatment, all ethylene receptors are in an activated form, which can physically interact with CTR1 and consequently recruit CTR1 protein to endoplasmic reticulum membrane to activate it. Activated CTR1 suppresses the downstream signal transduction by an unknown mechanism. Upon binding to its receptors, ethylene will inactivate the receptor/CTR1 module and in turn alleviate their inhibitory effect on two positive regulators acting downstream of CTR1： EIN2 and EIN3. Genetic study reveals that EIN2 is an essential component in the ethylene signaling pathway but its biochemical function remains a mystery. EIN3 is a plant-specific transcription factor and its protein abundance in the nucleus is rapidly induced upon ethylene treatment. In the absence of ethylene signal, EIN3 protein is degraded by an SCF complex containing one of the two F-box proteins EBF1/EBF2 in a 26S proteasome-dependent manner. EIN3 can bind to the promoter sequences of a number of downstream components, such as ERFs, which in turn bind to a GCC box, a c/s-element found in many ethylene-regulated defense genes. Ethylene has been shown to also regulate many other hormones＇ signaling pathways including auxin, abscisic acid and jasmonic acid, implying the existence of complicated signaling networks in the growth, development and defense responses of various plants.

Identification and Quantitative Analysis of Significantly Accumulated Proteins During the Arabidopsis Seedling De-etiolation Process

Proteomic analysis was performed on seedlings after different light treatments. A total of （1 350±31） protein spots was separated and visualized on each silver nitrate-stained two-dimensional gel using protein samples prepared from light-grown or etiolated seedlings with or without 6-9 h light treatment. Twenty-five protein spots （encoded by 19 genes） that were significantly accumulated upon light treatment were identified using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry method. Functional proteomics indicated that these proteins involved mainly in chloroplast development, energy metabolism, cell cycle progression and membrane electron transport. For 18 of the protein-coding genes we identified through an internet search, the transcript levels of 17 genes matched roughly with their protein content in etiolated and green seedlings, suggesting that these genes were regulated by light mainly at the transcriptional level. Despite a very significant increase in the amount of proteins upon light treatment, similar RNA levels were found in dark-grown or green seedlings for the carbonic anhydrase gene At3g05100, indicating a possible post-transcriptional regulatory mechanism. Elucidation of light-induced protein accumulation will undoubtedly enhance our understanding of plant photomorphogenesis.

Cloning and expression of a cDNA encoding ribosomal protein S4 from Rice (Oryza sativa)

A cDNA clone, pS4, has been isolated from a cDNA library prepared from rice anthers of about 1.0 mm in length. DNA sequence analysis and database search show that the cDNA encodes a protein which is highly homologous to eukaryotic 80S ribosomal protein subunit 4 (S4). Northern hybridization indicates that this gene expresses in all tissues analyzed although the expression level varies and it cannot be induced by mechanical wounding in leaves. Southern blot analysis demonstrates that this rice S4 gene is from a multigene

Cloning and Sequencing of Trichosanthin Gene and Its Expression in Escherichia coli and Tobacco Plant

A Trichosanthin gene was cloned from Trichosanthes kirilowii genomic DNA by polymerase chain reaction (PCR). Nucleotide sequence data indicated that we obtained the coding region of the mature Trichosanthin peptide as well as its signal peptide at the N-terminus. Comparisons of our sequence with the previously reported nucleotide sequences of this gene showed 99.25% homology, yet there were notable differences between the previously reported amino acid sequence and our deduced result. This gene was subcloned into a highlevel expression plasmid (pJLA502) of E. coli under the control of a P_RP_L promoter, and we observed the gene product after temperature induction. The gene was further cloned into plant intermediate vector pE3 under the control of a CaMV 35S promoter, and transferred into a tobacco genome using the agrobacterium-mediated gene transfer system. Western blotting analysis of the protein extracted from Escherichia coli and transgenic tobacco plants proved that the Trichosanthin gene has

Characterization of Arabidopsis MYB transcription factor gene AtMYB17 and its possible regulation by LEAFY and AGL15

MYB transcription factors compose one of the largest transcription factor families in Arabidopsis, which play important roles in vari- ous developmental processes as well as defense responses against environmental stresses. In this study, we report the characterization of AtMYB17 gene, a putative R2R3 type MYB gene family member in Arabidopsis. AtMYB17 was found exclusively localized in nuclear, with an activation domain at its C-terminus. AtMYBI7 was highly expressed in inflorescences and siliques, especially at early flower developmental stages. The level of AtMYB17 transcripts was also found to increase after imbibition during seed germination and gradually concentrate to the shoot apex. Bioinformatics analysis identified several binding sites of LEAFY （LFY） and AGL15 in the promoter re- gion of AtMYB17. Promoter-GUS fusion analysis showed that the LFY binding sites were important in fine-tuning regulation of the spatio-temporal expression ofAtMYB17 in transgenic plants. Moreover, AtMYB17 was up-regulated in 35S：：AGL15 plants. Taken together, our data suggest that LFY may be involved in the regulation of AtMYB17, possibly together with AGL 15, and thereafter in early inflores- cence development and seed germination.

Cotton GhPOX1 encoding plant class Ⅲ peroxidase may be responsible for the high level of reactive oxygen species production that is related to cotton fiber elongation

The accumulation of reactive oxygen species （ROS） is involved in plant cell development. In plant, class III peroxidases are heme-containing enzymes encoded by a large multi-gene family participated in the release or consumption of ROS. The specific function of each member of the family is still elusive. Here, we showed that ROS was significantly generated during cotton fiber initiation and elongation, whereas, application of NADPH oxidase inhibitor diphenyleneiodonium （DPI） and peroxidase inhibitor salicylhydroxamic acid （SHAM） to the wild-type cotton ovule culture significantly suppressed fiber growth, respectively. Their inhibitory effects were caused by the reduction of superoxide radical （O2^-）. Ten GhPOX genes （cDNAs） encoding cotton class III peroxidases were isolated, among them eight GhPOX genes were reported for the first time. Microarray analyses indicated that GhPOX1 was the mostly predominantly expressed in fast-elongating cotton fiber cells. Real-time quantitative PCR analysis revealed the transcript level of GhPOX1 was over 400-fold higher in growing fiber cells than in ovules, flowers, roots, stems and leaves. To reveal the role of GhPOX1 in plant development, its Arabidopsis orthologue atpox13 mutant was demonstrated to be defective in branch root development. Taken together, the data suggest that GhPOX1 plays an important role during fiber cell elongation possibly by mediating production of reactive oxygen species.

The epigenetic involvement in plant hormone signaling

The biosynthesis and signaling of plant hormones play a critical role in almost all biological processes.It is well-documented that phytohormones cross-talk with each other.Epigenetic mechanisms were suggested to regulate expression of downstream targets in hormone signaling pathways that help implement hormone functions.This new layer of complexities that integrate epigenetic information such as DNA methylation,chromatin remodeling,histone modification,microRNAs and siRNAs with plant hormone signaling and regulations of gene expression,has been gradually revealed.In this short review,the author tries to assemble recent progress to establish a molecular linkage between these two large and momentum research fields and also to help readers digest the literature.

TSdb:A database of transporter substrates linking metabolic pathways and transporter systems on a genome scale via their shared substrates

TSdb (http://tsdb.cbi.pku.edu.cn) is the first manually curated central repository that stores formatted information on the substrates of transporters. In total, 37608 transporters with 15075 substrates from 884 organisms were curated from UniProt functional annotation. A unique feature of TSdb is that all the substrates are mapped to identifiers from the KEGG Ligand com- pound database. Thus, TSdb links current metabolic pathway schema with compound transporter systems via the shared compounds in the pathways. Furthermore, all the transporter substrates in TSdb are classified according to their biochemical properties, biological roles and subcellular localizations. In addition to the functional annotation of transporters, extensive compound annotation that includes inhibitor information from the KEGG Ligand and BRENDA databases has been integrated, making TSdb a useful source for the discovery of potential inhibitory mechanisms linking transporter substrates and metabolic enzymes. User-friendly web interfaces are designed for easy access, query and download of the data. Text and BLAST searches against all transporters in the database are provided. We will regularly update the substrate data with evidence from new publications.

A nonsynonymous SNP in human cytosolic sialidase in a small Asian population results in reduced enzyme activity: potential link with severe adverse reactions to oseltamivir

oseltamivir 的使用，广泛地是的 stockpiled 为在可能的鸟的流行性感冒的使用的药之一流行，被报导了与 neuropsychiatricdisorders 和严重皮肤反应被联系，首先在日本。这里，我们在 dbSNP 数据库识别了非同义的 SNP (单个核苷酸多型性) ， R41Q 在 humancytosolic sialidase 的酶的活跃地点附近，是 oseltamivir 的目标的病毒 neuraminidase 的一个相当或相同事物。在欧洲、非洲的美国人口的 9.29% 亚洲人口和没有的这 SNPoccurred。Ourstructural 分析和 Ki 大小使用试管内 sialidase 试金显示这 SNPcould 增加人的 sialidase 的非计划中的有约束力的亲密关系到 oseltamivir 羧化物， oseltamivir 的活跃形式，因此减少 sialidase 活动。另外，这 SNP 自己与一项内在地更低的 sialidase 活动导致酶，由它的增加的 Km 证明 Vmax 珍视并且减少。理论上，到有这 SNP 的人的 oseltamivir 的管理可能进一步减少他们的 sialidase 活动。我们注意 oseltamivir 的 reportedneuropsychiatric 副酌和人的 sialidase-relateddisorders 的已知的症状的类似。我们建议这个充实亚洲人的 sialidase 变化由 SNP 引起了，在同型结合的形式可能，可以与对 oseltamivir 的某些严重不利反应被联系。

Cloning and analysis of a cDNA encoding acetohydroxy acid isomeroreductase from G2 pea

Using cDNA representational difference analysis (cDNA RDA) method, we have successfully isolated a gene fragment whose expression was specifically induced by external GAa application. Screening a G2 pea cDNA library using this fragment as a probe, we obtained a 2036 bp full-length cDNA. It contains a 1746 bp open reading frame and encodes a protein of 581 amino acids with a theoretical molecular weight of 64 ku. It shares high-level sequenceidentity with AAIR genes from other plant species. This cDNA was cloned into expression vector and recombinant E. coli DH5α cells with remarkable AAIR enzyme activity were obtained.

A brief summary of major advances in cotton functional genomics and molecular breeding studies in China

Cotton fibers, commonly known as cotton lint, are single-celled trichomes derived from epidermal lay- ers of cotton ovules. Despite of its importance in word trade, the molecular mechanisms of cotton fiber production is still poorly understood. Through transcriptome profiling, functional genomics, pro- teomics, metabolomics approaches as well as marker-assisted molecular breeding, scientists in China have made significant contributions in cotton research. Here, we briefly summarize major progresses made in Chinese laboratories, and discuss future directions and perspectives relative to the develop- ment of this unique crop plant.

Molecular cloning,expressional profiling,DNA binding and trans-activation property studies of QRAP2 from Arabidopsis thaliana

Based upon analysis of data obtained from theATH1 microarrays, a cDNA that was highly induced afterdrought treatment, was isolated from Arabidopsis seedlings.RT-PCR and Quantitative Real-Time (QRT)-PCR experi-ments showed that expression level of the gene increasedsignificantly upon drought, UV, abscisic acid, high salinityand salicylic acid treatments. It was classified as a DREBsubfamily member based on multiple sequence alignmentand phylogenetic characterization. Since it encoded a proteinwith a typical ERF/AP2 DNA-binding domain and containeda glutamine-rich region near its N terminus, we named itQRAP2 (for glutamine-rich AP2). Gel retardation assay re-vealed that QRAP2 was able to form a specific complex withthe previously characterized DRE element while did notshow any affinity to the GCC box or the mutant DRE box.When fused to the GAL4 DNA-binding domain, either full-length QRAP2 or its N-terminus functioned effectively as atrans-activator in the yeast one-hybrid assay with its C-ter-minus completely inactive. Our data indicate that QRAP2could be a new member of the AP2/EREBP transcriptionfactor family involved in activation of down-stream targetgenes in response to environmental stress, especially underdrought conditions.