Isolation and mapping of telomeric pentanucleotide (TAACC)(n) repeats of the pacific whiteleg shrimp, Penaeus vannamei, using fluorescence in situ hybridization

To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)(n) repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective I showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA),, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1 > P2 > P3 > P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

Proteomic analysis of differentially expressed proteins in lymphoid organ of Fenneropenaeus chinensis response to Vibrio anguillarum stimulation

To gain an insight into the function of shrimp lymphoid organ at protein level, we analyzed the proteome of lymphoid organ in healthy Chinese shrimp Fenneropenaeus chinensis (F. chinensis) through two-dimensional gel electrophoresis (2-DE) based proteomic approach. A total of 95 spots representing 75 protein entries were identified by liquid chromatography tandem mass spectrometry (LC-MS/MS) with both online and in-house database. According to Gene Ontology (GO) annotation of biological process, the identified proteins were classified into 13 categories. Among them, approximately 36% of proteins related to cytoskeleton are noticeable. Then, a comparative proteomic approach was employed to investigate the differentially expressed proteins in lymphoid organ of Vibrio anguillarum-challenged F. chinensis. At 24 h post-injection (hpi), 17 differentially expressed protein spots were successfully identified, including 4 up-regulated protein spots (represent 4 proteins: cathepsin L protein similar to squid CG16901-PC, protein kinase C and protein similar to T-complex Chaperonin 5 CG8439-PA), and 13 down-regulated protein spots (represent 9 proteins: actin, beta-actin, cytoplasmic actin CyII, alpha tubulin, beta tubulin, protein similar to proteasome delta, vacuolar ATP synthase subunit B, elongation factor 2, carboxypeptidase B). These data may help us to understand the function of lymphoid organ and the molecular immune mechanism of shrimp responsive to pathogen infection. (C) 2010 Elsevier Ltd. All rights reserved.

Molecular cloning, characterization and expression of a novel serine proteinase inhibitor gene in bay scallops (Argopecten irradians, Lamarck 1819)

Serine protease inhibitors, critical regulators of endogenous proteases, are found in all multicellular organisms and play crucial roles in host physiological and immunological effector mechanisms. The first mollusk serine proteinase inhibitor (designated AISPI) cDNA was obtained from the bay scallop Argopecten irradians by randomly sequencing a whole tissue cDNA library and rapid amplification of cDNA ends (RACE). The full-length cDNA of the scallop serine protease inhibitor was 1020 bp, consisting of a 5'-terminal untranslated region (UTR) of 39 bp, a 3'-terminal UTR of 147 bp with a canonical polyadenylation signal sequence AATAAA and a poly(A) tail, and an open reading frame of 834 bp. The AISPI cDNA encoded a polypeptide of 278 amino acids with a putative signal peptide of 22 amino acids and a mature protein of 256 amino acids. The deduced amino-acid sequence of AISPI contained six tandem and homologous domains similar to that of Kazal-type serine protease inhibitors, including the conserved sequence C-X(7)-C-X(6)-Y-X(3)-C-X(2,3)-C and six cysteine residues responsible for the formation of disulfide bridges, indicating that the AISPI protein from bay scallop should be a member of the Kazal-type serine protease inhibitor family. The temporal expression of AISPI was measured by semi-quantitative RT-PCR after injury or bacterial challenge. After the adductor muscle was wounded or injected with Vibrio anguillarum, the expression of AISPI mRNA in hemolymph was up-regulated and reached the maximum level at 8 and 16 h, respectively, and then progressively dropped back to the original level. The results indicated that AISPI could play an important role in injury healing and immune response in mollusks as it could be induced by injury and bacterial challenge. (c) 2005 Elsevier Ltd. All rights reserved.

考虑机器故障和有限缓冲器的级联生产线系统的建模和分析

本文在建立机器故障和系统阻塞的近似模型的基础上给出了系统的排队网络模型.利用这一模型,可以对问题解析地求解,以分析系统的性能,而不需要复杂的计算.仿真结果表明,其解的精度令人满意.

基于滑转率的六轮纵列式月球车驱动控制研究

基于车轮滑转率和车轮地面力学,研究了月球车在松软月面行驶时的车轮过度下陷问题.将月球车车轮下陷和车轮—土壤作用力表达为车轮滑转率的函数,结合车辆地面力学理论并考虑纵列式车轮多通过性土壤参数的修正,建立了月球车的动力学模型.判断车轮是否发生过度下陷的标准为土壤所提供给驱动轮的土壤推力能否克服土壤对车轮的阻力.利用建立的动力学模型,计算出能够保证车轮不会过度下陷的期望滑转率.考虑到月球车动力学系统的非线性和不确定性,设计了以车轮滑转率为状态变量的滑模驱动控制器.仿真结果表明,采用该控制器可以较快地跟踪期望滑转率,避免车轮的过度滑转下陷,保证月球车能够在软质路面上正常行驶.

Type-omega DPLs

Type-omega DPLs (Denotational Proof Languages) are languages for proof presentation and search that offer strong soundness guarantees. LCF-type systems such as HOL offer similar guarantees, but their soundness relies heavily on static type systems. By contrast, DPLs ensure soundness dynamically, through their evaluation semantics; no type system is necessary. This is possible owing to a novel two-tier syntax that separates deductions from computations, and to the abstraction of assumption bases, which is factored into the semantics of the language and allows for sound evaluation. Every type-omega DPL properly contains a type-alpha DPL, which can be used to present proofs in a lucid and detailed form, exclusively in terms of primitive inference rules. Derived inference rules are expressed as user-defined methods, which are "proof recipes" that take arguments and dynamically perform appropriate deductions. Methods arise naturally via parametric abstraction over type-alpha proofs. In that light, the evaluation of a method call can be viewed as a computation that carries out a type-alpha deduction. The type-alpha proof "unwound" by such a method call is called the "certificate" of the call. Certificates can be checked by exceptionally simple type-alpha interpreters, and thus they are useful whenever we wish to minimize our trusted base. Methods are statically closed over lexical environments, but dynamically scoped over assumption bases. They can take other methods as arguments, they can iterate, and they can branch conditionally. These capabilities, in tandem with the bifurcated syntax of type-omega DPLs and their dynamic assumption-base semantics, allow the user to define methods in a style that is disciplined enough to ensure soundness yet fluid enough to permit succinct and perspicuous expression of arbitrarily sophisticated derived inference rules. We demonstrate every major feature of type-omega DPLs by defining and studying NDL-omega, a higher-order, lexically scoped, call-by-value type-omega DPL for classical zero-order natural deduction---a simple choice that allows us to focus on type-omega syntax and semantics rather than on the subtleties of the underlying logic. We start by illustrating how type-alpha DPLs naturally lead to type-omega DPLs by way of abstraction; present the formal syntax and semantics of NDL-omega; prove several results about it, including soundness; give numerous examples of methods; point out connections to the lambda-phi calculus, a very general framework for type-omega DPLs; introduce a notion of computational and deductive cost; define several instrumented interpreters for computing such costs and for generating certificates; explore the use of type-omega DPLs as general programming languages; show that DPLs do not have to be type-less by formulating a static Hindley-Milner polymorphic type system for NDL-omega; discuss some idiosyncrasies of type-omega DPLs such as the potential divergence of proof checking; and compare type-omega DPLs to other approaches to proof presentation and discovery. Finally, a complete implementation of NDL-omega in SML-NJ is given for users who want to run the examples and experiment with the language.

Redundant Sensors for Mobile Robot Navigation

Redundant sensors are needed on a mobile robot so that the accuracy with which it perceives its surroundings can be increased. Sonar and infrared sensors are used here in tandem, each compensating for deficiencies in the other. The robot combines the data from both sensors to build a representation which is more accurate than if either sensor were used alone. Another representation, the curvature primal sketch, is extracted from this perceived workspace and is used as the input to two path planning programs: one based on configuration space and one based on a generalized cone formulation of free space.

Rapid authentication of ginseng species using microchip electrophoresis with laser-induced fluorescence detection

Ginseng is one of the most expensive Chinese herbal medicines and the effectiveness of ginseng depends strongly on its botanical sources and the use of different parts of the plants. In this study, a microchip electrophoresis method coupled with the polymerase chain reaction (PCR)-short tandem repeats (STR) technique was developed for rapid authentication of ginseng species. A low viscosity hydroxypropyl methylcellulose (HPMC) solution was used as the sieving matrix for separation of the amplified STR fragments. The allele sizing of the amplified PCR products could be detected within 240 s or less. Good reproducibility and accuracy of the fragment size were obtained with the relative standard deviation for the allele sizes less than 1.0% (n = 11). At two microsatellite loci (CT 12, CA 33), American ginseng had a different allele pattern on the electropherograms compared with that of the Oriental ginseng. Moreover, cultivated and wild American ginseng can be distinguished on the basis of allele sizing. This work establishes the feasibility of fast genetic authentication of ginseng species by use of microchip electrophoresis.

Development and application of a sol-gel immunosorbent-based method for the determination of isoproturon in surface water

An immunosorbent was fabricated by encapsulation Of monoclonal anti-isoproturon antibodies in sol-gel matrix. The immunosorbent-based loading, rinsing and eluting processes were optimized. Based on these optimizations, the sol-gel immunosorbent (SG-IS) selectively extracted isoproturon from an artificial mixture of 68 pesticides. In addition to this high selectivity, the SG-IS proved to be reusable. The SG-IS was combined with liquid chromatography-tandem mass spectrometry (LC-MS-MS) to determine isoproturon in surface water, and the linear range was up to 2.2 mu g/l with correlation coefficient higher than 0.99 and relative standard deviation (RSD) lower than 5% (n = 8). The limit of quantitation (LOQ) for 25-ml surface water sample was 5 ng/l. (c) 2006 Elsevier B.V. All rights reserved.

Caratterizzazione proteomica di fluidi e tessuti in diverse condizioni fisio-patologiche

This thesis has been focused on the proteomic characterization of human saliva from donors of different ages, starting from birth up to adult age, and pediatric brain tumor tissues. The first study has been performed in order to compare the acid-insoluble fraction of saliva from preterm with at-term newborns and adults and establish if differences exist. In the second study medulloblastoma and pilocytic astrocytoma pediatric brain tumor extracts have been compared. In both studies 2- DE analysis was coupled with high resolution tandem mass spectrometry (MS/MS). The proteomic characterization of the acid-insoluble fractions of saliva from preterm newborns allowed to integrate data previously obtained on the acid-soluble fraction by HPLC-electrospray ionization (ESI)-mass spectrometry (MS), and to evidence several differences between preterm newborns, at-term newborns and adults. Spots differentially expressed between the three groups, according to image analysis of the gels, were submitted to in-gel tryptic digestion and the peptide mixture analyzed by high performance HPLC-ESI-MS/MS for their characterization. By this strategy, we identified three over-expressed proteins in atterm newborns with respect to preterm newborns and adults (BPI fold-containing family A member 1, two proteoforms of annexin A1, and keratin type 1 cytoskeletal 13), and several over-expressed proteins in adults (fatty acid-binding protein, S100A6, S100A7, two proteoforms of S100A9, several proteoforms of prolactin-inducible protein, Ig kappa chain, two proteoforms of cystatin SN, one proteoform of cystatin S and several proteoforms of α-amylase 1). Moreover, for the first time, it was possible to assign by MS/MS four spots of human saliva 2-DE, already detected by other authors, to different proteoforms of S100A9. The strategy applied used a sequential staining protocol to the 2-DE gels, first with Pro-Q Diamond, that allows specific detection of phosphoproteins, and successively with total protein SYPRO Ruby stain. In the second study, proteomic analysis of two pediatric brain tumor tissues pointed out differences between medulloblastoma, the prevalent malignant tumor in childhood, and pilocytic astrocytoma, the most common, that only rarely shows a malignant progression. Due to the limited availability of bioptic tissue, the study was performed on pooled tumor tissues, and was focused on acid-insoluble fraction to integrate the characterization performed by a group of colleagues in Rome on the acid-soluble fraction by high performance HPLC-ESI-MS/MS. The results indicated that the two tumors exhibit different proteomic profiles and evidenced interesting differential expression of several proteins. Among them, peroxiredoxin- 1, peptidyl-prolyl cis–trans isomerase A, heterogeneous nuclear ribonucleoproteins A2/B1, mitochondrial isoform of malate dehydrogenase, nucleoside diphosphate kinase A, glutathione S-transferase P and fructose bisphosphate aldolase A resulted significantly over-expressed in medulloblastoma while glial fibrillary acidic protein, serotransferrin, α crystallin B chain, ferritin light chain, annexin A5, fatty acid-binding protein (brain), sorcin and apolipoprotein A-I resulted significantly over-expressed in pilocytic astrocytoma. In conclusion, the work done allowed to evidence the usefulness of using an integrated bottom-up/top-down approach, based on 2-DE-MS analysis and high performance MS in order to obtain a complete characterization of the proteome under investigation, revealing and identifying, not only peptides and small proteins, but also proteins with higher MW, that often it is not possible to identify by using exclusively a top-down ESI-MS approach.

Locational distribution of gene functional classes in Arabidopsis thaliana

Riley, M. C., Clare, A., King, R. D. (2007). Locational distribution of gene functional classes in Arabidopsis thaliana. BMC Bioinformatics 8, Article No: 112 Sponsorship: EPSRC / RAEng

Nuclear dispositions of subtelomeric and pericentromeric chromosomal domains during meiosis in asynaptic mutants of rye (Secale cereale L.)

EI Mikhailova, SP Sosnikhina, GA Kirillova, OA Tikholiz, VG Smirnov, RN Jones and G Jenkins (2001). Nuclear dispositions of subtelomeric and pericentromeric chromosomal domains during meiosis in asynaptic mutants of rye (Secale cereale L.). Journal of Cell Science, 114 (10), 1875-1882. Sponsorship: Russian Foundation for Basic Research (grants 00-04-48522/ 99-04-48182) RAE2008

Rola Francji i Niemiec w procesie integracji europejskiej w latach 1992-2007

Francja i Niemcy przez stulecia walczyły o zdobycie władzy i przejęcie wpływów na kontynencie europejskim i traktowały siebie nawzajem jako największe zagrożenie. Jednak tragiczna pierwsza połowa XX wieku przyniosła z jednej strony pragnienie zapewnienia, iż okropności wojny już nigdy się nie powtórzą, a z drugiej strony poczucie, że nieodzowna jest zmiana dwustronnych stosunków panujących między Berlinem a Paryżem. Konieczność stworzenia przestrzeni wolności i współpracy doprowadziła niegdysiejszych wrogów do stworzenia idei integracji najważniejszych części gospodarki. Pomysł zjednoczenia krajów Europy Zachodniej przekształcił się w kolejnych latach w symbol zaangażowania francusko-niemieckiego. Dwie republiki stały się rdzeniem europejskiej współpracy i spiritus movens zmian politycznych, ekonomicznych i instytucjonalnych w powojennej Europie. Po upadku komunizmu w 1989 roku ich rola zyskała nowy wymiar w odmiennych warunkach geopolitycznych - od momentu podpisania Traktatu z Maastricht w 1992 roku francusko-niemiecki duet powiększył swe znaczenie i wpływ na politykę nowej Unii Europejskiej. Realizacja zapisów Traktatu z Maastricht i kolejnych dokumentów, w tym Traktatu z Lizbony, koncentracja na kwestiach reform instytucjonalnych, jak również przygotowania do wschodniego rozszerzenia UE mogą być rozpatrywane jedynie w odniesieniu do wspólnych działań prowadzonych przez nadreński tandem. Realizacja trzech filarów integracji: współpracy w wymiarze ekonomicznym i społecznym, wspólnej polityki zagranicznej i bezpieczeństwa, jak również współpracy policyjnej i sądowej w sprawach karnych, podkreślają znaczenie couple franco-allemand i zwracają uwagę na rolę lidera, jaką Paryż i Berlin odgrywają w dziedzinie integracji.

Synteza i struktura nowych aminowych analogów ansamycynowego antybiotyku rifampicyny

Wydział Chemii: Zakład Biochemii

Identyfikacja domen WG/GW zaangażowanych w wiązanie białek Argonaute oraz analiza mechanizmów molekularnych odpowiedzialnych za ich zmienność

Wydział Biologii: Instytut Biologii Molekularnej i Biotechnologii