Use of Vertex Index in Structure-Activity Analysis and Design of Molecules

The last few decades have witnessed application of graph theory and topological indices derived from molecular graph in structure-activity analysis. Such applications are based on regression and various multivariate analyses. Most of the topological indices are computed for the whole molecule and used as descriptors for explaining properties/activities of chemical compounds. However, some substructural descriptors in the form of topological distance based vertex indices have been found to be useful in identifying activity related substructures and in predicting pharmacological and toxicological activities of bioactive compounds. Another important aspect of drug discovery e. g. designing novel pharmaceutical candidates could also be done from the distance distribution associated with such vertex indices. In this article, we will review the development and applications of this approach both in activity prediction as well as in designing novel compounds.

Anticancer property of Bryophyllum pinnata (Lam.) Oken. leaf on human cervical cancer cells

Background: Bryophyllum pinnata (B. pinnata) is a common medicinal plant used in traditional medicine of India and of other countries for curing various infections, bowel diseases, healing wounds and other ailments. However, its anticancer properties are poorly defined. In view of broad spectrum therapeutic potential of B. pinnata we designed a study to examine anti-cancer and anti-Human Papillomavirus (HPV) activities in its leaf extracts and tried to isolate its active principle. Methods: A chloroform extract derived from a bulk of botanically well-characterized pulverized B. pinnata leaves was separated using column chromatography with step-gradient of petroleum ether and ethyl acetate. Fractions were characterized for phyto-chemical compounds by TLC, HPTLC and NMR and Biological activity of the fractions were examined by MTT-based cell viability assay, Electrophoretic Mobility Shift Assay, Northern blotting and assay of apoptosis related proteins by immunoblotting in human cervical cancer cells. Results: Results showed presence of growth inhibitory activity in the crude leaf extracts with IC50 at 552 mu g/ml which resolved to fraction F4 (Petroleum Ether: Ethyl Acetate:: 50: 50) and showed IC50 at 91 mu g/ml. Investigations of anti-viral activity of the extract and its fraction revealed a specific anti-HPV activity on cervical cancer cells as evidenced by downregulation of constitutively active AP1 specific DNA binding activity and suppression of oncogenic c-Fos and c-Jun expression which was accompanied by inhibition of HPV18 transcription. In addition to inhibiting growth, fraction F4 strongly induced apoptosis as evidenced by an increased expression of the pro-apoptotic protein Bax, suppression of the anti-apoptotic molecules Bcl-2, and activation of caspase-3 and cleavage of PARP-1. Phytochemical analysis of fraction F4 by HPTLC and NMR indicated presence of activity that resembled Bryophyllin A. Conclusions: Our study therefore demonstrates presence of anticancer and anti-HPV an activity in B. pinnata leaves that can be further exploited as a potential anticancer, anti-HPV therapeutic for treatment of HPV infection and cervical cancer.

Differential Activities of the Two Closely Related Withanolides, Withaferin A and Withanone: Bioinformatics and Experimental Evidences

Background and Purpose: Withanolides are naturally occurring chemical compounds. They are secondary metabolites produced via oxidation of steroids and structurally consist of a steroid-backbone bound to a lactone or its derivatives. They are known to protect plants against herbivores and have medicinal value including anti-inflammation, anti-cancer, adaptogenic and anti-oxidant effects. Withaferin A (Wi-A) and Withanone (Wi-N) are two structurally similar withanolides isolated from Withania somnifera, also known as Ashwagandha in Indian Ayurvedic medicine. Ashwagandha alcoholic leaf extract (i-Extract), rich in Wi-N, was shown to kill cancer cells selectively. Furthermore, the two closely related purified phytochemicals, Wi-A and Wi-N, showed differential activity in normal and cancer human cells in vitro and in vivo. We had earlier identified several genes involved in cytotoxicity of i-Extract in human cancer cells by loss-of-function assays using either siRNA or randomized ribozyme library. Methodology/Principal Findings: In the present study, we have employed bioinformatics tools on four genes, i.e., mortalin, p53, p21 and Nrf2, identified by loss-of-function screenings. We examined the docking efficacy of Wi-N and Wi-A to each of the four targets and found that the two closely related phytochemicals have differential binding properties to the selected cellular targets that can potentially instigate differential molecular effects. We validated these findings by undertaking parallel experiments on specific gene responses to either Wi-N or Wi-A in human normal and cancer cells. We demonstrate that Wi-A that binds strongly to the selected targets acts as a strong cytotoxic agent both for normal and cancer cells. Wi-N, on the other hand, has a weak binding to the targets; it showed milder cytotoxicity towards cancer cells and was safe for normal cells. The present molecular docking analyses and experimental evidence revealed important insights to the use of Wi-A and Wi-N for cancer treatment and development of new anti-cancer phytochemical cocktails.

Volatiles in Protoplanetary Disks

Planets are assembled from the gas, dust, and ice in the accretion disks that encircle young stars. Ices of chemical compounds with low condensation temperatures (<200 K), the so-called volatiles, dominate the solid mass reservoir from which planetesimals are formed and are thus available to build the protoplanetary cores of gas/ice giant planets. It has long been thought that the regions near the condensation fronts of volatiles are preferential birth sites of planets. Moreover, the main volatiles in disks are also the main C-and O-containing species in (exo)planetary atmospheres. Understanding the distribution of volatiles in disks and their role in planet-formation processes is therefore of great interest.

This thesis addresses two fundamental questions concerning the nature of volatiles in planet-forming disks: (1) how are volatiles distributed throughout a disk, and (2) how can we use volatiles to probe planet-forming processes in disks? We tackle the first question in two complementary ways. We have developed a novel super-resolution method to constrain the radial distribution of volatiles throughout a disk by combining multi-wavelength spectra. Thanks to the ordered velocity and temperature profiles in disks, we find that detailed constraints can be derived even with spatially and spectrally unresolved data -- provided a wide range of energy levels are sampled. We also employ high-spatial resolution interferometric images at (sub)mm frequencies using the Atacama Large Millimeter Array (ALMA) to directly measure the radial distribution of volatiles.

For the second question, we combine volatile gas emission measurements with those of the dust continuum emission or extinction to understand dust growth mechanisms in disks and disk instabilities at planet-forming distances from the central star. Our observations and models support the idea that the water vapor can be concentrated in regions near its condensation front at certain evolutionary stages in the lifetime of protoplanetary disks, and that fast pebble growth is likely to occur near the condensation fronts of various volatile species.

Avaliação da defesa química e da influência dos corais invasores Tubastraea coccinea e Tubastraea tagusensis na estruturação das comunidades bentônicas da Baía da Ilha Grande RJ

A introdução de espécies invasoras marinhas tem causado danos econômicos e ecológicos consideráveis em todo o mundo. Algumas destas espécies incluindo corais escleractíneos possuem adaptações, tais como metabólitos secundários utilizados para evitar a predação e competição por espaço por outros organismos. Este arsenal químico e as interações entre espécies invasoras e nativas podem causar alterações na distribuição das espécies e na estrutura das comunidades de costões rochosos tropicais. Os objetivos deste estudo foram (1) caracterizar os metabólitos secundários produzidos pelos corais invasores Tubastraea tagusensis e T. coccinea na Baía da Ilha Grande, Brasil, (2) detectar os compostos químicos liberados pelos tecidos de Tubastraea tagusensis in situ utilizando um aparelho submersível; (3) testar no campo os extratos metanólicos produzidos por ambas as espécies de Tubastraea contra a predação por peixes generalistas e assentamento de outros organismos, (4) testar no campo se os compostos químicos produzidos por ambos os corais invasores variaram na concentração ou tipo quando os corais foram colocados próximos de competidores nativos e (5) determinar como as comunidades de costões rochosos da Baía da Ilha Grande foram afetadas pela expansão de Tubastraea coccinea e T. tagusensis em 8 locais estudados durante 2 anos. As principais classes de substâncias encontradas nos extratos metanólicos de Tubastraea foram identificados como esteróis, ácidos graxos, hidrocarbonetos, alcalóides, ésteres e alcoóis, entretanto, o aparelho submersível identificou somente hidrocarbonetos liberados por Tubastraea na água do mar. O extrato metanólico de T. tagusensis reduziu a predação por peixes generalistas e já os extratos de ambas as espécies mostraram efeitos espécie-específicos sobre organismos incrustantes no campo. No experimento de interação competitiva foi detectada a presença de necrose nos tecidos do coral endêmico Mussismilia hispida e isso provocou variação nas concentrações de esteróis, alcalóides e ácidos graxos nos tecidos de Tubastraea. Em contraste, a esponja Desmapsamma anchorata cresceu sobre os tecidos das colônias de ambos os corais invasores. A presença de Tubastraea nas comunidades bentônicas causou uma dissimilaridade média de 4,8% nas comunidades invadidas. Uma forte relação positiva foi encontrada entre a cobertura de Tubastraea e a mudança na estrutura da comunidade da Baía da Ilha Grande. Portanto, os efeitos negativos de ambos os corais invasores são suficientes para acarretar mudanças na estrutura das comunidades bentônicas tropicais.

Avaliação das concentrações de BTEX em ambiente indoor: estudo de caso da sala de spinning de uma academia de ginástica Rio de Janeiro / RJ.

Muitos dos locais onde as atividades são realizadas nas academias de ginásticas são salas pequenas e fechadas com sistema de climatização artificial, freqüentados por um grande número de alunos realizando seus exercícios e profissionais auxiliando as atividades. Com isso, há uma intensa transpiração desses indivíduos, uma freqüente rotina de limpeza do piso e de equipamentos com pequenos intervalos, possibilitando a alterações da qualidade do ar indoor. O presente trabalho busca mostrar as tendências de variações nos valores das concentrações dos poluentes atmosféricos BTEX em ambiente indoor, especificamente na sala de spinning de uma academia de ginástica do Rio de Janeiro. Para o monitoramento da qualidade do ar foram utilizados cartuchos de carvão ativado SKC, acoplado a uma bomba KNF com vazão de 1l min. Para a extração de cada amostra foi feita a análise cromatográfica com cromatógrafo a gás modelo 6890 acoplado a um espectrômetro de massa modelo 5973 da marca Agilent. Foram analisadas 34 amostras coletadas na salas de spinning durante as aulas com atividades aeróbicas, o que intensificava a respiração dos indivíduos, possibilitando uma maior inalação destes COVs. Em contrapartida, também foram coletadas 5 amostras outdoor, 4 delas pareadas indoor/ outdoor para uma análise comparativa das concentrações destes poluentes. Dentre os compostos orgânicos voláteis analisados, o tolueno é o BTEX mais abundante obtido neste trabalho, representando 81% destes COVs indoor. Todas as amostras medidas em pares indoor/ outdoor tiveram concentrações maiores no interior, exceto para o benzeno no dia 3/12/2010. Simples atividades usualmente realizadas pelo homem, como a inserção de piso emborrachado, manutenção do sistema de climatização artificial, e limpeza podem alterar o ar indoor. As conclusões alcançadas após as medições das concentrações de BTEX foram de que o ar indoor estava mais poluído do que o outdoor. Este monitoramento da qualidade do ar indoor ainda é escasso no Brasil. Alguns esforços tem sido feito em relação a ambientes confinados como a Portaria n˚3523 do Ministério da Saúde, regulamentando o controle dos ambientes climatizados e a Resolução n˚9 da Agência Nacional de Vigilância Sanitária, além da Resolução CONAMA n ˚3 estabelecendo padrões de qualidade do ar para alguns compostos químicos, porém muitos compostos químicos ainda não são legislados ou não possuem a devida atenção, não sendo suficientes para contemplar a complexidade do assunto

Impacto do aterro controlado Morro do Céu na atmosfera

O principal objetivo deste estudo é estimar o alcance dos poluentes emitidos pelo Aterro Controlado do Morro do Céu (ACMC), localizado em Niterói e as possíveis áreas afetadas. Utilizou-se um modelo matemático para o estudo do transporte e difusão dos poluentes que fornece a concentração nas vizinhanças, a partir dos dados de emissões, meteorológicos e topográficos. Foram analisados e tratados os dados meteorológicos e a topografia da região de alcance da pluma. As amostras foram coletadas por uma bomba de ar a uma vazão de 500 mL min-1 por um período de 10 min, em dois dias e horários diferentes. A câmara de fluxo empregada foi de 30 L e de PVC, no formato cilíndrico, cuja boca foi emborcada no solo por 5 cm e a amostragem realizada por uma válvula posicionada no fundo. Foram empregados como meios de amostragem cartuchos de carvão ativo de leito duplo e as análises químicas foram realizadas por cromatografia de fase gasosa com detecção por ionização na chama. Os resultados encontrados indicam que o ACMC pode conter quantidade significativa de vários compostos químicos, principalmente compostos orgânicos voláteis, impactando a vegetação, prejudicando a saúde e a qualidade de vida da população do seu entorno. Foram obtidos valores de compostos orgânicos voláteis acima de 400 g m-3 a menos que 500 m do ACMC. Considerando que o ACMC não será desativado em um tempo próximo, creches, escolas e postos de saúde devem ser deslocados para uma área onde o impacto dos poluentes atmosféricos seja menor, contribuindo para a melhoria da qualidade de vida da população

拮抗菌和化学物质的抑病机理及果实抗病相关基因的克隆

真菌病害是造成采后新鲜水果损失的一个主要原因。生物拮抗菌能有效地防治果实采后腐烂，降低杀菌剂的用量，从而增加了食品安全性和降低了潜在的环境危害。然而，与化学杀菌剂相比，单独使用生物拮抗菌对果实采后病害的控制效果有时不如化学杀菌剂明显。因此，为了提高拮抗菌的生防效力，有效控制果实的采后病害，本文主要研究了拮抗菌与化学物质使用的防病机理，并从冬枣果实中克隆β-1，3-葡聚糖酶基因并对其特性进行了初步分析。研究结果表明： 1. 酵母菌Cryptococcus laurentii和枯草芽孢杆菌Bacillus subtilis能够有效的防治冬枣果实采后青霉病和黑霉病的发生，而且C. laurentii对病害的防治效果比B. subtilis好。拮抗菌的抑病效果与使用浓度成正比。在接种C. laurentii的伤口上再接种病原菌可以显著刺激酵母菌的生长。然而，在接种B. subtilis的伤口上接种病原菌则不增加拮抗细菌的群体数量。 2. 不同酵母拮抗菌对四种杀菌剂（Deccozil，Sportak，Iprodine和Stroby）的敏感程度不同。其中，R. glutinis对Deccozil，Iprodione和Stroby最敏感。将低剂量的杀菌剂与酵母菌配合能显著增强酵母菌对采后病菌的抑制作用。C. laurentii与100 µl/L的Stroby配合能完全抑制青霉和黑霉病菌的孢子萌发。2%（w/v）的碳酸氢钠（SBC）与C. laurentii或T. pullulans配合使用显著抑制采后病菌(Penicillium expansum或Alternaria alternata)的孢子萌发和芽管伸长。SBC显著增强拮抗菌对梨果实采后青霉病和黑霉病的防治能力。C. laurentii对采后病害的防治效果好于T. pullulans的防治效果。 3. C. laurentii和B. subtilis对冬枣果实抗病性的诱导与接种距离和接种时间密切相关。距接种拮抗菌近的部位，抗性诱导就越强。酵母菌诱导果实的这种抗病性与诱导果实几丁质酶，β-1，3-葡聚糖酶， PAL，POD和PPO活性有关。 4. 采前喷施2 mM的水杨酸（SA）和0.2 mM的茉莉酸甲酯（MeJA）显著降低甜樱桃果实采后褐腐病的病斑直径， 并能诱导甜樱桃果实β-1，3-葡聚糖酶， PAL， POD和PPO活性以及乙烯含量的增加。采前处理对果实抗病性的诱导效果要好于采后处理。采前和采后SA或MeJA处理，贮藏于25C的甜樱桃果实β-1，3-葡聚糖酶和PAL活性显著高于贮藏于0C的甜樱桃果实的酶活性。2 mM的SA显著抑制了Monilinia fructicola的孢子萌发和菌丝扩展;而0.2 mM的MeJA则对M. fructicola几乎没有抑制作用。在贮藏早期，MeJA对果实β-1，3-葡聚糖酶和PAL活性的诱导作用要强于SA的诱导作用。 5. 1 × 108CFU/ml的C. laurentii，以及5 × 107CFU/ml的C. laurentii与0.2 mM的MeJA 配合使用均可诱导桃果实的抗性，并显著降低果实青霉病和褐腐病的病斑直径。0.2 mM的MeJA能促进C. laurentii生长，抑制P. expansum的菌丝扩展， 但对M. fructicola基本没有抑制作用。在25和0C，MeJA和C. laurentii单独或配合使用都诱导了桃果实几丁质酶，β-1，3-葡聚糖酶，PAL和POD活性的升高。这些抗病相关酶活性的升高可能与病斑扩展的程度是直接相关的。 6. 通过设计简并引物，采用降落PCR，扩增出β-1，3-葡聚糖酶基因的同源片段，分别克隆到两个彼此间同源性很低的β-1，3-葡聚糖酶的cDNA全长（Glu-1和Glu-2）。RT-PCR结果表明，Glu-1基因的表达受酵母拮抗菌C. laurentii处理所诱导，这一结果与酵母拮抗菌诱导果实β-1，3-葡聚糖酶活性的增加相呼应;而Glu-2基因的表达则不受C. laurentii处理所诱导。

西藏产雪莲花的化学成分研究

本学位论文报道了作为传统藏药材广泛使用的西藏产雪莲花化学成分的研究。论文由五章组成，第一章是三种西藏产雪莲花的化学成分的系统分离纯化和结构鉴定；第二章为西藏产雪莲花化学成分的液-质及串联质谱联用分析；第三章提出了以HPLC和TLC为检测方法的雪莲花药材质量标准草案；第四章给出了对西藏产雪莲花挥发油化学成分的气-质联用分析结果；第五章概述了雪莲花的化学成分及药理研究进展。 第一章包括三个部分。第一部分报道了绵头雪莲花(Saussurea laniceps Hand.-Mazz.)全草乙醇提取物化学成分的分离鉴定。采用正相硅胶柱层析及凝胶柱层析等分离方法，从西藏产绵头雪莲花的乙醇提取物中共分离鉴定出15个化合物。其中11个化合物为首次从该植物中分离得到，当中2个化合物系在凤毛菊属植物中首次发现。第二部分报道了水母雪莲花(Saussurea medusa Maxim.)全草乙醇提取物的化学成分。采用正、反相硅胶柱层析及凝胶柱层析等分离方法，共分离鉴定出15个化合物，其中1个为新化合物，另有4个化合物为首次从该植物中分离得到。新化合物结构通过质谱和一维及二维核磁共振等波谱解析方法及碱水解反应确定为巴豆酰基-高车前苷(M-7)。第三部分报道了三指雪莲花 (Saussurea tridactyla Sch.-Bip. ex Hook. f.)全草乙醇提取物的化学成分。采用正相硅胶柱层析及凝胶柱层析等分离方法，共分离鉴定出7个化合物，其中1个化合物为首次从该植物中分离得到。 第二章也包括三个部分。首先是采用液-质联用(HPLC-DAD-ESI-MSn)分析方法，对7个西藏不同产地的三指雪莲花化学成分进行了分析，通过与标准品的 UV和MS数据比较，共鉴定出14个峰，并对其中8个共有成分进行了定量测定。其次是关于八种西藏产雪莲花化学成分的液-质联用(HPLC-DAD-ESI-MSn)分析，通过与标准品的UV和MS数据比较，共鉴定出15个峰，并对其中8个共有成分进行了定量检测。最后通过对八种西藏产雪莲花主要化学成分的多级串联质谱(ESI-MSn)分析，快速、灵敏地鉴定出10个黄酮和3个香豆素化学成分。 第三章同样包括三个部分。首先是以绵头雪莲花中主要香豆素成分东莨菪素和伞形花内酯为对照品，通过TLC定性检测和HPLC含量测定，草拟出较严谨的药材质量标准。其次是将绵头雪莲花、三指雪莲花和雪兔子作为一个药材看待，草拟了以东莨菪素和伞形花内酯的TLC检测为指标的药材质量标准。最后是针对水母雪莲花，以主要黄酮成分芹菜素-7-O-b-D-葡萄糖苷为对照品作TLC检测，并草拟出该药材的质量标准草案。 第四章报道了西藏产雪莲花挥发油的化学成分分析。采用传统水蒸气蒸馏法分别从八种雪莲花全草中提取挥发油，利用气相色谱-质谱联用技术分别从水母雪莲花、绵头雪莲花、槲叶雪莲花、云状雪兔子、拉萨雪兔子、小果雪兔子、雪兔子和三指雪莲花中分别鉴定出83、83、56、34、21、20、24和20个化学成分，分别占其挥发油总量的70.7%、76.0%、82.2%、55.4%、49.7%、70.4 %、76.2%和 76.7%。 第五章为综述，总结和概括了雪莲花的化学和药理研究进展。 The dissertation reports the investigation of the chemical constituents of the genus Saussurea. Quite a lot of species in this genus are traditional Tibetan medicinal plants, and hence have been widely used in traditional Tibetan medicine. This dissertation consisted of five chapters. The first chapter is on the chemical constituents of three Saussurea plants. The second section is about the analysis of chemical constituents of Saussurea plants using HPLC-MS and ESI-MS/MS. In the third chapter, we proposed quality-control standards for the Genus Saussurea based on TLC (thin layer chromatography) and HPLC. The fourth chapter is about chemical compositions of the essential oil from the whole plant of Saussurea plants. The last chapter reviews the research progress of the Genus Saussurea. The first chapter consists of three parts. The first part is about chemical constituents of ethanol extracts from whole plant of Saussurea laniceps Hand.-Mazz. Fifteen compounds were isolated by column chromatography on normal phase silica gel and Sephadex LH-20. Among them, eleven compounds were isolated from this plant for the first time, and two compounds were isolated from Genus Saussurea for the first time. The second part is about chemical constituents of ethanol extracts from whole plant of Saussurea medusa Maxim. Fifteen compounds were isolated by column chromatography on normal phase, reversed phase silica gel and Sephadex LH-20. Five of them were isolated from this plant for the first time, and there is one new flavonoid glucoside which was identified as 6″-O-crotonoyl-homoplantaginin (M-7) based on the evidence of one- and two-dimensional nuclear magnetic resonance, mass spectrometry analysis, and alkaline hydrolysis reaction. The last part is about chemical constituents of ethanol extracts from whole plant of Saussurea tridactyla Sch.-Bip. ex Hook. f.. Seven compounds were isolated by column chromatography on normal phase silica gel and Sephadex LH-20. There is one compound which was isolated from this plant for the first time. The second chapter consists of three parts. In the first part, we analyzed the chemical constituents of S. tridactyla collected from seven different places in Tibet using HPLC-DAD-ESI-MSn. Fourteen peaks in the HPLC were identified by comparison of UV and MS spectra with those of authentic compounds, among which eight common peaks were quantified. In the second part, we analyzed the chemical constituents of eight Saussurea species using HPLC-DAD-ESI-MSn method. Fifteen peaks in the HPLC were identified by comparison of UV and MS spectra with those of authentic compounds and eight main peaks of them were quantified. In the last part, we analyzed the chemical compounds of the above eight Saussurea plants directly by ESI-MS/MS. Thirteen major compounds, including 10 flavonoids and 3 coumarins were easily rapidly identified. The third chapter consists of three parts. In the first part, we proposed a comparative high quality-control standard for S. laniceps, based on quality detection by TLC and quantity analysis by HPLC using two major compounds (umbelliferone and scopoletin) as standard compounds. In the second part, in viewing S. laniceps, S. tridactyla and S. gossypiphora as the members of one family of medicinal herbs, we suggested a quality-control standard based on the TLC detection of the two major compounds (umbelliferone and scopoletin). In the last part, we proposed a quality-control standard for S. medusa based on the TLC detection of its major component (apigenin 7-O-glucoside). The four chapter analyzed the chemical constituents of essential oil of eight Saussurea species. The essential oils were extracted from the whole plants of these samples with water stream distillation. By GC-MS analysis, we identified eighty-three compounds from S. medusa, eighty-three from S. laniceps, fifty-six from S. quercifolia, thirty-four from S. aster, twenty-one from S. kingii, twenty from S. simpsoniana, twenty-four from S. gossypiphora, and twenty from S. tridactyla respetively, which accounted for 70.7%, 76.0%, 82.2%, 55.4%, 49.7%, 70.4 %, 76.2% and 76.7% of the total essential oil, respectively. The last chapter reviews the research progress of the Genus Saussurea.

气相色谱过程的蒙特卡罗模拟

Based on Monte Carlo method the microscopic gas-phase adsorption chromatographic behaviors of volatile chemical compounds were simulated,and the migration process of those compounds followed by the carrier gases along the chromatographic surface and the process of adsorption-desorption were also described.The programs have been compiled to simulate the processes of thermochromatography and isothermal chromatography with different experimental conditions and properties.The calculated results agree well with ...中文摘要：用蒙特卡罗方法模拟了易挥发化合物的气相色谱微观动力学行为,描述了化合物随气流在固体色谱柱表面的迁移以及吸附-解吸等过程。按气相色谱微观动力学模型编译的计算机程序模拟了超重元素化合物在等温色谱及热色谱的动力学过程,并根据不同实验条件进行了大量计算。计算结果与实验数据较为吻合。讨论了超重元素的半衰期、吸附态的周期、载气流量以及化合物的质量密度等对实验结果的影响及该理论模型的优点和待改进的地方。

Micro and nanostructured impedance sensors for biological and biomedical applications

This thesis work covered the fabrication and characterisation of impedance sensors for biological applications aiming in particular to the cytotoxicity monitoring of cultured cells exposed to different kind of chemical compounds and drugs and to the identification of different types of biological tissue (fat, muscles, nerves) using a sensor fabricated on the tip of a commercially available needle during peripheral nerve block procedures. Gold impedance electrodes have been successfully fabricated for impedance measurement on cells cultured on the electrode surface which was modified with the fabrication of gold nanopillars. These nanostructures have a height of 60nm or 100nm and they have highly ordered layout as they are fabricated through the e-beam technique. The fabrication of the threedimensional structures on the interdigitated electrodes was supposed to improve the sensitivity of the ECIS (electric cell-substrate impedance sensing) measurement while monitoring the cytotoxicity effects of two different drugs (Antrodia Camphorata extract and Nicotine) on three different cell lines (HeLa, A549 and BALBc 3T3) cultured on the impedance devices and change the morphology of the cells growing on the nanostructured electrodes. The fabrication of the nanostructures was achieved combining techniques like UV lithography, metal lift-off, evaporation and e-beam lithography techniques. The electrodes were packaged using a pressure sensitive, medical grade adhesive double-sided tape. The electrodes were then characterised with the aid of AFM and SEM imaging which confirmed the success of the fabrication processes showing the nanopillars fabricated with the right layout and dimensions figures. The introduction of nanopillars on the impedance electrodes, however, did not improve much the sensitivity of the assay with the exception of tests carried out with Nicotine. HeLa and A549 cells appeared to grow in a different way on the two surfaces, while no differences where noticed on the BALBc 3T3 cells. Impedance measurements obtained with the dead cells on the negative control electrodes or the test electrodes with the drugs can be compared to those done on the electrodes containing just media in the tested volume (as no cells are attached and cover the electrode surface). The impedance figures recorded using these electrodes were between 1.5kΩ and 2.5 kΩ, while the figures recorded on confluent cell layers range between 4kΩ and 5.5kΩ with peaks of almost 7 kΩ if there was more than one layer of cells growing on each other. There was then a very clear separation between the values of living cell compared to the dead ones which was almost 2.5 - 3kΩ. In this way it was very easy to determine whether the drugs affected the cells normal life cycle on not. However, little or no differences were noticed in the impedance analysis carried out on the two different kinds of electrodes using cultured cells. An increase of sensitivity was noticed only in a couple of experiments carried out on A549 cells growing on the nanostructured electrodes and exposed to different concentration of a solution containing Nicotine. More experiments to achieve a higher number of statistical evidences will be needed to prove these findings with an absolute confidence. The smart needle project aimed to reduce the limitations of the Electrical Nerve Stimulation (ENS) and the Ultra Sound Guided peripheral nerve block techniques giving the clinicians an additional tool for performing correctly the peripheral nerve block. Bioimpedance, as measured at the needle tip, provides additional information on needle tip location, thereby facilitating detection of intraneural needle placement. Using the needle as a precision instrument and guidance tool may provide additional information as to needle tip location and enhance safety in regional anaesthesia. In the time analysis, with the frequency fixed at 10kHz and the samples kept at 12°C, the approximate range for muscle bioimpedance was 203 – 616 Ω, the approximate bioimpedance range for fat was 5.02 - 17.8 kΩ and the approximate range for connective tissue was 790 Ω – 1.55 kΩ. While when the samples were heated at 37°C and measured again at 10kHz, the approximate bioimpedance range for muscle was 100-175Ω. The approximate bioimpedance range of fat was 627 Ω - 3.2 kΩ and the range for connective tissue was 221-540Ω. In the experiments done on the fresh slaughtered lamb carcass, replicating a scenario close to the real application, the impedance values recorded for fat were around 17 kΩ, for muscle and lean tissue around 1.3 kΩ while the nervous structures had an impedance value of 2.9 kΩ. With the data collected during this research, it was possible to conclude that measurements of bioimpedance at the needle tip location can give valuable information to the clinicians performing a peripheral nerve block procedure as the separation (in terms of impedance figures) was very marked between the different type of tissues. It is then feasible to use an impedance electrode fabricated on the needle tip to differentiate several tissues from the nerve tissue. Currently, several different methods are being studied to fabricate an impedance electrode on the surface of a commercially available needle used for the peripheral nerve block procedure.

Identification of dyes on ancient Chinese paper samples using the subtracted shifted Raman spectroscopy method

The Stein Collection in the British Library contains the Diamond Sutra, the world's oldest, dated, printed document. The paper of the Diamond Sutra and other documents from the Stein collection is believed to be dyed yellow by a natural extract, called huangbo, from the bark of Phellodendron amurense, which contains three major yellow chromophores: berberine, palmatine, and jatrorrhizine, Conservation of these documents requires definite information on the chemical composition of the dyes but no suitable, completely noninvasive analytical method is known. Here we report resonance Raman studies of a series of prate dyes, of plant materials and extracts, and of dyed ancient and modern paper samples. Resonance Raman spectroscopy is used to enhance the spectra of the dyes over the signals from the paper matrixes in which they are held. The samples an give resonance Raman spectra which are dominated by intense fluorescence, but by using SSRS (subtracted shifted Raman spectroscopy) we have obtained reliable spectra of the pure dyes, native bark from the Phellodendron amurense, modern paper dyed with huangbo extracted from this bark, and ancient paper samples. For both ancient paper samples whose pigment bands were detected, the relative intensities of the bands due to berberine and palmatine suggest that the ancient paper is richer in berberine than its modern counterpart, This is the first nondestructive in situ method for detection of these pigments in manuscripts, and as such has considerable potential benefit for the treatment of irreplaceable documents that are believed to be dyed with huangbo but documents on which conservation work cannot proceed without definite identification of the chemical compounds that they contain.

Development of new approaches for the synthesis and decoding of one-bead one-compound cyclic peptide libraries

La plupart des processus cellulaires et biologiques reposent, à un certain niveau, sur des interactions protéine-protéine (IPP). Leur manipulation avec des composés chimiques démontre un grand potentiel pour la découverte de nouveaux médicaments. Malgré la demande toujours croissante en molécules capables d’interrompre sélectivement des IPP, le développement d’inhibiteurs d’IPP est fortement limité par la grande taille de la surface d’interaction. En considérant la nature de cette surface, la capacité à mimer des structures secondaires de protéines est très importante pour lier une protéine et inhiber une IPP. Avec leurs grandes capacités peptidomimétiques et leurs propriétés pharmacologiques intéressan-tes, les peptides cycliques sont des prototypes moléculaires de choix pour découvrir des ligands de protéines et développer de nouveaux inhibiteurs d’IPP. Afin d’exploiter pleinement la grande diversité accessible avec les peptides cycliques, l’approche combinatoire «one-bead-one-compound» (OBOC) est l’approche la plus accessible et puissante. Cependant, l’utilisation des peptides cycliques dans les chimiothèques OBOC est limitée par les difficultés à séquencer les composés actifs après le criblage. Sans amine libre en N-terminal, la dégradation d’Edman et la spectrométrie de masse en tandem (MS/MS) ne peuvent pas être utilisées. À cet égard, nous avons développé de nouvelles approches par ouverture de cycle pour préparer et décoder des chimiothèques OBOC de peptides cycliques. Notre stratégie était d’introduire un résidu sensible dans le macrocycle et comme ancrage pour permettre la linéarisation des peptides et leur largage des billes pour le séquençage par MS/MS. Tout d’abord, des résidus sensibles aux nucléophiles, aux ultraviolets ou au bromure de cyanogène ont été introduits dans un peptide cyclique et leurs rendements de clivage évalués. Ensuite, les résidus les plus prometteurs ont été utilisés dans la conception et le développement d’approches en tandem ouverture de cycle / clivage pour le décodage de chimiothèques OBOC de peptides cycliques. Dans la première approche, une méthionine a été introduite dans le macrocycle comme ancrage pour simultanément permettre l’ouverture du cycle et le clivage des billes par traitement au bromure de cyanogène. Dans la seconde approche, un résidu photosensible a été utilisé dans le macrocycle comme ancrage pour permettre l’ouverture du cycle et le clivage suite à une irradiation aux ultraviolets. Le peptide linéaire généré par ces approches peut alors être efficacement séquencé par MS/MS. Enfin, une chimiothèque OBOC a été préparée et criblée la protéine HIV-1 Nef pour identifier des ligands sélectifs. Le développement de ces méthodologies permttra l’utilisation de composés macrocycliques dans les chimiothèques OBOC et constitue une contribution importante en chimie médicinale pour la découverte de ligands de protéines et le développement d’inhibiteurs d’IPP.

Machine learning methods for quantitative structure-property relationship modeling

Tese de doutoramento, Informática (Bioinformática), Universidade de Lisboa, Faculdade de Ciências, 2014

Extração e caracterização de extratos de Jatropha gossypiifolia L.: avaliação da sua atividade antimicrobiana e antioxidante

Trabalho Final de Mestrado para obtenção do grau de mestre em Engenharia Química e Biológica