Uracil excision repair in Mycobacterium tuberculosis cell-free extracts

Uracil excision repair is ubiquitous in all domains of life and initiated by uracil DNA glycosylases (UDGs) which excise the promutagenic base, uracil, from DNA to leave behind an abasic site (AP-site). Repair of the resulting AP-sites requires an AP-endonuclease, a DNA polymerase, and a DNA ligase whose combined activities result in either short-patch or long-patch repair. Mycobacterium tuberculosis, the causative agent of tuberculosis, has an increased risk of accumulating uracils because of its G + C-rich genome, and its niche inside host macrophages where it is exposed to reactive nitrogen and oxygen species, two major causes of cytosine deamination (to uracil) in DNA. In vitro assays to study DNA repair in this important human pathogen are limited. To study uracil excision repair in mycobacteria, we have established assay conditions using cell-free extracts of M. tuberculosis and M. smegmatis (a fast-growing mycobacterium) and oligomer or plasmid DNA substrates. We show that in mycobacteria, uracil excision repair is completed primarily via long-patch repair. In addition, we show that M. tuberculosis UdgB, a newly characterized family 5 UDG, substitutes for the highly conserved family 1 UDG, Ung, thereby suggesting that UdgB might function as backup enzyme for uracil excision repair in mycobacteria. (C) 2011 Elsevier Ltd. All rights reserved.

Antihyperlipidemic potential of Cedrus deodara extracts in monosodium glutamate induced obesity in neonatal rats

Objective: To study the antihyperlipidemic effect of Cedrus deodara (C. deodara) against monosodium glutamate (MSG) induced obesity in neonatal rats. Materials and Methods: The studies were carried out on newborn neonatal rats and were injected intraperitoneally with 2 mg/g of MSG on the 2(nd) and 4(th) postnatal days and 4 mg/g on 6(th), 8(th) and 10(th) postnatal days. Ethanolic extract (EE) and acetone extract (AE) of C. deodara was administered in a dose of 100 and 200 mg/kg, p.o./day at the age of 65 days. On day 60 of treatment, body weight, locomotor activity, body temperature, and various biochemical parameters like serum glucose, total cholesterol, triglyceride, and organs weights were recorded. Results: There was a significant reduction in body weight, organs and increased body temperature, locomotor activity after treatment with extracts. C. deodara decreased serum glucose, total cholesterol and triglyceride, low density lipoprotein (LDL) and very low density lipoprotein (VLDL) levels and increased high density lipoprotein (HDL) significantly has compared to MSG-control rats. Conclusion: C. deodara extracts exhibited antihyperlipidemic effect and it possesses anti-obesity properties in MSG induced obese rats.

Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

Evaluation of hexane and ethyl acetate extracts of the sponge Jaspis diastra collected from Mauritius Waters on HeLa cells

Objectives Based on previous screening results, the cytotoxic effect of the hexane (JDH) and ethyl acetate extracts (JDE) of the marine sponge Jaspis diastra were evaluated on HeLa cells and the present study aimed at determining their possible mechanism of cell death. Methods Nuclear staining, membrane potential change, flow cytometry analysis of cell cycle distribution and annexin V staining were undertaken to investigate the effects of JDE and JDH. Electrospray ionization mass spectrometry (ESI-MS) and nuclear magnetic resonance were used to characterize an isolated bioactive molecule. Key findings JDE displayed an IC50 25 times more significant than the JDH. Flow cytometry analysis revealed JDE induced apoptosis in HeLa cells accompanied by the collapse of mitochondrial membrane potential. Fractionation of JDE resulted in the isolation of the known cytotoxic cyclodepsipeptide, Jaspamide. Conclusions Taking our results together suggest that JDE can be valuable for the development of anticancer drugs, especially for cervical cancer. Further investigations are currently in progress with the aim to determine and isolate other bioactive compounds from this extract.

Effects of Withania somnifera and Tinospora cordifolia Extracts on the Side Population Phenotype of Human Epithelial Cancer Cells: Toward Targeting Multidrug Resistance in Cancer

Recent reports suggest the existence of a subpopulation of stem-like cancer cells, termed as cancer stem cells (CSCs), which bear functional and phenotypic resemblance with the adult, tissue-resident stem cells. Side population (SP) assay based on differential efflux of Hoechst 33342 has been effectively used for the isolation of CSCs. The drug resistance properties of SP cells are typically due to the increased expression of ABC transporters leading to drug efflux. Conventionally used chemotherapeutic drugs may often leads to an enrichment of SP, revealing their inability to target the drug-resistant SP and CSCs. Thus, identification of agents that can reduce the SP phenotype is currently in vogue in cancer therapeutics. Withania somnifera (WS) and Tinospora cordifolia (TC) have been used in Ayurveda for treating various diseases, including cancer. In the current study, we have investigated the effects of ethanolic (ET) extracts of WS and TC on the cancer SP phenotype. Interestingly, we found significant decrease in SP on treatment with TC-ET, but not with WS-ET. The SP-inhibitory TC-ET was further fractionated into petroleum ether (TC-PET), dichloromethane (TC-DCM), and n-butyl alcohol (TC-nBT) fractions using bioactivity-guided fractionation. Our data revealed that TC-PET and TC-DCM, but not TC-nBT, significantly inhibited SP in a dose-dependent manner. Furthermore, flow cytometry-based functional assays revealed that TC-PET and TC-DCM significantly inhibited ABC-B1 and ABC-G2 transporters and sensitized cancer cells toward chemotherapeutic drug-mediated cytotoxicity. Thus, the TC-PET and TC-DCM may harbor phytochemicals with the potential to reverse the drug-resistant phenotype, thus improving the efficacy of cancer chemotherapy.

Spectrophotometric determination of molybdenum with Syzygium jambolanum DC leaf extracts

A new spectrophotometric method for the determination of molybdenum in industrial materials has been developed using the leaf extract of Syzygium jambolanum DC based on the reaction of Mo (VI) at pH 7.0 to produce an orange-yellow complex with an absorption maximum at 426 nm. The molar absorptivity of the complex is 4.27 x 10(4) l mol(-1) cm(-1) and the absorbance, is linear in the range 0.05-0.8 ppm. Sandell sensitivity coefficient was found to be 2.25 x 10(-3) mu g/cm(2). The method is ten times more sensitive than the aqueous thiocyanate system. It has been applied successfully in micronutrient fertilizer, artificial freshwater and sea-water analyses.

Effects of extracts of dried seeds of Toloache, Datura innoxia as anaesthesia on the African catfish Clarias gariepinus fingerlings

The effects of crude extract, pure extract, aqueous, fraction of pure and lipid fraction of pure extract of dried seeds of toloache. Datura innoxia as anaesthesia on the African catfish. Clarias gariepinus fingerlings were studied. The fish were exposed to various doses of the extract in aquaria tanks and the time taken for each fish to reach anaesthesia was recorded. The fish were anaesthetized up to 3.00g/l fingerlings reached anaesthesia is significantly (P<0.05) shorter time (1.004 minutes at 0.05gl) in pure unseparated extract than in crude extract (58.50 minutes at 3.00g/l concentrated). The time to reach anaesthesia decreased with an increase in concentration of the seed extract. Out the two fractions the lipid fraction had significantly (P>0.05) better anaesthetic on the fish. The control produced no observable anaesthetic effect on the fish within three hours. This suggests that the anaesthetizing active ingredent resided in the lipid fraction. All fish recovered from anaesthesia, swam and fed actively and no mortality was observed throughout the exposure period and thereafter. It is therefore recommended for use on C. gariepinus fingerlings

Studies of the effects from extracts from two local plants (Tephrosia vogelii and Parkia clappertoniana) on Clarias gariepinus (Tengels)

Studies were carried out using 96hr static toxicity bioassay to determine the effect of lethal concentrations of extracts from two local plants Tephrosia vogelii and Parkia clappertoniana which are known fish poison, on a species of mud fish. Clarias gariepinus Phytochemical analysis of the plant extracts was done and the extract from T. vogelii was found to contain alkaloids, tannins and flavonoids, while the extract from P. clappertoniana was formed to contain alkaloids tannins and saponins. Experimental fish were exposed to test water separately polluted by varying concentrations of extraction of both plant species ranging from 0.50mgl super(-1), 1.50mgl super(-1), 2.50mgl super(-1), 3.0mgl super(-1), 5.00mgl super(-1), 10.00mgl super(-1) in the case of T. vogelii and 5.00mgl super(-1), 7.50mgl super(-1), 10.00mgl super(-1), 15.00mgl super(-1), 20.00mgl super(-1) and 30.00mgl super(-1) in the case of P. clappertaniana. Behavioural hispathological and heamatological examinations were made. Both plant extracts were found to have lethal effects at the higher concentrations, affecting the gills and the central nervous system as well as having a depressive effect on the total count and increasing platelet and white blood cell count. Symptoms of toxicosis observed include, initial inactivation agitated swimming, tumbling movement air gulping, increased opercular beat and period of quiescence/knockdown before death. Marked differences were also observed in the hematological and histopathological analysis of poisoned fish. Lower concentrations of the extracts had sub lethal effects on the fish, which manifested as zigzag movement air gulping increased opercular movement etc. None of these effects were observed in the control experiment

TRANSFER OF ANALYTICAL METHODS FOR THE CHARACTERISATION OF NATURAL PRODUCTS TO R&D PROCESSES OF IDOKI

IDOKI SCF Technologies S.L. is a technology-based company, set up on September 2006 in Derio (Biscay) with the main scope of developing extraction and purification processes based on the use of supercritical fluid extraction technology (SFE) in food processing, extraction of natural products and the production of personal care products. IDOKI¿s researchers have been working on many different R&D projects so far, most of them using this technology. However, the optimization of a SFE method for the different matrices cannot be performed unless we have an analytical method for the characterisation of the extracts obtained in each experiment. The analytical methods are also essential for the quality control of the raw materials that are going to be used and also for the final product. This PhD thesis was born to tackle this problem and therefore, it is based on the development of different analytical methods for the characterisation of the extracts and products. The projects that we could include in this thesis were the following: the extraction propolis, the recovery of agroindustrial residues (soy and wine) and the dealcoholisation of wine.On the one hand, for the extraction of propolis, several UV-Vis spectroscopic methods were used in order to measure the antioxidant capacity and the total polyphenol and flavonoid content of the extracts. A SFC method was also developed in order to measure more specific phenolic compounds. On the other hand, for the recovery of agroindustrial residues UV-Vis spectroscopy was used to determine the total polyphenol content and two SFC methods were developed to analyse different phenolic compounds. Extraction methods such as MAE, FUSE and rotary agitation were also evaluated for the characterisation of the raw materials.Finally, for the dealcoholisation of wine, the development of a SBSE-TD-GC-MS and DHS-TD-GC-MS methods for the analysis of aromas and a NIR spectroscopic method for the determination of ethanol content with the help of chemometrics was necessary. Most of these methods are typically used in IDOKI¿s lab as routine analyses apart from others not included in this PhD thesis.

Cultura de tecidos e análise do potencial antioxidante de Passiflora alata Curtis

Passiflora alata Curtis, comumente conhecida como maracujá-doce, é uma das espécies do gênero Passiflora cultivadas comercialmente, sendo consumida in natura devido ao seu gosto adocicado. Ela também é utilizada em todo o mundo como ornamental e na medicina popular. O objetivo deste trabalho foi o estabelecimento de diferentes estratégias para a cultura in vitro de P. alata e a análise da produção de substâncias antioxidantes nos materiais obtidos in vitro, em comparação com as plantas in vivo. Diferentes tratamentos visando à quebra da dormência das sementes foram avaliados para a germinação in vitro ou in vivo, além da incubação das sementes sob tipos distintos de luz. Para o estabelecimento das culturas primárias, apices caulinares e segmentos nodais das plântulas derivadas da germinação in vitro foram cultivados em meio MSM . A taxa de alongamento dos brotos e o número de nós por brotos das culturas primárias foram aumentados pela adição de água de coco ao meio. Plantas derivadas dessas culturas foram utilizadas como fontes de explantes nodais, internodais e foliares. O potencial morfogênico de sementes sem tegumento foi também avaliado. Calos friáveis foram induzidos a partir de segmentos nodais e foliares na presença de PIC, e aqueles obtidos a partir de folhas em meio suplementado com PIC a 28,9 μM foram selecionados para o estabelecimento de culturas de células em suspensão. Após o desenvolvimento de diferentes estratégias in vitro para P. alata, folhas de plantas in vivo foram utilizadas para a avaliação de parâmetros que afetam a extração de substâncias antioxidante. O potencial antioxidante foi determinado pelo ensaio DPPH e o conteúdo de fenóis totais foi determinado utilizando o método Folin-Ciocalteau. Após o desenvolvimento do protocolo de extração, a atividade antioxidante dos diferentes materiais in vitro foi também avaliada. A eficiência antirradicalar variou entre os sistemas de cultura estudados, sendo diretamente proporcional ao conteúdo de fenóis totais dos extratos. Esses resultados indicam que as estratégias para cultura in vitro de P. alata desenvolvidas neste trabalho representam alternativas para a multiplicação de plantas e produção de substâncias fenólicas com ação antioxidante.

Determinação de atividade antioxidante, compostos fenólicos totais e teor de resveratrol em cinco cultivares brasileiras de Arachis hypogaea L. com a utilização de duas metodologias extrativas

O amendoim A. hypogaea L. é a quarta oleaginosa mais consumida no mundo e suas sementes são altamente energéticas, com grandes quantidades de lipídios, proteínas, vitaminas e carboidratos. Diversas atividades farmacológicas já foram observadas em extratos de raízes, folhas e sementes, sendo a principal delas a atividade antioxidante. Neste trabalho, foi realizada a comparação entre duas metodologias (por maceração e assistida por micro-ondas) para a extração de compostos antioxidantes, incluindo o resveratrol. Também foi realizada a comparação entre extratos de diferentes órgãos de cultivares brasileiras (IAC 886, IAC Caiapó, IAC Tatu ST, IAC 8112 e IAC 99-1) quanto à atividade antioxidante, por DPPH, ao teor de compostos fenólicos, por Folin-Ciocalteu, e ao teor de resveratrol, por HPLC. Por fim, foram estabelecidos protocolos de cultura de tecidos para explantes de sementes, visando à produção de calos e plantas in vitro para posterior dosagem de compostos de interesse, tendo em vista a possibilidade de modulação das condições in vitro. As melhores condições determinadas para a extração por maceração de antioxidantes de A. hypogaea foram 80% de etanol em água como solvente, trituração com almofariz e pistilo, 50 mL solvente por grama de material vegetal seco, 120 minutos de incubação e dois estágios de extração. As melhores condições para a extração de resveratrol assistida por micro-ondas foram o uso de 37 mL de solvente/g material vegetal seco, com agitação de 1200 rpm por 15 minutos, a 37C. De uma maneira geral, os extratos de raízes e oriundos de micro-ondas apresentaram maior atividade antioxidante (até 92,36 2,71%), teor de compostos fenólicos (até 54,15 1,39 mg EAG/g extrato) e teor de resveratrol (até 1,614 0,356 mg/g extrato). Dentre as cultivares estudadas, IAC Tatu e IAC 99-1 foram as que apresentaram os teores mais elevados. Brotos e calos friáveis foram obtidos a partir de cotilédones, eixos embrionários e folíolos embrionários cultivados em meios suplementados com BAP e picloram, respectivamente.