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1.
Foods ; 13(12)2024 Jun 13.
Article de Anglais | MEDLINE | ID: mdl-38928804

RÉSUMÉ

Cassava is a staple crop in developing countries because its starchy roots provide essential dietary carbohydrates. The aim of this research was to conduct a comprehensive inquiry and scientific evaluation of the nutritional value of cassava tubers. Eight nutritional characteristics were examined in native and imported cassava variants: starch, reduced sugar, anthocyanins, protein, dietary fiber, quinic acid, vitamin C, and dry matter content. Principal component analysis (PCA) was conducted to minimize the dimensionality of the nutritional markers. A scientific assessment technique was developed to calculate a composite score for the various cassava samples. Analysis of the data revealed noticeable variance among the samples' nutritional indicators, suggesting varying degrees of association. Starch had a substantial positive link with lower sugar, protein, and dry matter content (p < 0.01). Anthocyanins and quinic acid interacted favorably (p < 0.05), and a positive link between protein and dry matter content was observed (p < 0.05); however, protein and dietary fiber interacted negatively (p < 0.05). The contribution rate of the top three PCA factors was over 76%, demonstrating that these factors incorporated the primary information acquired from the eight original nutritional indices, while maintaining excellent representativeness and impartiality. The experimental results showed a preliminary nutritional grade for 22 cassava tuber samples. The top five types were Guangxi Muci, Gui Cassava 4, Glutinous Rice Cassava, Huifeng 60, and Dongguan Hongwei. In the cluster analysis, the levels of similarity between the data showed that the 22 types of cassava tubers could be grouped into five categories, each with their own set of nutrients. This study promotes the directed breeding of cassava species and offers a theoretical foundation for creating and using various cassava varieties. Furthermore, this work lays the groundwork for a systematic and dependable technique for the quality assessment, comprehensive evaluation, and reasonable classification of cassava species and similar crops.

2.
Heliyon ; 10(2): e24702, 2024 Jan 30.
Article de Anglais | MEDLINE | ID: mdl-38312664

RÉSUMÉ

The contagious COVID-19 has recently emerged and evolved into a world-threatening pandemic outbreak. After pursuing rigorous prophylactic measures two years ago, most activities globally reopened despite the emergence of lethal genetic strains. In this context, assessing and mapping activity characteristics-based hot spot regions facilitating infectious transmission is essential. Hence, our research question is: How can the potential hotspots of COVID-19 risk be defined intra-cities based on the spatial planning of commercial activity in particular? In our research, Zayed and October cities, Egypt, characterized by various commercial activities, were selected as testbeds. First, we analyzed each activity's spatial and morphological characteristics and potential infection risk based on the Centre for Disease Control and Prevention (CDCP) criteria and the Kriging Interpolation method. Then, using Google Mobility, previous reports, and semi-structured interviews, points of interest and population flow were defined and combined with the last step as interrelated horizontal layers for determining hotspots. A validation study compared the generated activity risk map, spatial COVID-19 cases, and land use distribution using logistic regression (LR) and Pearson coefficients (rxy). Through visual analytics, our findings indicate the central areas of both cities, including incompatible and concentrated commercial activities, have high-risk peaks (LR = 0.903, rxy = 0.78) despite the medium urban density of districts, indicating that urban density alone is insufficient for public health risk reduction. Health perspective-based spatial configuration of activities is advised as a risk assessment tool along with urban density for appropriate decision-making in shaping pandemic-resilient cities.

3.
Sci Total Environ ; 915: 170019, 2024 Mar 10.
Article de Anglais | MEDLINE | ID: mdl-38224877

RÉSUMÉ

Most coastal cities have been experiencing unprecedented urbanization-induced flood risk, climatic events, and haphazard anthropogenic activities, jeopardizing residents' lives and building environments. Despite mounting flood-related studies, analyzing the correlation between the spatiotemporal dynamics of Built-up Expansion patterns (BE) and flood risk remains unknown and holds divergent perspectives. In this context, the coastal city of Alexandria, Egypt, characterized by multiple urban patterns and experiencing heavy rainfall annually, was selected as a testbed. Our method defined the spatiotemporal rates of BE from 1995 to 2023, quantified flood risk spatially, and finally investigated the correlation between BE and flood risk through spatial and statistical analysis. Our results show the built-up area occupied 30.32 % of the total city area till 2023, and the infilling pattern dominated the BE growth by 45.21 % of the total built-up area, followed by leapfrogging and edge expansion by 33.25 % and 21.55 %, respectively. The unplanned-infilling pattern is predominantly highly correlated with the flood-vulnerable peaks (correlation coefficient (rk) = 0.975, p-value < 0.05) and lowers dramatically towards planned-infilling regions with flood protections. Meanwhile, a spatial mismatch exists between high-risk peaks and leapfrogging and edge expansion (rk = 0.118 and 0.662, respectively, with a p-value < 0.01), indicating that controlling the built-up amount is inadequate for mitigating flood risk. Porosity-based urban configuration and spatial distribution of built-up patches in harmony with nature-based solutions are recommended for shaping flood-resilient and effective urban planning.

4.
J Environ Manage ; 344: 118260, 2023 Oct 15.
Article de Anglais | MEDLINE | ID: mdl-37354590

RÉSUMÉ

Cities have experienced rapid urbanization-induced harsh climatic events, especially flooding, inevitably resulting in negative and irreversible consequences for urban resilience and endangering residents' lives. Numerous studies have analyzed the effects of anthropogenic practices (land use changes and urbanization) on flood forecasting. However, non-structural mitigation's effectiveness, like Nature-Based Solutions (NBS), has yet to receive adequate attention, particularly in the Middle East and North Africa (MENA) region, which have become increasingly significant and indispensable for operationalizing cities efficiently. Therefore, our study investigated the predictive influence of incorporating one of the most common NBS strategies called low-impact development tools (LID) (such as rain gardens, bio-retention cells, green roofs, infiltration trenches, permeable pavement, and vegetative swale) during the urban planning of Alexandria, Egypt, which experiences the harshest rainfall annually and includes various urban patterns. City characteristics-dependent 14 LID scenarios were simulated with recurrence intervals ranging from 2 to 100 years using the LID Treatment Train Tool (LID TTT), depending on calibrated data from 2015 to 2020, by the Nash-Sutcliffe efficiency index and deterministic coefficient, and root-mean-square error with values of 0.97, 0.91, and 0.31, respectively. Our findings confirmed the significant effectiveness of combined LID tools on total flood runoff volume reduction by 73.7%, revealing that different urban patterns can be used in flood-prone cities, provided LID tools are considered in city planning besides grey infrastructure to achieve optimal mitigation. These results, which combined multiple disciplines and were not explicitly mentioned in similar studies in developing countries, may assist municipalities' policymakers in planning flood-resistant, sustainable cities.


Sujet(s)
Urbanisme , Inondations , Villes , Urbanisation , Pluie , Mouvements de l'eau
5.
Appl Biochem Biotechnol ; 195(10): 5903-5915, 2023 Oct.
Article de Anglais | MEDLINE | ID: mdl-36719522

RÉSUMÉ

Most Ephedra species are adapted to arid and desert conditions and are widely used in folk medicine to treat several disorders. The design of the current study was to determine the functional properties of seeds of two Ephedra species (E. alata and E. altissima) naturally growing in Tunisian arid zones by evaluating their mineral contents and bioactive compounds. The flame atomic absorption spectrometry revealed that seeds contained remarkable amounts of sodium (Na), potassium (K), calcium (Ca), magnesium (Mg), copper (Cu), zinc (Zn), and iron (Fe). The colorimetric investigation revealed high total polyphenol, flavonoid, and condensed tannin contents. Furthermore, by utilizing high-performance liquid chromatography-electrospray ionization-mass spectrometry method (HPLC-ESI/MS), a total of 11 phenolics were identified and quantified including 7 flavonoid compounds and 4 phenolic acids that were mostly predominated by gallic acid and quercetrin. Results so far have been very encouraging and proved that Ephedra seeds are a valuable source of natural bioactive compounds and minerals which could potentially be used for industrial and pharmaceutical purposes.


Sujet(s)
Antioxydants , Ephedra , Antioxydants/analyse , Ephedra/composition chimique , Tunisie , Flavonoïdes/analyse , Graines/composition chimique , Chromatographie en phase liquide à haute performance/méthodes , Minéraux , Composés phytochimiques/analyse , Extraits de plantes/composition chimique , Spectrométrie de masse ESI/méthodes
6.
Food Sci Nutr ; 10(11): 3979-3992, 2022 Nov.
Article de Anglais | MEDLINE | ID: mdl-36348780

RÉSUMÉ

An edible coating was developed using gelatin extracted from the skin of gray triggerfish (Balistes capriscus) and applied to the fillet of the smooth-hound shark (Mustelus mustelus). Moringa oleifera leaf extract was added to gelatin coating solution to improve its preservative properties. The phenolic profiles and antioxidant and antibacterial activities of M. oleifera extracts were determined. Phenolic acids constituted the largest group representing more than 77% of the total compounds identified in the ethanol/water (MOE/W) extract, among which the quinic acid was found to be the major one (31.48 mg/g extract). The MOE/W extract presented the highest DPPH• scavenging activity (IC50 = 0.53 ± 0.02 mg/ml) and reducing (Fe3+) power (EC0.5 = 0.57 ± 0.02 mg/ml), as well as interesting inhibition zones (20-35 mm) for the most tested strains. Coating by 3% of gelatin solution significantly reduced most deterioration indices during chilled storage, such as malondialdehyde (MDA), total volatile basic nitrogen (TVB-N), weight loss, pH, and mesophilic, psychrophilic, lactic, and H2S-producing bacterial counts. Interestingly, coating with gelatin solution containing MOE/W extract at 20 µg/ml was more effective than gelatin applied alone. Compared with the uncoated sample, gelatin-MOE/W coating reduced the weight loss and MDA content by 26% and 70% after 6 days of storage, respectively. Texture analysis showed that the strength of uncoated fillet increased by 46%, while the strength of fillet coated with gelatin-MOE/W only increased by 12% after 6 days of storage. Fish fillet coated with gelatin-MOE/W had the highest sensory scores in terms of odor, color, and overall acceptability throughout the study period.

7.
J Chromatogr A ; 1673: 463057, 2022 Jun 21.
Article de Anglais | MEDLINE | ID: mdl-35477072

RÉSUMÉ

Aerial parts of the rare species Salvia aegyptiaca L. and S. verbenaca L. were collected from arid habitats in southern Tunisia. Their polar (ethanol-water) and mid-polar (ethyl acetate) extracts were analyzed non-targeted via a developed high-performance thin-layer chromatography profiling hyphenated with 12 effect-directed assays and 8 different physico-chemical detections. Bioactive compound zones were observed with inhibiting activities on α-glucosidase, ß-glucosidase, ß-glucuronidase, acetylcholinesterase, butyrylcholinesterase and tyrosinase, with radical scavenging (antioxidative) effects, and with activities against Gram-negative and Gram-positive bacteria. The effect-directed profile patterns showed common bioactive zones for different collection sites of the same species and distinct differences between species. Such characteristic profiles can be used to prove authenticity. Genotoxic, estrogen-like and androgen-like compounds were not detected even at higher amounts applied (for extracts from 1.6 mg sample). In the physico-chemical profiling, further organic substances were selectively detected, which highlighted the complexity of the multi-component mixture. The Tunisian sage profiles were further compared to the frequently used S. folium L. and S. officinalis L. leaves, and to reference mixtures containing phenolic acids and tanshinones. Selected bioactive zones in the S. verbenaca extracts were characterized by high-resolution mass spectrometry, and some mass signals were attributed to a caffeic acid derivative and to oleanolic and ursolic acids. Such effect-directed non-target profiling allows straightforward comparison not only of sage but of plant extracts in general.


Sujet(s)
Salvia , Acetylcholinesterase/composition chimique , Antioxydants/analyse , Butyrylcholine esterase/analyse , Chromatographie sur couche mince/méthodes , Extraits de plantes/composition chimique , Feuilles de plante/composition chimique
8.
Environ Geochem Health ; 44(11): 4045-4061, 2022 Nov.
Article de Anglais | MEDLINE | ID: mdl-34850307

RÉSUMÉ

The present article aims to assess the phytotoxic effects of copper and zinc oxide nanoparticles (Cu NPs, ZnO NPs) on mung bean (Vigna radiata L.) and their possible risk on food quality and safety. We also study the molecular mechanisms underlying the toxicity of nanosized Cu and ZnO. Seeds of mung bean were germinated under increasing concentrations of Cu NPs and ZnO NPs (10, 100, 1000, 2000 mg/L). We analyzed levels of free amino acids, total soluble sugars, minerals, polyphenols and antioxidant capacity. Our results showed that depending on the concentrations used of Cu NPs and ZnO NPs, the physiology of seed germination and embryo growth were modified. Both free metal ions and nanoparticles themselves may impact plant cellular and physiological processes. At 10 mg/L, an improvement of the nutritive properties, in terms of content in free amino acids, total soluble sugars, essential minerals, antioxidant polyphenols and flavonoids, was shown. However, higher concentrations (100-2000 mg/L) caused an alteration in the nutritional balance, which was revealed by the decrease in contents and quality of phenolic compounds, macronutrients (Na, Mg, Ca) and micronutrients (Cu, Fe, Mn, Zn, K). The overall effects of Cu and ZnO nanoparticles seem to interfere with the bioavailability of mineral and organic nutrients and alter the beneficial properties of the antioxidant phytochemicals, mineral compounds, phenolic acids and flavonoids. This may result in a potential hazard to human food and health, at some critical doses of nanofertilizers. This study may contribute in the guidelines to the safe use of nanofertilizers or nanosafety, for more health benefit and less potential risks.


Sujet(s)
Fabaceae , Vigna , Oxyde de zinc , Humains , Oxyde de zinc/toxicité , Cuivre/toxicité , Cuivre/métabolisme , Antioxydants , Fabaceae/composition chimique , Flavonoïdes/toxicité , Polyphénols , Minéraux , Qualité alimentaire , Ions , Micronutriments , Acides aminés , Sucres
9.
Plant Physiol Biochem ; 168: 305-320, 2021 Nov.
Article de Anglais | MEDLINE | ID: mdl-34673320

RÉSUMÉ

In Sabkha biotope, several environmental factors (i.e., salinity, drought, temperature, etc.) especially during dry season affect halophytes developments. To cope with these harmful conditions, halophytes use multiple mechanisms of adaptations. In this study, we focused on the effect of environmental condition changes over a year in the Sabkha of Aïn Maïder (Medenine - Tunisia) on the physiological and biochemical behavior of Limoniastrum guyonianum using a modeling approach. Our study showed that the model depicted well (R2 > 0.75) the monthly fluctuations of the studied parameters in this habitat. During the dry period (June to September), the salinity of the soil increased remarkably (high level of EC and Na+ content), resulting in high Na+ content in the aerial parts followed by a nutrient deficiency in K+, Ca2+, and Mg2+. As a result of this disruption, L. guyonianum decreased its water potential to more negative values to maintain osmotic potential using inorganic osmolytes (i.e., Na+) and organic osmolytes (i.e., sugars: sucrose, fructose, glucose, and xylitol, and organic acids: citric and malic acids). In addition, CO2 assimilation rate, stomatal conductance, transpiration rate, and photosynthetic pigments decreased significantly with increasing salinity. The phenolic compounds contents and the antioxidant activity increased significantly in the dry period as a result of increased levels of H2O2 and lipid peroxidation. This increase was highly correlated with soil salinity and air temperature. The maintenance of tissue hydration (i.e., moderate decrease of relative water content), the accumulation of sugars and organic acids, the enhancement of phenolic compounds amounts, and the increase of antioxidant activity during the dry period suggest that L. guyonianum possesses an efficient tolerance mechanism that allows the plant to withstand the seasonal fluctuations of climatic conditions in its natural biotope.


Sujet(s)
Peroxyde d'hydrogène , Plumbaginaceae , Antioxydants/métabolisme , Photosynthèse , Plumbaginaceae/métabolisme , Salinité , Saisons , Tunisie
10.
Andrologia ; 53(9): e14181, 2021 Oct.
Article de Anglais | MEDLINE | ID: mdl-34219269

RÉSUMÉ

This study aimed to investigate the effects of heavy metals on measures of male fertility. One hundred and two infertile men with occupational exposure and thirty fertile men were included in this study. Blood and urinary levels of lead, cadmium, zinc and copper were measured by atomic absorption spectrophotometry. Semen parameters and a motile sperm organelle morphology examination were also performed. Measures of hormonal levels, oxidation-reduction potential, DNA fragmentation index and chromatin condensation were assessed for all participants. Heavy metals levels, oxidative stress and DNA quality were significantly higher in the infertile group compared to controls. FSH and testosterone levels were lower in the infertile group. A urinary cadmium level was positively associated with abnormal sperm morphology (r = .225, p < .05). Normal morphology was inversely correlated with the duration of the exposure (r = -.227, p = .022). The blood lead level was positively related to the level of testosterone (r = .223, p = .031). Cadmium and lead blood levels were positively correlated with the level of chromatin decondensation (r = .528, p < .001; r = .280, p = .017). Our study showed that occupational exposure to heavy metals is very harmful to reproductive health. DNA quality and oxidative stress investigations must be recommended for reprotoxic exposed patients prior to in vitro fertilisation treatment.


Sujet(s)
Infertilité masculine , Plomb , Cadmium/toxicité , Cuivre , Humains , Infertilité masculine/induit chimiquement , Plomb/toxicité , Mâle , Sperme , Mobilité des spermatozoïdes , Spermatozoïdes , Zinc
11.
Prep Biochem Biotechnol ; 51(10): 1018-1025, 2021.
Article de Anglais | MEDLINE | ID: mdl-33729901

RÉSUMÉ

This study was carried out to evaluate the effect of extraction methods (direct maceration (DM) and successive maceration (SM)) and solvents (dichloromethane (DCM), ethyl acetate (EAc), butanol (But), and aqueous extraction (Aqu)) on the phenolic composition and biological activities of Moringa oleifera leaves cultivated for the first time in Tunisia. Total polyphenol content (TPC), total flavonoid content (TFC) and LC-MS analysis were performed for all extracts. Antioxidant potential by DPPH, metal chelating, and FRAP assays, antibacterial activity against Staphylococcus aureus (ATCC 29213) and Escherichia coli (ATCC 25922) by the minimum inhibitory concentration method (MIC) and cytotoxic properties against lung cancer cells (A549), were determined. Phenolic compounds and biological activities of M. oleifera leaves depend on the method and the solvent used for the extraction of these bioactive substances. The But extract prepared by SM method exhibited the highest amounts of TPC (103.06 ± 0.5 mg GAE/g DE) and showed the strongest potential antioxidant (CI50 = 0.26 mg/mL on DPPH test), antibacterial (MIC = 250 µg/mL) and cytotoxic activities (GI50 = 69.9 µg/mL). LC-MS analysis showed that 28 phenolic compounds of 33 tested standards were found in M. oleifera leaves. The But extract obtained by SM method exhibited the highest amounts of rutin, quercetin and syringic acid.


Sujet(s)
Moringa oleifera/composition chimique , Phénols/analyse , Extraits de plantes/composition chimique , Feuilles de plante/composition chimique , Antibactériens/analyse , Antibactériens/isolement et purification , Antibactériens/pharmacologie , Antioxydants/analyse , Antioxydants/isolement et purification , Antioxydants/pharmacologie , Flavonoïdes/analyse , Flavonoïdes/isolement et purification , Flavonoïdes/pharmacologie , Phénols/isolement et purification , Phénols/pharmacologie , Extraits de plantes/isolement et purification , Extraits de plantes/pharmacologie , Polyphénols/analyse , Polyphénols/isolement et purification , Polyphénols/pharmacologie , Solvants
12.
Food Chem ; 339: 127824, 2021 Mar 01.
Article de Anglais | MEDLINE | ID: mdl-32882624

RÉSUMÉ

Despite the interest of legumes for food and feed purposes, the phytochemicals of Astragalus armatus (AA), A. caprinus (AC), and A. gombiformis (AG) have not been reported in-depth yet. Thus, the lipid contents, fatty acids composition, proteins, and bioactive compounds in the seeds of these species were investigated. Total lipids were ranged from 12.2 (AG) to 36.5 g 100 g-1 DW (AC) and consisted of oleic acid, linoleic acid, α-linolenic acid, and palmitic acid. The crude protein contents were in the range from 52.2 (AG) to 54.7 g 100 g-1 DW (AA). Globulin and albumin were the predominant soluble protein fractions. The seeds consisted significantly of different contents of total polyphenols (3.4-6.5 mg GAEg-1 DW), total flavonoids (1.24-5.15 mg QEg-1 DW), and total condensed tannins (12-23.2 mg CEg-1 DW). The extracts mainly consisted of quinic acid, p-coumaric acid, and cirsiliol. All these findings can be assets for functional foods and/or food ingredients.


Sujet(s)
Astragalus/composition chimique , Lipides/analyse , Composés phytochimiques/analyse , Protéines végétales/analyse , Graines/composition chimique , Antioxydants/analyse , Antioxydants/composition chimique , Acides gras/analyse , Flavonoïdes/analyse , Extraits de plantes/composition chimique , Huiles végétales/composition chimique , Polyphénols/analyse , Acide quinique/analyse , Tanins/analyse
13.
Genes (Basel) ; 11(8)2020 08 05.
Article de Anglais | MEDLINE | ID: mdl-32764325

RÉSUMÉ

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.


Sujet(s)
Medicago/génétique , Polymorphisme de nucléotide simple , Similitude de séquences , Trigonella/génétique , Caractère quantitatif héréditaire , Graines/génétique
14.
J Therm Biol ; 81: 73-81, 2019 Apr.
Article de Anglais | MEDLINE | ID: mdl-30975426

RÉSUMÉ

This study aims to investigate the thermoprotective properties of Opuntia ficus-indica f. inermis. Extracts were prepared from cladodes (CE) and mesocarps (ME), then subjected to a spectrophotometric and LC-MS analyses. Lymphocytes were isolated from peripheral blood of non-stressed sheep, supplemented with CE, ME, betanin or α-tocopherol, and subjected to two thermal treatments: 40 and 41 °C, for 6 h. Viable lymphocytes and H2O2 production were evaluated. The antioxidant activity of ME was 3.43 folds higher than CE. The LC-MS analysis of CE and ME allowed identifying 11 phenolic acids, 2 flavanones, 6 flavones, 3 flavonols and 1 betanin type betacyanin. Lymphocytes mortality increased linearly as function of the severity and the duration of heat stress. This mortality was correlated with H2O2 production. At 41 °C, only ME allowed maintaining lymphocytes viability. Moreover, ME was more efficient than CE in reducing H2O2 production. This thermoprotection was ensured by betaxanthin and betacyanin pigments. Interestingly, betanin was more efficient than α-tocopherol in preventing hyperthermia-induced lymphocytes' mortality. We report here for the first time the thermoprotective properties of cladodes and mesocarps of Opuntia ficus-indica f. inermis. Betanin was able to maintain lymphocyte viability through reducing H2O2 production, and therefore the oxidative-induced heat stress.


Sujet(s)
Antioxydants/administration et posologie , Réaction de choc thermique , Lymphocytes/physiologie , Opuntia/composition chimique , Extraits de plantes/administration et posologie , Agents protecteurs/administration et posologie , Phénomènes physiologiques nutritionnels chez l'animal , Animaux , Antioxydants/composition chimique , Bétacyanines/administration et posologie , Bétacyanines/isolement et purification , Bétacyanines/métabolisme , Survie cellulaire/effets des médicaments et des substances chimiques , Compléments alimentaires , Peroxyde d'hydrogène/métabolisme , Extraits de plantes/composition chimique , Extraits de plantes/isolement et purification , Ovis , alpha-Tocophérol/administration et posologie , alpha-Tocophérol/isolement et purification
15.
Proteins ; 84 Suppl 1: 87-104, 2016 09.
Article de Anglais | MEDLINE | ID: mdl-26492194

RÉSUMÉ

The CASP experiment is a biannual benchmark for assessing protein structure prediction methods. In CASP11, RBO Aleph ranked as one of the top-performing automated servers in the free modeling category. This category consists of targets for which structural templates are not easily retrievable. We analyze the performance of RBO Aleph and show that its success in CASP was a result of its ab initio structure prediction protocol. A detailed analysis of this protocol demonstrates that two components unique to our method greatly contributed to prediction quality: residue-residue contact prediction by EPC-map and contact-guided conformational space search by model-based search (MBS). Interestingly, our analysis also points to a possible fundamental problem in evaluating the performance of protein structure prediction methods: Improvements in components of the method do not necessarily lead to improvements of the entire method. This points to the fact that these components interact in ways that are poorly understood. This problem, if indeed true, represents a significant obstacle to community-wide progress. Proteins 2016; 84(Suppl 1):87-104. © 2015 Wiley Periodicals, Inc.


Sujet(s)
Biologie informatique/statistiques et données numériques , Modèles moléculaires , Modèles statistiques , Protéines/composition chimique , Logiciel , Algorithmes , Bactéries/composition chimique , Biologie informatique/méthodes , Simulation numérique , Bases de données de protéines , Humains , Coopération internationale , Internet , Pliage des protéines , Motifs et domaines d'intéraction protéique , Structure secondaire des protéines
16.
Wellcome Open Res ; 1: 24, 2016 Dec 09.
Article de Anglais | MEDLINE | ID: mdl-28317030

RÉSUMÉ

Determining the structure of a protein by any method requires various contributions from experimental and computational sides. In a recent study, high-density cross-linking/mass spectrometry (HD-CLMS) data in combination with ab initio structure prediction determined the structure of human serum albumin (HSA) domains, with an RMSD to X-ray structure of up to 2.5 Å, or 3.4 Å in the context of blood serum. This paper reports the blind test on the readiness of this technology through the help of Critical Assessment of protein Structure Prediction (CASP). We identified between 201-381 unique residue pairs at an estimated 5% FDR (at link level albeit with missing site assignment precision evaluation), for four target proteins. HD-CLMS proved reliable once crystal structures were released. However, improvements in structure prediction using cross-link data were slight. We identified two reasons for this. Spread of cross-links along the protein sequence and the tightness of the spatial constraints must be improved. However, for the selected targets even ideal contact data derived from crystal structures did not allow modellers to arrive at the observed structure. Consequently, the progress of HD-CLMS in conjunction with computational modeling methods as a structure determination method, depends on advances on both arms of this hybrid approach.

17.
Nucleic Acids Res ; 43(W1): W343-8, 2015 Jul 01.
Article de Anglais | MEDLINE | ID: mdl-25897112

RÉSUMÉ

RBO Aleph is a novel protein structure prediction web server for template-based modeling, protein contact prediction and ab initio structure prediction. The server has a strong emphasis on modeling difficult protein targets for which templates cannot be detected. RBO Aleph's unique features are (i) the use of combined evolutionary and physicochemical information to perform residue-residue contact prediction and (ii) leveraging this contact information effectively in conformational space search. RBO Aleph emerged as one of the leading approaches to ab initio protein structure prediction and contact prediction during the most recent Critical Assessment of Protein Structure Prediction experiment (CASP11, 2014). In addition to RBO Aleph's main focus on ab initio modeling, the server also provides state-of-the-art template-based modeling services. Based on template availability, RBO Aleph switches automatically between template-based modeling and ab initio prediction based on the target protein sequence, facilitating use especially for non-expert users. The RBO Aleph web server offers a range of tools for visualization and data analysis, such as the visualization of predicted models, predicted contacts and the estimated prediction error along the model's backbone. The server is accessible at http://compbio.robotics.tu-berlin.de/rbo_aleph/.


Sujet(s)
Conformation des protéines , Logiciel , Algorithmes , Internet , Modèles moléculaires , Analyse de séquence de protéine
18.
Pak J Pharm Sci ; 26(1): 145-52, 2013 Jan.
Article de Anglais | MEDLINE | ID: mdl-23261740

RÉSUMÉ

Chloroacetonitrile is a disinfectant by-product of chlorination of drinking water and is considered as a direct-acting mutagenic and carcinogenic agent. Time-course and dose-response studies were performed to examine the mechanism of chloroacetonitrile-induced hepatotoxicity. In the time-course study, animals were scarified at 2, 4, 6 and 12 h after a single oral dose of chloroacetonitrile (38 mg/kg, p.o.). In the dose-response study, rats were scarified at 2 h after a single oral dose of chloroacetonitrile (9, 19, 38, and 76 mg/kg). In the time-course study chloroacetonitrile induced a significant decrease of hepatic glutathione, and activities of glutathione-S-transferase, glutathione proxidase and superoxide dismutase accompanied with an increase of hepatic malondialdehyde, plasma cytokines (IL-6 & 10 and TNF-α), serum aminotransferases and total bilirubin after 2 h of administration. Maximal alteration of the estimated parameters was observed at 4 h and returned to normal value at 6 h and/or 12 h after chloroacetonitrile treatment. Moreover, the alterations in oxidant, antioxidant parameters, inflammatory cytokines and the liver function tests were dose dependant. Histopathological findings supported the biochemical results. These data indicate that the mechanism of chloroacetonitrile-induced hepatotoxicity may be mediated through depletion of antioxidants, induction of oxidative stress and inflammatory cytokines.


Sujet(s)
Acétonitriles/toxicité , Lésions hépatiques dues aux substances/étiologie , Foie/effets des médicaments et des substances chimiques , Polluants chimiques de l'eau/toxicité , Purification de l'eau , Animaux , Bilirubine/sang , Lésions hépatiques dues aux substances/immunologie , Lésions hépatiques dues aux substances/métabolisme , Lésions hépatiques dues aux substances/anatomopathologie , Cytokines/sang , Relation dose-effet des médicaments , Glutathion/métabolisme , Glutathione peroxidase/métabolisme , Glutathione transferase/métabolisme , Médiateurs de l'inflammation/sang , Foie/immunologie , Foie/métabolisme , Foie/anatomopathologie , Tests de la fonction hépatique , Mâle , Malonaldéhyde/métabolisme , Stress oxydatif/effets des médicaments et des substances chimiques , Rats , Rat Wistar , Superoxide dismutase/métabolisme , Facteurs temps , Transaminases/sang
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