Biomedical and biological applications of scanning electron microscopy

This article summarizes the basic principles of scanning electron microscopy and the capabilities of the technique with different examples ofapplications in biomedical and biological research.

Phytochemical investigation of alpine plants : the cottonsedges Eriophorum scheuchzeri Hoppe, E. angustifolium Honck. and E. latifolium Hoppe (CYPERACEAE)

Résumé: Alpine plants living at high altitudes undergo a series of climatic stress factors (chilling, enhanced UV radiation, short growing season, low nutriment supply...) which may influence their secondary compounds composition. Many publications showed in these last years that plants under stress conditions do synthesize a range of specific defence compounds (terpenes, flavonoids, coumarines...). A careful phytochemical investigation of those plants could therefore lead to the discovery of active molecules. Thus, for the biological and chemical screening, about 30 alpine plants have been collected above 2000 metres, in the alpine grass-lands. Eriophorum scheuchzeri Hoppe (Cyperaceae), not yet investigated phytochemically, revealed in its lipophilic and polar extracts the presence of various radical scavengers in a TLC autography with the DPPH (2,2-dipheny1-1- picrylhydrazyl) radical as spray reagent, as well as several antifungal compounds acitve against Cladosporium cucumerinum and Candida albi cans. The first part of this study consisted in the detection, isolation and characterization of the bioactive natural compounds present in the lipophilic extract of Eriophorum scheuchzeri. Among the eight isolated compounds, six were isoflavones. No isoflavones have been reported in the Cyperaceae family yet, nor in related families such as Poaceae or Juncaceae. Besides, isoflavones are generally rare in the plant kingdom and and they occur only in some families, such as Fabaceae, Rosaceae or Myristicaceae. In addition, out of these six isoflavones, three were new isoflavones. The known compounds were parvisoflavone A and B and cajanin which are already known isoflavones in the Fabaceae family. Two of the new isoflavones were particular, as they were C-methylated on the B-ring at the C-3' position. Methylated flavonoids are particularly rare in the plant kingdom. At present, no C-methylated isoflavones with methyl groups on the B-ring have ever been reported. The fourth new compound was a prenylated flavanone. Flavanones are also rare in the Cyperaceae family since they were found only in two genera (Cyperus and Schoenus). Finally, the widespread flavone tricin, characteristic of the Cyperaceae and Poaceae family has also been isolated. The second part of this study consisted in the characterization of the polar components present in the Me0H extract. In order to obtain mass and UV information about the secondary compounds present in the Eriophorum scheuchzeri methanolic extract, a LC-UV/DAD-APCl/MSn analysis has been performed as a first dereplication step. The UV/DAD spectra showed the presence of polyphenol compounds (phenylpropanoids and flavonoids). The LC-APCI/MSn analysis allowed the determination of the molecular weight of these compounds. Moreover, the fragmentation pattern of the [M+H]+ ions indicated presence of mono-, di- and tri-glycosides. LC-UV in combination with UV shift reagents added post-column was used in a second phase for the structural elucidation of the flavonoids. It allowed the positioning of the sugars on the aglycones. Finally, LC-NMR was used for a more detailed structural investigation of the compounds present in the crude MEOH extract. Thus, 10 fiavonoids have been totally or partially characterized by LC-UV-MS and LC-1H-RMN and UV-shift reagents added post column. However, the information obtained on-line was not always sufficient to allow a complete identification of all the compounds. Some of these compounds especially those with more than two sugar units attached to them, have been isolated in order to proceed to their complete characterization. Moreover, the Eriophorum scheuchzeri species was compared to two other species from the same genus. A LC-UV-ESI/MS analysis enabled a survey of the chemical composition of the DCM extracts of two related species E. angustifolium (Honck) and E. latifolium (Hoppe). The chromatograms of the three species showed some similarities in their flavonoid contents, especially by the recurrent presence of three compounds. The MEOH extracts of all three species have been compared by means of LC-UV-APCl/MS analyses. The chromatographic profile of all the three species showed even closer similarities than those found in the DCM extracts. E. angustifolium Honck. and E. latifolium species showed 7 compounds in common. Finally, the pure compounds obtained from the DCM (CH2Cl2) fraction were tested at different concentration, in order to evaluate their chemical and biological activities. All eight compounds showed an anti-scavenger activity against the DPPH radical, and four compounds showed antifungal activities against Cladosporium cucumerinum and Candida albicans. The pure compounds isolated from the MeOH extract were tested only for their biological activities as their antioxidant activity is already well documented in the literature. No compound showed a biological activity against Cladosporium cucumerinum and Candida albicans. Résumé: De nombreux travaux ont démontré ces dernières décennies que les plantes soumises à différents types de stress (basse température, UV, stress hydrique) synthétisent des composés secondaires (fiavonoides, coumarines, terpènes...) de protection et de défense. Les plantes d'altitude par exemple qui sont exposées à des conditions climatiques et environnementales difficiles, ont tendance à synthétiser des substances antioxydantes et antiradicalaires. Une investigation phytochirnique de ces plantes a conduit à la découverte de nouvelles molécules actives. Ainsi plusieurs plantes alpines ont été sélectionnées en fonction de leur habitat en vue de les soumettre aux tests biologiques (antifongiques) et chimiques (antiradicalaires) menés en routine dans notre laboratoire. Dans ce criblage biologique préliminaire, les extraits d'Eriophorum scheuchzeri Hoppe (Cyperaceae) ont réagi positivement aux différents tests. Il a donc été décidé d'entreprendre l'isolement des composés actifs. La première partie de ce travail a consisté à détecter, isoler et caractériser les composés naturels actifs présents dans l'extrait apolaire d' Eriophorum scheuchzeri. Parmi les huit composés isolés, quatre d'entre eux sont nouveaux. Un de ces produits est une flavanone et trois sont de nouvelles isoflavones, particulièrement intéressantes car elles possèdent des groupements C-méthylés au niveau du cycle B. Les flavonoides C-méthylés sont peu répandus dans le règne végétal et les rares exemples connus sont généralement C-méthylés sur le cycle A. Les quatre autres composés isolés n'ont jamais été décrits dans cette famille. Il s'agit d' isoflavones, les parvisoflavones A et B et la cajanine. Enfin, la flavone tricine, flavonoide caractéristique des Cyperaceae et des Poaceae a également été isolée. La deuxième partie de ce travail a consisté à caractériser les constituants polaires présents dans l'extrait methanolique. L'extrait a été analysé par chromatographie analytique couplée à différentes méthodes spectroscopiques (LC-UV-MS et LC-UV-1H RMN). De cette façon, douze flavonoides et un dérivé du phénylpropane, l'acide chlorogénique ont été identifiés. Les flavonoides tri-glycosylés ont dû être isolés afin de déterminer la nature et l'enchaînement des sucres. Finalement, l'espèce Eriophorum scheuchzeri a été comparée à deux autres espèces d' Eriophorum, soit E. angustifolium et E. latifolium. En conclusion, cette étude phytochimique a abouti à l'isolement de plusieurs nouvelles isoflavones aux activités antioxydantes et antifongiques ainsi qu'oestrogéniques.

Department of Biological Sciences Newsletter, Fall 2005

The University of Iowa Department of Biology is devoted to providing students with an education that prepares them for a multitude of careers that depend on a solid understanding of biology. Students will gain valuable experience through our programs.

Department of Biological Sciences Newsletter, Fall 2006

The University of Iowa Department of Biology is devoted to providing students with an education that prepares them for a multitude of careers that depend on a solid understanding of biology. Students will gain valuable experience through our programs.

Prediction of soil shear strength in agricultural and natural environments of the Brazilian Cerrado

The objective of this work was to develop uni- and multivariate models to predict maximum soil shear strength (τmax) under different normal stresses (σn), water contents (U), and soil managements. The study was carried out in a Rhodic Haplustox under Cerrado (control area) and under no-tillage and conventional tillage systems. Undisturbed soil samples were taken in the 0.00-0.05 m layer and subjected to increasing U and σn, in shear strength tests. The uni- and multivariate models - respectively τmax=10(a+bU) and τmax=10(a+bU+cσn) - were significant in all three soil management systems evaluated and they satisfactorily explain the relationship between U, σn, and τmax. The soil under Cerrado has the highest shear strength (τ) estimated with the univariate model, regardless of the soil water content, whereas the soil under conventional tillage shows the highest values with the multivariate model, which were associated to the lowest water contents at the soil consistency limits in this management system.

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largely through direct effects within the kidney and highlight important cell types and biological pathways.

Enzymes of yeast polyphosphate metabolism: structure, enzymology and biological roles.

Inorganic polyphosphate (polyP) is found in all living organisms. The known polyP functions in eukaryotes range from osmoregulation and virulence in parasitic protozoa to modulating blood coagulation, inflammation, bone mineralization and cellular signalling in mammals. However mechanisms of regulation and even the identity of involved proteins in many cases remain obscure. Most of the insights obtained so far stem from studies in the yeast Saccharomyces cerevisiae. Here, we provide a short overview of the properties and functions of known yeast polyP metabolism enzymes and discuss future directions for polyP research.

Food Safety Testing: Rapid Molecular Methods for Chemical and Biological Hazards

The central goal of food safety policy in the European Union (EU) is to protect consumer health by guaranteeing a high level of food safety throughout the food chain. This goal can in part be achieved by testing foodstuffs for the presence of various chemical and biological hazards. The aim of this study was to facilitate food safety testing by providing rapid and user-friendly methods for the detection of particular food-related hazards. Heterogeneous competitive time-resolved fluoroimmunoassays were developed for the detection of selected veterinary residues, that is coccidiostat residues, in eggs and chicken liver. After a simplified sample preparation procedure, the immunoassays were performed either in manual format with dissociation-enhanced measurement or in automated format with pre-dried assay reagents and surface measurement. Although the assays were primarily designed for screening purposes providing only qualitative results, they could also be used in a quantitative mode. All the developed assays had good performance characteristics enabling reliable screening of samples at concentration levels required by the authorities. A novel polymerase chain reaction (PCR)-based assay system was developed for the detection of Salmonella spp. in food. The sample preparation included a short non-selective pre-enrichment step, after which the target cells were collected with immunomagnetic beads and applied to PCR reaction vessels containing all the reagents required for the assay in dry form. The homogeneous PCR assay was performed with a novel instrument platform, GenomEra^™, and the qualitative assay results were automatically interpreted based on end-point time-resolved fluorescence measurements and cut-off values. The assay was validated using various food matrices spiked with sub-lethally injured Salmonella cells at levels of 1-10 colony forming units (CFU)/25 g of food. The main advantage of the system was the exceptionally short time to result; the entire process starting from the pre-enrichment and ending with the PCR result could be completed in eight hours. In conclusion, molecular methods using state-of-the-art assay techniques were developed for food safety testing. The combination of time-resolved fluorescence detection and ready-to-use reagents enabled sensitive assays easily amenable to automation. Consequently, together with the simplified sample preparation, these methods could prove to be applicable in routine testing.

The impact of FTAs on MENA trade in agricultural and industrial products

This paper analyses the impact of Free Trade Agreements (FTAs) on Middle East and North African Countries (MENA) trade for the period 1994-2010. The analysis distinguishes between industrial and agricultural trade to take into account the different liberalisation schedules. An augmented gravity model is estimated using up-to-date panel data techniques to control for all time-invariant bilateral factors that influence bilateral trade as well as for the so-called multilateral resistance factors. We also control for the endogeneity of the agreements and test for self-selection bias due to the presence of zero trade in our sample. The main findings indicate that North-South-FTAs and South-South- FTAs have a differential impact in terms of increasing trade in MENA countries, with the former being more beneficial in terms of exports for MENA countries, but both showing greater global market integration. We also find that FTAs that include agricultural products, in which MENA countries have a clear comparative advantage, have more favourable effects for these countries than those only including industrial products. JEL code: F10, F15

Synthesis and biological activity of n-{5-(4-methylphenyl) diazenyl-4-phenyl-1, 3-thiazol-2-yl}benzamide derivatives

In the present study, various amides of 2-amino-5-(4-methylphenyl)-diazenyl-4-phenyl-1, 3-thiazole was synthesized and their biological activities were evaluated. All the synthesized compounds were characterized by the combination of elemental analysis and standard spectroscopic methods. They are screened for anti-bacterial activity against Escherichia coli and Staphylococcus aureus as well as screened for antifungal activity against Aspergillus niger and Apergillus oryzae by cup plate method at 1 µg/ mL concentration in DMF.

SYNTHESIS AND BIOLOGICAL ACTIVITY OF NEW SERIES OF ORGANOTIN(IV) ESTERS WITH N,N-DIACETYLGLYCINE

A bioactive N,N-diacetylglycine (NNDAG) and new organotin(IV) complexes (OTCs) (1-7) were synthesized. Spectroscopic techniques were employed to characterize NNDAG and OTCs. FTIR was employed to verify N,N protection of glycine by acetyl groups. The disappearance of υ(OH) at 3000-2600 cm-1 showed de-protonation of free ligand. The Δυ 150<200 cm-1 of OTCs 4-7 verified bidentate coordination with tetrahedral geometry. The Δυ of OTCs1 and 3 was <200 cm-1 exhibitingtrans -octahedral geometry while OTC 2 dimer was assigned a unique sinusoidal view. The 1H NMR spectra of OTCs verified their synthesis by de-protonation of NNDAG and no chemical shift was found downfield for carboxylic acid proton. The 13C, 119Sn NMR and Mass spectrometric data also supported FTIR and 1H NMR descriptions. The OTCs 4, 5, 6 and7 (500 ppm) proved twice as active against Escherichia coli as the standard antibiotic enoxacin (1000 ppm). The promising property of the OTCs (4, 5, 6 and7) is clearly due to their tetrahedral. The OTCs 4and 5 exhibited excellent activity against M. minimum and good activity against T. castaneum.LD50 of all the compounds were determined and OTCs4, 5 and 7 were found to be active.

New [18F]Tracers for Alzheimer's Disease Imaging. Labeling Synthesis And Biological Testing

Alzheimer’s disease (AD) is the most common form of dementia. Characteristic changes in an AD brain are the formation of β-amyloid protein (Aβ) plaques and neurofibrillary tangles, though other alterations in the brain have also been connected to AD. No cure is available for AD and it is one of the leading causes of death among the elderly in developed countries. Liposomes are biocompatible and biodegradable spherical phospholipid bilayer vesicles that can enclose various compounds. Several functional groups can be attached on the surface of liposomes in order to achieve long-circulating target-specific liposomes. Liposomes can be utilized as drug carriers and vehicles for imaging agents. Positron emission tomography (PET) is a non-invasive imaging method to study biological processes in living organisms. In this study using nucleophilic 18F-labeling synthesis, various synthesis approaches and leaving groups for novel PET imaging tracers have been developed to target AD pathology in the brain. The tracers were the thioflavin derivative [18F]flutemetamol, curcumin derivative [18F]treg-curcumin, and functionalized [18F]nanoliposomes, which all target Aβ in the AD brain. These tracers were evaluated using transgenic AD mouse models. In addition, 18F-labeling synthesis was developed for a tracer targeting the S1P3 receptor. The chosen 18F-fluorination strategy had an effect on the radiochemical yield and specific activity of the tracers. [18F]Treg-curcumin and functionalized [18F]nanoliposomes had low uptake in AD mouse brain, whereas [18F]flutemetamol exhibited the appropriate properties for preclinical Aβ-imaging. All of these tracers can be utilized in studies of the pathology and treatment of AD and related diseases.

A conceptual and practical overview of cDNA microarray technology: implications for basic and clinical sciences

cDNA microarray is an innovative technology that facilitates the analysis of the expression of thousands of genes simultaneously. The utilization of this methodology, which is rapidly evolving, requires a combination of expertise from the biological, mathematical and statistical sciences. In this review, we attempt to provide an overview of the principles of cDNA microarray technology, the practical concerns of the analytical processing of the data obtained, the correlation of this methodology with other data analysis methods such as immunohistochemistry in tissue microarrays, and the cDNA microarray application in distinct areas of the basic and clinical sciences.

The Alberta Dilemma: Optimal Sharing of a Water Resource by an Agricultural and an Oil Sector

The purpose of this paper is to characterize the optimal time paths of production and water usage by an agricultural and an oil sector that have to share a limited water resource. We show that for any given water stock, if the oil stock is sufficiently large, it will become optimal to have a phase during which the agricultural sector is inactive. This may mean having an initial phase during which the two sectors are active, then a phase during which the water is reserved for the oil sector and the agricultural sector is inactive, followed by a phase during which both sectors are active again. The agricultural sector will always be active in the end as the oil stock is depleted and the demand for water from the oil sector decreases. In the case where agriculture is not constrained by the given natural inflow of water once there is no more oil, we show that oil extraction will always end with a phase during which oil production follows a pure Hotelling path, with the implicit price of oil net of extraction cost growing at the rate of interest. If the natural inflow of water does constitute a constraint for agriculture, then oil production never follows a pure Hotelling path, because its full marginal cost must always reflect not only the imputed rent on the finite oil stock, but also the positive opportunity cost of water.

Distribution of diatom communities in agricultural and mining watersheds of Southwest Spain

Els sistemes aquàtics continental representen un dels ecosistemes més amenaçats a nivell mundial, com a conseqüència de l'ús intensiu quel'home en fa. La conca del Guadiana no està lliure d'aquestes pressions antròpiques. Les grans infraestructures hidràuliques i l'escorrentia provinent de l'agricultura són només exemples dels greus problemes que pateix la conca. Aquests problemes es fan especialment palesos en la zona alta de la conca, on l'escassetat d'aigua no fa més que agreujar el problema.Tot això ha generat la necessitat urgent d'avaluar l'estat de conservació d'aquests ecosistemes aquàtics continentals, poder determinar la mesura i la magnitud de les pertorbacions que els estan afectant i així proposar mesures de gestió destinades a restaurar-ne la integritat ecològica. El principal objectiu que presenta aquest és determinar els patrons de distribució de les comunitats de algals (amb una menció especial en el grup de les diatomees) i de les seves causes en la conca del Guadiana i associades, amb la finalitat d'establir i proposar eines que permetin avaluar l'estat de conservació de les masses d'aigua d'aquestes conques.