Determination and structural characterisation of dermatan sulfate in the presence of other galactosaminoglycans

Chondroitin sulfate and dermatan sulfate are galactosaminoglycans that have similar size and charge density thus making difficult their separation and accurate determination from tissue preparations. A procedure was developed, which was based on the specific action of chondroitinase B, that allowed the determination of dermatan sulfate content in a mixture of chondroitin sulfate/dermatan sulfate, its molecular mass (M_r), and iduronic acid content and distribution throughout the chain. According to this procedure, the galactosaminoglycan sample was treated with chondroitinase B and its profile, upon gel chromatography on Sepharose CL-6B, was compared to that of the initial sample. The differences in uronic acid content of the fractions of the gel chromatographies were plotted and a secondary profile was constructed, which corresponded to the elution profile of intact dermatan sulfate in the sample. From this profile, the size distribution of dermatan sulfate was obtained and its M_r was calculated. In addition, the accurate content of dermatan sulfate in the sample was determined. The digest contained oligosaccharides of variable size that were separated on BioGel P-10. From the separated oligosaccharides the distribution of iduronic acid throughout the dermatan sulfate chains was determined. The procedure was applied to the determination and partial characterisation of dermatan sulfate from sheep nasal cartilage, in which it is reported for the first time that it contains a significant proportion of dermatan sulfate chains of low iduronic acid content.     

Characterization of the myoglobin of the lampreyPetromyzon marinus

Summary Myoglobin has been identified in the myocardium of the lampreyPetromyzon marinus, one of the most primitive of all vertebrates. This protein was isolated by ammonium sulphate fractionation and purified by successive chromatography on Ultrogel AcA 54, DEAE-Sephadex and CM-23 cellulose. The molecule differs substantially from the monomeric hemoglobins found in the lamprey as evidenced by its elution profile on DEAE-Sephadex and the fingerprint pattern of its enzymically-produced peptides. The functional significance of this protein in Agnatha is discussed.     

Changes in galactolipid composition of the cold freshwater dinoflagellate Borghiella dodgei in response to temperature

The freshwater dinoflagellate Borghiella dodgei is adapted to cold temperatures. We investigated the effects of small temperature changes on its galactolipid composition, choosing 3 and 7°C as deviations from its optimal growth temperature (5°C). The galactolipid profile, important for maintenance of membrane fluidity, was determined by liquid chromatography–mass spectrometry and the influence of temperature on galactolipids was investigated by one-way ANOVA. We found 24 different galactolipid species, including novel tri-galactosyldiacylglycerols (TGDGs). The overall amount of mono- (MGDG), di- (DGDG) and tri- (TGDG) galactosyldiacylglycerols remained stable while single galactolipids varied with temperature. Few changes were found from 3 to 5°C, instead 11 galactolipid species changed from 5 to 7°C. Concomitantly with the unsaturation index of MGDGs, the more unsaturated galactolipids decreased at higher temperature, and the less abundant and less unsaturated galactolipids in each lipid class accumulated. Changes in the galactolipid profile of Borghiella underlined its cold-stenothermal nature: it can adapt to relatively ‘higher’ temperatures by reducing the synthesis of the more unsaturated MGDGs, DGDGs and TGDGs, but remains restricted by its lower growth rate. Based on our results, we predict that with climate change the galactolipid profile of cold-stenothermal algae will change with important repercussions on their consumers.     

New antifungal agents for the systemic mycoses

The azoles are the prominent broad spectrum oral antifungal agents in use or under clinical investigation for the systemic mycoses. This class of antifungal agents is represented by the marketed drug ketoconazole (Nizoral) and the experimental triazoles furthest along in clinical trials in the United States, itraconazole and fluconazole. Ketoconazole use is limited by its side effect profile and activity spectrum. Itraconazole appears to be better tolerated and less toxic to liver function, does not cause adrenal suppression and is more active against Aspergillus and Sporothrix schenckii. Fluconazole appears to be a highly promising agent due its highly favorable pharmacokinetic profile; it is water soluble, is well tolerated, is not metabolized to inactive constituents, it has a long half-life and, unlike the other azoles, high cerebrospinal fluid levels are readily attained for consideration in meningeal mycoses. It remains to be determined what place these new triazoles have in managing immunosuppressed patients including those with acquired immune deficiency syndrome known as AIDS. Other experimental antifungal agents, including ambruticin, amphotericin B methyl ester and saramycetin are also described. Sales figures are presented of drugs marketed in the United States for the systemic mycoses and reflect the growing problem of fungal diseases in the population.Presented as part of the Everett S. Beneke Symposium in Mycology, May 27, 1988.     

Fiber‐type composition in the perivertebral musculature of lizards: Implications for the evolution of the diapsid trunk muscles

The perivertebral musculature of lizards is critical for the stabilization and the mobilization of the trunk during locomotion. Some trunk muscles are also involved in ventilation. This dual function of trunk muscles in locomotion and ventilation leads to a biomechanical conflict in many lizards and constrains their ability to breathe while running (“axial constraint”) which likely is reflected by their high anaerobic scope. Furthermore, different foraging and predator‐escape strategies were shown to correlate with the metabolic profile of locomotor muscles in lizards. Because knowledge of muscle's fiber‐type composition may help to reveal a muscle's functional properties, we investigated the distribution pattern of muscle fiber types in the perivertebral musculature in two small lizard species with a generalized body shape and subjected to the axial constraint (Dipsosaurus dorsalis, Acanthodactylus maculatus) and one species that circumvents the axial constraint by means of gular pumping (Varanus exanthematicus). Additionally, these species differ in their predator‐escape and foraging behaviors. Using refined enzyme‐histochemical protocols, muscle fiber types were differentiated in serial cross‐sections through the trunk, maintaining the anatomical relationships between the skeleton and the musculature. The fiber composition in Dipsosaurus and Acanthodactylus showed a highly glycolytic profile, consistent with their intermittent locomotor style and reliance on anaerobic metabolism during activity. Because early representatives of diapsids resemble these two species in several postcranial characters, we suggest that this glycolytic profile represents the plesiomorphic condition for diapsids. In Varanus, we found a high proportion of oxidative fibers in all muscles, which is in accordance with its high aerobic scope and capability of sustained locomotion. J. Morphol., 2013. © 2012 Wiley Periodicals, Inc.     

CFD Validation of the Optimal Arrangement of the Propulsive Dorsal Fin of Gymnarchus niloticus

Gymnarchus niloticus, a typical freshwater fish, swims by undulations of a long-based dorsal fin aided by the two pectoral fins, while commonly it holds its body rigid and straight. The long flexible dorsal fin is the main propulsor of G niloticus; it has also considerable influence on the streamline profile. This paper proposes a CFD approach to validate that the natural arrangement of the propulsive dorsal fin is optimal. Using morphological data and a smoothness-keeping algorithm, the dorsal fin is ‘virtually＇ moved forward and backward with several displacements from the natural location. For each case, we reconstruct geometry, generate CFD grids, and calculate the pressure, viscous and total drag coefficients respectively. The results show that the pressure and total drag coefficients increase whether the dorsal fin is displaced forward or backward, and that greater displacement from its original position leads to greater pressure and total drag coefficients. This suggests that the natural position of the dorsal fin is significant for maintaining the fish＇s streamline profile and reducing drag.     

New equations for the dose under pulsative/periodic conditions in the design of coated stents

The notion of dose that comes from the biologists has been introduced by Delfour et al. (2005 SIAM J. Appl. Math. 65(3):858–881) in the context of coated stents to control restenosis. Assuming a stationary velocity profile of the blood flow in the lumen, it leads to a time-independent equation for the dose that considerably simplifies the analysis and the design problem. Under stable conditions the blood flow is pulsative, that is the velocity field can be assumed to be periodic. So it is necessary to justify the replacement of the periodic field by its time average over the pulsation period. In this paper, firstly we introduce the new unfolded dose and its equations without a priori constraint on the size of the period. So it can be used in biochemical problems where the period is large compared to the time constants of the system. Secondly, we show that, as the period goes to zero, the velocity field can be replaced by its average over the period. Numerical tests on a one-dimensional example are included to illustrate the theory.     

Passive Membrane Penetration of the Serotonin Precursor 5‐Hydroxytryptophan is Controlled by Its Zwitterion

Species‐specific partition coefficients in the octanol/water system were determined for the neurotransmitter serotonin (5‐HT) and its precursor 5‐hydroxytryptophan (5‐HTP). The pH‐independent partition coefficients (p) of the individual microspecies were determined by combination of experimentally measured distribution constants and a custom‐tailored evaluation method, using highly similar auxiliary compounds. Experimental microscopic partition coefficients for triprotic molecules have only been reported before for thyroxine and its derivatives. The parabolic pH‐distribution profile of 5‐HT shows the dominance of the lipophilic non‐charged microspecies, with a log p of 0.66. However, the most lipophilic non‐charged form of 5‐HTP, with a log p of 0.31, has no significant contribution to the distribution coefficient at any pH value. Instead, the less lipophilic zwitterionic protonation isomer dominates the distribution in the pH range 2.10 – 11.11. Although the non‐charged microspecies of 5‐HTP is 151 times more lipophilic than its zwitterionic protonation isomer, the overwhelming dominance of the zwitterionic form ensures that its contribution to the overall lipophilicity exceeds 1320 times that of the non‐charged one. This fact is another counter‐example of the widespread belief that passive diffusion into lipophilic media is predominated by the non‐charged species. The lipophilicity profile of 5‐HT and 5‐HTP is depicted in terms of species‐specific lipophilicities.     

Patterns of morphological evolution of the cephalic region in damselfishes (Perciformes: Pomacentridae) of the Eastern Pacific

Pomacentridae are one of the most abundant fish families inhabiting reefs of tropical and temperate regions. This family, comprising 29 genera, shows a remarkable diversity of habitat preferences, feeding, and behaviours. Twenty‐four species belonging to seven genera have been reported in the Eastern Pacific region. The present study focuses on the relationship between the diet and the cephalic profile in the 24 endemic damselfishes of this region. Feeding habits were determined by means of underwater observations and the gathering of bibliographic data. Variations in cephalic profile were analyzed by means of geometric morphometrics and phylogenetic methods. The present study shows that the 24 species can be grouped into three main trophic guilds: zooplanktivores, algivores, and an intermediate group feeding on small pelagic and benthic preys. Shape variations were low within each genus except for Abudefduf. Phylogenetically adjusted regression reveals that head shape can be explained by differences in feeding habits. The morphometric phylogeny recovered the subfamily Stegastinae and the relationship between Abudefduf troschelii and Chromis species. The cephalic profile of damselfishes contains a clear and strong phylogenetic signal. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 593–613.     

The evolutionary and molecular features of the broad-host-range plant pathogen Sclerotinia sclerotiorum

Sclerotinia sclerotiorum is a pathogenic fungus that infects hundreds of plant species, including many of the world's most important crops. Key features of S. sclerotiorum include its extraordinary host range, preference for dicotyledonous plants, relatively slow evolution, and production of protein effectors that are active in multiple host species. Plant resistance to this pathogen is highly complex, typically involving numerous polymorphisms with infinitesimally small effects, which makes resistance breeding a major challenge. Due to its economic significance, S. sclerotiorum has been subjected to a large amount of molecular and evolutionary research. In this updated pathogen profile, we review the evolutionary and molecular features of S. sclerotiorum and discuss avenues for future research into this important species.     

Homoplasy corrected estimation of genetic similarity from AFLP bands,and the effect of the number of bands on the precision of estimation

AFLP is a DNA fingerprinting technique, resulting in binary band presence–absence patterns, called profiles, with known or unknown band positions. We model AFLP as a sampling procedure of fragments, with lengths sampled from a distribution. Bands represent fragments of specific lengths. We focus on estimation of pairwise genetic similarity, defined as average fraction of common fragments, by AFLP. Usual estimators are Dice (D) or Jaccard coefficients. D overestimates genetic similarity, since identical bands in profile pairs may correspond to different fragments (homoplasy). Another complicating factor is the occurrence of different fragments of equal length within a profile, appearing as a single band, which we call collision. The bias of D increases with larger numbers of bands, and lower genetic similarity. We propose two homoplasy- and collision-corrected estimators of genetic similarity. The first is a modification of D, replacing band counts by estimated fragment counts. The second is a maximum likelihood estimator, only applicable if band positions are available. Properties of the estimators are studied by simulation. Standard errors and confidence intervals for the first are obtained by bootstrapping, and for the second by likelihood theory. The estimators are nearly unbiased, and have for most practical cases smaller standard error than D. The likelihood-based estimator generally gives the highest precision. The relationship between fragment counts and precision is studied using simulation. The usual range of band counts (50–100) appears nearly optimal. The methodology is illustrated using data from a phylogenetic study on lettuce.     

Flavonoid evidence for allopolyploidy in the Chenopodium album aggregate (Amaranthaceae)

The flavonoid chemistry of 16 species of Chenopodium was investigated, with an emphasis on C. album and its relatives. The chief compounds seen were 3-O-glycosides of quercetin, kaempferol and isorhamnetin. The latter two classes show a mutually exclusive distribution among the diploid and all but one tetraploid species. C. polyspermum is unusual in possessing O-methylation at the 4-, 6- and 7-positions, and C. murale is the only taxon to have 7-O-glycosylation. Acylated glycosides are common. C. album and related hexaploid taxa display a single flavonoid profile, providing no support for the recognition of more than one species. The hexaploid flavonoid profile represents an almost perfect summation of those of the diploids, C. suecicum and C. ficifolium. This apparent additive inheritance supports the hypothesis that these species (or taxa very similar to them) are involved in the ancestry of C. album. Chromosome numbers are reported for 14 of the species.     

Easy differentiation of Mycobacterium mucogenicum from other species of the Mycobacterium fortuitum complex by thin-layer and gas chromatography of fatty esters and alcohols

The mycolate pattern of a recently recognized mycobacterial pathogen, Mycobacterium mucogenicum (formerly Mycobacterium chelonae-like organism), was established for the first time. The reference strains, together with 31 environmental and clinical isolates belonging to this species, were examined for their mycolate composition by thin-layer chromatography. All strains tested exhibited the same mycolate profile. Mycolates were identified as belonging to the type without additional oxygenated chemical groups (mycolate I) and the type with a dicarboxylic group (mycolate VI); the identification of the latter was reinforced by the presence of 2-octadecanol, as seen by gas-liquid capillary chromatography. This mycolate profile permits the clear differentiation of M. mucogenicum from other related species, as members of the Mycobacterium fortuitum complex. This fact is especially important because strains of M. mucogenicum are very difficult to differentiate from other species of the M. fortuitum complex by means of conventional biochemical tests. Moreover, the characteristic mycolate profile exhibited by the strains of M. mucogenicum supports the recent proposal which considers them as members of a new species.     

Diurnal and seasonal changes in blood composition of the free-living Egyptian fruit bat (Rousettus aegyptiacus)

We studied the blood profile of the free-living fruit bat (Rousettus aegyptiacus) during the beginning of the activity period (around various feeding trees) and upon return to the day roost during 1994–1995. Results of the present study suggest that during winter and early spring bats are characterized by a poor physical and physiological state as reflected in the blood profile, revealing elevated urea and uric acid concentrations. It was found that at the end of the resting phase, R. aegyptiacus was in a mild state of dehydration (increased hematocrit and hemoglobin levels). At the end of activity, upon return to the day roost, both hematocrit and hemoglobin levels decreased but bats still maintained a high plasma osmolality. Several components in the blood are effected by the feeding time and show a cyclic change in concentration. The reverse relationship between glucose and triglyceride levels may indicate that glucose is the energy source during the active phase and that fat is the energy source during the resting period. The low cholesterol level in the blood reflects its absence in the fruit diet. Accepted: 5 February 1999     

A study of the anti‐plasmodium activity of angiotensin II analogs

Controlling the dissemination of malaria requires the development of new drugs against its etiological agent, a protozoan of the Plasmodium genus. Angiotensin II and its analog peptides exhibit activity against the development of immature and mature sporozoites of Plasmodium gallinaceum. In this study, we report the synthesis and characterization of angiotensin II linear and cyclic analogs with anti‐plasmodium activity. The peptides were synthesized by a conventional solid‐phase method on Merrifield's resin using the t‐Boc strategy, purified by RP‐HPLC and characterized by liquid chromatography/ESI (+) MS (LC‐ESI(+)/MS), amino acid analysis, and capillary electrophoresis. Anti‐plasmodium activity was measured in vitro by fluorescence microscopy using propidium iodine uptake as an indicator of cellular damage. The activities of the linear and cyclic peptides are not significantly different (p < 0.05). Kinetics studies indicate that the effects of these peptides on plasmodium viability overtime exhibit a sigmoidal profile and that the system stabilizes after a period of 1 h for all peptides examined. The results were rationalized by partial least‐square analysis, assessing the position‐wise contribution of each amino acid. The highest contribution of polar amino acids and a Lys residue proximal to the C‐terminus, as well as that of hydrophobic amino acids in the N‐terminus, suggests that the mechanism underlying the anti‐malarial activity of these peptides is attributed to its amphiphilic character. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.     

Effect of Vernalization and Red Light Illumination of Seedlings of Bread Wheat (Triticum aestivum L.) on the Temperature Profile of cAMP Phosphodiesterase Activity

Phenotypic manifestations of Vrn(vernalization) and Ppd (photoperiod) genes responsible for transition of bread wheat Triticum aestivumL. to generative growth (flowering) are mutually related. Since the mechanism of phytochrome-induced photoperiodism involves the enzymes of cyclic adenosine monophosphate metabolism, and phosphodiesterase in particular, we tested involvement of phosphodiesterase in the process of winter wheat vernalization and formation of flowering competence in alternate wheat requiring a long photoperiod but no vernalization for its transition to flowering. We studied temperature dependence of phosphodiesterase activity in vernalized and unvernalized winter wheat on the one hand and in etiolated and red light illuminated seedlings of alternate wheat on the other hand. Short-term experiments demonstrated that red light illumination is similar to long photoperiod by the effect on the long-day plants. Both influences induced a pronounced inversion of the temperature profile of phosphodiesterase activity in the 28–45°C range. We propose that phosphodiesterase is involved in vernalization and can serve as a receptor of low temperature in winter wheat. Changed temperature profile is a radical control mechanism of phosphodiesterase activity in response to the influences (red light and vernalizing temperatures) responsible for competence of various bread wheat forms for generative growth.     

Studies on the transmission of some Fusarium spp. to potato progeny tubers from mother plants and its biological control

Fusarium spp. attack potato roots causing root-rot, damping-off and wilt disease in Assuit Governorate. Forty-five Fusarium isolates were isolated from F. nygamai, F. acutatum, F. solani, F. proliferatum, F. subglutinans, and F. oxysporum. Isolates were tested for their pathogenic capability on Burn potato variety during growing season 2007/2008. Isolates infect potato plants causing either damping-off or wilt symptoms. Isolates varied in their virulence. Role of potato tuber seed in the transmission of the causal pathogen to daughter using Electrophoresis. Protein profiles of the tested isolates divided into four sub-clusters at similarity levels 93.79, 91.55 and 92.62% while isolate of Fusarium profile No. 11 formed separate sub-clusters at similarity level 69.79%. F. nygamai and F. solani were notable exception because profile No. 4 of F. nygamai from roots and profile No. 4 from sprouts were almost identical (similarity level 96.81%); similarity level between profile No. 8 from roots and profile no/8 from sprouts was 95.44%. Results prove that F. nygamai and F. solani are potato tuber seed-borne fungus. T. harzianum, T. viride, T. longibrachiatum, G. virens and E. nigrum or its filtrate inhibited the growth of F. nygamai, F. acutatum, F. solani, F. proliferatum, F. subglutinans and F. oxysporum. The formulation of T. harzianum, T. longibrachiatum and G. virens against tested pathogenic fungi reduce disease incidence under greenhouse conditions.     

Detection of Methicillin-Resistant Staphylococcus aureus Using mecA/nuc Genes and Antibiotic Susceptibility Profile of Malaysian Clinical Isolates

The aim of this study is to compare methicillin-resistant Staphylococcus aureus (MRSA) detection methods and to generate antibiogram profile of S. aureus clinical isolates from two teaching hospitals in Malaysia including three reference isolates from American Type Culture Collection (ATCC). The mecA/nuc gene PCR amplification, spot inoculation test and oxacillin disc diffusion test were applied to compare its MRSA detection abilities. No disagreement between the three methods was observed. From 29 bacterial isolates (including the ATCC strains) tested, 19 isolates were confirmed as S. aureus with 14 isolates exhibiting multidrug-resistance. All isolates are still susceptible to vancomycin as indicated by the E-test result. Current biochemical tests are comparable with the molecular detection method for MRSA used in this study while multidrug-resistance traits are present in both MRSA and MSSA clinical isolates. Presently, mupirocin seems to be the best alternative for vancomycin against multidrug-resistant S. aureus infections in Malaysia. Susceptibility profile of 19 S. aureus isolates acquired from two teaching hospitals and ATCC towards 16 selected antibiotics was analyzed and an antibiogram was generated. Findings also indicated resistance against many of the available antibiotics and thus an urgent need to search for alternative antibiotics.     

Stromatoporoid palaeoecology in the Frasnian (Upper Devonian) Belgian platform,and its applications in interpretation of carbonate platform environments

Abstract: Stromatoporoid faunas in the Frasnian of southern Belgium are abundant in the carbonate platform environments present in this area. Stromatoporoids dominate the large skeletal organisms and occur principally in biostromes. The stromatoporoid assemblage is represented by a small number of taxa. Stromatoporoid genera include Actinostroma, Amphipora, Atelodictyon, Clathrocoilona, Salairella, Stachyodes, Stictostroma, Stromatopora and Trupetostroma which are present in environments ranging from the outer, outer intermediate, inner intermediate and inner zones and associated biostromes. Most large skeletal stromatoporoids are low profile, which reinforces the conclusions of previous studies that low‐profile growth forms were the most successful stromatoporoid forms. These low‐profile forms are likely to have been important sediment stabilisers that may have led to expansion of the carbonate factory. Growth forms vary between facies, indicating some degree of environmental control on form; for example, laminar in the intermediate zone, bulbous and domical in the inner and outer zones. Stromatoporoid taxa vary in occurrence across the environmental gradient from shallow to deep. There is some taxonomic control on growth forms, with some taxa showing more variability than others in different environments.