Identification of Races of Selected Isolates of Uromyces appendiculatus from Minas Gerais (Brazil) Based on the new international classification system

Twelve single-pustule isolates of Uromyces appendiculatus, the etiological agent of common bean rust, were collected in the state of Minas Gerais, Brazil, and classified according to the new international differential series and the binary nomenclature system proposed during the 3rd Bean Rust Workshop. These isolates have been used to select rust-resistant genotypes in a bean breeding program conducted by our group. The twelve isolates were classified into seven different physiological races: 21-3, 29-3, 53-3, 53-19, 61-3, 63-3 and 63-19. Races 61-3 and 63-3 were the most frequent in the area. They were represented by five and two isolates, respectively. The other races were represented by just one isolate. This is the first time the new international classification procedure has been used for U. appendiculatus physiological races in Brazil. The general adoption of this system will facilitate information exchange, allowing the cooperative use of the results obtained by different research groups throughout the world. The differential cultivars Mexico 309, Mexico 235 and PI 181996 showed resistance to all of the isolates that were characterized. It is suggested that these cultivars should be preferentially used as sources for resistance to rust in breeding programs targeting development lines adapted to the state of Minas Gerais.

Identification of hemolytic and neuroactive fractions in the venom of the sea anemone Bunodosoma cangicum

Sea anemones are a rich source of biologically active substances. In crayfish muscle fibers, Bunodosoma cangicum whole venom selectively blocks the I K(Ca) currents. In the present study, we report for the first time powerful hemolytic and neuroactive effects present in two different fractions obtained by gel-filtration chromatography from whole venom of B. cangicum. A cytolytic fraction (Bcg-2) with components of molecular mass ranging from 8 to 18 kDa elicited hemolysis of mouse erythrocytes with an EC50 = 14 ��g/ml and a maximum dose of 22 ��g/ml. The effects of the neuroactive fraction, Bcg-3 (2 to 5 kDa), were studied on isolated crab nerves. This fraction prolonged the compound action potentials by increasing their duration and rise time in a dose-dependent manner. This effect was evident after the washout of the preparation, suggesting the existence of a reversible substance that was initially masking the effects of an irreversible one. In order to elucidate the target of Bcg-3 action, the fraction was applied to a tetraethylammonium-pretreated preparation. An additional increase in action potential duration was observed, suggesting a blockade of a different population of K+ channels or of tetraethylammonium-insensitive channels. Also, tetrodotoxin could not block the action potentials in a Bcg-3-pretreated preparation, suggesting a possible interaction of Bcg-3 with Na+ channels. The present data suggest that B. cangicum venom contains at least two bioactive fractions whose activity on cell membranes seems to differ from the I K(Ca) blockade described previously.

Identification of Albizia lebbeck seed coat chitin-binding vicilins (7S globulins) with high toxicity to the larvae of the bruchid Callosobruchus maculatus

Seed coat is a specialized maternal tissue that interfaces the embryo and the external environment during embryogenesis, dormancy and germination. In addition, it is the first defensive barrier against penetration by pathogens and herbivores. Here we show that Albizia lebbeck seed coat dramatically compromises the oviposition, eclosion and development of the bruchid Callosobruchus maculatus. Dietary supplementation of bruchid larvae with A. lebbeck seed coat flour causes severe weight loss and reduces survival. By means of protein purification, mass spectrometry and bioinformatic analyses, we show that chitin-binding vicilins are the main source of A. lebbeck tegumental toxicity to C. maculatus. At concentrations as low as 0.1%, A. lebbeck vicilins reduce larval mass from 8.1 �� 1.7 (mass of control larvae) to 1.8 �� 0.5 mg, which corresponds to a decrease of 78%. Seed coat toxicity constitutes an efficient defense mechanism, hindering insect predation and preventing embryo damage. We hypothesize that A. lebbeck vicilins are good candidates for the genetic transformation of crop legumes to enhance resistance to bruchid predation.

Identification of main contamination points by hygiene indicator microorganisms in beef processing plants

The microbiological quality of beef and meat products is strongly influenced by the conditions of hygiene prevailing during their production and handling. Without proper hygienic control, the environment in slaughterhouses and butcher shops can act as an important source of microbiological contamination. To identify the main points of microbiological contamination in the beef processing chain, 443 samples of equipment, installations and products were collected from 11 establishments (1 slaughterhouse and 10 butcher shops) located in the state of Paran��, Brazil. The microbiological quality of all the samples was evaluated using Petri dishes to obtain counts of mesophilic aerobes (AC), total coliforms, Escherichia coli (EC), yeasts and molds (YM). The main contamination points identified in butcher shops, in decreasing order, were stainless steel boxes, beef tenderizers, grinders, knives, mixers, sausage stuffers, plastic boxes, floors and drains. In the slaughterhouse, these points were sausage stuffers, platforms, floors and drains. The most severely contaminated products were fresh sausages and ground beef. This information about the main points of microbiological contamination in the beef processing chain is expected to aid professionals responsible for hygiene in similar establishments to set up proper hygienic procedures to prevent or reduce microbiological contamination of beef and meat products.

Identification and characterisation of phenolic compounds extracted from Moroccan olive mill wastewater

Olive mill wastewater, hereafter noted as OMWW was tested for its composition in phenolic compounds according to geographical areas of olive tree, i.e. the plain and the mountainous areas of Tadla-Azilal region (central Morocco). Biophenols extraction with ethyl acetate was efficient and the phenolic extract from the mountainous areas had the highest concentration of total phenols' content. Fourier-Transform-Middle Infrared (FT-MIR) spectroscopy of the extracts revealed vibration bands corresponding to acid, alcohol and ketone functions. Additionally, HPLC-ESI-MS analyses showed that phenolic alcohols, phenolic acids, flavonoids, secoiridoids and derivatives and lignans represent the most abundant phenolic compounds. N��zhenide, naringenin and long chain polymeric substances were also detected. Mountainous areas also presented the most effective DPPH scavenging potential compared to plain areas; IC50 values were 11.7 �� 5.6 ��g/ml and 30.7 �� 4.4 ��g/ml, respectively. OMWW was confirmed as a rich source of natural phenolic antioxidant agents.

The identification and characterization of inter- and intra-species genetic diversity derived from retrotransposons in humans

Retrotransposons, which used to be considered as ���junk DNA���, have begun to reveal their immense value to genome evolution and human biology due to recent studies. They consist of at least ~45% of the human genome and are more or less the same in other mammalian genomes. Retrotransposon elements (REs) are known to affect the human genome through many different mechanisms, such as generating insertion mutations, genomic instability, and alteration in gene expression. Previous studies have suggested several RE subfamilies, such as Alu, L1, SVA and LTR, are currently active in the human genome, and they are an important source of genetic diversity between human and other primates, as well as among humans. Although several groups had used Retrotransposon Insertion Polymorphisms (RIPs) as markers in studying primate evolutionary history, no study specifically focused on identifying Human-Specific Retrotransposon Element (HS-RE) and their roles in human genome evolution. In this study, by computationally comparing the human genome to 4 primate genomes, we identified a total of 18,860 HS-REs, among which are 11,664 Alus, 4,887 L1s, 1,526 SVAs and 783 LTRs (222 full length entries), representing the largest and most comprehensive list of HS-REs generated to date. Together, these HS-REs contributed a total of 14.2Mb sequence increase from the inserted REs and Target Site Duplications (TSDs), 71.6Kb increase from transductions, and 268.2 Kb sequence deletion of from insertion-mediated deletion, leading to a net increase of ~14 Mb sequences to the human genome. Furthermore, we observed for the first time that Y chromosome might be a hot target for new retrotransposon insertions in general and particularly for LTRs. The data also allowed for the first time the survey of frequency of TE insertions inside other TEs in comparison with TE insertion into none-TE regions. In summary, our data suggest that retrotransposon elements have played a significant role in the evolution of Homo sapiens.

Identification and characterization of a Catharanthus roseus mutant altered in monoterpenoid indole alkaloid biosynthesis

The Madagascar periwinkle [Catharanthus roseus (L.) G. Don] is a commercially important horticultural flower species and is the only source for several pharmaceutically valuable monoterpenoid indole alkaloids (MIAs), including the powerful antihypertensive ajmalicine and the antineoplastic agents vincristine and vinblastine. While biosynthesis of MIA precursors has been elucidated, conversion of the common MIA precursor strictosidine to MIAs of different families, for example ajmalicine, catharanthine or vindoline, remains uncharacterized. Deglycosylation of strictosidine by the key enzyme Strictosidine beta-glucosidase (SGD) leads to a pool of uncharacterized reaction products that are diverted into the different MIA families, but the downstream reactions are uncharacterized. Screening of 3600 EMS (ethyl methane sulfonate) mutagenized C. roseus plants to identify mutants with altered MIA profiles yielded one plant with high ajmalicine, and low catharanthine and vindoline content. RNA sequencing and comparative bioinformatics of mutant and wildtype plants showed up-regulation of SGD and the transcriptional repressor Zinc finger Catharanthus transcription factor (ZCT1) in the mutant line. The increased SGD activity in mutants seems to yield a larger pool of uncharacterized SGD reaction products that are channeled away from catharanthine and vindoline towards biosynthesis of ajmalicine when compared to the wildtype. Further bioinformatic analyses, and crossings between mutant and wildtype suggest a transcription factor upstream of SGD and ZCT1 to be mutated, leading to up-regulation of Sgd and Zct1. The crossing experiments further show that biosynthesis of the different MIA families is differentially regulated and highly complex. Three new transcription factors were identified by bioinformatics that seem to be involved in the regulation of Zct1 and Sgd expression, leading to the high ajmalicine phenotype. Increased cathenamine reductase activity in the mutant converts the pool of SGD reaction products into ajmalicine and its stereoisomer tetrahydroalstonine. The stereochemistry of ajmalicine and tetrahydroalstonine biosynthesis in vivo and in vitro was further characterized. In addition, a new clade of perakine reductase-like enzymes was identified that reduces the SGD reaction product vallesiachotamine in a stereo-specific manner, characterizing one of the many reactions immediately downstream of SGD that determine the different MIA families. This study establishes that RNA sequencing and comparative bioinformatics, in combination with molecular and biochemical characterization, are valuable tools to determine the genetic basis for mutations that trigger phenotypes, and this approach can also be used for identification of new enzymes and transcription factors.

Identification et localisation des pr��occupations fonctionnelles dans un code l��gataire Java

Traditionnellement, les applications orient��es objets l��gataires int��grent diff��rents aspects fonctionnels. Ces aspects peuvent ��tre dispers��s partout dans le code. Il existe diff��rents types d���aspects : ��� des aspects qui repr��sentent des fonctionnalit��s m��tiers ; ��� des aspects qui r��pondent �� des exigences non fonctionnelles ou �� d���autres consid��rations de conception comme la robustesse, la distribution, la s��curit��, etc. G��n��ralement, le code qui repr��sente ces aspects chevauche plusieurs hi��rarchies de classes. Plusieurs chercheurs se sont int��ress��s �� la probl��matique de la modularisation de ces aspects dans le code : programmation orient��e sujets, programmation orient��e aspects et programmation orient��e vues. Toutes ces m��thodes proposent des techniques et des outils pour concevoir des applications orient��es objets sous forme de composition de fragments de code qui r��pondent �� diff��rents aspects. La s��paration des aspects dans le code a des avantages au niveau de la r��utilisation et de la maintenance. Ainsi, il est important d���identifier et de localiser ces aspects dans du code l��gataire orient�� objets. Nous nous int��ressons particuli��rement aux aspects fonctionnels. En supposant que le code qui r��pond �� un aspect fonctionnel ou fonctionnalit�� exhibe une certaine coh��sion fonctionnelle (d��pendances entre les ��l��ments), nous proposons d���identifier de telles fonctionnalit��s �� partir du code. L���id��e est d���identifier, en l���absence des paradigmes de la programmation par aspects, les techniques qui permettent l���impl��mentation des diff��rents aspects fonctionnels dans un code objet. Notre approche consiste �� : ��� identifier les techniques utilis��es par les d��veloppeurs pour int��grer une fonctionnalit�� en l���absence des techniques orient��es aspects ��� caract��riser l���empreinte de ces techniques sur le code ��� et d��velopper des outils pour identifier ces empreintes. Ainsi, nous pr��sentons deux approches pour l���identification des fonctionnalit��s existantes dans du code orient�� objets. La premi��re identifie diff��rents patrons de conception qui permettent l���int��gration de ces fonctionnalit��s dans le code. La deuxi��me utilise l���analyse formelle de concepts pour identifier les fonctionnalit��s r��currentes dans le code. Nous exp��rimentons nos deux approches sur des syst��mes libres orient��s objets pour identifier les diff��rentes fonctionnalit��s dans le code. Les r��sultats obtenus montrent l���efficacit�� de nos approches pour identifier les diff��rentes fonctionnalit��s dans du code l��gataire orient�� objets et permettent de sugg��rer des cas de refactorisation.

Isolation and identification of native microalgae for biodiesel production

La demande croissante en carburants, ainsi que les changements climatiques dus au r��chauffement plan��taire poussent le monde entier �� chercher des sources d�����nergie capables de produire des combustibles alternatifs aux combustibles fossiles. Durant les derni��res ann��es, plusieurs sources potentielles ont ��t�� identifi��es, les premi��res �� ��tre consid��r��es sont les plantes ol��agineuses comme source de biocarburant, cependant l���utilisation de v��g��taux ou d���huiles v��g��tales ayant un lien avec l���alimentation humaine peut engendrer une hausse des prix des denr��es alimentaires, sans oublier les questions ��thiques qui s���imposent. De plus, l'usage des huiles non comestibles comme sources de biocarburants, comme l���huile de jatropha, de graines de tabac ou de jojoba, r��v��le un probl��me de manque de terre arable ce qui oblige �� r��duire les terres cultivables de l'industrie agricole et alimentaire au profit des cultures non comestibles. Dans ce contexte, l'utilisation de microorganismes aquatiques, tels que les microalgues comme substrats pour la production de biocarburant semble ��tre une meilleure solution. Les microalgues sont faciles �� cultiver et peuvent croitre avec peu ou pas d'entretien. Elles peuvent ainsi se d��velopper dans des eaux douces, saum��tres ou sal��es de m��me que dans les terres non cultivables. Le rendement en lipide peut ��tre largement sup��rieur aux autres sources de biocarburant potentiel, sans oublier qu���elles ne sont pas comestibles et sans aucun impact sur l'industrie alimentaire. De plus, la culture intensive de microalgues pour la production de biodiesel pourrait ��galement jouer un r��le important dans l'att��nuation des ��missions de CO2. Dans le cache de ce travail, nous avons isol�� et identifi�� morphologiquement des esp��ces de microalgues natives du Qu��bec, pour ensuite examiner et mesurer leur potentiel de production de lipides (biodiesel). L�����chantillonnage fut r��alis�� dans trois r��gions diff��rentes du Qu��bec: la r��gion de Montr��al, la gasp��sie et le nord du Qu��bec, et dans des eaux douces, saum��tres ou sal��es. Cent souches ont ��t�� isol��es �� partir de la r��gion de Montr��al, caract��ris��es et s��lectionn��es selon la teneur en lipides et leur ��limination des nutriments dans les eaux us��es �� des temp��ratures diff��rentes (10 �� 2��C et 22 �� 2��C). Les esp��ces ayant une production potentiellement ��lev��e en lipides ont ��t�� s��lectionn��es. L���utilisation des eaux us��es, comme milieu de culture, diminue le co��t de production du biocarburant et sert en m��me temps d'outil pour le traitement des eaux us��es. Nous avons compar�� la biomasse et le rendement en lipides des souches cultiv��es dans une eau us��e par apport �� ceux dans un milieu synth��tique, pour finalement identifi�� un certain nombre d'isolats ayant montr�� une bonne croissance �� 10��C, voir une teneur ��lev��e en lipides (allant de 20% �� 45% du poids sec) ou une grande capacit�� d'��limination de nutriment (>97% d'��limination). De plus, nous avons caract��ris�� l'une des souches int��ressantes ayant montr�� une production en lipides et une biomasse ��lev��e, soit la microalgue Chlorella sp. PCH90. Isol��e au Qu��bec, sa phylog��nie mol��culaire a ��t�� ��tablie et les ��tudes sur la production de lipides en fonction de la concentration initiale de nitrate, phosphate et chlorure de sodium ont ��t�� r��alis��es en utilisant de la m��thodologie des surfaces de r��ponse. Dans les conditions appropri��es, cette microalgue pourrait produire jusqu'�� 36% de lipides et croitre �� la fois dans un milieu synth��tique et un milieu issu d'un flux secondaire de traitement des eaux us��es, et cela �� 22��C ou 10��C. Ainsi, on peut conclure que cette souche est prometteuse pour poursuivre le d��veloppement en tant que productrice potentielle de biocarburants dans des conditions climatiques locales.

Ecological and Biochemical Studies On Cyanobacteria of Cochin Estuary and Their Application as Source of Antioxidants

The main objectives of the present investigation were to evaluate the qualitative and quantitative distribution of natural cyanobacterial population and their ecobiological properties along the Cochin estuary and their application in aquaculture systems as a nutritional supplement due to their nutrient-rich biochemical composition and antioxidant potential. This thesis presents a detailed account of the distribution of cyanobacteria in Cochin estuary, an assessment of physico-chemical parameters and the nutrients of the study site, an evaluation of the effect of physico-chemical parameters on cyanobacterial distribution and abundance, isolation, identification and culturing of cyanobacteria, the biochemical composition an productivity of cyanobacteria, and an evaluation of the potential of the selected cyanobacteria as antioxidants against ethanol induced lipid peroxidation. The pH, salinity and nutritional requirements were optimized for low-cost production of the selected cyanobacterial strains. The present study provides an insight into the distribution, abundance, diversity and ecology of cyanobacteria of Cochin estuary. From the results, it is evident that the ecological conditions of Cochin estuary support a rich cyanobacterial growth.

Code clones in program test sequence identification

Code clones are portions of source code which are similar to the original program code. The presence of code clones is considered as a bad feature of software as the maintenance of software becomes difficult due to the presence of code clones. Methods for code clone detection have gained immense significance in the last few years as they play a significant role in engineering applications such as analysis of program code, program understanding, plagiarism detection, error detection, code compaction and many more similar tasks. Despite of all these facts, several features of code clones if properly utilized can make software development process easier. In this work, we have pointed out such a feature of code clones which highlight the relevance of code clones in test sequence identification. Here program slicing is used in code clone detection. In addition, a classification of code clones is presented and the benefit of using program slicing in code clone detection is also mentioned in this work.

Perceptual compensation for effects of echo and of reverberation on speech identification

In an ideal "reverberant" room, the energy of the impulse responses decays smoothly, at a constant rate of dB/s, so that gradually-decaying tails are added at the ends of sounds. Conversely, a single echo gives a flat energy-decay up to the echo's arrival time, which then drops abruptly, so that sounds with only echoes lack the decaying-tail feature of reverberation. The perceptual effects of these types of reflection pattern were measured with test-words from a continuum of steps between "sir" and "stir", which were each embedded in a carrier phrase. When the proportion of reflected sound in test-words is increased, to a level above the amount in the carrier, the test words sound more like "sir". However, when the proportion of reflected sound in the carrier is also increased, to match the amount in the test word, there can be a perceptual compensation where test words sound more like "stir" again. A reference condition used real-room reverberation from recordings at different source to receiver distances. In a synthetic-reverberation condition, the reflection pattern was from a "colorless" impulse response, comprising exponentially-decaying reflections that were spaced at intervals. In a synthetic-echo condition, the reflection pattern was obtained from the synthetic reverberation by removing the intervals between reflections before delaying the resulting cluster relative to the direct sound. Compensation occurred in the reference condition and in different types of synthetic reverberation, but not in synthetic-echo conditions. This result indicates that the presence of tails from reverberation informs the compensation mechanism.

Identification of components of the Sigma B Regulon in Listeria monocytogenes that contribute to acid and salt tolerance

Sigma B (��B) is an alternative sigma factor that controls the transcriptional response to stress in Listeria monocytogenes and is also known to play a role in the virulence of this human pathogen. In the present study we investigated the impact of a sigB deletion on the proteome of L. monocytogenes grown in a chemically defined medium both in the presence and in the absence of osmotic stress (0.5 M NaCl). Two new phenotypes associated with the sigB deletion were identified using this medium. (i) Unexpectedly, the strain with the ��sigB deletion was found to grow faster than the parent strain in the growth medium, but only when 0.5 M NaCl was present. This phenomenon was independent of the carbon source provided in the medium. (ii) The ��sigB mutant was found to have unusual Gram staining properties compared to the parent, suggesting that ��B contributes to the maintenance of an intact cell wall. A proteomic analysis was performed by two-dimensional gel electrophoresis, using cells growing in the exponential and stationary phases. Overall, 11 proteins were found to be differentially expressed in the wild type and the ��sigB mutant; 10 of these proteins were expressed at lower levels in the mutant, and 1 was overexpressed in the mutant. All 11 proteins were identified by tandem mass spectrometry, and putative functions were assigned based on homology to proteins from other bacteria. Five proteins had putative functions related to carbon utilization (Lmo0539, Lmo0783, Lmo0913, Lmo1830, and Lmo2696), while three proteins were similar to proteins whose functions are unknown but that are known to be stress inducible (Lmo0796, Lmo2391, and Lmo2748). To gain further insight into the role of ��B in L. monocytogenes, we deleted the genes encoding four of the proteins, lmo0796, lmo0913, lmo2391, and lmo2748. Phenotypic characterization of the mutants revealed that Lmo2748 plays a role in osmotolerance, while Lmo0796, Lmo0913, and Lmo2391 were all implicated in acid stress tolerance to various degrees. Invasion assays performed with Caco-2 cells indicated that none of the four genes was required for mammalian cell invasion. Microscopic analysis suggested that loss of Lmo2748 might contribute to the cell wall defect observed in the ��sigB mutant. Overall, this study highlighted two new phenotypes associated with the loss of ��B. It also demonstrated clear roles for ��B in both osmotic and low-pH stress tolerance and identified specific components of the ��B regulon that contribute to the responses observed.

Source splitting via the point source method

We introduce a new algorithm for source identification and field splitting based on the point source method (Potthast 1998 A point-source method for inverse acoustic and electromagnetic obstacle scattering problems IMA J. Appl. Math. 61 119���40, Potthast R 1996 A fast new method to solve inverse scattering problems Inverse Problems 12 731���42). The task is to separate the sound fields uj, j = 1, ..., n of sound sources supported in different bounded domains G1, ..., Gn in from measurements of the field on some microphone array���mathematically speaking from the knowledge of the sum of the fields u = u1 + + un on some open subset �� of a plane. The main idea of the scheme is to calculate filter functions , to construct u��� for ��� = 1, ..., n from u|�� in the form We will provide the complete mathematical theory for the field splitting via the point source method. In particular, we describe uniqueness, solvability of the problem and convergence and stability of the algorithm. In the second part we describe the practical realization of the splitting for real data measurements carried out at the Institute for Sound and Vibration Research at Southampton, UK. A practical demonstration of the original recording and the splitting results for real data is available online.

The neurochemically diverse intermedius nucleus of the medulla as a source of excitatory and inhibitory synaptic input to the nucleus tractus solitarii

Sensory afferent signals from neck muscles have been postulated to influence central cardiorespiratory control as components of postural reflexes, but neuronal pathways for this action have not been identified. The intermedius nucleus of the medulla (InM) is a target of neck muscle spindle afferents and is ideally located to influence such reflexes but is poorly investigated. To aid identification of the nucleus, we initially produced three-dimensional reconstructions of the InM in both mouse and rat. Neurochemical analysis including transgenic reporter mice expressing green fluorescent protein in GABA-synthesizing neurons, immunohistochemistry, and in situ hybridization revealed that the InM is neurochemically diverse, containing GABAegric and glutamatergic neurons with some degree of colocalization with parvalbumin, neuronal nitric oxide synthase, and calretinin. Projections from the InM to the nucleus tractus solitarius (NTS) were studied electrophysiologically in rat brainstem slices. Electrical stimulation of the NTS resulted in antidromically activated action potentials within InM neurons. In addition, electrical stimulation of the InM resulted in EPSPs that were mediated by excitatory amino acids and IPSPs mediated solely by GABA(A) receptors or by GABA(A) and glycine receptors. Chemical stimulation of the InM resulted in (1) a depolarization of NTS neurons that were blocked by NBQX (2,3-dioxo-6-nitro-1,2,3,4-tetrahydrobenzo[f]quinoxaline-7-sulfonoamide) or kynurenic acid and (2) a hyperpolarization of NTS neurons that were blocked by bicuculline. Thus, the InM contains neurochemically diverse neurons and sends both excitatory and inhibitory projections to the NTS. These data provide a novel pathway that may underlie possible reflex changes in autonomic variables after neck muscle spindle afferent activation.