Structural studies on tobacco streak virus coat protein: Insights into the pleomorphic nature of ilarviruses

Tobacco streak virus (TSV), the type member of Ilarvirus genus, is a major plant pathogen. TSV purified from infected plants consists of a ss-RNA genome encapsidated in spheroidal particles with diameters of 27, 30 and 33 nm constructed from multiple copies of a single species of coat protein (CP) subunits. Apart from protecting the viral genome, CPs of ilarviruses play several key roles in the life cycle of these viruses. Unlike the related bromo and cucumoviruses, ilarvirus particles are labile and pleomorphic, which has posed difficulties in their crystallization and structure determination. In the current study, a truncated TSV-CP was crystallized in two distinct forms and their structures were determined at resolutions of 2.4 angstrom and 2.1 angstrom, respectively. The core of TSV CP was found to possess the canonical beta-barrel jelly roll tertiary structure observed in several other viruses. Dimers of CP with swapped C-terminal arms (C-arm) were observed in both the crystal forms. The C-arm was found to be flexible and is likely to be responsible for the polymorphic and pleomorphic nature of TSV capsids. Consistent with this observation, mutations in the hinge region of the C-arm that reduce the flexibility resulted in the formation of more uniform particles. TSV CP was found to be structurally similar to that of Alfalfa mosaic virus (AMV) accounting for similar mechanism of genome activation in alfamo and ilar viruses. This communication represents the first report on the structure of the CP from an ilarvirus. (C) 2015 Elsevier Inc. All rights reserved.

Letras, 2002, nº 45 (número completo)

Contenido: “Ni razón ni palabra” de Edgar Bayley: momento de transición / María Amelia Arancet Ruda – Metonimia y fantasma. Modalidades del ectoplasma en el Río de la Plata / José Mariano García – “Hombres de maíz”, una rapsodia americana / Graciela Maturo – Autobiografía y ficción en “Un verano en Tenerife” de Dulce María Loynaz / María Lucía Puppo – La condición posmoderna en la narrativa española / Analía Vélez de Villa – La armoniosa poesía de Francisco Luis Bernárdez / Gloria Videla de Rivero – Borges y Schopenhauer / Carmen Balzer – El catálogo de los ejércitos: un motivo tradicional en “The lord of the rings” / Jorge Ferro – Función y significado de las historias en “Stiller” de Max Frisch / María Esther Mangariello – La ciudad de New York a comienzos del siglo XX, bajo las miradas de Henry James y Edith Wharton / Rosa E. M. D. Penna – Reseñas bibliográficas

Sexual Reproduction and Early Development in the Estuarine Sea Anemone, Nematostella vectensis Stephenson, 1935

This dissertation: 1) determines the factor(s) responsible for spawning induction in NematosteJla vectensis; 2) isolates, describes, and documents the source of jelly from egg masses of N. vectensis; and 3) describes N. vectensis' early development. Namatostella vectensis were maintained on a 7-day mussel feeding/water change regime over 159 days. Within 36 hours of mussel feeding/water change. 69.1% of females and 78.5% of males spawned reliably. Through manipulation of feeding, water change, oxygen and nitrogenous waste concentrations, spawning induction was found to be triggered by the oxygen concentration associated with water change, and not by feeding. Ammonia, anemones' major waste product, inhibited this induction in a concentration-dependent manner. Female N. vectensis release eggs in a persistent jellied egg mass which is unique among the Actiniaria. The major component of this egg mass jelly was a positive periodic acid-Schiffs staining, 39.5-40.5 kD glycoprotein. Antibodies developed in rabbits against this glycoprotein bound to jelly of intact egg masses and to granules (~ 2.8 IJm in diameter) present in female anemone mesenteries and their associated filaments. Antibodies did not label male tissues. Nematostella vecfensis embryos underwent first karyokinesis -60 minutes following the addition of sperm to eggs. Second nuclear division took place, followed by first cleavage, 90-120 minutes later. Each of the 4 blastomeres that resulted from first cleavage contained a single nucleus. Arrangement of these blastomeres ranged from radial to pseudospiral. Embryonic development was both asynchronous and holoblastic. Following formation of the 4-cell stage, 71% of embryos proceeded to cleave again to form an 8-cell stage. In each of the remaining 29% of embryos, a fusion of from 2-4 blastomeres resulted in 4 possible patterns which had no affect on either cleavage interval timing or subsequent development. The fusion event was not due to ooplasmic segregation. Blastomeres isolated from 4-celled embryos were regulative and developed into normal planula larvae and juvenile anemones that were 1/4 the size of those that developed from intact 4-celled embryos. Embryos exhibiting the fusion phenomenon were examined at the fine structural level. The fusion phenomenon resulted in formation of a secondary syncytium and was not a mere compaction of blastomeres.

Electric fishing survey of the gravel addition sites on the River Wyre, Grizedale Beck and Joshua's Beck.

Although geographically the River Wyre lies between two rivers containing major migrations of adult salmon and sea trout, its rod & line fisheries have for a number of years produced exceptionally low catches. In order to determine the causes of this the Wyre Salmon and Sea trout Restoration Group (WSSRG) was conceived in 1994 as a partnership between the then National Rivers Authority (now Environment Agency), local landowners, angling clubs and interested parties. Two studies of 1994 and 1995 stated that there is a shortage of useable spawning gravels on the river. This is compounded by Abbeystead Reservoir acting as a gravel trap, the siltation of gravels on several side becks and problems with access to available gravels by returning adults. There was also perceived to be a need for accurate fishery data from the river encompassing redd counts, catch data and surveys of fry populations. The 1995 report suggested a number of management proposals which might be adopted in order to improve and create available spawning habitat for migratory salmonids. Funding was made available to create three spawning gravels on each of two side becks (Grizedale Beck and Joshua's Beck) and the addition of gravels to a site oh the main river below Abbeystead Reservoir. Modifications were also made to the fish pass at Abbeystead to allow easier passage of fish. These improvements were made in the autumn of 1995. Salmonid spawning redd counting was undertaken on the whole Wyre catchment in 1995/1996 and specific surveys by electric fishing on the gravel enhancement sites in the summer of 1996. This report details the current state of the improvement works that were undertaken and presents the results of electric fishing surveys in September 1996. A number of lessons have been learnt which will be of great benefit to the Fisheries Function in other parts of the Wyre catchment and the Central Area in general.

A preliminary account and review of the simple methods for determining the operational parameters of fishing gear, underwater, with notes on its application

An account and review of the simple methods for determining the operational parameters of fishing gear, underwater, such a tilt of otter boards (outwards or inwards, forwards or afterwards), vertical height of net, its horizontal spread, angle of divergence at bosom, spread between wing tips, angle of inclination of danlenos, butterfly, slope of legs and sweep-line has been given. The relationship of distance between the otter boards spread and the vertical height of net has been obtained as generally linear. The possibilities of regulating the vertical height of net (dependent variate) and spread of otter boards (independent variate) for increasing the fishing efficiency has been discussed. The angle of attack of oval shaped otter boards used during the operations still remain undetermined, however, it has been explained how the best angle of attack for increasing the efficiency of gear can be obtained by regulating the ratio of depth to warp for a given net. The inadequacy of the mere indices of catch per hour of trawling in comparing the relative efficiency of trawls in gear research studies has been indicated. The importance of estimating the operational parameters and its application to commercial fisheries depending upon the distribution pattern of fish and in gear research has been discussed. The efficiency of the jelly bottle method has been compared statistically with the observations made on the trawl gear underwater with instruments.

Small scale manufacture of crude agar from Gracilaria seaweeds

A simplified process was worked out to prepare crude agar from red seaweeds (Gracilaria sp.). The process required careful preliminary cleaning and bleaching (sun-drying) of the weed. The agar was extracted by boiling with water in a mixture (2%) strong enough to set as a jelly. Freezing the jelly over a 3—day period in an ice-making machine, adjusted to work slowly, separated out ice and agar. The blocks were thawed out and the agar dried in the sun. The efficiency of extraction was over 800/A.

Agar from Gracilaria lichenoides and Gracilaria confervoides from Ceylon

"Agar-agar" is a name derived from the jelly obtained from certain red algae in Malaya. In Sri Lanka agar is prepared from the red seaweeds Gracilaria confervoides and Gracilaria lichenoides. They are commonly known as Sri Lanka moss and the local names are "kandha parsi or sanchow parsi". The uses of agar are given together with details of the method of extraction of this substance from Gracilaria lichenoides and Gracilaria confervoides.

Sequential analysis for testing quality standard of fish ham and sausage

Fish sausages are finely ground fish flesh, either of a single species or mixed, homogenised with starch, sugar, fat, spices and preservatives, generally filled in cylindrical synthetic or natural casings and pasteurised. Similar products containing small pieces of quality fish and lard are termed "fish ham". They are highly relished products in Japan, annual consumption exceeding 2 lakh tones. Preliminary studies have shown that they can catch a lucrative market in our country. However, being a pasteurised product which is often consumed as such without any further cooking, strict quality control measures have to be enforced so as to avoid food poisoning hazards. Besides physical characteristics like absence of damages, pin-holes, curliness and air pockets as well as jelly strength, texture and flavour, chemical characteristics like pH and acid values, moisture, carbohydrate and fat contents and volatile bases have to be assessed. A very important test that has to be carried out along with the above, before passing a lot for free distribution is the bacteriological examination to avoid the presence of pathogenic organisms.

High temperature processing of fish sausage 3. - Studies on some of the storage characteristics

The proximate composition of the high temperature processed fish sausage was found to be 14.56% protein, 4.65% fat, 69.14% moisture, 2.12% ash and 8.12% carbohydrate. The quality of the product during storage was assessed on the basis of the changes observed in the physical, chemical and microbiological parameters. The results of the different tests such as pH, volatile base nitrogen (VBN), trimethyl amine nitrogen (TMA-N) and jelly strength are summarized and discussed. The total bacterial load increased gradually during storage but was not proportional to the initial load.

A novel C1q-domain-containing protein from Zhikong scallop Chlamys farreri with lipopolysaccharide binding activity

The C1q-domain-containing (C1qDC) proteins are a family of proteins characterized by a globular C1q (gC1q) domain in their C-terminus. They are involved in various processes of vertebrates and supposed to be an important pattern recognition receptor in innate immunity of invertebrates. In this study, a novel member of C1q-domain-containing protein family was identified from Zhikong scallop Chlamys farreri (designated as CfC1qDC) by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) approaches. The full-length cDNA of CfC1qDC was of 777 bp, consisting of a T-terminal untranslated region (UTR) of 62 bp and a 3' UTR of 178 bp with a polyadenylation signal sequence AATAAA and a poly (A) tail. The CfC1qDC cDNA encoded a polypeptide of 178 amino acids, including a signal peptide and a C1q-domain of 158 amino acids with the theoretical isoelectric point of 5.19 and the predicted molecular weight of 17.2 kDa. The C1q-domain in CfC1qDC exhibited homology with those in sialic acid binding lectin from mollusks and C1qDC proteins from higher vertebrates. The typical 10 beta-strand jelly-roll folding topology structure of C1q-domain and the residues essential for effective packing of the hydrophobic core were well conserved in CfC1qDC. By fluorescent quantitative real-time PCR, mRNA transcripts of CfC1qDC were mainly detected in kidney, mantle, adductor muscle and gill, and also marginally detectable in hemocytes. In the bacterial challenge experiment, after the scallops were challenged by Listonella anguillarum, there was a significant up-regulation in the relative expression level of CfC1qDC and at 6 h post-injection, the mRNA expression reached the maximum level and was 4.55-fold higher than that of control scallops. Similarly, the expression of CfC1qDC mRNA in mixed primary cultures of hemocytes stimulated by lipopolysaccharides (LPS) was up-regulated and reached the maximum level at 6 h post-stimulation, and then dropped back to the original level gradually. In order to investigate its function, the cDNA fragment encoding the mature peptide of CfC1qDC was recombined and expressed in Escherichia coli BL21 (DE3). The recombinant CfC1qDC protein displayed a significantly strong activity to bind LIDS from E. coli, although no obvious antibacterial or agglutinating activity toward Gram-negative bacteria E. coli JM109, L. anguillarum and Gram-positive bacteria Micrococcus luteus was observed. These results suggested that CfC1qDC was absolutely a novel member of the C1qDC protein family and was involved in the recognition of invading microorganisms probably as a pattern recognition molecule in mollusk. (c) 2008 Elsevier Ltd. All rights reserved.

AiC1qDC-1, a novel gC1q-domain-containing protein from bay scallop Argopecten irradians with fungi agglutinating activity

The globular C1q-domain-containing (C1qDC) proteins are a family of versatile pattern recognition receptors via their globular C1q (gC1q) domain to bind various ligands including several PAMPs on pathogens. In this study, a new gC1q-domain-containing protein (AiC1qDC-1) gene was cloned from Argopecten irradians by rapid amplification of cDNA ends (RACE) approaches and expressed sequence tag (EST) analysis. The full-length cDNA of AiC1qDC-1 was composed of 733 bp, encoding a signal peptide of 19 residues and a typical gC1q domain of 137 residues containing all eight invariant amino acids in human C1qDC proteins and seven aromatic residues essential for effective packing of the hydrophobic core of AiC1qDC-1. The gC1q domain of AiC1qDC-1, which possessed the typical 10-stranded beta-sandwich fold with a jelly-roll topology common to all C1q family members, showed high homology not only to those of Cl qDC proteins in mollusk but also to those of C1qDC proteins in human. The AiC1qDC-1 transcripts were mainly detected in the tissue of hepatopancreas and also marginally detectable in adductor, heart, mantle, gill and hemocytes by fluorescent quantitative real-time PCR. In the microbial challenge experiment, there was a significant up-regulation in the relative expression level of AiC1qDC-1 in hepatopancreas and hemocytes of the scallops challenged by fungi Pichia pastoris GS115, Gram-positive bacteria Micrococcus luteus and Gram-negative bacteria Listonella anguillarum. The recombinant AiC1qDC-1 (rAiC1qDC-1) protein displayed no obvious agglutination against M. luteus and L. anguillarum, but it aggregated P. pastoris remarkably. This agglutination could be inhibited by D-mannose and PGN but not by LPS, glucan or D-galactose. These results indicated that AiC1qDC-1 functioned as a pattern recognition receptor in the immune defense of scallops against pathogens and provided clues for illuminating the evolution of the complement classical pathway. (C) 2010 Elsevier Ltd. All rights reserved.

A dual role for ErbB2 signaling in cardiac trabeculation.

Cardiac trabeculation is a crucial morphogenetic process by which clusters of ventricular cardiomyocytes extrude and expand into the cardiac jelly to form sheet-like projections. Although it has been suggested that cardiac trabeculae enhance cardiac contractility and intra-ventricular conduction, their exact function in heart development has not been directly addressed. We found that in zebrafish erbb2 mutants, which we show completely lack cardiac trabeculae, cardiac function is significantly compromised, with mutant hearts exhibiting decreased fractional shortening and an immature conduction pattern. To begin to elucidate the cellular mechanisms of ErbB2 function in cardiac trabeculation, we analyzed erbb2 mutant hearts more closely and found that loss of ErbB2 activity resulted in a complete absence of cardiomyocyte proliferation during trabeculation stages. In addition, based on data obtained from proliferation, lineage tracing and transplantation studies, we propose that cardiac trabeculation is initiated by directional cardiomyocyte migration rather than oriented cell division, and that ErbB2 cell-autonomously regulates this process.

THE PERFORMER’S INFLUENCE ON FRANCO-BELGIAN COMPOSITIONS FROM 1870 TO 1930

The turn of the 20th century marked an ascendancy of the Franco-Belgian school of composers. French composers were inspired by the great German composers of the Romantic era, and they created their own defined national style that emerged toward the end of the 19th century. The Franco-Belgian composers’ special emphasis on tone, timbre and color encouraged a more individual, personally interpretative approach. These devices underscore the importance and influence a performer can have on the outcome of a piece. I researched the relationship between composers and violinists at a time when the Franco-Belgian style developed and flourished. The Franco-Belgian school of violin playing emerged from the Paris and Brussels conservatories as well as the symbiotic relationship between the performers and composers. Three recitals in collaboration with pianist David Ballena, which comprise this dissertation project, were performed at the University of Maryland. Each recital featured music for violin and piano from 1870 through 1930. The repertoire was chosen to reflect a performer’s influence on a composer. I examined specific composer/performer relationships that helped shape the birth of a newly defined “French” style of playing. My research focused on the stylistic interactions composers, such as César Franck, his disciple Guillaume Lekeu had with the leading prominent Belgian violinist Eugène Ysaye and between Maurice Ravel and the Hungarian violinist Jelly d’Aranyi. I also looked into the personal relationship between friends who inspired each other: Gabriel Fauré and Paul Viardot, Edouard Lalo and Pablo de Sarasate, Claude Debussy and Arthur Hartmann, and the young Lili Boulanger and Yvonne Astruc. Furthermore, I looked into the unfulfilled love between Maurice Ravel and Hélène Jourdan-Morhange, as well as the marriage of Olivier Messiaen with Claire Delbos, both relationships resulting in masterpieces for violin that have remained a part of the standard violin repertoire. My research led me to understand what type of violin playing each composer had in mind while composing, all of which led me to understand the importance a performer has in preserving national styles. The recitals were recorded on compact discs and archived within the Digital Repository at the University of Maryland (DRUM).

Finding our way through phenotypes.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.