Dissecting pi-helices: sequence, structure and function

A new procedure for the identification of regular secondary structures using a C-alpha trace has identified 659 pi-helices in 3582 protein chains, solved at high resolution. Taking advantage of this significantly expanded database of pi-helices, we have analysed the functional and structural roles of helices and determined the position-wise amino acid propensity within and around them. These helices range from 5 to 18 residues in length with the average twist and rise being 85.2 +/- 7.2 and 1.28 +/- 0.31 angstrom, respectively. A total of 546 (similar to 83%) out of 659 pi-helices occur in conjunction with alpha-helices, with 101 pi-helices being interspersed between two alpha-helices. The majority of interspersed pi-helices were found to be conserved across a large number of structures within a protein family and produce a significant bend in the overall helical segment as well as local distortions in the neighbouring a-helices. The presence of a pi-helical fragment leads to appropriate orientation of the constituent residues, so as to facilitate favourable interactions and also help in proper folding of the protein chain. In addition to intra helical 6 -> 1 N H center dot center dot center dot O hydrogen bonds, pi-helices are also stabilized by several other non-bonded interactions. pi-Helices show distinct positional residue preferences, which are different from those of a-helices.

Correlation equations for average deposition rate coefficients of nanoparticles in a cylindrical pore

Nanoparticle deposition behavior observed at the Darcy scale represents an average of the processes occurring at the pore scale. Hence, the effect of various pore-scale parameters on nanoparticle deposition can be understood by studying nanoparticle transport at pore scale and upscaling the results to the Darcy scale. In this work, correlation equations for the deposition rate coefficients of nanoparticles in a cylindrical pore are developed as a function of nine pore-scale parameters: the pore radius, nanoparticle radius, mean flow velocity, solution ionic strength, viscosity, temperature, solution dielectric constant, and nanoparticle and collector surface potentials. Based on dominant processes, the pore space is divided into three different regions, namely, bulk, diffusion, and potential regions. Advection-diffusion equations for nanoparticle transport are prescribed for the bulk and diffusion regions, while the interaction between the diffusion and potential regions is included as a boundary condition. This interaction is modeled as a first-order reversible kinetic adsorption. The expressions for the mass transfer rate coefficients between the diffusion and the potential regions are derived in terms of the interaction energy profile. Among other effects, we account for nanoparticle-collector interaction forces on nanoparticle deposition. The resulting equations are solved numerically for a range of values of pore-scale parameters. The nanoparticle concentration profile obtained for the cylindrical pore is averaged over a moving averaging volume within the pore in order to get the 1-D concentration field. The latter is fitted to the 1-D advection-dispersion equation with an equilibrium or kinetic adsorption model to determine the values of the average deposition rate coefficients. In this study, pore-scale simulations are performed for three values of Peclet number, Pe = 0.05, 5, and 50. We find that under unfavorable conditions, the nanoparticle deposition at pore scale is best described by an equilibrium model at low Peclet numbers (Pe = 0.05) and by a kinetic model at high Peclet numbers (Pe = 50). But, at an intermediate Pe (e.g., near Pe = 5), both equilibrium and kinetic models fit the 1-D concentration field. Correlation equations for the pore-averaged nanoparticle deposition rate coefficients under unfavorable conditions are derived by performing a multiple-linear regression analysis between the estimated deposition rate coefficients for a single pore and various pore-scale parameters. The correlation equations, which follow a power law relation with nine pore-scale parameters, are found to be consistent with the column-scale and pore-scale experimental results, and qualitatively agree with the colloid filtration theory. These equations can be incorporated into pore network models to study the effect of pore-scale parameters on nanoparticle deposition at larger length scales such as Darcy scale.

Nanomechanical Mapping, Hierarchical Polymer Dynamics, and Miscibility in the Presence of Chain-End Grafted Nanoparticles

To improve the spatial distribution of nano particles in a polymeric host and to enhance the interfacial interaction with the host, the use of chain-end grafted nanoparticle has gained popularity in the field of polymeric nanocomposites. Besides changing the material properties of the host, these grafted nanoparticles strongly alter the dynamics of the polymer chain at both local and cooperative length scales (relaxations) by manipulating the enthalpic and entropic interactions. It is difficult to map the distribution of these chain-end grafted nanoparticles in the blend by conventional techniques, and herein, we attempted to characterize it by unique technique(s) like peak force quantitative nanomechanical mapping (PFQNM) through AFM (atomic force microscopy) imaging and dielectric relaxation spectroscopy (DRS). Such techniques, besides shedding light on the spatial distribution of the nanoparticles, also give critical information on the changing elasticity at smaller length scales and hierarchical polymer chain dynamics in the vicinity of the nanoparticles. The effect of one-dimensional rodlike multiwall carbon nanotubes (MWNTs), with the characteristic dimension of the order of the radius of gyration of the polymeric chain, on the phase miscibility and chain dynamics in a classical LCST mixture of polystyrene/ poly(vinyl methyl ether) (PS/PVME) was examined in detail using the above techniques. In order to tune the localization of the nanotubes, different molecular weights of PS (13, 31, and 46 kDa), synthesized using RAFT (reversible addition fragmentation chain transfer) polymerization, was grafted onto MWNTs in situ. The thermodynamic miscibility in the blends was assessed by low-amplitude isochronal temperature sweeps, the spatial distribution of MWNTs in the blends was evaluated by PFQNM, and the hierarchical polymer chain dynamics was studied by DRS. It was observed that the miscibility, concentration fluctuation, and cooperative relaxations of the PS/PVME blends are strongly governed by the spatial distribution of MWNTs in the blends. These findings should help guide theories and simulations of hierarchical chain dynamics in LCST mixtures containing rodlike nanoparticles.

Nanomechanical Mapping, Hierarchical Polymer Dynamics, and Miscibility in the Presence of Chain-End Grafted Nanoparticles

To improve the spatial distribution of nano particles in a polymeric host and to enhance the interfacial interaction with the host, the use of chain-end grafted nanoparticle has gained popularity in the field of polymeric nanocomposites. Besides changing the material properties of the host, these grafted nanoparticles strongly alter the dynamics of the polymer chain at both local and cooperative length scales (relaxations) by manipulating the enthalpic and entropic interactions. It is difficult to map the distribution of these chain-end grafted nanoparticles in the blend by conventional techniques, and herein, we attempted to characterize it by unique technique(s) like peak force quantitative nanomechanical mapping (PFQNM) through AFM (atomic force microscopy) imaging and dielectric relaxation spectroscopy (DRS). Such techniques, besides shedding light on the spatial distribution of the nanoparticles, also give critical information on the changing elasticity at smaller length scales and hierarchical polymer chain dynamics in the vicinity of the nanoparticles. The effect of one-dimensional rodlike multiwall carbon nanotubes (MWNTs), with the characteristic dimension of the order of the radius of gyration of the polymeric chain, on the phase miscibility and chain dynamics in a classical LCST mixture of polystyrene/ poly(vinyl methyl ether) (PS/PVME) was examined in detail using the above techniques. In order to tune the localization of the nanotubes, different molecular weights of PS (13, 31, and 46 kDa), synthesized using RAFT (reversible addition fragmentation chain transfer) polymerization, was grafted onto MWNTs in situ. The thermodynamic miscibility in the blends was assessed by low-amplitude isochronal temperature sweeps, the spatial distribution of MWNTs in the blends was evaluated by PFQNM, and the hierarchical polymer chain dynamics was studied by DRS. It was observed that the miscibility, concentration fluctuation, and cooperative relaxations of the PS/PVME blends are strongly governed by the spatial distribution of MWNTs in the blends. These findings should help guide theories and simulations of hierarchical chain dynamics in LCST mixtures containing rodlike nanoparticles.

Length-frequency estimation for yellowfin tuna (Thunnus albacares) caught by commercial fishing gear in the Eastern Pacific Ocean

ENGLISH: Methods of collecting samples for the purpose of estimating the numbers and weights of fish caught, by length interval, are described. Several models for two-stage sampling are described, and the equations for the estimators and their variances are given. The results from a brief simulation study are used to show the differences between estimates made with the different models. Estimators for the average weights of fish in the catch and their variances are also described. These average weights are used to provide improved estimates of the total annual catches of yellowfin taken from the eastern Pacific Ocean, east of 150°W, between 1955 and 1990. SPANISH: Se describen los métodos de recoger de muestreo para estimar el número o peso de peces capturados, por intervalo de talla. Se describen varios modelos para el muestreo de dos etapas, y se presentan las ecuaciones para los estimadores y sus varianzas. Se usan los resultados de un breve estudio de simulación para indicar las diferencias entre estimaciones realizadas con los distintosmodelos. También se describe un estimador para el peso promedio de peces en la captura y su varianza. Se usan estos estimadores para calcular estimaciones mejoradas de las capturas anuales totales de aleta amarilla tomadas del Océano Pacífico oriental, al este de 150°W, entre 1955 y 1990. (PDF contains 41 pages.)

Studies on 4S and 5S RNA of HeLa cells

SECTION I

Section I is concerned with a partial sequence analysis conducted on 5S RNA from HeLa cells. Analysis of the oligonucleotide pattern after pancreatic ribonuclease digestion of a highly-purified preparation of 5S RNA gave results which were in general agreement with those published for KB cells, both with respect to the identity and the frequency of the partial sequences. However, the presence of a trinucleotide not found in the KB 5S pattern, together with the reproducibly much lower than expected molar yield of the larger oligonucleotides strongly suggested the occurrence of alternate sequences at various sites in the 5S molecules of human cells. The presence of ppGp and pppGp at the 5'-terminus of HeLa 5S RNA was clearly demonstrated. The implications of this finding with regard to the origin of 5S RNA are discussed.

SECTION II

In Section II the proportion of the HeLa cell genome complementary to tRNA was investigated by using RNA- DNA hybridization. The value for saturation of the HeLa DNA by tRNA was found to be 1.1 x 10^-5, which corresponds to about 4900 sites for tRNA per HeLa cell in an exponentially growing culture. Analysis of the nucleotide composition of the hybridized tRNA revealed significant differences from the nucleotide composition of the input tRNA, with the purine to pyrimidine ratio indicating, however, that these differences were not produced by excessive RNase attack of the hybrid. The size of the hybridized tRNA was only moderately smaller than that of the input RNA; the average S value in formaldehyde was 2.7 (corresponding to a length of about 65 nucleotides), suggesting that a relatively small portion near the ends of the hybridized 4S chains had been removed by RNase.

SECTION III

The proportion of the HeLa cell genome complementary to 5S RNA was investigated by using RNA-DNA hybridization. The value for saturation of the HeLa DNA by 5S RNA was found to be 2.3 x 10^-5, which corresponds to about 7,000 sites for 5S RNA per HeLa cell in an exponentially growing culture. Analysis of the nucleotide composition of the hybridized 5S RNA revealed no significant difference from the nucleotide composition of the input RNA. At the RNA to DNA input ratio of 1:1000, the average S value in formaldehyde of the hybridized 5S RNA corresponded to a polynucleotide chain about two-thirds the size of the input RNA.

Entanglement negativity in the harmonic chain out of equilibrium

We study the entanglement in a chain of harmonic oscillators driven out of equilibrium by preparing the two sides of the system at different temperatures, and subsequently joining them together. The steady state is constructed explicitly and the logarithmic negativity is calculated between two adjacent segments of the chain. We find that, for low temperatures, the steady-state entanglement is a sum of contributions pertaining to left-and right-moving excitations emitted from the two reservoirs. In turn, the steady-state entanglement is a simple average of the Gibbs-state values and thus its scaling can be obtained from conformal field theory. A similar averaging behaviour is observed during the entire time evolution. As a particular case, we also discuss a local quench where both sides of the chain are initialized in their respective ground states.

Utilização de sistema multiplex de marcadores do tipo INDELs em identificação humana por DNA

Os INDELs são polimorfismos de comprimento, gerados a partir de inserções e/ou deleções de um ou mais nucleotídeos. Os marcadores INDELs, que estão amplamente distribuídos pelo genoma e se caracterizam pela alta estabilidade devido à baixa taxa mutacional (10-9), podem ser analisados a partir da amplificação por PCR (Reação em Cadeia da Polimerase). A facilidade de análise e a possibilidade de construção de sistemas multiplex capazes de gerar amplicons curtos (menores que 100 pb) tornam os INDELs uma importante ferramenta para identificação humana por DNA. Para avaliar a eficiência e validar a metodologia que emprega os polimorfismos de inserção/deleção na identificação humana, utilizamos o sistema Indel-plex ID, capaz de amplificar simultaneamente 38 loci INDELs bialélicos de cromossomos autossomos. Diferentes amostras biológicas (cabelo, saliva, sangue, sêmen e urina) foram genotipadas apresentando reprodutibilidade entre todas as tipagens. A concentração mínima de DNA necessária para amplificação dos 38 loci INDELs foi de 0,5 ng. Artefatos do tipo split peaks foram observados em algumas amostras. Os produtos da PCR foram purificados em resina Sephadex proporcionando melhores condições de análise, redução de artefatos e aumento na intensidade média de fluorescência dos alelos amplificados. A eficiência do sistema Indel-plex ID na amplificação de DNA degradado foi verificada durante as análises das amostras de DNA extraídas de restos mortais (ossos e dentes). Comparativamente ao sistema Identifiler, o Indel-plex ID, se mostrou mais eficiente em termos de número de loci genotipados e qualidade de amplificação. Nas investigações de vínculos genéticos realizadas com o sistema Indel-plex ID foi possível corroborar resultados anteriores obtidos pela análise de marcadores STR. Nas análises com amostras in vivo foram obtidos valores máximos de Probabilidades de Paternidade de 99,99998%. Para casos envolvendo supostos pais falecidos, o sistema Indel-plex ID reforçou resultados obtidos com o sistema Identifiler e Minifiler. A Probabilidade de Paternidade de 99,953%, obtida com o sistema Indel-plex ID, conjugada com a Probabilidade de Paternidade de 99,957%, obtida como o sistema Minifiler, possibilitou um índice final de 99,99998%. Os resultados evidenciaram que os loci INDELs do sistema Indel-plex ID são altamente informativos, constituindo uma ferramenta importante em estudos de identificação humana e de relações de parentesco

Surface plasmons and effects of losses in propagating modes in a chain of silver nanoparticles

In this work a chain of 4000 silver nanoparticles embedded in a glass medium is considered, and its leftmost particle is excited by an electric field pulse of Gaussian shape. Considering Drude’s model, losses of the system are taken into account by γ factor, which stands for the Ohmic losses, and different quantities, such as frequencies of excited modes and group velocities are calculated. Besides, these results are compared to those obtained from the dispersion relation of an infinite chain. The increase of losses affects the lifetime and propagation length of the plasmon; besides, although the response dispersion relation for an infinite chain seems to remain invariable, this is not the case for a finite chain. The mismatches are bigger for higher losses. Furthermore, plasmon propagation velocities are analysed, and an explanation for the mismatch of longitudinal modes close to the intersection point with the dispersion of light is suggested. Finally, some concepts to treat this problem from the energy transport point of view are introduced.

VPA estimates of fishing mortality and exploited biomass from Sardinella aurita catch-at-length data in eastern Venezuela

In this study, length-frequency data on Spanish sardine (Sardinella aurita) from northeastern Venezuela were analyzed for the period 1967-1989. Average growth parameters for the von Bertalanffy equation were established as L sub( infinity )= 26.6 cm (TL) and K = 1.26 year super(-1). The number of recruits to the fishing area, estimated from length-structured Virtual Population Analysis, varied from <10 super(8) in the late 1960s to >10 super(9) at the end of the 1980s. Exploited biomass estimates for the same period varied from less than 20,000 t in the first year to more than 100,000 in 1989. Both recruitment and exploited biomass showed different seasonal patterns between 1976-1983 and 1984-1988. Despite some uncertainty regarding these estimates, it is considered that major population tendencies are adequately represented by this analysis

Growth and length-weight parameters of Pacific mackerel (Scomber japonicus) in the Gulf of Guayaquil, Ecuador

The seasonally oscillating growth parameters and length-weight relationships for Scomber japonicus caught in the Gulf of Guayaquil, Ecuador, were determined based on length-frequency data from 1989 to 1996, using the FiSAT software package of Gayanilo et al. (1996). Estimates of growth parameters are in general agreement with previous studies on the same species. Results also imply that the growth of Scomber japonicus slows down during the cold season by approximately 50% with respect to the average growth. The mean value of the power b is significantly larger than 3, indicating that the model of allometric growth should be used for the length-weight relationship and calculation of the condition factor.

Condition factor and length-weight relationship of Nemipterus japonicus (Bloch) off Bombay coast

Fluctuations in the K values of Nemipterus japonicus (Bloch) off Bombay coast were interpreted regarding sex, month and females maturity stage. These indicate differential growth rates in males and females. Males and females attain first maturity at 145 mm and 115 mm respectively, second maturity is attained by both the sexes at 195 mm. First spawning occurs when both are of 155 mm length and at second spawning males and females attain 215 and 205 mm of length respectively. The fish mature and breed at "O" year; the main spawning period is from August to November with peak spawning activities in October. It grows about 155 mm in first year at 12.91mm per month and about 215 mm in the second year at 5.0 mm per month on an average. Length-weight relationships for males and females are given. The rate of growth of females by weight was found to be slower below 150 mm, but faster than that of males above 150 mm specimens.

Wadge Bank trawl fishery studies. Pt. 4. An analysis of the length frequency measurements of the sea bream (Lethrinus nebulosus) made in 1949 and 1953 to 1958

Length frequency distributions of the sea bream collected during the period 1953 to 1958 have been analysed. The increase in average sizes of the sea bream with depth suggests a movement to deeper waters with increase in size. By numbers, the sea bream is more abundant between 21 and 30 fathoms than in deeper areas. The recruitment was continuous and regular. There is no sign of entry or progression of a dominant brood throughout the period under study. Length frequency distribution shows three distinct modes. The first mode occurs regularly but does not progress beyond 40cm, recruitment being balanced by natural and fishing mortality. The other two which are not regular are probably the result of fishing outside regular areas. Short sections of “growth” lines which fit into one another when extrapolated, are evident. The larger lines obtained by extrapolation are parallel to one another. These tentative "growth lines" indicate that this species which enters the fishing grounds, when 15 cm or larger in length are exploited by the trawl fishery for a period of three to four years. This species appears to be six months old when it enters the fishing grounds and increases in length by about 37.5 cm in the next 30 months. Later growth slows down. The average size of the specimens sampled continued to get smaller from 1953 till 1957. It is shown that this reduction in size is due to increased fishing effort.

Marketing of value-added products from silver carp and involvement of rural people in the production and marketing chain

Cost-profit analysis and market testing of some value-added products from silver carp such as fish mince block, fish sausage, fish ball, fish stick and fish burger were analyzed during April 2001 to March 2002. The study also explored the possibility to involve rural low-income people in the production and marketing of such products. The production of silver carp was higher in greater Jessore and Mymensingh districts but the price remained low during the peak-harvesting season in October to November. The price varied with size of the fish, season, market characteristics and effective demand of the buyers. Price of about 500 g size fish was found to be Tk. 20-25/kg in the rural markets. The average size of fish in the rural markets was 3S0-550 g while that in the urban markets it was 700-1,200 g. The cost of production of the value added products and profit margin were assessed on the basis of market price of the raw material as well as that of the finished products, transportation, storage and marketing costs. The profit margins of 34%, 39%, 81% and 31% of their sales price were obtained for fish sausage, fish ball, fish stick and fish burger, respectively. Actual production cost could be minimized if the fish is purchased directly from the farmers. Consumer's acceptance and marketability tests showed that both rural and urban people preferred fish ball than fish sausage. However, response towards the taste, flavor and color of fish ball and fish sausage was found to vary with occupations and age of the consumers. A correlation was observed between age group and acceptance of new products. Fish ball, fish stick and fish burger were found to be the most preferable items to the farmers because of easy formulation process with common utensils. Good marketing linkage and requirement of capital had been identified as the prerequisites for operating small-scale business on value-added fish products.

Effect of two green algae species (Chlorella sp. & Scenedesmus obliquus) enriched with B group vitamins on food chain of Rutilus frisii kutum (Kamensky, 1901) fry

The Effect of two freshwater green algae species Chlorella sp. & Scenedesmus obliquus enriched (from the beginning of culture and after 96 hours) with different dosages of B group vitamins (0, 0.5, 1, and 2 ml of enriching solution per each liter of algae medium) on fecundity of Daphnia magna and growth of Rutilus frisii kutum fry were investigated in a research from spring, 2008 to autumn, 2009. First, each of the green algae species were cultured purely and massively in the Zander (Z-8+N) medium and then the nutritional value (the amount of protein, lipid, and carbohydrate) of enriched algae were meausered. In this study, enriching of Chlorella sp. & S. obliquus with a suitable mix of B group vitamins significantly improved their nutritive value. So the highest amount of nutritional value of Chlorella sp. was obtained because of enriching with dosage 0.5 ml.l-1 (366.654Kcal) and for Scenedesmus obliquus with dosage of 1 ml.l-1 (376.95Kcal). The acquired amount from control group showed an increase of respectively 42% and 11%. According to the results, increased dosages of enriching solution caused Daphnia fecundity to increase (at both stages : enrichment from the beginning of culture and after 96 hours). So the highest average of D. magna reproduction rate was obtained through being fed with Chlorella sp. and S. obliquus enriched with dosage of 2 ml enriching solution per liter of algae medium. The average fecundity of D. magna fed with Chlorella sp. enriched with dosage of 2 ml.l-1 enriching solution from the beginning of culture and after 96 hours was obtained respectively 2.128 ± 0.375 and 2.1 ± 0.69 and the average fecundity of D. magna fed with S. obliquus enriched with dosage of 2 ml enriching solution from the beginning of culture and after 96 hours was obtained respectively 2.128 ± 0.375 and 2.1 ± 0.69 which showed respectively an increase of 61 ٪, 91٪, 77 ٪, and 83٪ in proportion to the acquired amount from control group. When enriching solution was added to either algae culture medium from the beginning of culture, showed statistically significant differences (P<0.05) between dosages of 0 and 2 ml.l-1, 1 and 2 ml.l-1, and 0.5 and 2 ml enriching solution per each liter of Chlorella sp. culture medium and between dosages of 0 and 1 ml.l-1, and 0 and 2 ml enriching solution per each liter of S. obliquus culture medium. The highest average of body weight gain percentage and specific growth rate of kutum fry was obtained respectively 21.19%, 26.63%, 1.92, and 2.34 from the beginning of culture and after 96 hours with dosage of 1 ml B group vitamins per each liter of Chlorella sp. culture medium, which showed respectively an increase of 50%, 70%, 46%, and 62% in proportion to the acquired amount from control group. In the cases which Chlorella sp. were grown in the medium containing vitamin, from point of view of the average percentage of weight and specific growth rate of kutum fry significant differences were observed on the basis of the result of One-way ANOVA between dosages of 0 and 1, 1 and 2 , 0.5 and 1 ml B group vitamins per each liter. The highest average of body weight gain percentage and specific growth rate of kutum fry was obtained respectively 32.02%, 29.42%, 2.78, and 2.34 from the beginning of culture and after 96 hours with dosage of 2 ml B group vitamins per each liter of S. obliquus culture medium, which showed respectively an increase of 32%, 19%, 28%, and 17% in proportion to the acquired amount from control group. In the cases which S. obliquus were grown in the medium containing vitamin, from point of view of the average percentage of weight and specific growth rate of kutum fry significant differences were observed on the basis of the result of One-way ANOVA between dosages of 0 and 1, 0 and 2. According to the results of the present research we can say that considerable enhancement in the quality of the food of D. magna can be made by manipulation of the nutritional value of fresh water unicellular green algae with suitable mixture of B group vitamins, so that both the fecundity of D. magna will increase and the nutritional requirements of the kutum fry will be filled in this way.