The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Ray tracing based path-length calculations for polarized light tomographic imaging

A ray tracing based path length calculation is investigated for polarized light transport in a pixel space. Tomographic imaging using polarized light transport is promising for applications in optical projection tomography of small animal imaging and turbid media with low scattering. Polarized light transport through a medium can have complex effects due to interactions such as optical rotation of linearly polarized light, birefringence, diattenuation and interior refraction. Here we investigate the effects of refraction of polarized light in a non-scattering medium. This step is used to obtain the initial absorption estimate. This estimate can be used as prior in Monte Carlo (MC) program that simulates the transport of polarized light through a scattering medium to assist in faster convergence of the final estimate. The reflectance for p-polarized (parallel) and s-polarized (perpendicular) are different and hence there is a difference in the intensities that reach the detector end. The algorithm computes the length of the ray in each pixel along the refracted path and this is used to build the weight matrix. This weight matrix with corrected ray path length and the resultant intensity reaching the detector for each ray is used in the algebraic reconstruction (ART) method. The proposed method is tested with numerical phantoms for various noise levels. The refraction errors due to regions of different refractive index are discussed, the difference in intensities with polarization is considered. The improvements in reconstruction using the correction so applied is presented. This is achieved by tracking the path of the ray as well as the intensity of the ray as it traverses through the medium.

Comparison between weight loss of bends in a pneumatic conveyor and erosion rate obtained in a centrifugal erosion tester for the same materials

In order to find a link between results obtained from a laboratory erosion tester and tests carried out on a pneumatic conveyor, a comparison has been made between weight loss from bends on an industrial-scale pneumatic conveyor and erosion rates obtained in a small centrifugal erosion tester, for the same materials. Identical test conditions have been applied to both experiments so that comparable test results have been obtained. The erosion rate of mild steel commonly used as the wall material of conveyor pipes and pipe bends was determined individually on both test rigs. A relationship between weight loss from the bends and erosion rate determined from the tester has been developed. A discussion based on the results and their applicability to the prediction of wear in pneumatic conveyors concludes the paper. © 2004 Elsevier B.V. All rights reserved.

Semi-weight function method on computation of stress intensity factors in dissimilar materials

Semi-weight function method is developed to solve the plane problem of two bonded dissimilar materials containing a crack along the bond. From equilibrium equation, stress and strain relationship, conditions of continuity across interface and free crack surface, the stress and displacement fields were obtained. The eigenvalue of these fields is lambda. Semi-weight functions were obtained as virtual displacement and stress fields with eigenvalue-lambda. Integral expression of fracture parameters, K-I and K-II, were obtained from reciprocal work theorem with semi-weight functions and approximate displacement and stress values on any integral path around crack tip. The calculation results of applications show that the semi-weight function method is a simple, convenient and high precision calculation method.

Length of concentrate finishing affects the fatty acid composition of grass-fed andgenetically lean beef: an emphasis on trans-18:1 and conjugated linoleic acid profiles

2.4. The author may post the VoR version of the article (in PDF or HTML form) in the Institutional Repository of the institution in which the author worked at the time the article was first submitted, or (for appropriate journals) in PubMed Central or UK PubMed Central or arXiv, no sooner than one year after first publication of the article in the Journal, subject to file availability and provided the posting includes a prominent statement of the full bibliographical details, a copyright notice in the name of the copyright holder (Cambridge University Press or the sponsoring Society, as appropriate), and a link to the online edition of the Journal at Cambridge Journals Online.

Catch-per-unit-effort and biological parameters from the Massachusetts coastal lobster (Homarus americanus) resource: Description and trends

Acomprehensive description of the Massachusetts coastal lobster (Homarus americanus) resou,rce was obtained by sampling commercial catches coastwide at sea and at dealerships between 1981 and 1986. Acommercial lobster sea-sampling program, wherein six coastal regions were sampled monthly, with an areal and temporal data weighting design, was the primary source of data. An improved index of catch per trap haul/set-over-day was generated by modeling the relationship between catch and immersion time and standardizing effort. This 6-year time-series of mean annual catch rates tracked closely the landings trend for territorial waters. During the study period there was a gradual increase in indices of exploitation and total annual mortality which corresponded to a gradual decline in mean carapace length of marketable lobster. The frequency of culls escalated from 10.0% in 1981 to 20.9% in 1986, while the percentage of lobster found dead in traps was consistently less than 1%. The sex ratio (%F:%M) was significantly different from 50:50 and approximated a 60:40 relationship during the study period. Male and female weight-length relationships were significantly different. Females weighed more than males at smaller sizes and less than males at larger sizes. A north-south clinal trend was evident wherein lobster north of Cape Cod weighed less at length than those from regions south of Cape Cod. Functional size-maturity relationships were developed for female lobster by staging cement gland development. Proportions mature at size represent more realistic values than those obtained by analyses of percent of females ovigerous. Regional variation occurred in most of the parameters studied. Three lobster groups, differing in major population descriptors, are defined by our data.(PDF file contains 28 pages.)

The age and growth of the tongue sole Cynoglossus canariensis (Steind 1882)

The geometric mean regression equation for the weight; length relationship of Cynoglossus canariensis was W = 0.0025 L super(3.1770). The Von Bertalanffy constants Woo, Loo, K, and to were 507.5852 g, 47.3683 cm, 0.3333 and 0.1397 for males and 839.0753 g, 54.4720 cm, 0.3062 and 0.1737 for females. Total mortality coefficient Z ranged from 0.6482 and 0.8021

The relationship between otolith increments and time for yellowfin and skipjack tuna marked with tetracycline

ENGLISH: The rate at which increments are deposited on the sagittal otoliths of yellowfin (Thunnus albacares) and skipjack (Katsuwonus p elamis) tunas is determined by a markrecapture experiment using tetracycline. During growth in fork length from 40 to 110 em, and for a period of up to 389 days, yellowfin of the Revillagigedo Islands- Baja California region deposit one increment per day in either the postrostrum or rostrum position of the otolith. For skipjack of the same region, rostrum increments underestimate time by approximately 24 percent during growth from 42 to 64 cm and over the maximum interval of 249 days. The growth rate of each species is estimated from the recapture fork length and the linear change in an otolith dimension following tetracycline injection. Over specific ranges in fork length the rates are 3.06 and 1.15 em per month for yellowfin and skipjack, respectively. SPANISH: La rapidez (tasa) en la que se depositan los incrementos en los otolitos sagitales del aleta amarilla (Thunnus albacares) y el barrilete (Katsuwonus pelamis) se determina mediante un experimento al recapturar los peces que han sido marcados con tetraciclina. Durante el crecimiento de la longitud de horquilla de 40 a 110 cm y por un período hasta de 389 días, se forma en el aleta amarilla de la región de las Islas Revillagigedo-Baja California, un incremento diario ya sea en el parte del postrostrum o rostrum de los otolitos. Con respecto al barrilete de la misma region los incrementos en el rostrum subestiman aproximadamente el tiempo en un 24 por ciento durante el crecimiento de 42 a 64 cm y sobre un intervalo máximo de 249 días. El índice de crecimiento de cada especie se estima en la recaptura según la longitud de horquilla y el cambio lineal en la dimensión de un otolito después de la inyección de tetraciclina. La variación específica sobre la longitud de horquilla de los índices son 3.06 y 1.15 cm por mes para el aleta amarilla y el barrilete, respectivamente. (PDF contains 54 pages.)

Growth of yellowfin tuna, Thunnus albacares, in the Eastern Pacific Ocean based on otolith increments

ENGLISH: The growth of yellowfin tuna in the eastern Pacific is described in terms of several measurements taken from the fish and their otoliths (sagittae). Equations are also developed to predict age from the readily available dimensions of fork length and head length. The data for all of these relationships were obtained from a sample of 196 fish collected during 1977 through 1979 from purse seiners fishing north of the equator and east of 137°W. The fork-length range of the sample was 30-170 cm. The number of increments on a sagitta of each fish was used as a direct estimate of its age in days. The correspondence between increments and days has been validated for yellowfin in the length range of 40-110 cm. Circumstantial evidence indicates that the relationship also applies in the intervals of 0-40 cm and 110-170 cm. This circumstancial evidence was derived from: 1) literature on validated increments during early growth for other species, 2) knowledge that structures assumed to be daily increments on yellowfin otoliths have subsequently been validated in the corresponding zone on bluefin otoliths, and 3) a comparison of the growth curve based on increments to others obtained from length frequency modal analysis. Based on this information the age estimates over the entire size range of sampled fish are believed to be accurate. In addition to the general growth and age-predictive relationships, the major conclusions of the study are that: 1) Sexually dimorphic growth exists in terms of fork length, fish weight and the length of the otolith counting path for the entire data set. Examination of the data for 1977 and 1979 also revealed that the fork-length growth of each sex differed within years. 2) For combined sexes there were significant differences among the fork-length growth curves for yellowfin sampled in different years. 3) Yellowfin caught inshore (within 275 miles of the coast) were heavier than those caught offshore for fork lengths between 30 and 110 cm. The situation was reversed for lengths greater than 110 cm. 4) Back-calculated spawning months were distributed uniformly throughout the year in 1974 and 1977, but in 1975-1976 and 1978 spawning activity was apparently concentrated in the latter half of the year. SPANISH: El crecimiento del atún aleta amarilla en el Pacífico oriental se describe en términos de varias medidas obtenidas de peces y otolitos (sagita). Se formularon también ecuaciones para pronosticar la edad, según las dimensiones fácilmente disponibles de la longitud horquilla y longitud de la cabeza. Los datos de todas estas relaciones fueron obtenidos mediante una muestra de 196 peces recolectados desde 1977hasta 1979, en barcos cerqueros que estaban pescando al norte de la línea ecuatorial y al este de los 137°W. El intervalo de la longitud horquilla de la muestra fue de 30-170 cm. Se empleó el número de incrementos en la sagita de cada pez como un estimado directo de la edad en días. Se ha comprobado la relación entre los incrementos y los días en el intervalo de longitud de 40-110 cm del aleta amarilla. La evidencia circunstancial indica que se aplica también la relación a los intervalos de 0-40 cm y 110-170 cm. Esta evidencia circunstancial se dedujo: 1) de las publicaciones sobre incrementos comprobados de otras especies durante el primer crecimiento, 2) del conocimientoque las estructuras que se supone son incrementos diarios en los otolitos del aleta amarilla han sido comprobadas luego en la parte correspondiente de otolitos del aleta azul y 3) por una comparación de la curva de crecimiento, basada en incrementos relacionados a otras curvas obtenidas según el análisis modal frecuencia-talla. Se cree, basados en esta información, que las estimaciones de la edad sobre toda la amplitud de talla de los peces muestreados, es acertada. Además de la relación del crecimiento general y del pronóstico de la edad, las principales conclusiones de este estudio son: 1) En toda la serie de datos existe el crecimiento sexualmente dimórfico en términos de longitud horquilla, peso del pez y longitud del plano de conteo del otolito. El examen de los datos de 1977 y 1979, revelan también que el crecimiento longitud horquilla de cada sexo es diferente en los años. 2) En los sexos combinados hubo diferencias significativas entre las curvas de crecimiento longitud horquilla del aleta amarilla muestreado en diferentes años. 3) El aleta amarilla capturado cerca a la costa (en las primeras 275 millas) fue más pesado que el capturado en las aguas mar afuera, correspondiente a la longitud horquilla entre 30 y 110 cm. La situación fue inversa para tallas de más de 110 cm. 4) En 1974 y 1977, los meses retrocalculados del desove se distribuyeron uniformemente durante el año, pero en 1975-1976 y 1978, la actividad del desove se concentró aparentemente en el último semestre del año. (PDF contains 62 pages.)

Sexual maturity, fecundity and egg size of wild and cultured samples of Bagrus bayad macropterus

Twenty four matured samples of Bagrus bayad macropterus from the wild (Shiroro Lake, Nigeria) and under captivity, size ranging from 412.69-3300.00 g total body weight, were analysed for sexual maturity,fecundity and egg size. The average fecundity obtained were 53352.59 and 21028.32 eggs for the wild and cultured fish respectively.Positive relationship was observed between fecundity, body size and gonad weight. Fecundity increased as body size increased. A more positive and linear relationship was observed between fecundity and gonad weight than fecundity and total body weight. Egg diameter,length and weight were determined from the egg samples. The mean size range of eggs for cultured fish was 0.74-1.05 mm of diameter; 1.01-1.20 mm of length and 0.25-0.40 mg of weight. Wild samples had mean size range of 0.68-l.09 mm of diameter, 0.85-1.38 mm of length and egg mean weight range was 0.15- 0.40 mg. Sexual maturity is dependent on size (1 kg and above). The egg diameter, egg length and weight bear no relationship with each other. Gonad development study indicated that gonad development was faster under captivity than in wild

Birth Weight, Working Memory and Epigenetic Signatures in IGF2 and Related Genes: A MZ Twin Study

Neurodevelopmental disruptions caused by obstetric complications play a role in the etiology of several phenotypes associated with neuropsychiatric diseases and cognitive dysfunctions. Importantly, it has been noticed that epigenetic processes occurring early in life may mediate these associations. Here, DNA methylation signatures at IGF2 (insulin-like growth factor 2) and IGF2BP1-3 (IGF2-binding proteins 1-3) were examined in a sample consisting of 34 adult monozygotic (MZ) twins informative for obstetric complications and cognitive performance. Multivariate linear regression analysis of twin data was implemented to test for associations between methylation levels and both birth weight (BW) and adult working memory (WM) performance. Familial and unique environmental factors underlying these potential relationships were evaluated. A link was detected between DNA methylation levels of two CpG sites in the IGF2BP1 gene and both BW and adult WM performance. The BW-IGF2BP1 methylation association seemed due to non-shared environmental factors influencing BW, whereas the WM-IGF2BP1 methylation relationship seemed mediated by both genes and environment. Our data is in agreement with previous evidence indicating that DNA methylation status may be related to prenatal stress and later neurocognitive phenotypes. While former reports independently detected associations between DNA methylation and either BW or WM, current results suggest that these relationships are not confounded by each other.

Reprodução de peixes de riachos: uma abordagem comparativa entre as estratégias r e K

No presente trabalho, objetivou-se caracterizar a estratégia reprodutiva, enfatizando o investimento energético, de duas espécies de peixe do rio Ubatiba, Maricá, Rio de Janeiro: Parotocinclus maculicauda (K-estrategista) e Astyanax hastatus (r-estrategista). Foram realizadas coletas bimestrais de Junho de 2010 a Abril de 2011 totalizando 236 exemplares amostrados de A. hastatus e 234 de P. maculicauda. Para cada exemplar foram registrados os dados de comprimento padrão (Cp, cm), peso total (Pt, g), peso gonadal (Pg, g), sexo e estádio de maturação. Através da estrutura de tamanho, observamos que as fêmeas atingem maior comprimento, em relação aos machos, para as duas espécies. A relação peso/ comprimento evidenciou para ambas as espécies, crescimento alométrico negativo (inferior a 3), demonstrando crescimento mais longelíneo. Para a proporção sexual, o teste χ2 foi aplicado e indicou que, para as duas espécies, há significativamente mais fêmeas. A distribuição sexual no ano mostrou que as fêmeas se mantêm em maioria durante todo o ano para P. maculicauda. Para A. hastatus este padrão também se mantém, porém com exceção do bimestre Novembro/Dezembro, quando o número de machos torna-se um pouco maior. O tamanho de primeira maturação mostrou-se o mesmo para ambas as espécies (2,5 a 3,0 cm). A variação temporal da freqüência de indivíduos reprodutivos e não reprodutivos juntamente com a distribuição temporal dos valores individuais de IGS mostrou que P. maculicauda se reproduz com maior intensidade nas estações chuvosas (Setembro a Abril), reduzindo sua atividade reprodutiva de maneira significativa nas estações secas (Maio a Agosto). Já A. hastatus demonstrou regular atividade reprodutiva durante todo o ano com pequeno pico no bimestre Novembro/ Dezembro. Desova do tipo total foi registrada para Astyanax, enquanto que para Parotocinclus registrou-se desova parcelada em três lotes. Em ambas as espécies foi observada relação inversa entre volume e a quantidade de ovócitos produzidos, com A. hastatus produzindo muitos ovócitos (fecundidade: 463 + 213 ovócitos/grama de peixe) de reduzido volume (diâmetro = 800 μm e volume = 0,26 mm3) e P. maculicauda produzindo número bem inferior (fecundidade: 47 + 13 ovócitos/grama de peixe), porém com volume superior (diâmetro = 1.600 μm e volume = 2,14 mm3). Com isso o valor energético relativo também se mostrou superior, com A. hastaus produzindo ovócitos vitelogênicos com 0,4+ 0,08 cal/unidade e P. maculicauda produzindo os mesmos ovócitos com 1,8+ 1,1 cal/unidade. Para a produção energética total investida na produção de gametas, foi considerado o tipo de desova de cada espécie, com Astyanax investindo 50,5 + 24 calorias/grama/grama de peixe e Parotocinclus investindo 88,4 + 72,46 cal/grama/grama de peixe, porém sem diferenças significativas (Mann-Whitney; U =235,0, p=0,08), indicando, portanto que independente da estratégia adotada (r ou K), o gasto energético na produção de ovócitos é a mesma.

A-SCALA: an age-structured statistical catch-at-length analysis for assessing tuna stocks in the eastern tropical Pacific Ocean

English: We describe an age-structured statistical catch-at-length analysis (A-SCALA) based on the MULTIFAN-CL model of Fournier et al. (1998). The analysis is applied independently to both the yellowfin and the bigeye tuna populations of the eastern Pacific Ocean (EPO). We model the populations from 1975 to 1999, based on quarterly time steps. Only a single stock for each species is assumed for each analysis, but multiple fisheries that are spatially separate are modeled to allow for spatial differences in catchability and selectivity. The analysis allows for error in the effort-fishing mortality relationship, temporal trends in catchability, temporal variation in recruitment, relationships between the environment and recruitment and between the environment and catchability, and differences in selectivity and catchability among fisheries. The model is fit to total catch data and proportional catch-at-length data conditioned on effort. The A-SCALA method is a statistical approach, and therefore recognizes that the data collected from the fishery do not perfectly represent the population. Also, there is uncertainty in our knowledge about the dynamics of the system and uncertainty about how the observed data relate to the real population. The use of likelihood functions allow us to model the uncertainty in the data collected from the population, and the inclusion of estimable process error allows us to model the uncertainties in the dynamics of the system. The statistical approach allows for the calculation of confidence intervals and the testing of hypotheses. We use a Bayesian version of the maximum likelihood framework that includes distributional constraints on temporal variation in recruitment, the effort-fishing mortality relationship, and catchability. Curvature penalties for selectivity parameters and penalties on extreme fishing mortality rates are also included in the objective function. The mode of the joint posterior distribution is used as an estimate of the model parameters. Confidence intervals are calculated using the normal approximation method. It should be noted that the estimation method includes constraints and priors and therefore the confidence intervals are different from traditionally calculated confidence intervals. Management reference points are calculated, and forward projections are carried out to provide advice for making management decisions for the yellowfin and bigeye populations. Spanish: Describimos un análisis estadístico de captura a talla estructurado por edad, A-SCALA (del inglés age-structured statistical catch-at-length analysis), basado en el modelo MULTIFAN- CL de Fournier et al. (1998). Se aplica el análisis independientemente a las poblaciones de atunes aleta amarilla y patudo del Océano Pacífico oriental (OPO). Modelamos las poblaciones de 1975 a 1999, en pasos trimestrales. Se supone solamente una sola población para cada especie para cada análisis, pero se modelan pesquerías múltiples espacialmente separadas para tomar en cuenta diferencias espaciales en la capturabilidad y selectividad. El análisis toma en cuenta error en la relación esfuerzo-mortalidad por pesca, tendencias temporales en la capturabilidad, variación temporal en el reclutamiento, relaciones entre el medio ambiente y el reclutamiento y entre el medio ambiente y la capturabilidad, y diferencias en selectividad y capturabilidad entre pesquerías. Se ajusta el modelo a datos de captura total y a datos de captura a talla proporcional condicionados sobre esfuerzo. El método A-SCALA es un enfoque estadístico, y reconoce por lo tanto que los datos obtenidos de la pesca no representan la población perfectamente. Además, hay incertidumbre en nuestros conocimientos de la dinámica del sistema e incertidumbre sobre la relación entre los datos observados y la población real. El uso de funciones de verosimilitud nos permite modelar la incertidumbre en los datos obtenidos de la población, y la inclusión de un error de proceso estimable nos permite modelar las incertidumbres en la dinámica del sistema. El enfoque estadístico permite calcular intervalos de confianza y comprobar hipótesis. Usamos una versión bayesiana del marco de verosimilitud máxima que incluye constreñimientos distribucionales sobre la variación temporal en el reclutamiento, la relación esfuerzo-mortalidad por pesca, y la capturabilidad. Se incluyen también en la función objetivo penalidades por curvatura para los parámetros de selectividad y penalidades por tasas extremas de mortalidad por pesca. Se usa la moda de la distribución posterior conjunta como estimación de los parámetros del modelo. Se calculan los intervalos de confianza usando el método de aproximación normal. Cabe destacar que el método de estimación incluye constreñimientos y distribuciones previas y por lo tanto los intervalos de confianza son diferentes de los intervalos de confianza calculados de forma tradicional. Se calculan puntos de referencia para el ordenamiento, y se realizan proyecciones a futuro para asesorar la toma de decisiones para el ordenamiento de las poblaciones de aleta amarilla y patudo.

Length-fecundity relationships of Nigerian fish populations

Parameters of the exponential body length (L)-fecundity (F) relationship of the form F=a.L super(b) are presented for 47 populations and 26 species of Nigerian fishes. Estimates of b varied between 1.563 (Ilisha africana) and 5.771 (Barbus callipterus) with a mean of 3.054 (s.d. = 1.024). The maximum sizes of fish populations examined did not significantly influence the relative magnitudes of b. The parameters Alpha and Beta of the linear length-fecundity relationships of the form F = Alpha + BetaL are also presented for five fish populations. Estimates of Beta ranged from 243.5 (Chrysichthys walkeri) to 1,334,895 (Tilapia mariae).

Weight-fecundity relationships of Nigerian fish populations

Parameters a and b of the power body weight (W) - fecundity (F=a W super(b)) are presented for 25 populations comprising 15 species of Nigerian fishes. Estimates of b varied between 0.511 (Parauchenoglanis akin) and 1.654 (Periophthalmus barbarus) with a mean of 1.087 (s.d.=0.520). The maximum weight of populations examined did not significantly influence the relative magnitude of b. The parameters proportional to and beta of the linear weight-fecundity relationship (F= proportional to + beta W) are also presented for 27 fish populations from 22 species. Estimates of beta ranged from 4.22 (Chromidotilapia guntheri) to 2,062.94 (Pellunula min), with a mean of 243.80 (s.d.=477.89). The magnitude of beta declined with increasing maximum weights of fishes examined.