Length and age at maturity of female petrale sole (Eopsetta jordani) determined from samples collected prior to spawning aggregation

The problem of bias in female petrale sole age and length-at-maturity relationships caused by sampling from spawning aggregations was investigated. Samples were collected prior to aggregation, and histological methods were used to determine maturity status. Mature and immature fish were classified by inspecting oocytes for the presence of yolk in September, when substantial divergence in yolked and unyolked oocyte diameters had been observed. Comparison of macroscopic and microscopic assessment of maturity showed that maturity status cannot be determined accurately by using macroscopic inspection during the summer. Female petrale sole from the central Oregon coast were 50% mature at 33 cm and 5 years of age. Comparison of data from our study with data used in recent petrale sole stock assessments showed that both sampling bias and the use of samples from sea-sons when status cannot be accurately determined have likely caused errors in fitted maturity relationships.

Lunar, diurnal and tidal periodicity in relation to the prawn abundance and migration in the Godavari estuarine systems

Preliminary investigations to study the lunar, diurnal and tidal periodicity in abundance and migrations of prawns were made in the Bairavapalam distributary of the Goutami branch of the Godavari estuary during the period of November 1961 to July 1962. The study was based on observation of the catches of a stake net (bag net) operated near the mouth of the estuary. Records of the catches were maintained tidewise daily. Comparative estimates of abundance were made on the basis of catch per hour's operation. It was generally observed that the catches were higher during the darker half of the month than in the brighter fortnight. The landings during low tides were generally higher than those during high tides and usually heavier catches were made during nocturnal low tides than during the day low tides. A continuous inward and outward (immigration and emigration) movement of prawns of all size groups was observed in the estuary from November to July. In general, more penaeid prawns were found to be immigrating at dawn than at dusk. Similarly, the number of emigrants was also found to be generally higher during the new moon period than during the full moon. Metapenaeus monoceros showed an almost distinct nocturnal periodicity in migration, while no such periodicity was observed, distinctly, in other species. In the case of Penaeus indicus the movement of migrants was prolonged. In M. brevicornis the migrants were scarce till March and thereafter increased numerically. The migrant forms of Metapenaeus dobsoni continued to be abundant till May with peak periods in January and February. The migratory pattern of Metapenaeus affinis was similar to that of Metapenaeus brevicornis, though the migrants of the former species appeared a month earlier than the latter. Intensive studies over extended areas for longer periods are required to understand clearly the migratory pattern of the various species. The phenomenon of immigration of prawns can be clearly understood only by vital staining or tagging studies. Perhaps the emigrants might be returning with the succeeding changing life. To verify this, laboratory experiments, by vital stains, were conducted. The marked specimens, if released during the low tides on a large scale, may be recaptured during the subsequent high tides and the duration also may be calculated. At least some percentage of the emigrants remains in the sea for maturity and breeding.

Characterization of YBCO Bulk samples by local AC-susceptometry

Melt processed HTSC bulk samples usually show a high inhomogeneity. These inhomogeneities influence application-relevant properties such as the lévitation force or the trapped field. In this contribution a technique is presented which allows investigation of these inhomogeneous properties. The measurements are performed by scanning the sample surface with a small coil system and detecting the first and third harmonic of the inductive response. The critical current density jc is calculated from the measured signal using a modified critical state model. Jcdistributions yielded by this technique are shown. © 1997 IEEE.

Growth of the buccaneer anchovy Encrasicholina punctifer off Mozambique, based on samples collected in research surveys

Growth of Encrasicholina punctifer (Engraulididae) is estimated, based on samples obtained during five surveys on Sofala Bank (central Mozambique). The estimated values of the von Bertalanffy growth function, TL∞=12 cm and K=2.0 yearˉ¹ are compared with results of growth studies elsewhere in the Indo-Pacific region, based mainly on the index Φ=log(sub)10 K+2*log(sub)10L∞ assumed to be constant within species. This comparison is rendered difficult by the uncertain taxonomical status of stolephorid anchovies.

Phylogenetic study of complete cytochrome b genes in musk deer (genus Moschus) using museum samples

As an endangered animal group, musk deer (genus Moschus) are not only a great concern of wildlife conservation, but also of special interest to evolutionary studies due to long-standing arguments on the taxonomic and phylogenetic associations in this group. Using museum samples, we sequenced complete mitochondrial cytochrome b genes (1140 bp) of all suggested species of musk deer in order to reconstruct their phylogenetic history through molecular information. Our results showed that the cytochrome b gene tree is rather robust and concurred for all the algorithms employed (parsimony, maximum likelihood, and distance methods). Further, the relative rate test indicated a constant sequence substitution rate among all the species, permitting the dating of divergence events by molecular clock. According to the molecular topology, M. moschiferus branched off the earliest from a common ancestor of musk deer (about 700,000 years ago); then followed the bifurcation forming the M. berezouskii lineage and the lineage clustering M. fuscus, M. chrysogaster, and M. leucogaster (around 370,000 years before present), interestingly the most recent speciation event in musk deer happened rather recently (140,000 years ago), which might have resulted from the diversified habitats and geographic barriers in southwest China caused by gigantic movements of the Qinghai-Tibetan Plateau in history. Combining the data of current distributions, fossil records, and molecular data of this study, we suggest that the historical dispersion of musk deer might be from north to south in China. Additionally, in our further analyses involving other pecora species, musk deer was strongly supported as a monophyletic group and a valid family in Artiodactyla, closely related to Cervidae. (C) 1999 Academic Press.

Methylation of tumor associated genes in tissue and plasma samples from liver disease patients

To investigate whether aberrant hypermethylation in plasma DNA could be used as diagnosis makers for hepatocellular carcinoma (HCC), we performed methylation-specific PCR (MSP) to check the methylation status of five tumor associated genes in 36 cases of

Observation on the lunar and tidal influence on gill netting in the Bay of Bengal

The effect of lunar and tidal influence on the landing of pelagic fish with drift gill nets has been studied for the first time from Bay of Bengal along the Orissa coast. The catchability of the gear was highest during the first quarter and lowest in the fourth quarter of the moon. The variation in catch rates during the four different quarters was not statistically significant. Contrary to the earlier belief, landing with gill net was not poor during the moonlit nights. The extensive use of bluish grey nylon twine matching with seawater in place of indigenous hemp or cotton twine, has largely eliminated the visibility of gear during the brighter phase of the moon. The rate of exploitation was found to be significantly higher during the nights of neap tide, compared to those of spring tide. A plausible explanation for this phenomenon has been offered.

Preliminary observations on the lunar and tidal influences on the catches of seer by gill nets

The paper deals with the lunar and tidal influences on the catches of seer by gill nets. The landings during full moon and new moon nights, during low and high tides and during different quarters of the lunar month for three fishing seasons are discussed.

Neutrality tests using DNA polymorphism from multiple samples

The polymorphism of a gene or a locus is studied with increasing frequency by multiple laboratories or the same group at different times. Such practice results in polymorphism being revealed by different samples at different regions of the locus. Tests of neutrality have been widely conducted for polymorphism data but commonly used statistical tests cannot be applied directly to such data. This article provides a procedure to conduct a neutrality test and details are given for two commonly used tests. Applying the two new tests to the chemokine-receptor gene (CCR5) in humans, we found that the hypothesis that all mutations are selectively neutral cannot explain the observed pattern of DNA polymorphism.

Estimating material elasticity by spherical indentation load-relaxation tests on viscoelastic samples of finite thickness

A two-step viscoelastic spherical indentation method is proposed to compensate for 1) material relaxation and 2) sample thickness. In the first step, the indenter is moved at a constant speed and the reaction force is measured. In the second step, the indenter is held at a constant position and the relaxation response of the material is measured. Then the relaxation response is fit with a multi-exponential function which corresponds to a three-branch general Maxwell model. The relaxation modulus is derived by correcting the finite ramp time introduced in the first step. The proposed model takes into account the sample thickness, which is important for applications in which the sample thickness is less than ten times the indenter radius. The model is validated numerically by finite element simulations. Experiments are carried out on a 10% gelatin phantom and a chicken breast sample with the proposed method. The results for both the gelatin phantom and the chicken breast sample agree with the results obtained from a surface wave method. Both the finite element simulations and experimental results show improved elasticity estimations by incorporating the sample thickness into the model. The measured shear elasticities of the 10% gelatin sample are 6.79 and 6.93 kPa by the proposed finite indentation method at sample thickness of 40 and 20 mm, respectively. The elasticity of the same sample is estimated to be 6.53 kPa by the surface wave method. For the chicken breast sample, the shear elasticity is measured to be 4.51 and 5.17 kPa by the proposed indentation method at sample thickness of 40 and 20 mm, respectively. Its elasticity is measured by the surface wave method to be 4.14 kPa. © 2011 IEEE.

Secondary structural analysis of the mRNA regions encoding the hemagglutinin cleavage site basic amino acids of the avian influenza virus H5N1 subtype samples

Here we report the codon bias and the mRNA secondary structural features of the hemagglutinin (HA) cleavage site basic amino acid regions of avian influenza virus H5N1 subtypes. We have developed a dynamic extended folding strategy to predict RNA secondar

The study of maturational progress in the whitespotted rabbitfish (Siganus sutor) under different photoperiod and light intensity conditions

The rule of light on the timing of maturation and spawning in tropical and subtropical regions is not clear well, because the reproductive cycle in these systems is lunar synchronized. In this study, thus, the effects of different light regimes were investigated on maturational progress of whitespotted rabbitfish, Siganus sutor, the commercial species in Persian Gulf and Oman Sea. During prespawning season, 50 adult fish were randomly divided into ten 300-l tanks (n=5). The fish in control tank received indoor light condition and the fish in each other tanks were exposed to nine different combinations of photoperiod (8L: 16D, 12L: 12D, 16L: 8D) and light intensity (1000, 2000, 3000 lux). After 60 days, GSI and HSI values, serum levels of estradiol (E2), testosterone (T), 17-α hydroxyprogestrone (OHP), calcium (Ca2+) and gonad histology were evaluated for females and males. In females the GSI mean values of exposed fish increased in comparison with control except for fish were kept under 8L, 2000 lux (tank 8). These differences were significant only for fishes in tank 7 (8L, 3000 lux). In the cases of HSI, the results were converse, so that, the most of thanks showed significant decreasing than fishes reared under indoor condition. Morphology and histology study of Ovaries showed three developmental phases including 3, 4 and chiefly 5 that were parallel with GSI values. Fortheremore the serum levels of E2 was recorded between 0.54-15.8 ng/ml in different fish and their mean values were lower than control in all treatmants (P> 0.05). In males, the similar results were obtained. The GSI and HSI mean values in experimental regimes compared with control were upper and lower, respectively, except for fishes were reared in tank 1 (16L, 3000 lux). Testes histology of fishes were reared under different regimes showed signs of stage 5, since no blood vessels observed and thick milt exuded on slight pressure. The mean values of testosterone consentration in fishes were kept in tanks 1 and 6 (12L, 1000 lux) were higher and in other ones were lower than control group. It is also noted that the OHP and Ca2+ had diverse results including increasing and decreasing mean values than control. So, these factors contrary to E2 and T were not suitable to evaluation of maturity in both sexes. On the basis of ovarian structure in stage 5, oocyte development pattern in this species was group synchronous. So, increased mean of GSI versus decreased values of HSI, E2 and perhaps Ca2+ were the signs of improved maturation. But in males, reduced levels of T and similarity of testes morphology in all samples caused that GSI mean value was the only indicator for differentiating among treatments. These findings suggest that alternations were used in light regimes have been the reason of improved maturity in all treatments except fishes reared in tank 8. The ١٠٧ rule of light intensity on induction of maturity was cleared by comparision between fishes in tanks 4, 5, 6 and control group. Because day length was the same whereas fishes in tanks 4, 5 and 6 were exposed to increased light intensity compared with control. This fact verified by results was obtained from fishes in tanks 9 and especially 7, since photoperiod in this group was lower than control. So, higher intensity was considered as the reason of alternations. Contrasting with indoor condition, Induced maturity was also cleared for fishes were kept in tanks 1, 2 and 3, where both of light duration and intensity were increased. But, the rule of photoperiod was individually demonstrated when obtained results were compared with similar light intensities in other treatments. In conclusion, with comparison among different light regimes it is declared that siganids were kept under light condition of tank 2 including 16h light duration combined with 2000 lux intensity showed the best signs of sexual maturation in both sexes. On the basis of this study, setting up the spring light condition during prespawning season induces maturation in withspotted rabbitfish. This improvement not only by influence of photoperiod or light intensity, separately, but obtained through interaction between them. Thus, determination of threshold and resistance to light be recommended before exposure, although using proper regime during suitable time are necessary to achieve purposes considerably.

Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.