Morphological studies in modern teratological investigations

Despite the variety of modern molecular techniques available, examination of foetal anatomy is still a fundamental part of teratological studies in evaluating the developmental toxicity of xenobiotics or other non-chemical factors. The article presents contemporary methods of embryotoxicity and foetotoxicity assessment. A single alizarin red S and double alcian blue followed by alizarin red S staining, as well as various methods of soft tissue examination are discussed

Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover

<p>Abstract</p> <p>Background</p> <p>Natural acquisition of novel genes from other organisms by horizontal or lateral gene transfer is well established for microorganisms. There is now growing evidence that horizontal gene transfer also plays important roles in the evolution of eukaryotes. Genome-sequencing and EST projects of plant and animal associated nematodes such as <it>Brugia</it>, <it>Meloidogyne</it>, <it>Bursaphelenchus </it>and <it>Pristionchus </it>indicate horizontal gene transfer as a key adaptation towards parasitism and pathogenicity. However, little is known about the functional activity and evolutionary longevity of genes acquired by horizontal gene transfer and the mechanisms favoring such processes.</p> <p>Results</p> <p>We examine the transfer of cellulase genes to the free-living and beetle-associated nematode <it>Pristionchus pacificus</it>, for which detailed phylogenetic knowledge is available, to address predictions by evolutionary theory for successful gene transfer. We used transcriptomics in seven <it>Pristionchus </it>species and three other related diplogastrid nematodes with a well-defined phylogenetic framework to study the evolution of ancestral cellulase genes acquired by horizontal gene transfer. We performed intra-species, inter-species and inter-genic analysis by comparing the transcriptomes of these ten species and tested for cellulase activity in each species. Species with cellulase genes in their transcriptome always exhibited cellulase activity indicating functional integration into the host's genome and biology. The phylogenetic profile of cellulase genes was congruent with the species phylogeny demonstrating gene longevity. Cellulase genes show notable turnover with elevated birth and death rates. Comparison by sequencing of three selected cellulase genes in 24 natural isolates of <it>Pristionchus pacificus </it>suggests these high evolutionary dynamics to be associated with copy number variations and positive selection.</p> <p>Conclusion</p> <p>We could demonstrate functional integration of acquired cellulase genes into the nematode's biology as predicted by theory. Thus, functional assimilation, remarkable gene turnover and selection might represent key features of horizontal gene transfer events in nematodes.</p

A Genome Wide Association Study of arabinoxylan content in 2-row spring barley grain

In barley endosperm arabinoxylan (AX) is the second most abundant cell wall polysaccharide and in wheat it is the most abundant polysaccharide in the starchy endosperm walls of the grain. AX is one of the main contributors to grain dietary fibre content providing several health benefits including cholesterol and glucose lowering effects, and antioxidant activities. Due to its complex structural features, AX might also affect the downstream applications of barley grain in malting and brewing. Using a high pressure liquid chromatography (HPLC) method we quantified AX amounts in mature grain in 128 spring 2-row barley accessions. Amounts ranged from ~ 5.2 μg/g to ~ 9 μg/g. We used this data for a Genome Wide Association Study (GWAS) that revealed three significant quantitative trait loci (QTL) associated with grain AX levels which passed a false discovery threshold (FDR) and are located on two of the seven barley chromosomes. Regions underlying the QTLs were scanned for genes likely to be involved in AX biosynthesis or turnover, and strong candidates, including glycosyltransferases from the GT43 and GT61 families and glycoside hydrolases from the GH10 family, were identified. Phylogenetic trees of selected gene families were built based on protein translations and were used to examine the relationship of the barley candidate genes to those in other species. Our data reaffirms the roles of existing genes thought to contribute to AX content, and identifies novel QTL (and candidate genes associated with them) potentially influencing the AX content of barley grain. One potential outcome of this work is the deployment of highly associated single nucleotide polymorphisms markers in breeding programs to guide the modification of AX abundance in barley grain

NIST interlaboratory study on glycosylation analysis of monoclonal antibodies : comparison of results from diverse analytical methods

Glycosylation is a topic of intense current interest in the development of biopharmaceuticals since it is related to drug safety and efficacy. This work describes results of an interlaboratory study on the glycosylation of the Primary Sample (PS) of NISTmAb, a monoclonal antibody reference material. Seventy‑six laboratories from industry, university, research, government, and hospital sectors in Europe, North America, Asia, and Australia submitted a total of 103 reports on glycan distributions. The principal objective of this study was to report and compare results for the full range of analytical methods presently used in the glycosylation  analysis of mAbs. Therefore, participation was unrestricted, with laboratories choosing their own measurement techniques. Protein glycosylation was determined in various ways, including at the level of intact mAb, protein fragments, glycopeptides, or released glycans, using a wide variety of methods for derivatization, separation, identification, and quantification. Consequently, the diversity of results was enormous, with the number of glycan compositions identified by each laboratory ranging from 4 to 48. In total, one hundred sixteen glycan compositions were reported, of which 57 compositions could be assigned consensus abundance values. These consensus medians provide community-derived values for NISTmAb PS. Agreement with the consensus medians did not depend on the specific method or laboratory type.. The study provides a view of the current state-of-the-art for biologic glycosylation measurement and suggests a clear need for harmonization of glycosylation analysis methods

Improved lumping friction model for liquid pipe flow

Normally, during one-dimensional pipe flow, the friction terms are calculated with the use of a numerical method (for example MOC – method of characteristics) at every computational node along the pipe and at every time step. This procedure tends to increase the computational effort greatly. A considerable increase in computational speed can be archived by calculating the frequency-dependent friction at the end of the pipe only. To avoid possible problems (no damping at closed walls, underestimate damping on high impedance components) the frequency-dependent friction term is calculated from the flow waves. The lumping friction model in this work is based on a modificated Schohl convolution integral solution. In addition, the work examined the impact of using of simplified effective weighting function on the obtained results of numerical simulations. The modified method in conjunction with the use of simplified weighting function allow determination of real-time estimate of the basic parameters representing the fluid flow in complex hydraulic systems, water supply, etc

Convolution integral in transient pipe flow

This paper is devoted to the modeling of hydraulic losses during transient flow of liquids in pressure lines. Unsteady pipe wall shear stress is presented in the form of a convolution integral of liquid acceleration and a weighting function. The weighting function depends on the dimensionless time and the Reynolds number. In its first revision (Zielke W 1968 J. ASME 90 109) it had a complex and inefficient mathematical structure (featured power growth of computational time). Therefore, further work aimed at developing the so-called efficient models for correct estimation of hydraulic resistance with simultaneous linear loading of the computer's operating memory was needed. The work compared the methods of numerical solving of the convolution integral known from the literature (classic by Zielke W 1968 J. ASME 90 109 and Yardy A E and Brown J M B 2010 J. Hydratd. Eng. 136 (7) 453 and efficient by Trikha A K 1975 J. Fluids Eng. p. 97. Kagawa T et at. 1983 Trans. Jpn. Soc. Mech. Eng. 49 (447) 2638 and Schohl G A 1993 J. Fluids Eng. 115 420). The comparison highlighted the level of usefulness of the analyzed models in simulating the water hammer and revealed the demand for further research for the improvement of efficiency of the solutions

Nowe efektywne funkcje wagowe umożliwiające symulację niestacjonarnych oporów hydraulicznych podczas przepływówniestacjonarnych oporów hydraulicznych podczas przepływów cieczy w przewodach ciśnieniowych

Most papers dealing with calculations and simulations of the unsteady liquid pipe flow are based on the assumption that the formula for quasi-steady friction (Darcy-Weisbach formula) can be applied. In the case of fast changes, like fast transients e.g. water hammer, it fails. In this work, the wall shear stress is presented as a sum of quasi-steady and unsteady component. The unsteady component of the wall shear stress is modeled as a convolution of local fluid acceleration and a weighting function. The original weighting function has usually a very complicated structure, and what is more, makes impossible to carry out an efficient simulation of dynamical runs. In this paper, in order to enable efficient calculation of the unsteady component of the wall shear stress, new weighting functions are presented as sums of exponential components.W dużej części prac, dotyczących obliczania oraz symulacji niestacjonarnego przepływu cieczy w przewodach ciśnieniowych, opory wyznacza się jedynie z dobrze znanej formuły Darcy-Weisbacha. Niestety w szybkozmiennych przepływach, takich jak np. uderzenie hydrauliczne, założenie quasi-stacjonarności oporów jest poważnym błędem. Wponiższej pracy naprężenie styczne na ściance przewodu wyznacza się z sumy quasi-stacjonarnego składnika oraz niestacjonarnego. Niestacjonarny składnik naprężenia stycznego modelowany jest jako splot lokalnego przyśpieszenia cieczy oraz funkcji wagi. Klasyczne funkcje wagi mają skomplikowaną postać, co uniemożliwia efektywne wyznaczanie oporów. W tej pracy przedstawione zostały nowe efektywne postacie funkcji wagowych o rozszerzonych zakresach stosowalności

Transient cavitating pipe flow: Computation models and methods

The paper presents four key mathematical models of a transient cavitating pipe flow, i.e. the column separation model (CSM), the gas cavitation model (CSMG), Adamkowski’s model (CSMA) and the bubbly cavitation model (BCM). All models investigated in the paper take into account unsteady frictional loss models. The equations describing all models have been solved using the method of characteristics at first and the finite differences method then. The results of numerical simulations have been compared with the results obtained in the experiments. Transients which have taken into account the unsteady wall shear stress fit well with the results of experiments in comparison with the quasi-steady wall shear stress model

Uniwersalna funkcja wagi w modelowaniu niestacjonarnych przepływów z kawitacją występujących w przewodach ciśnieniowych

This work concerns modeling of time-varying resistance during transient cavitating liquid pipe flow. The wall shear stress is presented in the way introduced by Zielke as the integral convolution of liquid local velocity changes and a weighting function. A new procedure for determination, so-called, a universal laminar-turbulent weighting function, which combines functions of Zielke and Vardy and Brown or Zielke and Zarzycki, is presented. Based on these weighting functions, the method of simulation transients in the pressure lines in a wide range of Reynolds numbers is presented. It eliminates numerical problems associated with the change of laminar flow into turbulent and vice versa. An example application of this method for simulation of water hammer is presented. The calculation results are compared against experiments presented by Bergant and Simpson, and good agreement is found.Praca dotyczy modelowania zmiennych w czasie oporów podczas nieustalonego przepływu cieczy w przewodach ciśnieniowych. Naprężenie styczne na ściance przewodu przedstawione zostało w klasyczny sposób (wg. Zielke) jako całka splotowa z przyśpieszenia cieczy i pewnej funkcji wagowej. Przedstawiono procedury wyznaczania dwóch uniwersalnych funkcji wagowych laminarnoturbulentnych (wg. Zielke i Vardy-Browna oraz wg. Zielke i Zarzyckiego).W oparciu o te funkcje przedstawiono metodę modelowania (symulacji) przebiegów przejściowych w przewodach ciśnieniowych w szerokim zakresie liczb Reynoldsa. Eliminuje on problemy natury numerycznej związane z przechodzeniem min. z przepływu laminarnego w turbulentny i odwrotnie. Podano przykład zastosowania opracowanej metody do symulacji uderzenia hydraulicznego. Wyniki obliczeń porównano z wynikami eksperymentalnymi wg. Berganta i Simpsona, otrzymując dobrą zgodność