Semiquantitative RT-PCR measurement of gene expression in rat tissues including a correction for varying cell size and number

Background: Current methodology of gene expression analysis limits the possibilities of comparison between cells/tissues of organs in which cell size and/or number changes as a consequence of the study (e.g. starvation). A method relating the abundance of specific mRNA copies per cell may allow direct comparison or different organs and/or changing physiological conditions. Methods: With a number of selected genes, we analysed the relationship of the number of bases and the fluorescence recorded at a present level using cDNA standards. A lineal relationship was found between the final number of bases and the length of the transcript. The constants of this equation and those of the relationship between fluorescence and number of bases in cDNA were determined and a general equation linking the length of the transcript and the initial number of copies of mRNA was deduced for a given pre-established fluorescence setting. This allowed the calculation of the concentration of the corresponding mRNAs per g of tissue. The inclusion of tissue RNA and the DNA content per cell, allowed the calculation of the mRNA copies per cell. Results: The application of this procedure to six genes: Arbp, cyclophilin, ChREBP, T4 deiodinase 2, acetyl-CoA carboxylase 1 and IRS-1, in liver and retroperitoneal adipose tissue of food-restricted rats allowed precise measures of their changes irrespective of the shrinking of the tissue, the loss of cells or changes in cell size, factors that deeply complicate the comparison between changing tissue conditions. The percentage results obtained with the present methods were essentially the same obtained with the delta-delta procedure and with individual cDNA standard curve quantitative RT-PCR estimation. Conclusion: The method presented allows the comparison (i.e. as copies of mRNA per cell) between different genes and tissues, establishing the degree of abundance of the different molecular species tested.

Terrestrial laser scanning for landslides deformation monitoring

Within last few years a new type of instruments called Terrestrial Laser Scanners (TLS) entered to the commercial market. These devices brought a possibility to obtain completely new type of spatial, three dimensional data describing the object of interest. TLS instruments are generating a type of data that needs a special treatment. Appearance of this technique made possible to monitor deformations of very large objects, like investigated here landslides, with new quality level. This change is visible especially with relation to the size and number of the details that can be observed with this new method. Taking into account this context presented here work is oriented on recognition and characterization of raw data received from the TLS instruments as well as processing phases, tools and techniques to do them. Main objective are definition and recognition of the problems related with usage of the TLS data, characterization of the quality single point generated by TLS, description and investigation of the TLS processing approach for landslides deformation measurements allowing to obtain 3D deformation characteristic and finally validation of the obtained results. The above objectives are based on the bibliography studies and research work followed by several experiments that will prove the conclusions.

Optimal management of microgrids

Desenvolupament dels models matemàtics necessaris per a controlar de forma òptima la microxarxa existent als laboratoris del Institut de Recerca en Energia de Catalunya. Els algoritmes s'implementaran per tal de simular el comportament i posteriorment es programaran directament sobre els elements de la microxarxa per verificar el seu correcte funcionament.. Desenvolupament dels models matemàtics necessaris per a controlar de forma òptima la microxarxa existent als laboratoris del Institut de Recerca en Energia de Catalunya. Els algoritmes s'implementaran per tal de simular el comportament i posteriorment es programaran directament sobre els elements de la microxarxa per verificar el seu correcte funcionament.

Gleevec, an Abl family inhibitor, produces a profound change in cell shape and migration (in press)

The issue of how contractility and adhesion are related to cell shape and migration pattern remains largely unresolved. In this paper we report that Gleevec (Imatinib), an Abl family kinase inhibitor, produces a profound change in the shape and migration of rat bladder tumor cells (NBTII) plated on collagen-coated substrates. Cells treated with Gleevec adopt a highly spread D-shape and migrate more rapidly with greater persistence. Accompanying this more spread state is an increase in integrin-mediated adhesion coupled with increases in the size and number of discrete adhesions. In addition, both total internal reflection fluorescence microscopy (TIRFM) and interference reflection microscopy (IRM) revealed a band of small punctate adhesions with rapid turnover near the cell leading margin. These changes led to an increase in global cell-substrate adhesion strength, as assessed by laminar flow experiments. Gleevec-treated cells have greater RhoA activity which, via myosin activation, led to an increase in the magnitude of total traction force applied to the substrate. These chemical and physical alterations upon Gleevec treatment produce the dramatic change in morphology and migration that is observed.

Spottier Targets Are Less Attractive to Tabanid Flies: On the Tabanid-Repellency of Spotty Fur Patterns

During blood-sucking, female members of the family Tabanidae transmit pathogens of serious diseases and annoy their host animals so strongly that they cannot graze, thus the health of the hosts is drastically reduced. Consequently, a tabanid-resistant coat with appropriate brightness, colour and pattern is advantageous for the host. Spotty coats are widespread among mammals, especially in cattle (Bos primigenius). In field experiments we studied the influence of the size and number of spots on the attractiveness of test surfaces to tabanids that are attracted to linearly polarized light. We measured the reflection-polarization characteristics of living cattle, spotty cattle coats and the used test surfaces. We show here that the smaller and the more numerous the spots, the less attractive the target (host) is to tabanids. We demonstrate that the attractiveness of spotty patterns to tabanids is also reduced if the target exhibits spottiness only in the angle of polarization pattern, while being homogeneous grey with a constant high degree of polarization. Tabanid flies respond strongly to linearly polarized light, and we show that bright and dark parts of cattle coats reflect light with different degrees and angles of polarization that in combination with dark spots on a bright coat surface disrupt the attractiveness to tabanids. This could be one of the possible evolutionary benefits that explains why spotty coat patterns are so widespread in mammals, especially in ungulates, many species of which are tabanid hosts

Grain size analyses in tin-lead glazes based on 2d-sections

A problem in the archaeometric classification of Catalan Renaissance pottery is the fact, thatthe clay supply of the pottery workshops was centrally organized by guilds, and thereforeusually all potters of a single production centre produced chemically similar ceramics.However, analysing the glazes of the ware usually a large number of inclusions in the glaze isfound, which reveal technological differences between single workshops. These inclusionshave been used by the potters in order to opacify the transparent glaze and to achieve a whitebackground for further decoration.In order to distinguish different technological preparation procedures of the single workshops,at a Scanning Electron Microscope the chemical composition of those inclusions as well astheir size in the two-dimensional cut is recorded. Based on the latter, a frequency distributionof the apparent diameters is estimated for each sample and type of inclusion.Following an approach by S.D. Wicksell (1925), it is principally possible to transform thedistributions of the apparent 2D-diameters back to those of the true three-dimensional bodies.The applicability of this approach and its practical problems are examined using differentways of kernel density estimation and Monte-Carlo tests of the methodology. Finally, it istested in how far the obtained frequency distributions can be used to classify the pottery

A finite-population revenue management model and a risk-ratio procedure for the joint estimation of population size and parameters

Many dynamic revenue management models divide the sale period into a finite number of periods T and assume, invoking a fine-enough grid of time, that each period sees at most one booking request. These Poisson-type assumptions restrict the variability of the demand in the model, but researchers and practitioners were willing to overlook this for the benefit of tractability of the models. In this paper, we criticize this model from another angle. Estimating the discrete finite-period model poses problems of indeterminacy and non-robustness: Arbitrarily fixing T leads to arbitrary control values and on the other hand estimating T from data adds an additional layer of indeterminacy. To counter this, we first propose an alternate finite-population model that avoids this problem of fixing T and allows a wider range of demand distributions, while retaining the useful marginal-value properties of the finite-period model. The finite-population model still requires jointly estimating market size and the parameters of the customer purchase model without observing no-purchases. Estimation of market-size when no-purchases are unobservable has rarely been attempted in the marketing or revenue management literature. Indeed, we point out that it is akin to the classical statistical problem of estimating the parameters of a binomial distribution with unknown population size and success probability, and hence likely to be challenging. However, when the purchase probabilities are given by a functional form such as a multinomial-logit model, we propose an estimation heuristic that exploits the specification of the functional form, the variety of the offer sets in a typical RM setting, and qualitative knowledge of arrival rates. Finally we perform simulations to show that the estimator is very promising in obtaining unbiased estimates of population size and the model parameters.

The size and distribution of donations: Effects of numbers of potential recipients

Whereas much literature exists on choice overload, little is known about effects of numbers of alternatives in donation decisions. How do these affect both the size and distribution of donations? We hypothesize that donations are affected by the reputation of recipients and increase with their number, albeit at a decreasing rate. Allocations to recipients reflect different concepts of fairness equity and equality. Both may be employed but, since they differ in cognitive and emotional costs, numbers of recipients are important. Using a cognitive (emotional) argument, distributions become more uniform (skewed) as numbers increase. In a survey, respondents indicated how they would donate lottery winnings of 50 Euros. Results indicated that more was donated to NGO s that respondents knew better. Second, total donations increased with the number of recipients albeit at a decreasing rate. Third, distributions of donations became more skewed as numbers increased. We comment on theoretical and practical implications.

Finite-size scaling analysis of the avalanches in the three-dimensional Gaussian random-field Ising model with metastable dynamics

A numerical study is presented of the third-dimensional Gaussian random-field Ising model at T=0 driven by an external field. Standard synchronous relaxation dynamics is employed to obtain the magnetization versus field hysteresis loops. The focus is on the analysis of the number and size distribution of the magnetization avalanches. They are classified as being nonspanning, one-dimensional-spanning, two-dimensional-spanning, or three-dimensional-spanning depending on whether or not they span the whole lattice in different space directions. Moreover, finite-size scaling analysis enables identification of two different types of nonspanning avalanches (critical and noncritical) and two different types of three-dimensional-spanning avalanches (critical and subcritical), whose numbers increase with L as a power law with different exponents. We conclude by giving a scenario for avalanche behavior in the thermodynamic limit.

Finite-size scaling investigation of the liquid-liquid critical point in ST2 water and its stability with respect to crystallization.

The liquid-liquid critical point scenario of water hypothesizes the existence of two metastable liq- uid phases low-density liquid (LDL) and high-density liquid (HDL) deep within the supercooled region. The hypothesis originates from computer simulations of the ST2 water model, but the stabil- ity of the LDL phase with respect to the crystal is still being debated. We simulate supercooled ST2 water at constant pressure, constant temperature, and constant number of molecules N for N ≤ 729 and times up to 1 μs. We observe clear differences between the two liquids, both structural and dynamical. Using several methods, including finite-size scaling, we confirm the presence of a liquid-liquid phase transition ending in a critical point. We find that the LDL is stable with respect to the crystal in 98% of our runs (we perform 372 runs for LDL or LDL-like states), and in 100% of our runs for the two largest system sizes (N = 512 and 729, for which we perform 136 runs for LDL or LDL-like states). In all these runs, tiny crystallites grow and then melt within 1 μs. Only for N ≤ 343 we observe six events (over 236 runs for LDL or LDL-like states) of spontaneous crystal- lization after crystallites reach an estimated critical size of about 70 ± 10 molecules.

First genome size estimations for some eudicot families and genera

First genome size estimations for some eudicot families and genera.- Genome size diversity in angiosperms varies roughly 2400-fold, although approximately 45% of angiosperm families lack a single genome size estimation, and therefore, this range could be enlarged. To contribute completing family and genera representation, DNA C-Values are here provided for 19 species from 16 eudicot families, including first values for 6 families, 14 genera and 17 species. The sample of species studied is very diverse, including herbs, weeds, vines, shrubs and trees. Data are discussed regarding previous genome size estimates of closely related species or genera, if any, their chromosome number, growth form or invasive behaviour. The present research contributes approximately 1.5% new values for previously unreported angiosperm families, being the current coverage around 55% of angiosperm families, according to the Plant DNA C-Values Database.

The effect of age at the first mating and herd size on the lifetime productivity of sows

The effect of age at the first mating and herd size were evaluated in the reference Spanish Databank (BDporc) of 37 698 sows born between 1991 and 1995 and with individual lifetime records. The data included dates of births at entrance and culling, first mating, repetitive mating and conception, first farrowing and weaning records. Individual records were validated before the analysis by screening them through a tolerance “filter” in order to eliminate the extreme values from the analysis. The total database of the sows was classified in 7 classes according to age at the first mating (< 210, 210–220, 221–230, 231–240, 241–250, 251–270, and > 270 days) and in 6 classes of herd size (< 200, 200–300, 301–400, 401–600, 601–800, and > 800 sows). The total number of litters and number of weaned piglets obtained from each sow during the lifetime production were significantly (P < 0.05) greater for gilts between 221 and 240 d of age at the first mating. There was a significant (P < 0.001) effect of the herd size on the reproductive performance of the sow, and the best performance was obtained with herds with 401 to 600 sows compared to < 200 or > 800 sow-herds. Furthermore, a significant (P < 0.001) interaction between age at the first mating and herd size was detected and can be associated with a particular pattern for the herd size class 401–600 sows with the best performances obtained for the sows first mated at less than 200 days. For the other herd sizes, the results indicated that sows mated for the first time at the right age, 221–240 days, are more productive, both in the number and size of the parities throughout lifetime production.