A pipeline to study structural interactions among Spodoptera frugiperda serine proteinases and plant proteinase inhibitors.

We propose here a computational biology pipeline to identify and analyze possible structural determinants that could explain some level of insensitivity by S. frugiperda serine proteinases (SPs) against plant PIs observed in a real time PCR experiment.GA 330

Bichromatic Local Oscillator for Detection of Two-Mode Squeezed States of Light

We present a new technique for the detection of two-mode squeezed states of light that allows for a simple characterization of these quantum states. The usual detection scheme, based on heterodyne measurements, requires the use of a local oscillator with a frequency equal to the mean of the frequencies of the two modes of the squeezed field. As a result, unless the two modes are close in frequency, a high-frequency shot-noise-limited detection system is needed. We propose the use of a bichromatic field as the local oscillator in the heterodyne measurements. By the proper selection of the frequencies of the bichromatic field, it is possible to arbitrarily select the frequency around which the squeezing information is located, thus making it possible to use a low-bandwidth detection system and to move away from any excess noise present in the system.Comment: 11 pages, 3 figure

Effects of acute aerobic exercise on rats serum extracellular vesicles diameter, concentration and small RNAs content

Physical exercise stimulates organs, mainly the skeletal muscle, to release a broad range of molecules, recently dubbed exerkines. Among them, RNAs, such as miRNAs, piRNAs, and tRNAs loaded in extracellular vesicles (EVs) have the potential to play a significant role in the way muscle and other organs communicate to translate exercise into health. Low, moderate and high intensity treadmill protocols were applied to rat groups, aiming to investigate the impact of exercise on serum EVs and their associated small RNA molecules. Transmission electron microscopy, resistive pulse sensing, and western blotting were used to investigate EVs morphology, size distribution, concentration and EVs marker proteins. Small RNA libraries from EVs RNA were sequenced. Exercise did not change EVs size, while increased EVs concentration. Twelve miRNAs were found differentially expressed after exercise: rno-miR-128-3p, 1033p, 330-5p, 148a-3p, 191a-5p, 10b-5p, 93-5p, 25-3p, 142-5p, 3068-3p, 142-3p, and 410-3p. No piRNA was found differentially expressed, and one tRNA, trna8336, was found down-regulated after exercise. The differentially expressed miRNAs were predicted to target genes involved in the MAPK pathway. A single bout of exercise impacts EVs and their small RNA load, reinforcing the need for a more detailed investigation into EVs and their load as mediators of health-promoting exercise

Improved methods for detection of β-galactosidase (lacZ) activity in hard tissue

The ß-galactosidase gene (lacZ) of Escherichia coli is widely used as a reporter gene. The expression of lacZ can be detected by enzyme-based histochemical staining using chromogenic substrates such as 5-bromo-4-chloro-3-indolyl-ß-D: -galactoside (X-gal). Because the enzymatic activity of lacZ is vulnerable to high temperatures and acid treatment for demineralization, detection of lacZ on paraffinized sections is difficult, especially for hard tissues, which require demineralization before sectioning in paraffin. To circumvent this problem, whole-mount X-gal staining before sectioning is performed. However, detection of lacZ activity in the center of larger portions of hard whole adult tissues is challenging. In this study, focusing on fixation procedures, we determined the conditions conducive to improved detection of lacZ activity in deeper areas of whole tissues. We used an annexin a5 (Anxa5)-lacZ reporter mouse model in which the Anxa5 expression in hard tissue is indicated by lacZ activity. We found that lacZ activity could be detected throughout the periodontal ligament of adult mice when fixed in 100% acetone, whereas it was not detected in the periodontal ligament around the root apex fixed in glutaraldehyde and paraformaldehyde. This staining could not be detected in wild-type mice. Acetone maintains the lacZ activity within 48 h of fixation at both 4°C and at room temperature. In conclusion, acetone is the optimal fixative to improve permeability for staining of lacZ activity in large volumes of adult hard tissues

Thermodynamic Properties of the One-Dimensional Extended Quantum Compass Model in the Presence of a Transverse Field

The presence of a quantum critical point can significantly affect the thermodynamic properties of a material at finite temperatures. This is reflected, e.g., in the entropy landscape S(T; c) in the vicinity of a quantum critical point, yielding particularly strong variations for varying the tuning parameter c such as magnetic field. In this work we have studied the thermodynamic properties of the quantum compass model in the presence of a transverse field. The specific heat, entropy and cooling rate under an adiabatic demagnetization process have been calculated. During an adiabatic (de)magnetization process temperature drops in the vicinity of a field-induced zero-temperature quantum phase transitions. However close to field-induced quantum phase transitions we observe a large magnetocaloric effect

The Effect of Transposable Element Insertions on Gene Expression Evolution in Rodents

Background:Many genomes contain a substantial number of transposable elements (TEs), a few of which are known to be involved in regulating gene expression. However, recent observations suggest that TEs may have played a very important role in the evolution of gene expression because many conserved non-genic sequences, some of which are know to be involved in gene regulation, resemble TEs. Results:Here we investigate whether new TE insertions affect gene expression profiles by testing whether gene expression divergence between mouse and rat is correlated to the numbers of new transposable elements inserted near genes. We show that expression divergence is significantly correlated to the number of new LTR and SINE elements, but not to the numbers of LINEs. We also show that expression divergence is not significantly correlated to the numbers of ancestral TEs in most cases, which suggests that the correlations between expression divergence and the numbers of new TEs are causal in nature. We quantify the effect and estimate that TE insertion has accounted for ~20% (95% confidence interval: 12% to 26%) of all expression profile divergence in rodents. Conclusions:We conclude that TE insertions may have had a major impact on the evolution of gene expression levels in rodents

A straightforward multiallelic significance test for the Hardy-Weinberg equilibrium law

Much forensic inference based upon DNA evidence is made assuming Hardy-Weinberg Equilibrium (HWE) for the genetic loci being used. Several statistical tests to detect and measure deviation from HWE have been devised, and their limitations become more obvious when testing for deviation within multiallelic DNA loci. The most popular methods-Chi-square and Likelihood-ratio tests-are based on asymptotic results and cannot guarantee a good performance in the presence of low frequency genotypes. Since the parameter space dimension increases at a quadratic rate on the number of alleles, some authors suggest applying sequential methods, where the multiallelic case is reformulated as a sequence of “biallelic” tests. However, in this approach it is not obvious how to assess the general evidence of the original hypothesis; nor is it clear how to establish the significance level for its acceptance/rejection. In this work, we introduce a straightforward method for the multiallelic HWE test, which overcomes the aforementioned issues of sequential methods. The core theory for the proposed method is given by the Full Bayesian Significance Test (FBST), an intuitive Bayesian approach which does not assign positive probabilities to zero measure sets when testing sharp hypotheses. We compare FBST performance to Chi-square, Likelihood-ratio and Markov chain tests, in three numerical experiments. The results suggest that FBST is a robust and high performance method for the HWE test, even in the presence of several alleles and small sample sizes

Toward a global description of the nucleus-nucleus interaction

Extensive systematization of theoretical and experimental nuclear densities and of optical potential strengths exctracted from heavy-ion elastic scattering data analyses at low and intermediate energies are presented.The energy-dependence of the nuclear potential is accounted for within a model based on the nonlocal nature of the interaction.The systematics indicate that the heavy-ion nuclear potential can be described in a simple global way through a double-folding shape,which basically depends only on the density of nucleons of the partners in the collision.The poissibility of extracting information about the nucleon-nucleon interaction from the heavy-ion potential is investigated.Comment: 12 pages,12 figure