Multitrait analysis of quantitative trait loci using Bayesian composite space approach

<p>Abstract</p> <p>Background</p> <p>Multitrait analysis of quantitative trait loci can capture the maximum information of experiment. The maximum-likelihood approach and the least-square approach have been developed to jointly analyze multiple traits, but it is difficult for them to include multiple QTL simultaneously into one model.</p> <p>Results</p> <p>In this article, we have successfully extended Bayesian composite space approach, which is an efficient model selection method that can easily handle multiple QTL, to multitrait mapping of QTL. There are many statistical innovations of the proposed method compared with Bayesian single trait analysis. The first is that the parameters for all traits are updated jointly by vector or matrix; secondly, for QTL in the same interval that control different traits, the correlation between QTL genotypes is taken into account; thirdly, the information about the relationship of residual error between the traits is also made good use of. The superiority of the new method over separate analysis was demonstrated by both simulated and real data. The computing program was written in FORTRAN and it can be available for request.</p> <p>Conclusion</p> <p>The results suggest that the developed new method is more powerful than separate analysis.</p

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Diagnostic value of cancer-testis antigen mRNA in peripheral blood from hepatocellular carcinoma patients

AIM: To evaluate the diagnostic value of cancer-testis antigen (CTA) mRNA in peripheral blood samples from hepatocellular carcinoma (HCC) patients

Composite Film Based on Pulping Industry Waste and Chitosan for Food Packaging

Wood auto-hydrolysates (WAH) are obtained in the pulping process by the hydrothermal extraction, which contains lots of hemicelluloses and slight lignin. WAH and chitosan (CS) were introduced into this study to construct WAH-based films by the casting method. The FT-IR results revealed the crosslinking interaction between WAH and CS due to the Millard reaction. The morphology, transmittance, thermal properties and mechanical properties of composite WAH/CS films were investigated. As the results showed, the tensile strength, light transmittances and thermal stability of the WAH-based composite films increased with the increment of WAH/CS content ratio. In addition, the results of oxygen transfer rate (OTR) and water vapor permeability (WVP) suggested that the OTR and WVP values of the films decreased due to the addition of CS. The maximum value of tensile strengths of the composite films achieved 71.2 MPa and the OTR of the films was low as 0.16 cm3&#183;&#956;m&#183;m&#8722;2&#183;24 h&#8722;1&#183;kPa&#8722;1, these properties are better than those of other hemicelluloses composite films. These results suggested that the barrier composite films based on WAH and CS will become attractive in the food packaging application for great mechanical properties, good transmittance and low oxygen transfer rate

8-pCPT-cGMP stimulates αβγ-ENaC activity in oocytes as an external ligand requiring specific nucleotide moieties

Epithelial sodium channels (ENaC) are regulated by protein kinase A, in addition to a broad spectrum of other protein kinases. It is not clear whether cGMP/PKG signaling might regulate ENaC activity. We examined the responses of αβγ-ENaC channels expressed in Xenopus oocytes to 8-(4-chlorophenylthio)-cGMP (8-pCPT-cGMP), a cell-permeable cGMP analog. This compound stimulated human αβγ-ENaC activity in a dose-dependent fashion, but cell-impermeable cGMP had no effect. Similar stimulatory effects of cGMP were observed in oocytes expressing either mouse or rat αβγ-ENaC channels. The identical ion selectivity and amiloride sensitivity of the 8-pCPT-cGMP-activated currents to those of αβγ-ENaC channels suggest that the cGMP-activated currents are associated with expressed ENaC. The PKGI activator Sp isomer of β-phenyl-1,N2-etheno-8-bromo-cGMP did not elicit a rise in ENaC current and that the 8-pCPT-cGMP-induced activation of ENaC channels was blocked by incubating oocytes with a PKG inhibitor, but not with other cGMP-sensitive kinase inactivators for PKA, MEK, MAP, and PKC. Surprisingly, both site-directed mutation of putative consensus PKG phosphorylation sites and truncation of entire cytosolic NH2- and COOH-terminal tails did not alter the response to 8-pCPT-cGMP. The ENaC activity was activated to the same extent by 8-pCPT-cGMP in cells in which PKGII expression was knocked down using small interfering RNA. Analog to 8-CPT-cAMP, 8-pCPT-cGMP was capable of activating ENaC in the identical manner in cell-free outside-out patches. We conclude that the rapid upregulation of human αβγ-ENaC activity in oocytes by external 8-pCPT-cGMP and 4-chlorothiolphenol-cAMP depends on the para-chlorophenylthiol and the hydroxy groups, and 8-pCPT-cGMP may serve as a novel ENaC ligand in addition to activating PKG signal

β-Hydroxybutyric Sodium Salt Inhibition of Growth Hormone and Prolactin Secretion via the cAMP/PKA/CREB and AMPK Signaling Pathways in Dairy Cow Anterior Pituitary Cells

β-hydroxybutyric acid (BHBA) regulates the synthesis and secretion of growth hormone (GH) and prolactin (PRL), but its mechanism is unknown. In this study, we detected the effects of BHBA on the activities of G protein signaling pathways, AMPK-α activity, GH, and PRL gene transcription, and GH and PRL secretion in dairy cow anterior pituitary cells (DCAPCs). The results showed that BHBA decreased intracellular cAMP levels and a subsequent reduction in protein kinase A (PKA) activity. Inhibition of PKA activity reduced cAMP response element-binding protein (CREB) phosphorylation, thereby inhibiting GH and PRL transcription and secretion. The effects of BHBA were attenuated by a specific Gαi inhibitor, pertussis toxin (PTX). In addition, intracellular BHBA uptake mediated by monocarboxylate transporter 1 (MCT1) could trigger AMPK signaling and result in the decrease in GH and PRL mRNA translation in DCAPCs cultured under low-glucose and non-glucose condition when compared with the high-glucose group. This study identifies a biochemical mechanism for the regulatory action of BHBA on GH and PRL gene transcription, translation, and secretion in DCAPCs, which may be one of the factors that regulate pituitary function during the transition period in dairy cows