Wright-Fisher diffusion bridges

The trajectory of the frequency of an allele which begins at $x$ at time $0$ and is known to have frequency $z$ at time $T$ can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when $x=z=0$ are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time $T$. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time $t\in (0,T)$. In a bridge with allele frequencies of 0 at times 0 and $T$ the coalescence structure is that the population coalesces in two directions from $t$ to $0$ and $t$ to $T$ such that there is just one lineage of the allele under consideration at times $0$ and $T$. The genealogy in Wright-Fisher diffusion bridges with selection is more complex than in the neutral model, but still with the property of the population branching and coalescing in two directions from time $t\in (0,T)$. The density of the frequency of an allele at time $t$ is expressed in a way that shows coalescence in the two directions. A new algorithm for exact simulation of a neutral Wright-Fisher bridge is derived. This follows from knowing the density of the frequency in a bridge and exact simulation from the Wright-Fisher diffusion. The genealogy of the neutral Wright-Fisher bridge is also modelled by branching P\'olya urns, extending a representation in a Wright-Fisher diffusion. This is a new very interesting representation that relates Wright-Fisher bridges to classical urn models in a Bayesian setting. This paper is dedicated to the memory of Paul Joyce

Methylation of RASSFIA in primary gastric cancer and corresponding normal tissue by MSP

<p><b>Copyright information:</b></p><p>Taken from "Association of diminished expression of RASSF1A with promoter methylation in primary gastric cancer from patients of central China"</p><p>http://www.biomedcentral.com/1471-2407/7/120</p><p>BMC Cancer 2007;7():120-120.</p><p>Published online 3 Jul 2007</p><p>PMCID:PMC1925110.</p><p></p> Lane 3, 4 and lane 6, 7 show a representative result from a tumor and normal sample, respectively. U: amplified product with primer recognizing unmethylated sequences; M: amplified product with primer recognizing methylated sequences. Genomic DNA, methylated in vitro by CpG methylase (Sss I) was used as a positive control. Water blank was used as a negative control. The PCR products were resolved on a 8% polyacrylamide gel

Protein expression of RASSF1A in primary gastric cancer (T) and corresponding normal tissue (N)

<p><b>Copyright information:</b></p><p>Taken from "Association of diminished expression of RASSF1A with promoter methylation in primary gastric cancer from patients of central China"</p><p>http://www.biomedcentral.com/1471-2407/7/120</p><p>BMC Cancer 2007;7():120-120.</p><p>Published online 3 Jul 2007</p><p>PMCID:PMC1925110.</p><p></p> Protein level of RASSF1A was quantified by Western-blotting compared with GAPDH

Anthranilamides as Bioinspired Molecular Electrets: Experimental Evidence for a Permanent Ground-State Electric Dipole Moment

As electrostatic equivalents of magnets, organic electrets offer unparalleled properties for impacting energy conversion and electronic applications. While biological systems have evolved to efficiently utilize protein α-helices as molecular electrets, the synthetic counterparts of these conjugates still remain largely unexplored. This paper describes a study of the electronic properties of anthranilamide oligomers, which proved to be electrets based on their intrinsic dipole moments as evident from their spectral and dielectric properties. NMR studies provided the means for estimating the direction of the intrinsic electric dipoles of these conjugates. This study sets the foundation for the development of a class of organic materials that are de novo designed from biomolecular motifs and possess unexplored electronic properties

Pulsed Direct Current Arc-Induced Nanoelectrospray Ionization Mass Spectrometry

This study explores the innovative field of pulsed direct current arc-induced nanoelectrospray ionization mass spectrometry (DCAI-nano-ESI-MS), which utilizes a low-temperature direct current (DC) arc to induce ESI during MS analyses. By employing a 15 kV output voltage, the DCAI-nano-ESI source effectively identifies various biological molecules, including angiotensin II, bradykinin, cytochrome C, and soybean lecithin, showcasing impressive analyte signals and facilitating multicharge MS in positive- and negative-ion modes. Notably, results show that the oxidation of fatty acids using a DC arc produces [M + O – H]− ions, which aid in identifying the location of CC bonds in unsaturated fatty acids and distinguishing between isomers based on diagnostic ions observed during collision-induced dissociation tandem MS. This study presents an approach for identifying the sn-1 and sn-2 positions in phosphatidylcholine using phosphatidylcholine and nitrate adduct ions, accurately determining phosphatidylcholine molecular configurations via the Paternò–Büchi reaction. With all the advantages above, DCAI-nano-ESI holds significant promise for future analytical and bioanalytical applications

BSP Gene Silencing Inhibits Migration, Invasion, and Bone Metastasis of MDA-MB-231BO Human Breast Cancer Cells

<div><p>Bone sialoprotein (BSP) has been implicated in a variety of physiological and pathophysiological events, including tumor cell invasion, bone homing, adhesion, and matrix degradation. To explore the potential involvement of BSP in human breast cancer cell invasion and metastasis, we used retrovirus-mediated RNAi to deplete BSP levels in the human bone-seeking breast cancer cell line MDA-MB-231BO (231BO) and established the 231BO-BSP27 and 231BO-BSP81 cell clones. Cell proliferation, colony formation, wound healing, and the ability to invade into matrigel of these BSP-depleted clones were all decreased. Both 231BO-BSP27 cells and 231BO-BSP81 cells showed a significant (15.4% and 28.6% respectively) reduction of bone metastatic potential following intracardiac injection as determined by X-ray detection and by hematoxylin and eosin staining. Moreover, the expression of integrins αvβ3 and β3 was decreased in the BSP-silenced cells whereas ectopic BSP expression increased the integrins αvβ3 and β3 levels. These results together suggest that BSP silencing decreased the integrin αvβ3 and β3 levels, in turn inhibiting cell migration and invasion and decreasing the ability of the cells to metastasize to bone.</p></div

Silencing BSP inhibits 231BO cell growth and colony formation.

<p>(A) Growth curves of 231BO-BSP27, 231BO-BSP81, 231BO-BSP100, 231BO-Scrambled, and 231BO cells detected by MTT assay showing that the viability of 231BO-BSP27 and 231BO-BSP81 cells is significantly decreased from the fourth day on. (B). The numbers of colonies formed by the 231BO-BSP27 and 231BO-BSP81 cells are decreased at the endpoint of 2 weeks. *p<0.05 <i>vs</i> 231BO; **p<0.001 <i>vs</i> 231BO.</p

The levels of BSP and integrins.

<p>(A) Flow cytometry (FCM) analyses of αvβ3 protein in the 231BO-BSP27 and 23BO-Scrambled cells, with their negative control in front. The αvβ3 level is lower in the 231-BSP27 cells than in the 231BO-Scrambled cells. (B) FCM analyses for EGFP are used to detect the percentage of the pIRES2-EGFP and pIRES2-hBSP-EGFP transfected cells, while FCM analyses for αvβ3 detect the effect of BSP on the αvβ3 expression. The αvβ3 level is decreased in BSP-depleted cells but is restored by transfection with the pIRES2-hBSP-EGFP. (C) Western blots show that the β3 level is decreased in BSP-depleted cells but is restored by BSP re-expression, with GAPDH as the loading control. (D) Comparisons of the αvβ3, β3 and BSP levels in four cell clones. **p<0.001 <i>vs</i> 231BO-Scrambled.</p

Metastasis in nude mice.

<p>(A) HE staining of brain and lung tissues. Arrows point to pathological mitotic figure. (B) X-ray scanning of bone lesions in nude mice. (C) HE staining, TRAP staining and immunohistochemical staining of tibias and femurs. (D) Metastatic incidences in the bone, lung and brain, as the percentage of the nude mice that show the lesion. “n” indicates the number of nude mice in each group.</p

Generating Electrospray Ionization on Ballpoint Tips

In this study, we report a simple and economical ballpoint electrospray ionization mass spectrometry (BP-ESI-MS) technique. This combines a small ballpoint tip with a syringe pump for the direct loading and ionization of various samples in different phases (including solution, semisolid, and solid) and allows for additional applications in surface analysis. The tiny metal ball on the ballpoint tip exhibits a larger surface for ionization than that of a conventional sharp tip end, resulting in higher ionization efficiency and less sample consumption. The adamant properties of the ballpoint tip allow sampling by simply penetrating or scraping various surfaces, such as a fruit peel, paper, or fabric. Complex samples, such as fine herbal powders and small solid samples, could be stored in the hollow space in the ballpoint socket and subsequently extracted online, which greatly facilitated MS analysis with little to no sample preparation. Positive ion mode was attempted, and various compounds, including amino acids, carbohydrates, flavonoids, and alkaloids, were detected from different types of samples. The results demonstrated that the special and excellent physical characteristics of ballpoint tips allowed for fast and convenient sampling and ionization for mass spectrometry analysis by the BP-ESI-MS method