A data-driven,high-throughput methodology to determine tissue-specific differentially methylated regions able to discriminate body fluids

Tissue-specific differentially methylated regions (tDMRs) are regions of the genome with methylation patterns that modulate gene expression in those tissue types. The detection of tDMRs in forensic evidence can permit the identification of body fluids at trace levels. In this report, we have performed a bioinformatic analysis of an existing array dataset to determine if new tDMRs could be identified for use in body fluid identification from forensic evidence. Once these sites were identified, primers were designed and bisulfite modification was performed. The relative methylation level for each body fluid at a given locus was then determined using qPCR with high-resolution melt analysis (HRM). After screening 127 tDMR's in multiple body fluids, we were able to identify four new markers able to discriminate blood (2 markers), vaginal epithelia (1 marker) and buccal cells (1 marker). One marker for each target body fluid was also tested with pyrosequencing showing results consistent with those obtained by HRM. This work successfully demonstrates the ability of in silico analysis to develop a novel set of tDMRs capable of being differentiated by real time PCR/HRM. The method can rapidly determine the body fluids left at crime scenes, assisting the triers of fact in forensic casework.     

From superhydrophobic‐ to superhydrophilic‐patterned poly(vinylidene fluoride‐co‐chlorotrifluoroethylene) architectures as a novel platform for biotechnological applications

The manufacture of three‐dimensional patterned electroactive poly(vinylidene fluoride‐co‐chlorotrifluoroethylene) microstructures with tailored architecture, morphology, and wettability is presented. The patterned microstructures are fabricated using a simple, effective, low cost, and reproducible technique based on microfluidic technology. These novel structures can represent innovative platforms for advanced strategies in a wide range of biotechnological applications, including tissue engineering, drug delivery, microfluidic, and sensors and actuators devices. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1802–1810     

Exchange energy density of inhomogeneous electron gas near a metal surface

Using the first-order density matrix of an infinite barrier model of a metal surface, the exchange energy density can be evaluated exactly as a function of the distance z from the barrier. This result is compared with the local approximation $\text{?}\text{3}\text{4}\text{e}{}^2\text{(}\text{3}\text{π}\text{)}{}^{\mathrm{<mtext>1</mtext><mtext>3</mtext>}}\text{[?(z)]}{}^{\mathrm{<mtext>4</mtext><mtext>3</mtext>}}$ where the electron density in the model. The local approximation follows the exact result quite closely at all z but leads to a large percentual error in the integrated surface exchange energy.     

Atomic-scale pathway of the pyramid-to-dome transition during ge growth on Si(001)

By high resolution scanning tunneling microscopy, we investigate the morphological transition from pyramid to dome islands during the growth of Ge on Si(001). We show that pyramids grow from top to bottom and that, from a critical size on, incomplete facets are formed. We demonstrate that the bunching of the steps delimiting these facets evolves into the steeper dome facets. Based on first principles and Tersoff-potential calculations, we develop a microscopic model for the onset of the morphological transition, able to reproduce closely the experimentally observed behavior.     

Stereoselective access to the versatile 4-aminohex-5-ene-1,2,3-triol pattern

We developed a stereocontrolled route allowing potential access to the eight isomers of 4-benzylaminohex-5-ene-1,2,3-triol in two or four steps and ca. 50% yield from readily available chiral nonracemic cis- or trans-alpha,beta-epoxyimine precursors. A new (NH(4))(2)CO(3)-based carboxylation/intramolecular cyclization sequence allowed regio- and stereocontrolled C-3 epoxide opening while neat C-2 hydrolysis was ensured by simple aqueous acidic treatment.     

Morphological and compositional evolution of the ge/si(001) surface during exposure to a si flux

By using scanning tunneling microscopy we found that the surface reconstruction of Ge/Si(001) epilayers evolves from (M x N) to (2 x N), and eventually to (2 x 1), during exposure to a Si flux. This sequence appears to be just the inverse of that observed during the growth of Ge or SiGe alloys on Si(001). However, molecular dynamics simulations supported by ab initio calculations allow us to interpret this morphological evolution in terms of Si migration through the epilayer and complex Si-Ge intermixing below the top Ge layer.     

Phonon dispersion curves and densities of lithium-intercalated iron phosphorus trisulfide

Summary The lattice dynamics of Li-intercalated FePS₃ has been studied by means of a force constant model generated by a set of short-range two-body potentials. The intercalated phases have been investigated for the three stoichiometric compositions: Li_0.5FePS₃, LiFePS₃, Li_1.5FePS₃, with the aim of analysing the evolution of the host lattice normal modes as a function of the concentration, and of finding the dispersion of the new phonon branches induced by lithium. The above special values of lithium concentration have been chosen because the size of the unit cell keeps the same as in the host material. The force constants are fitted to the infrared data and the phonon dispersion curves and the phonon energy densities have been calculated. A spectroscopic method for monitoring lithium migration in the host material is proposed.     

Daily variations in human plasma fluoride concentrations

This study investigated the variations in human plasma fluoride concentrations ([F]) and sought to determine the causes. Five subjects (27-33 years old) received a low-F diet during the 5 days of the study. Plasma samples and urine were collected every 3 h from 8 a.m. to 8 p.m. F, PTH, Ca and P were analyzed with the electrode, by chemiluminescence, AAS and colorimetry, respectively. A trend for the plasma [F] was found. The peak [F], 0.55 ± 0.11 μmol L⁻¹, occurred at 11 a.m. and the lowest [F], 0.50 ± 0.06 μmol L⁻¹ occurred between 5 and 8 p.m. Plasma [F] were positively correlated with urinary F excretion rates and with serum PTH levels, but not with the Ca or P levels. Serum PTH levels were positively correlated with urinary F excretion rates and negatively correlated with plasma Ca. The results suggest that the renal system seems to control the daily fluctuations in plasma [F].     

Novel and facile solution-phase synthesis of 2,5-diketopiperazines and O-glycosylated analogs

This work describes the synthesis in solution of a series of related diketopiperazines with potential biological activities: cyclo(l-Pro-l-Ser), cyclo(l-Phe-l-Ser), cyclo(d-Phe-l-Ser) and the corresponding glycosylated analogs of the latter, cyclo[d-Phe-l-Ser(αGlcNAc)] and cyclo[d-Phe-l-Ser(βGlcNAc)]. The synthetic approach involved coupling reactions of -OH or O-glycosylated serine benzyl esters with NFmoc-protected amino acids (Pro or Phe), followed by one-pot deprotection-cyclization reaction in the presence of 20% piperidine in DMF.     

Binary boron-rich borides of magnesium: single-crystal investigations and properties of MgB(7) and the new boride Mg(∼5)B(44)

Single crystals of dark-red MgB(7) were grown from the elements in a Cu-melt. The crystal structure (Pearson symbol oI64; space group Imma; a = 10.478(2) ?, b = 5.977(1) ?, c = 8.125(2) ?, 2842 reflns, 48 params, R(1)(F) = 0.018, R(2)(I) = 0.034) consists of a hexagonal-primitive packing of B(12)-icosahedra and B(2)-units in trigonal-prismatic voids. According to the UV-vis spectra and band structure calculations MgB(7) is semiconducting with an optical gap of 1.9 eV. The long B-B distance of 2.278 ? within the B(2)-unit can be seen as a weak bonding interaction. The new Mg(～5)B(44) occurs beside the well-known MgB(12) as a byproduct. Small fragments of the black crystals are dark-yellow and transparent. The crystal structure (Pearson symbol tP196, space group P4(1)2(1)2, a = 10.380(2) ?, c = 14.391(3) ?, 4080 reflns, 251 params, R(1)(F) = 0.025, R(2)(I) = 0.037) is closely related to tetragonal boron-II (t-B(192)). It consists of B(12)-icosahedra and B(19+1)-units. With a charge of -6 for the B(19+1)-units and a Mg-content of ～20 Mg-atoms per unit cell the observed Mg content in Mg(～5)B(44) is quite close to the expected value derived from simple electron counting rules. All compositions were confirmed by EDXS. The microhardness was measured on single crystals for MgB(7) (H(V) = 2125, H(K) = 2004) and MgB(12) (H(V) = 2360, H(K) = 2459).