Ancestry Inference Using the ForenSeqTM DNA Signature Prep Kit

Objective To evaluate the effect of 56 ancestry informative single nucleotide polymorphism （aiSNP） genetic markers in the ForenSeq^TM DNA Signature Prep Kit on ancestry inference. Methods A total of 85 samples from five populations including Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population, Xinjiang Uygur autonomous region Uygur population and Nigerian population were collected. The library was constructed with the ForenSeq^TM DNA Signature Prep Kit and sequencing was performed based on the MiSeq FGx Forensic Genomics System. Using universal analysis software （UAS） of ForenSeq^TM, principal component analysis （PCA）, Structure and likelihood ratio method was used on the genotyping data of 56 aiSNP markers, respectively, and the genetic relationships between populations and inference of the origin of ancestors were analyzed. Results Among the five populations tested, the four ethnic populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population, Tibet autonomous region Tibetan population and Xinjiang Uygur autonomous region Uygur population） could be significantly distinguished from Nigerian population. Xinjiang Uygur autonomous region Uygur individuals were shown as having mixed origins of ancestors and could be distinguished from the other three Chinese populations. However, the other three populations in China （Hebei Han population, Inner Mongolia autonomous region Mongolian population and Tibet autonomous region Tibetan population） could not be effectively distinguished by the system. Conclusion The 56 aiSNP markers in the ForenSeq^TM DNA Signature Prep Kit can make accurate ancestry inference from the intercontinental level, but it is not yet able to distinguish between Chinese subpopulations.

Label-Free Alignment of Nonmagnetic Particles in a Small Uniform Magnetic Field

Label-free manipulation of biological entities can minimize damage, increase viability and improve efficiency of subsequent analysis. Understanding the mechanism of interaction between magnetic and nonmagnetic particles in an inverse ferrofluid can provide a mechanism of label-free manipulation of such entities in a uniform magnetic field. The magnetic force, induced by relative magnetic susceptibility difference between nonmagnetic particles and surrounding magnetic particles as well as particle-particle interaction were studied. Label-free alignment of nonmagnetic particles can be achieved by higher magnetic field strength (Ba), smaller particle spacing (R), larger particle size (rp1), and higher relative magnetic permeability difference between particle and the surrounding fluid (Rμr). Rμr can be used to predict the direction of the magnetic force between both magnetic and nonmagnetic particles. A sandwich structure, containing alternate layers of magnetic and nonmagnetic particle chains, was studied. This work can be used for manipulation of nonmagnetic particles in lab-on-a-chip applications.

Magnetic Janus particles synthesized using droplet micro-magnetofluidic techniques for protein detection

Magnetic droplets on a microfluidic platform can act as micro-robots, providing wireless, remote, and programmable control. This field of droplet micro-magnetofluidics (DMMF) is useful for droplet merging, mixing and synthesis of Janus structures. Specifically, magnetic Janus particles (MJP) are useful for protein and DNA detection as well as magnetically controlled bioprinting. However, synthesis of MJP with control of the functional phases is a challenge. Hence, we developed a high flow rate, surfactant-free, wash-less method to synthesize MJP by integration of DMMF with hybrid magnetic fields. The effects of the flow rate, flow rate ratio, and hybrid magnetic field on the magnetic component of the Janus droplets and the MJP were investigated. It was found that the magnetization, particle size, and phase distribution inside MJP could be readily tuned by the flow rates and the magnetic field. The magnetic component in the MJP could be concentrated after mixing at flow rate ratio values less than 7.5 and flow rates less than 3 ml h^-1. The experimental results and our simulations are in good agreement. The synthesized magnetic-fluorescent Janus particles were used for protein detection, with BSA as a model protein.

Multi-chamber microfluidic platform for high-precision skin permeation testing

The established in vitro tool used for testing the absorption and penetration of chemicals through skin in pharmacology, toxicology and cosmetic science is the static Franz diffusion cell. While widespread, Franz cells are relatively costly, low-throughput and results may suffer from poor reproducibility. Microfluidics has the potential to overcome these drawbacks. In this paper, we present a novel microfluidic skin permeation platform and validate it rigorously against the Franz cell by comparing the transport of 3 model chemicals of varying lipophilicity: caffeine, salicylic acid and testosterone. Permeation experiments through silicone membranes show that the chip yields higher sensitivity in permeant cumulative amounts and comparable or lower coefficients of variation. Using a skin organotypic culture, we show that the chip decreases the effect of unstirred water layers that can occur in static Franz cells. The validation reported herein sets the stage for efficient skin permeation and toxicity screening and further development of microfluidic skin-on-chip devices.

[Full Sibling Identification by IBS Scoring Method and Establishment of the Query Table of Its Critical Value]

OBJECTIVES

To establish a query table of IBS critical value and identification power for the detection systems with different numbers of STR loci under different false judgment standards.

METHODS

Samples of 267 pairs of full siblings and 360 pairs of unrelated individuals were collected and 19 autosomal STR loci were genotyped by Goldeneye™ 20A system. The full siblings were determined using IBS scoring method according to the 'Regulation for biological full sibling testing'. The critical values and identification power for the detection systems with different numbers of STR loci under different false judgment standards were calculated by theoretical methods.

RESULTS

According to the formal IBS scoring criteria, the identification power of full siblings and unrelated individuals was 0.764 0 and the rate of false judgment was 0. The results of theoretical calculation were consistent with that of sample observation. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci was successfully established.

CONCLUSIONS

The IBS scoring method defined by the regulation has high detection efficiency and low false judgment rate, which provides a relatively conservative result. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci provides an important reference data for the result judgment of full sibling testing and owns a considerable practical value.

Magnetic Trapping of Bacteria at Low Magnetic Fields

A suspension of non-magnetic entities in a ferrofluid is referred to as an inverse ferrofluid. Current research to trap non-magnetic entities in an inverse ferrofluid focuses on using large permanent magnets to generate high magnetic field gradients, which seriously limits Lab-on-a-Chip applications. On the other hand, in this work, trapping of non-magnetic entities, e.g., bacteria in a uniform external magnetic field was studied with a novel chip design. An inverse ferrofluid flows in a channel and a non-magnetic island is placed in the middle of this channel. The magnetic field was distorted by this island due to the magnetic susceptibility difference between this island and the surrounding ferrofluid, resulting in magnetic forces applied on the non-magnetic entities. Both the ferromagnetic particles and the non-magnetic entities, e.g., bacteria were attracted towards the island, and subsequently accumulate in different regions. The alignment of the ferrimagnetic particles and optical transparency of the ferrofluid was greatly enhanced by the bacteria at low applied magnetic fields. This work is applicable to lab-on-a-chip based detection and trapping of non-magnetic entities bacteria and cells.

"Fluid color" sign: a useful indicator for discrimination between pleural thickening and pleural effusion

Color Doppler imaging has been applied traditionally in the evaluation of cardiovascular diseases. Recently it was observed that color signal may appear within the fluid collection in the pleural space during respiratory and cardiac cycles ("fluid color sign"). We performed this applicability of fluid color sign to the detection of pleural fluid capable of being removed to assess needle aspiration. From July 1992 to February 1994, we prospectively analyzed 76 patients who were suspected of having minimal pleural effusion on the basis of their chest radiographs. All patients were examined by color Doppler ultrasonography for the presence of fluid color sign, which was followed by needle aspiration to verify the presence of pleural effusion. Among the 65 patients with aspiratable fluid, 58 demonstrated positive fluid color sign (sensitivity 89.2%). None of the patients with solid pleural thickening showed fluid color sign (specificity 100%). With its relatively high sensitivity and specificity, the fluid color sign may be a useful diagnostic aid to real-time, gray scale ultrasonography for minimal or loculated effusion.

Image comparison of real-time gray-scale ultrasound and color Doppler ultrasound for use in diagnosis of minimal pleural effusion

To assess the value of color Doppler ultrasound in distinguishing minimal pleural effusion from pleural thickening, a prospective analysis was done on the ultrasonographic findings in 51 patients. Real-time, gray-scale, and color Doppler chest ultrasound examinations were carried out by different sonographers who had no clinical information concerning the patients. The sonographer evaluated the images for internal echogenicity of the effusion, pleural lesions that change shape with respiration, and movable septa and echo-densities in pleural space in conventional gray-scale as well as color signal in color Doppler ultrasound. Of the 35 patients with true effusion, 33 had positive color signal (sensitivity 94.3%, 95% confidence intervals [CI] 89 to 98.6%); in 16 patients without effusion, none had color signal (specificity 100%, 95% CI 83 to 100%). Although real-time, gray-scale ultrasound is also sensitive for detecting minimal effusion (sensitivity 100%, 95% CI 92 to 100%), it is less specific (specificity 68.7%, 95% CI 46 to 91.5%). Five of 16 examinations showing fluid-like lesions were found to be deceptive. With relatively high sensitivity and specificity, this method proved to be a useful diagnostic aid to real-time, gray-scale ultrasound for diagnosis of minimal or loculated effusion.

Ultrasound guided pericardial drainage and intrapericardial instillation of mitomycin C for malignant pericardial effusion

BACKGROUND

Conservative treatment of malignant pericardial effusion by intrapericardial instillation of a sclerosing agent may be an alternative to surgery.

METHODS

Twenty patients with malignant pericardial effusion were treated by ultrasound guided pericardiocentesis and the intrapericardial instillation of mitomycin C.

RESULTS

Mitomycin C was effective in controlling the pericardial effusion in 70% of patients without causing side effects, except for pericardial constriction seven months later in one subject.

CONCLUSIONS

Ultrasound guided intrapericardial instillation of mitomycin C is a suitable alternative in the management of malignant pericardial effusion.

Interterminal distance and flexibility of a triantennary glycopeptide as measured by resonance energy transfer

Three geometric isomers of a single triantennary glycopeptide, each containing two fluorophores attached to terminal positions in the molecule, were used to probe distance and flexibility of the oligosaccharide in solution. A dansyl group (energy acceptor) was attached to the C6 of Gal at either position 6', 6, or 8, and a naphthyl-2-acetyl group (energy donor) was coupled to the N terminus of the Ala-Asn peptide. (formula; see text) Resonance energy-transfer measurements revealed an average distance of approximately 22, 18, and 17 A between the donor and the acceptor attached to either the 6, 8, or 6' Gal residue, respectively. The lifetime of the donor's emission was nearly a single-exponential decay of 27 ns (96%), whereas the decay of the donor with proximally attached acceptor was fit by nonlinear least-squares analysis to a multiexponential for each glycopeptide probe. Fitting with a Lorentzian function revealed spatially distinct donor/acceptor distances presumably arising from glycopeptide branch flexibility. The results suggest that the acceptor located at Gal 8 is the most rigid relative to the donor with a single population of distances centered at 18.4 A. In contrast, the acceptor attached to either Gal 6' or 6 displayed two populations of different distances from the donor. The Gal 6 isomer contained a major population with average donor/acceptor separation distance of 21.7 A and a minor population with average separation distance of 9.7 A. Similarly, the Gal 6' isomer showed a major population with donor/acceptor separation distance of 18.3 A and a minor population with separation distance of 11.7 A. These data support the earlier conclusions that the Man alpha(1----6)Man linkage found in the core pentasaccharide of all branched N-linked oligosaccharides is flexible. In addition, the data suggest that the branch containing Gal 6 is also flexible in the triantennary glycopeptide.