MAGI: Methylation analysis using genome information

By incorporating annotation information into the analysis of next-generation sequencing DNA methylation data, we provide an improvement in performance over current testing procedures. Methylation analysis using genome information (MAGI) is applicable for both unreplicated and replicated data, and provides an effective analysis for studies with low sequencing depth. When compared with current tests, the annotation-informed tests provide an increase in statistical power and offer a significance-based interpretation of differential methylation.     

Subset Selection Procedures for Randomized Designs

Starting from the principle that there exists a randomization procedure that assigns treatments to experimental units, four subset selection rules for the problem of selecting the best treatment from a set of different treatments are proposed. Two of these are extensions of already existing subset selection procedures, which were defined for unbalanced designs, and need a separate selection constant for each individual treatment. The other two rules proposed are new and need only one selection constant for all treatments. The various procedures are compared, and illustrated by application to a plant breeding variety trial.     

Exact Test Procedures for Generalized Kendall Correlation Coefficients

An exact test of KENDALL'S tau is presented, useful in small samples when the asymptotic test may not be adequate. The procedure is proposed especially for situations when ties and/or censored observations are present in the variables to be analyzed by KENDALL'S tau. The paper describes generalizations of the procedure, presents calculated examples and offers a computer program, which facilitates the usage of the proposed procedure.     

Effects of freeze-thaw on the biomechanical and structural properties of the rat Achilles tendon

Rodent models are commonly used to investigate tendon healing, with the biomechanical and structural properties of the healed tendons being important outcome measures. Tendon storage for later testing becomes necessary when performing large experiments with multiple time-points. However, it is unclear whether freezing rodent tendons affects their material properties. Thus the aim of this study was to determine whether freezing rat Achilles tendons affects their biomechanical or structural properties. Tendons were frozen at either −20 °C or −80 °C directly after harvesting, or tested when freshly harvested. Groups of tendons were subjected to several freeze-thaw cycles (1, 2, and 5) within 3 months, or frozen for 9 months, after which the tendons were subjected to biomechanical testing. Additionally, fresh and thawed tendons were compared morphologically, histologically and by transmission electron microscopy. No major differences in biomechanical properties were found between fresh tendons and those frozen once or twice at −20 °C or −80 °C. However, deterioration of tendon properties was found for 5-cycle groups and both long-term freezing groups; after 9 months of freezing at −80 °C the tear resistance of the tendon was reduced from 125.4 ± 16.4N to 74.3 ± 18.4N (p = 0.0132). Moreover, tendons stored under these conditions showed major disruption of collagen fibrils when examined by transmission electron microscopy. When examined histologically, fresh samples exhibited the best cellularity and proteoglycan content of the enthesis. These properties were preserved better after freezing at −80 °C than after freezing at −20 °C, which resulted in markedly smaller chondrocytes and less proteoglycan content. Overall, the best preservation of histological integrity was seen with tendons frozen once at −80 °C. In conclusion, rat Achilles tendons can be frozen once or twice for short periods of time (up to 3 months) at −20 °C or −80 °C for later testing. However, freezing for 9 months at either −20 °C or −80 °C leads to deterioration of certain parameters.     

无创产前筛查(NIPT)的"不准确性"与阳性结果的验证

无创产前筛查(Non-Invasive Prenatal Testing, NIPT)通过检测孕妇外周血中的游离胎儿DNA来筛查胎儿常见非整倍体,已成为产前筛查中重要的一项技术,甚至可作为高龄孕妇初步筛查的首选方式。但因为难免会出现假阴性和假阳性,所以其阴性结果也并不能总是保证胎儿正常。而对于阳性结果,需通过有创产前诊断进行验证。目前,我国临床主要采用的有创产前诊断方法有绒毛活检(Chorionic Villous Sampling, CVS)、羊膜腔穿刺(Amniocentesis, AC)和脐血穿刺。绒毛活检和羊膜腔穿刺术是NIPT阳性结果验证的主要方式。本文主要对造成NIPT假阳性和假阴性结果的原因及其阳性结果的验证进行综述。     

Purification and Characterization of Class Alpha and Mu Glutathione S-Transferases From Porcine Liver

Six cytosolic GSTs from porcine liver were purified by a combination of glutathione affinity chromatography and ion-exchange HPLC. The isoenzymes were characterized by SDS-PAGE, gel filtration, isoelectric focusing, immunoblotting analysis and determination of substrate specificities and inhibition characteristics. The purified GSTs belong to the alpha and mu classes, respectively. No class pi isoenzyme was isolated or detected. The class alpha GST pA1-1* exists as a homodimer (M_r = 25.3 kDa), whereas GST pA2-3* consists of two subunits with different M_r values (27.0 and 25.3 kDa). The estimated pI values were 9.5 and 8.8, respectively. Furthermore, four class mu porcine GSTs, pM1-1*, pM1-2*, pM3-?* and pM4-?*, were isolated. The isoenzyme pM1-1* possesses a relative molecular mass of 27.2 kDa and a pI value of 6.2. Additional pM1 isoenzymes hybridize with the subunit pM2* (M_r = 25.2) to furnish a heterodimer, which shows a pI value of 5.8. The other class mu isoenzymes are heterodimers with pI values of 5.45 and 5.05. Substrate specificities and inhibition characteristics correlate very well with those of the corresponding human isoenzymes. The results are discussed with regard to the usefulness of porcine GSTs as an in vitro testing model.