Preimplantation Genetic Diagnosis for Aneuploidy and Translocations Using Array Comparative Genomic Hybridization

At least 50% of human embryos are abnormal, and that increases to 80% in women 40 years or older. These abnormalities result in low implantation rates in embryos transferred during in vitro fertilization procedures, from 30% in women <35 years to 6% in women 40 years or older. Thus selecting normal embryos for transfer should improve pregnancy results. The genetic analysis of embryos is called Preimplantation Genetic Diagnosis (PGD) and for chromosome analysis it was first performed using FISH with up to 12 probes analyzed simultaneously on single cells. However, suboptimal utilization of the technique and the complexity of fixing single cells produced conflicting results. PGD has been invigorated by the introduction of microarray testing which allows for the analysis of all 24 chromosome types in one test, without the need of cell fixation, and with staggering redundancy, making the test much more robust and reliable. Recent data published and presented at scientific meetings has been suggestive of increased implantation rates and pregnancy rates following microarray testing, improvements in outcome that have been predicted for quite some time. By using markers that cover most of the genome, not only aneuploidy can be detected in single cells but also translocations. Our validation results indicate that array CGH has a 6Mb resolution in single cells, and thus the majority of translocations can be analyzed since this is also the limit of karyotyping. Even for translocations with smaller exchanged fragments, provided that three out of the four fragments are above 6Mb, the translocation can be detected.     

Arecoline induces TNF-alpha production and Zonula Occludens-1 redistribution in mouse Sertoli TM4 cells

Background

Arecoline, a major alkaloid in Areca nut has the ability to induce oxidative stress. The effect of Areca nut, arecoline on reducing sperm quality and quantity were documented previously using several animal models. Junction disruption by down-regulation of the junction-adhesive protein via oxidative stress is an important route mediating abnormal spermatogenesis. Therefore, in this present study, we investigated the functional role of arecoline on junctional proteins.

Results

To analyze direct effects of arecoline on testis cells, confluent mouse testicular Sertoli cell line TM4 was exposed to arecoline. Arecoline decreased insoluble zonula occludens-1 (ZO-1) protein expression in TM4 cells, however, arecoline treatment increased TNF-alpha production in both TM4 and monocytic THP1 cells. In addition, ERK1/2 inhibitor PD98059 reversed arecoline effects on TNF-alpha and ZO-1.

Conclusions

Arecoline increases the production of TNF-alpha and induces protein redistribution of ZO-1. All these results explain the role of arecoline in male reproductive dysfunction, besides its cytotoxic induction.

Electronic supplementary material

The online version of this article (doi:10.1186/s12929-014-0093-z) contains supplementary material, which is available to authorized users.     

The evaluation of human papillomavirus genotyping in cervical liquid-based cytology specimens; using the Roche Linear Array HPV genotyping assay

Objective:  To ascertain the usefulness of the Roche Linear Array human papillomavirus (HPV) genotyping assay for assessing HPV genotypes in liquid-based cytology (LBC) samples and to evaluate this methodology within a cytopathology laboratory. These tests are of importance as persistent infection with high-risk HPV genotypes is considered a causal factor in the development of cervical cancer.
Methods:  A total of 175 cervical LBC samples were tested using the Roche Linear Array HPV genotyping test. The suitability of the assay use in routine cytopathology laboratory was considered. HPV genotypes were matched to the cervical cytology results, which included negative, borderline nuclear abnormalities, mild, moderate and severe dyskaryosis.
Results:  The assay could be applied to screening samples with the combined result available at the reporting stage. There were no test failures. All samples used after cytological analysis had sufficient DNA for testing. The results were reproducible and easily read and there was concordance of results between biomedical scientists. The results of the assay showed co-infection with multiple HPV genotypes was common in both high-grade and low-grade cytology samples. The percentage of HPV+ samples in the normal cytology samples (although in this grouping the number of samples was low) was 37%. In the cytology samples reported as severe dyskaryosis the HPV genotypes most commonly found were HPV16 and HPV51.
Conclusion:  The assay was able to detect multiple HPV infection with a wide range of genotypes in LBC samples sent for routine cytological analysis. It would be suitable for use in a cytopathology laboratory. The results of the assay show that the genotype profile has some variation from other geographical regions, and more work is needed to determine population prevalence, to ascertain the impact of the HPV vaccine, to evaluate test for cure and HPV triage management.     

Cloning of hHRI, Human Heme-regulated Eukaryotic Initiation Factor 2α Kinase: Down-regulated in Epithelial Ovarian Cancers

Protein synthesis is regulated in response to environmental stimuli by covalent modification, phosphorylating the components of the translational machinery. Phosphorylation of the subunit of eIF-2 is one of the bestcharacterized mechanisms for down-regulating protein synthesis in higher eukaryotes in response to various stress conditions. One of mammalian eIF-2 kinases is a hemeregulated inhibitor kinase (HRI), which is activated by heme deficiency and plays an important role in translational control. In this work, we have analyzed the differentially expressed genes between epithelial ovarian cancer and normal ovary. We have screened a total of 1,408 genes isolated from a human dermal papilla cell cDNA library by cDNA array hybridization. Among many differentially expressed genes, eIF2 kinase, a heme regulated inhibitor was down-regulated in ovarian epithelium cancer. The down-regulation of hHRI was also confirmed in other ovarian cancer tissues by Northern blot hybridization. The hHRI gene is 2,887 bp in length and the amino acid sequence deduced from the cDNA clone encodes a protein of 630 amino acids with molecular mass of 73 kDa. It contains all 12 catalytic domains of the protein kinases with consensus sequences of the proteinserine/threonine kinases. The expression pattern of hHRI mRNA showed approximately 3.0 kb bands which were expressed ubiquitously in all human tissues examined, which indicates that eIF-2 kinase could play an important role in the translational regulation of nonerythroid tissues.     

Relationship between innervation zone width and mean muscle fiber conduction velocity during a sustained isometric contraction

Objectives:

To examine the relationship between the biceps brachii muscle innervation zone (IZ) width and the mean muscle fiber conduction velocity (MFCV) during a sustained isometric contraction.

Methods:

Fifteen healthy men performed a sustained isometric elbow flexion exercise at their 60% maximal voluntary contraction (MVC) until they could not maintain the target force. Mean MFCV was estimated through multichannel surface electromyographic recordings from a linear electrode array. Before exercise, IZ width was quantified. Separate non-parametric one-way analyses of variance (ANOVAs) were used to examine whether there was a difference in each mean MFCV variable among groups with different IZ width. In addition, separate bivariate correlations were also performed to examine the relationships between the IZ width and the mean MFCV variables during the fatiguing exercise.

Results:

There was a significant difference in the percent decline of mean MFCV (%ΔMFCV) among groups with different IZ width (χ² (3)=11.571, p=0.009). In addition, there was also a significant positive relationship between the IZ width and the %ΔMFCV (Kendall’s tau= 0.807; p<0.001).

Conclusions:

We believe that such relationship is likely influenced by both muscle fiber size and the muscle fiber type composition.     

Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling,Glycan-array Data,and Mass Spectrometry

1. Download : Download high-res image (107KB)
2. Download : Download full-size image

Highlights

• •Method to probe the isomeric variants of the glycans attached to purified proteins.
• •Uses multiple rounds of glycosidase cleavage and lectin profiling.
• •Computation integration of lectin-binding, glycan-array, and mass spectrometry data.
• •Applied to microspots for compatibility with analyzing low-abundance proteins.

     

Genomic DNA extraction methods using formalin-fixed paraffin-embedded tissue

As new technologies come within reach for the average cytogenetic laboratory, the study of chromosome structure has become increasingly more sophisticated. Resolution has improved from karyotyping (in which whole chromosomes are discernible) to fluorescence in situ hybridization and comparative genomic hybridization (CGH, with which specific megabase regions are visualized), array-based CGH (aCGH, examining hundreds of base pairs), and next-generation sequencing (providing single base pair resolution). Whole genome next-generation sequencing remains a cost-prohibitive method for many investigators. Meanwhile, the cost of aCGH has been reduced during recent years, even as resolution has increased and protocols have simplified. However, aCGH presents its own set of unique challenges. DNA of sufficient quantity and quality to hybridize to arrays and provide meaningful results is required. This is especially difficult for DNA from formalin-fixed paraffin-embedded (FFPE) tissues. Here, we compare three different methods for acquiring DNA of sufficient length, purity, and “amplifiability” for aCGH and other downstream applications. Phenol–chloroform extraction and column-based commercial kits were compared with adaptive focused acoustics (AFA). Of the three extraction methods, AFA samples showed increased amplicon length and decreased polymerase chain reaction (PCR) failure rate. These findings support AFA as an improvement over previous DNA extraction methods for FFPE tissues.     

A hierarchical clustering method for estimating copy number variation

Microarray technologies allow for simultaneous measurement of DNA copy number at thousands of positions in a genome. Gains and losses of DNA sequences reveal themselves through characteristic patterns of hybridization intensity. To identify change points along the chromosomes, we develop a marker clustering method which consists of 2 parts. First, a "circular clustering tree test statistic" attaches a statistic to each marker that measures the likelihood that it is a change point. Then construction of the marker statistics is followed by outlier detection approaches. The method provides a new way to build up a binary tree that can accurately capture change-point signals and is easy to perform. A simulation study shows good performance in change-point detection, and cancer cell line data are used to illustrate performance when regions of true copy number changes are known.