Rapid Generation of Whole Chromosome Painting Probes (WCPs) by Chromosome Microdissection (2023)

Aneuploidy is considered a widespread genetic variation in such cell populations as yeast strains, cell lines and cancer cells, and spontaneous changes in the chromosomal copy number may have implications for data interpretation. Thus, aneuploidy monitoring is essential during routine laboratory practice, especially while conducting biochemical and/or gene expression analyses. In the present study, we constructed a panel of whole chromosome painting probes (WCPPs) to monitor aneuploidy in a single yeast Saccharomyces cerevisiae cell. The WCPP-based system was validated using “normal” haploid and diploid cells, as well as disomic cells both with and without cell synchronisation. FISH that utilised WCPPs was combined with DNA cell cycle analysis (imaging cytometry) to provide a detailed analysis of signal variability during the cell cycle. Chromosome painting can be utilised to detect spontaneously formed disomic chromosomes and study aneuploidy-promoting conditions. For example, the frequency of disomic chromosomes was increased in cells lacking NAD⁺-dependent histone deacetylase Sir2p compared with wild-type cells (p<0.05). In conclusion, WCPPs may be considered to be a powerful molecular tool to identify individual genomic differences. Moreover, the WCPP-based system may be used at the single-cell level of analysis to supplement array-based techniques and high-throughput analyses at the population scale.

Deletions in 4q, 13q and 16q were frequently detected in hepatocellular carcinoma (HCC) by comparative genomic hybridization (CGH) studies. However, detailed chromosome structural aberrations are not fully explored. Using CGH combined with multiplex-color FISH (M-FISH) with chromosome region-specific probes (CRPs), chromosome structural aberrations in 4q, 13q and 16q in six HCC cell lines were studied. All CRPs, which were generated from microdissected DNA, were specific, strong in intensity and sensitive enough to detect chromosome structural aberrations including translocation and deletion. FISH with BAC probes was used to further characterize translocation breakpoints and deletions. A breakpoint at 16q22 was localized at a BAC clone (RP11-341K23) and another breakpoint at 4q28 was localized within a 620kb-region. A minimal deleted region at 13q21 was found between BAC clones RP11-240M20 and RP11-435P18. This study demonstrated that the combination of CGH, M-FISH and BAC-FISH is a very useful tool to detect and characterize translocation breakpoint.

This chapter surveys the methods for analyzing mouse chromosomes, both mitotic and meiotic. In addition, references for methodology and examples of the kinds of information that can be obtained using the various methods are also provided in the chapter. Both genome sequencing and the availability of sequence have contributed to a virtual explosion in a number of cytogenetic applications. Cytogenetic mapping can be used to relate genetic linkage maps to cytologically identified chromosomal regions, reciprocal translocations, and genes being scored in the same linkage cross. However, new resources are continually becoming available and the explosion of activity in mouse and mammalian molecular cytogenetics points towards recent knowledge in this field. Advances in genomics and imaging and nanotechnology continue to bring new and useful methods to the field. Nonetheless, the basic technologies reviewed in the chapter remain useful for probing the structure of mouse chromosomes and for evaluation of de novo and heritable defects of chromosome structure and number.

This chapter surveys the methods for analyzing mouse chromosomes, both mitotic and meiotic. In addition, references for methodology and examples of the kinds of information that can be obtained using the various methods are also provided in the chapter. Both genome sequencing and the availability of sequence have contributed to a virtual explosion in a number of cytogenetic applications. Cytogenetic mapping can be used to relate genetic linkage maps to cytologically identified chromosomal regions, reciprocal translocations, and genes being scored in the same linkage cross. However, new resources are continually becoming available and the explosion of activity in mouse and mammalian molecular cytogenetics points towards recent knowledge in this field. Advances in genomics and imaging and nanotechnology continue to bring new and useful methods to the field. Nonetheless, the basic technologies reviewed in the chapter remain useful for probing the structure of mouse chromosomes and for evaluation of de novo and heritable defects of chromosome structure and number.

Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, Volume 10, 2014, pp. 44-51

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the gill samples of Takifugu rubripes analyzed by using Illumina HiSeq 2000 platform to identify gene-associated SNPs from the transcriptome of T. rubripes gill. A total of 27,085,235 unique-mapped-reads from 55,061,524 raw data reads were generated. A total of 56,972 putative SNPs were discovered, which were located in 11,327 genes. 35,839 SNPs were transitions (Ts), 21,074 SNPs were transversions (Tv) and 88.1% of 56,972 SNPs were assigned to the 22 chromosomes. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analyses were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 63.4% of SNPs (34/52) were true SNPs. RNA-Seq is a cost-effective way to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies. The results of our study can also offer some useful information as molecular makers to help select and cultivate T. rubripes.

Nanomedicine: Nanotechnology, Biology and Medicine, Volume 10, Issue 5, 2014, pp. e879-e888

Optik, Volume 127, Issue 24, 2016, pp. 12048-12055

With the purpose of augmenting immersive perception, 3D video coding extension of High Efficiency Video Coding (3D-HEVC) standard is developed. This extension employs Multiview Video plus Depth (MVD) format in which immediate virtual view texture videos can be rendered by adjacent depth maps, so that bitrates and coding runtime of multiview video are saved. A good preservation of depth map is vital to synthesize high-quality virtual view texture videos. Hence, several new depth map coding tools have been introduced into 3D-HEVC, such as Depth Modeling Mode (DMM) decision. However, the numerous DMM candidates result in a huge computational complexity, which prevents 3D-HEVC for practical use. To this end, we propose an efficient DMM decision algorithm for 3D-HEVC depth map coding, which incorporates unnecessary depth blocks skipping approach and Contour pattern early termination method. Simulated experiment results state that the proposed efficient DMM decision method can save about 31.33% coding time on average with only 0.01dB of PSNR drop and just 0.60% bitrate increase on average compared to the original 3D-HEVC encoder.

Medical Engineering & Physics, Volume 36, Issue 11, 2014, pp. 1428-1435

T₂ mapping is a powerful noninvasive technique providing quantitative biological information of the inherent tissue properties. However, its clinical usage is limited due to the relative long scanning time. This paper proposed a novel model-based method to address this problem. Typically, we directly estimated the relaxation values from undersampled k-space data by exploiting the sparse property of proton density and T₂ map in a penalized maximum likelihood formulation. An alternating minimization approach was presented to estimate the relaxation maps separately. Both numerical phantom and in vivo experiment dataset were used to demonstrate the performance of the proposed method. We showed that the proposed method outperformed the state-of-the-art techniques in terms of detail preservation and artifact suppression with various reduction factors and in both moderate and heavy noise circumstances. The superior reconstruction performance validated its promising potential in fast T₂ mapping applications.

Scientia Horticulturae, Volume 183, 2015, pp. 130-135

Allotriploid lilies can produce aneuploid or euploid functional female gametes and can be used as the maternal parents in lily introgression breeding. In this study, the genome composition of 14 allopolyploid progenies, including 5 progenies which were derived from LLO×TTTT, 5 progenies which were derived from LLO×OTOT, and 4 BC₂ progenies which were derived from MAD×AA/AAAA, were analyzed using genomic in situ hybridization (GISH) technique. The GISH results indicated that all of the 10 progenies which were derived from LLO×TTTT/OTOT were aneuploids, 4 BC₂ progenies were euploids. Moreover, LLO always produced aneuploid functional female gametes, giving rise to aneuploid progenies, and MAD produced euploid functional female gametes including n or 2n gametes. Most interestingly, T/O recombinant chromosomes, which were caused by abnormal meiosis, were observed in 2 progenies of LLO×OTOT. Based on the analysis, we proposed that aneuploids might provide a promising approach for lily breeding.

Surface and Coatings Technology, Volume 283, 2015, pp. 129-134

Generally, amorphous carbon films sliding against Al₂O₃ ceramic ball exhibited low friction. However, the low friction mechanism was still not well understood. Since the atomic interaction has difficulty in observing from the experimental method. Thus, in this paper, we probed the origin of low friction mechanism of amorphous carbon films against Al₂O₃ ceramic ball based on first principles calculations. The work of separation did not well illustrate the low friction mechanism. The calculated results of the potential energy surface showed that the minimum energy paths, which defined as a series of low energy regimes of the potential energy surface, were in charge of the low friction.