Cultivation and Biological Characterization of Chicken Primordial Germ Cells

Meng, Jiao; Guan, Weijun; Gao, Yuhua; Li, Lü; Bai, Chunyu; Ma, Yue; Li, Xiangchen

doi:10.1590/1678-4324-2016150374

Cited by 6 publications

(5 citation statements)

References 30 publications

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“…Twice diploid karyotype and the stably characteristic chromosome number, shape and structure are the prerequisite for the cell growth and functioning (32). Therefore, karyotype analysis is a simple and practical method for distinguishing normal cells from variants.…”

Section: Discussionmentioning

confidence: 99%

Biological characterization of sheep kidney-derived mesenchymal stem cells

Meng

Bai

et al. 2016

Experimental and Therapeutic Medicine

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The aim of the present study was to isolate, culture and characterize sheep metanephric mesenchymal stem cells (MMSCs). The MMSCs were isolated from the kidney tissue of six-week-old sheep fetus. This study investigated whether primary MMSCs could be grown for 26 passages and expressed Oct-4, which is involved in the self-renewal of undifferentiated pluripotent stem cells. The MMSCs also expressed the renal lineage marker gene PAX2, and mesenchymal cell marker genes CD44, FN1 and VIM. Expression of these genes was detected using immunofluorescence and reverse transcription-polymerase chain reaction assays. Additionally, we observed that the MMSCs are able to differentiate into adipocyte, hepatocyte and chondrocyte cells. Karyotype analyses showed that these cells were 95% diploid and thus differentiated. These results indicate that the MMSCs obtained from sheep fetuses possessed certain characteristics of multipotent stem cells. Therefore, MMSCs may potentially offer utility for tissue engineering and cellular transplantation therapy, and further studies are required to investigate these uses.

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Section: Discussionmentioning

confidence: 99%

Biological characterization of sheep kidney-derived mesenchymal stem cells

Meng

Bai

et al. 2016

Experimental and Therapeutic Medicine

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“…For some species, preparing the correct set of chromosomes may be even more complex, e. g., in the freshwater planarian (Schmidtea mediterranea) a large translocation between two chromosomes determines whether they reproduce sexually or asexually [25]. Microchromosomes are especially hard to estimate because their size is closer to the image resolution and they easily get out of focus [26].…”

Section: Discussionmentioning

confidence: 99%

Estimating chromosome sizes from karyotype images enables validation of de novo genome assemblies

Pippel

Ludwig

Dibrov

et al. 2023

Preprint

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Owing to decreased costs over time, the genomes of an increasing number of species are being sequenced. However, chromosome-scale genome assembly is affected by scaffolding errors, resulting in incorrect chromosome sizes. Here, we present KICS, a semi-automated and cost-efficient approach for examining the validity of the assembly by estimating relative chromosome sizes from karyotype images. The method employs threshold-based image segmentation and uses the extracted chromosome areas as proxies for the actual chromosome sizes. A strong correlation between chromosomal area and DNA confirmed the suitability of our approach, as assessed from karyotype images of multiple species. KICS can be applied to microchromosomes, and we identified assembly errors made by HiC sequencing in the horseshoe bat genome. By using the human genome as a reference, for which telomere-to-telomere data are available, we estimate an error of our tool of ∼6Mb. We foresee that KICS will be routinely used as an inexpensive and intuitive tool to validate the de novo assembly of new genomes.

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“…Microchromosomes are especially hard to estimate because their size is closer to the image resolution and they easily get out of focus [20].…”

Section: Discussionmentioning

confidence: 99%

“…For some species, this may be even more complex, e.g., in the freshwater planarian (Schmidtea mediterranea) a large translocation between two chromosomes determines whether they reproduce sexually or asexually [36]. Microchromosomes are especially hard to estimate because their size is closer to the image resolution and they easily get out of focus [20].…”

Section: Discussionmentioning

confidence: 99%

Estimating chromosome sizes from karyotype images enables validation of de novo assemblies

Ludwig

Dibrov

Myers

et al. 2022

Preprint

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Highly contiguous genome assemblies are essential for genomic research. Chromosome-scale assembly is feasible with the modern sequencing techniques in principle, but in practice, scaffolding errors frequently occur, leading to incorrect number and sizes of chromosomes. Relating the observed chromosome sizes from karyotype images to the generated assembly scaffolds offers a method for detecting these errors.Here, we present KICS, a semi-automated approach for estimating relative chromosome sizes from karyotype images and their subsequent comparison to the corresponding assembly scaffolds. The method relies on threshold-based image segmentation and uses the computed areas of the chromosome-related connected components as a proxy for the actual chromosome size. We demonstrate the validity and practicality of our approach by applying it to karyotype images of humans and various amphibians, birds, fish, insects, mammals, and plants. We found a strong linear relationship between pixel counts and the DNA content of chromosomes. Averaging estimates from eight human karyotype images, KICS predicts most of the chromosome sizes within an error margin of just 6 Mb.Our method provides additional means of validating genome assemblies at low costs. An interactive implementation of KICS is available at https://github.com/mpicbg-csbd/napari-kics.

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Cultivation and Biological Characterization of Chicken Primordial Germ Cells

Cited by 6 publications

References 30 publications

Biological characterization of sheep kidney-derived mesenchymal stem cells

Biological characterization of sheep kidney-derived mesenchymal stem cells

Estimating chromosome sizes from karyotype images enables validation of de novo genome assemblies

Estimating chromosome sizes from karyotype images enables validation of de novo assemblies

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