Chromosome dynamic changes in two cultured chinese human embryonic stem cell lines: Single nucleotide polymorphism, copy number variation and loss of heterozygosity

The quality and safety of human embryonic stem cells (hESCs) in clinical application depend on gene stability. Two Chinese hESC lines, Zh1 and Zh21, were incubated over a long period. We observed and compared the gene stability in the passage numbers 20, 17 for Zh1 cell line and passage numbers 27, 60, 68 for Zh21 cell line. Single nucleotide polymorphisis analysis indicated that hESCs in early passages had relative gene stability; and with the increase in passage number, gene instability became strong. We also found that there were copy number variations (CNVs) in both Zh21 and Zh1. We analyzed the CNVs of Chinese Han Beijing man (CHB; normal Chinese people) and found that the all CNV forms were the loss in Zh21, Zh1, and CHB. We also analyzed and compared the related pathways of the mutant genes. We propose three steps to ensure hESC safety. Firstly, besides the conventional methods such as pluripotent genes, chromosome G‐banding and teratoma, high‐resolution DNA chip analysis should also be adopted; secondly, chromosomal properties are monitored every 10 passages in less than passage 50 and every 5 passages in more than passage 50; thirdly, the related pathways of mutant genes should be observed because only the mutant genes with variations of their related pathways may affected cell functions. J. Cell. Biochem. 113: 3520–3527, 2012. © 2012 Wiley Periodicals, Inc.     

Frequencies in the Japanese Population of HFE Gene Mutations

We studied the frequencies of C282Y and H63Dmutations in the HFE gene, thought to be responsible forhereditary hemochromatosis (HH), in 504 chromosomesobtained from 252 unrelated Japanese. Allele-specific PCR and PCRrestriction fragment lengthpolymorphism methods revealed that the C282Y mutationwas not found and the H63D mutation was low in frequency(at only 0.99%) compared with data from European people. Since most HH is thought to be associated withthe HFE gene mutation, the low incidence of thesemutations is a likely reason for the rarity of thisdisease in the Japanese population.     

Simulation Based Investigation of Deleterious nsSNPs in ATXN2 Gene and Its Structural Consequence Toward Spinocerebellar Ataxia

Spinocerebellar degeneration, termed as ataxia is a neurological disorder of central nervous system, characterized by limb in‐coordination and a progressive gait. The patient also demonstrates specific symptoms of muscle weakness, slurring of speech, and decreased vibration senses. Expansion of polyglutamine trinucleotide (CAG) within ATXN2 gene with 35 or more repeats, results in spinocerebellar ataxia type‐2. Protein ataxin‐2 coded by ATXN2 gene has been reported to have a crucial role in translation of the genetic information through sequestering the histone acetyl transferases (HAT) resulting in a state of hypo‐acetylation. In the present study, we have evaluated the outcome for 122 non synonymous single nucleotide polymorphisms (nsSNPs) reported within ATXN2 gene through computational tools such as SIFT, PolyPhen 2.0, PANTHER, I‐mutant 2.0, Phd‐SNP, Pmut, MutPred. The apo and mutant (L305V and Q339L) form of structures for the ataxin‐2 protein were modeled for gaining insights toward 3D spatial arrangement. Further, molecular dynamics simulations and structural analysis were performed to observe the brunt of disease associated nsSNPs toward the strength and secondary properties of ataxin‐2 protein structure. Our results showed that, L305V is a highly deleterious and disease causing point substitution. Analysis based on RMSD, RMSF, Rg, SASA, number of hydrogen bonds (NH bonds), covariance matrix trace, projection analysis for eigen vector demonstrated a significant instability and conformation along with rise in mutant flexibility values in comparison to the apo form of ataxin‐2 protein. The study provides a blue print of computational methodologies to examine the ataxin‐blend SNPs. J. Cell. Biochem. 119: 499–510, 2018. © 2017 Wiley Periodicals, Inc.     

SDS-PAGE Pattern Polymorphism of X-Chromosomal Glue Proteins in Natural Populations of Two Drosophila nasuta Subgroup Species

For the first time, the glue protein patternpolymorphism in natural populations of D. n.nasuta and D. s. neonasuta has beenanalyzed by SDS-PAGE. The study involving 200 and 185isofemale lines comprising 2028 and 1900 individuals of D. n.nasuta and D. s. neonasuta, respectively,revealed the occurrence of eight variant glue proteinphenotypes in D. n. nasuta and seven in D.s. neonasuta. The number and frequency of variant phenotypes in differentpopulations of both species were found to vary. Analysisof glue protein patterns in the F₁ progeny ofcrosses involving parents with variant glue proteinphenotypes revealed that the polymorphic fractions areproduced by co-dominant genes located on the Xchromosome. More than 87% of the naturally inseminatedadult females were found to produce polymorphic progeny. The heterozygous female larvae were found toexceed the homozygotes in the isofemale line progeny ofmost of the populations.     

Extensive Genetic Polymorphism of Peptidases A, B, C, and D, in Wild Rabbit (Oryctolagus cuniculus) Populations from the Iberian Peninsula

Genetic polymorphism of peptidases A, B, C, andD in the wild rabbit (Oryctolagus cuniculus)was assessed by horizontal starch gel electrophoresis,in a total of 1003 individuals comprising 16 Iberian and 2 French populations and 1 domestic stock.Twenty-five different alleles were detected: 6 in PEPA,4 in PEPB, 8 in PEPC, and 7 in PEPD. The highest valuesof observed heterozygosity averaged over the four loci were obtained for the southwestern Iberianpopulations and a clinal loss of variability in anortheastern direction was detected. A clear separationbetween the two putative subspecies O. c.cuniculus and O. c. algirus was notobtained.     

Closely Linked Polymorphic Markers for Determining the Autosomal Dominant Allele (Cy) in Rat Polycystic Kidney Disease

The Han:SPRD strain is an SD-background strainknown to be a model of polycystic kidney disease (PKD)expressed through an autosomal dominant gene (Cy).However, different genotypes of this strain cannot be identified in the neonatal period. First, toestablish an accurate method of determining thegenotypes (Cy/Cy, Cy/+, +/+) which cause differentdisease progressions, we used polymorphic markers on rat chromosome 5. PCR products of tissue DNAtemplated with D5Rat9 showed distinct patterns onelectrophoresis indicating three genotypes. Second, todetermine whether the same locus plays a major role inexpressing PKD, we performed linkage analyses in a [BN X(BN X Han:SPRD)F₁] backcross. Cy/Cy and Cy/+also caused PKD in a BN background. In this backcross,we discovered that D5Rat11 is located closer to the Cy locus than D5Mgh10, which is regardedas one of the closest loci. We conclude that D5Rat9 andD5Rat11 are useful markers for determining the presenceof the Cy allele, which is regarded as the gene responsible for PKD.     

Aerial and underground biomasses of three Sphagnum-dwelling liverworts

Abstract

The few studies that have investigated levels of genetic variation in liverworts have found very little polymorphism. Our electrophoretic data show, however, that the leafy liverwort Porella platyphylla maintains high levels of genetic variation in at least some natural populations from the southeastern United States. Within a single population from southwestern North Carolina, we detected 26 distinct multilocus genotypes and more than 80% of the enzyme loci we surveyed were polymorphic. It seems likely that earlier studies of mostly thalloid species from glaciated regions of Europe have presented a biased picture of levels of variation in liverwort populations.     

Electrophoretic Polymorphisms and Their Taxonomic Implications in Callitrichini (Primates, Platyrrhini)

Five hundred forty-three blood samples from 15populations of the four genera of callitrichin primateswere studied electrophoretically. Polymorphism andgenetic distances were estimated for 20 loci, 13 of which were polymorphic. The lion tamarin(Leontopithecus) studied here exhibited theleast variability for these loci, while the monospecificCebuella showed the most. The genetic distancesobserved between Callithrix andCebuella genera support previous evidenceindicating a close taxonomic relationship between them.Genetic distance values obtained in this study alsosupport the synonimization of the kuhli form with Callithrix jacchuspenicillata.