The technique of simultaneous G banding and in situ hybridization has been developed in plants for the first time.Using this technique.RFLP marker umc58 closely linked with the hm1 gene dictating Helminthosporium carb...The technique of simultaneous G banding and in situ hybridization has been developed in plants for the first time.Using this technique.RFLP marker umc58 closely linked with the hm1 gene dictating Helminthosporium carbonum susceptibility1 was localized onto 1L3(chromosome 1,long arm,the third band from the centromere to the end of the arm),5L5 and 9L5.Theresults demonstrated that umc58 was a tripli cated sequence.It was deduced that umc58 probably was in a duplicated region that includes a part of Helminthosporium carbonum susceptibility genes(hm1 and hm2),as the hybridization sites of umc58 in chro mosomes 1 and 9 were those at which the genes localize.The techniques of simultaneous G banding and ISH in plants are discussed.展开更多
The Maximum Effective Moment(MEM)criterion predicts that the initial orientation of ductile shear zones and shear bands is^55°relative to the maximum principal stress axis(σ1)and that the kinematic vorticity num...The Maximum Effective Moment(MEM)criterion predicts that the initial orientation of ductile shear zones and shear bands is^55°relative to the maximum principal stress axis(σ1)and that the kinematic vorticity number(Wk)is^0.94.These preferred orientations should be reflected in the pattern of quartz<c>-fabrics in shear zones and shear bands.Common quartz<c>-fabrics in plane strain can be divided into low-temperature(L)and high-temperature(H)fabrics,with each group showing three patterns.A steady flow with a constant value of Wk≈0.94 gives rise to L-1 and H-1 patterns,which are commonly characterized by a single<c>axis girdle normal to the shear zone and a single<c>-point maximum parallel to the shear zone.Once the conjugate set develops,L-1 and H-1 have opening angles of^70°and^110°,respectively.L-2 and H-2 are asymmetric patterns associated with variable deformation partitioning and vorticity values of0<Wk<0.94.In contrast,L-3 and H-3 are symmetric patterns associated with 100%deformation partitioning and Wk=0.The opening angle in quartz<c>-fabrics is implicitly linked to the temperature during deformation.The opening angle is^70°at low temperature and^110°at high temperature.However,a linear correction between the opening angle and the temperature cannot be established.During deformation partitioning,synthetic shear bands form earlier than antithetic bands and are more easily developed.This may result in opening angles of<70°for low-temperature fabrics and of>110°for high-temperature fabrics.The following criteria can be used to recognize reworked shear zones that have experienced multiple orogenic phases and changes in the stress state:1)the initial Wk is larger or smaller than^0.94;2)the change in Wk is abrupt,rather than progressive;3)inconsistent shear senses are inferred for the different phases of deformation;and4)a negative value of Wk is found in reworked shear zones.展开更多
Haynaldia villosa (2n=2X= 14, VV), a relative of wheat, plays important roles in wheat improvement mainly owing to its disease resistance. Powdery mildew resistance gene Pm21 has been successfully transferred into w...Haynaldia villosa (2n=2X= 14, VV), a relative of wheat, plays important roles in wheat improvement mainly owing to its disease resistance. Powdery mildew resistance gene Pm21 has been successfully transferred into wheat by Cytogenetic Institute, Nanjing Agricultural University, China, and is widely used in the current wheat breeding programs. In this research, our objective is to further transfer and utilize the beneficial genes such as eye-spot resistance, yellow rust resistance, and gene of the tufted bristles on the glume ridge (a remarkable morphology) mapped on 2V of Haynaldia villosa. A disomic addition line with gametocidal chromosome 3C ofAegilops triuncialis added in Norin-26 was crossed to the wheat-H, villosa disomic substitution 2V(2D) and the hybrid F1 was then self-crossed. Chromosome C-banding, genomic in situ hybridization (GISH), and meiotic analysis in combination with molecular markers were applied to detect the chromosome variations derived from hybrids Fz and F3. To date, four translocations including one small segmental translocation T6BS·6BL-2VS, two whole arm translocations (preliminarily designed as T3DS·2VL and T2VS.7DL) and one intercalary translocation T2VS·2VL-W-2VL, one deletion Del. 2VS·2VL-, one monotelosomic Mt2VS, and one isochromosome 2VS·2VS line have been developed and characterized. One wheat SSR marker Xwmc25.120 tagging 2VS and one wheat STS marker NAU/STSBCD135-1 (2BL) tagging 2VL were successfully used to confirm the alien chromosome segments involved in the seven lines. The tufted bristles on the glume ridge appeared in lines T2VS-7DL, Mt2VS, 2VS-2VS as well as the parent DS2V(2D), whereas in T3DS·2VL, this trait did not appear. The gene controlling the tufted bristles was located on 2VS. Gametocidal chromosome 3C ofAegilops triuncialis could successfully induce chromosome 2V structural changes.展开更多
Background: The Great Plains of the United States includes a large number of hybrid and contact zones between bird species. The amount of gene flow between sister species in these zones ranges from very rare hybridiza...Background: The Great Plains of the United States includes a large number of hybrid and contact zones between bird species. The amount of gene flow between sister species in these zones ranges from very rare hybridization events to widespread and prevalent introgression. Some of these avian systems have been studied extensively, while others have been indeterminate of whether hybridization exists in areas of sympatry. Using genomic-level approaches allows investigation of genomic patterns of hybridization and gene flow between species—or lack thereof.Methods: We investigated a narrow zone of sympatry in Nebraska, USA between pewee species(Contopus sordidulus and C. virens), for which no hybridization has been confirmed. We used thousands of single nucleotide polymorphisms to identify potential hybridization and investigate genomic patterns of differentiation between these two species.Results: We found evidence of multiple hybrid individuals in the contact zone. Little genomic variation was fixed between species, but a large proportion had differentiated allele frequencies between species. There was a positive relationship between genetic differentiation and chromosome size.Conclusions: We provided the first conclusive evidence of hybridization between C. sordidulus and C. virens, in a region where secondary contact likely occurred due to human disturbance and habitat modification. The genomic patterns of differentiation affirm that these species split in the relatively recent past. Finally, the relationship of chromosome size and genetic differentiation may have resulted from differential rates of chromosomal recombination in songbirds and genetic differentiation between species largely due to genetic drift(possibly in concert with selection).展开更多
Background: Over 1100 genes have been annotated for human chromosome 9, including disease genes implicated in inflammation, atherosclerosis, cancer and neurodegeneration. The serine palmitoyltransferase-1, SPTLC1, gen...Background: Over 1100 genes have been annotated for human chromosome 9, including disease genes implicated in inflammation, atherosclerosis, cancer and neurodegeneration. The serine palmitoyltransferase-1, SPTLC1, gene is at the 9q22.2 cytogenetic band, a high G+C content region with common genetic alterations sufficient to modify cellular behavior. The sequence is highly conserved among diverse species from bacteria to humans, including a recently discovered 126 nucleotide alternate open reading frame, AltORF. The protein encoded by the reading frames has domains of biological interest and considerable overlapping molecular functions associated with cellular behavior and cancer progression. Methods: Here we examined molecular features of SPTLC1 in a group of inflammation associated cancer cell lines SKN-SH, MDA-PCa, Glioma LN18, PC3 and 647V. Subcellular localization of SPTLC1 was assessed by immunofluorescence microscopy and recombinant green fluorescent protein expression. In addition, PCR, DNA sequencing and bioinformatics analysis were used for molecular profiling of the SPTLC1 genomic and reverse transcribed cDNA fragments. Results: SPTLC1 is detected in all cell lines examined, with intense peri-nuclear staining, consistent with localization in the cytoplasm. Genomic DNA sample, but not the cD NA of SKN cells could be amplified with an AltORF primer set. The PC3 and MDA-PCa cancer cell lines which are both of prostate origin, show differences in SPTLC1 PCR amplification. Similar levels of SPTLC1 AltORF transcripts were detected by quantitative RT-PCR in all cell lines, except the PC3 cell line with low transcript level whose cDNA did not generate nucleotide base sequence information. Conclusions: This is the first reported transcriptional expression of the SPTLC1 AltORF for the inflammation associated human cancer cell lines. Interestingly, it is proximate of oncogenic cancer susceptibility genes and distal of tumor suppressor genes, the high content of short nucleotide repeats in the SPTLC1 AltORF sequence suggesting the region may be genetically unstable. This nominal functional genomics report on the human SPTLC1 AltORF will contribute to compiling a more detailed SPTLC1 gene ontology and is expected to help shed more insight into unique molecular attributes of SPTLC1 in the context of cancer cell behavior, malignant progression and the design of treatment for inflammation associated cancers.展开更多
We analyze correlations and patterns of oxidative activity of 3D DNA at DNA fluorescence in complete sets of chromosomes in neutrophils of peripheral blood. Fluorescence of DNA is registered by method of flow cytometr...We analyze correlations and patterns of oxidative activity of 3D DNA at DNA fluorescence in complete sets of chromosomes in neutrophils of peripheral blood. Fluorescence of DNA is registered by method of flow cytometry with nanometer spatial resolution. Experimental data present fluorescence of many ten thousands of cells, from different parts of body in each population, in various blood samples. Data is presented in histograms as frequency distributions of flashes in the dependence on their intensity. Normalized frequency distribution of information in these histograms is used as probabilistic measure for definition of Shannon entropy. Data analysis shows that for this measure of Shannon entropy common sum of entropy, i.e. total entropy E, for any histogram is invariant and has identical trends of changes all values of E (r) = lnr at reduction of rank r of histogram. This invariance reflects informational homeostasis of chromosomes activity inside cells in multi-scale networks of entropy, for varied ranks r. Shannon entropy in multi-scale DNA networks has much more dense packing of correlations than in “small world” networks. As the rule, networks of entropy differ by the mix of normal D 2 and abnormal D > 2 fractal dimensions for varied ranks r, the new types of fractal patterns and hinges for various topology (fractal dimension) at different states of health. We show that all distributions of information entropy are divided on three classes, which associated in diagnostics with a good health or dominants of autoimmune or inflammatory diseases. This classification based on switching of stability at transcritical bifurcation in homeostasis regulation. We defined many ways for homeostasis regulation, coincidences and switching patterns in branching sequences, the averages of Hölder for deviations of entropy from homeostasis at different states of health, with various saturation levels the noises of entropy at activity of all chromosomes in support regulation of homeostasis.展开更多
Objeclive The aim of this study was to investigate R-band of Cervus nippon hortulorum chromosomes and to provide references for genetic variation and gene location of Cervus nippon hortulorum. [Metbod] Cell division w...Objeclive The aim of this study was to investigate R-band of Cervus nippon hortulorum chromosomes and to provide references for genetic variation and gene location of Cervus nippon hortulorum. [Metbod] Cell division was synchronized by the pepripheral blood lymphocyte culture and the excessive dosage of thymine deoxyribonucleoside, and R-band of Cervus nippon hortulorum chromosomes was also analyzed by RBG-banding technique. Result The number of haploid chromosome banding increased to 400. The R-band of No. 1, No. 2, No. 3, No. 4, chromosome X and Y were almost just opposite to the high-resolution G band of them. The terminal of chromosomes except No. 21, No. 24 and No. 28 were all pos- itive deeply stained. E Conclusion] R-band of Cervus nippon hortulorum chromosomes can be manifested by RBG-binding technique.展开更多
文摘The technique of simultaneous G banding and in situ hybridization has been developed in plants for the first time.Using this technique.RFLP marker umc58 closely linked with the hm1 gene dictating Helminthosporium carbonum susceptibility1 was localized onto 1L3(chromosome 1,long arm,the third band from the centromere to the end of the arm),5L5 and 9L5.Theresults demonstrated that umc58 was a tripli cated sequence.It was deduced that umc58 probably was in a duplicated region that includes a part of Helminthosporium carbonum susceptibility genes(hm1 and hm2),as the hybridization sites of umc58 in chro mosomes 1 and 9 were those at which the genes localize.The techniques of simultaneous G banding and ISH in plants are discussed.
基金funded by the National Natural Science Foundation of China(Grant No.41772207)
文摘The Maximum Effective Moment(MEM)criterion predicts that the initial orientation of ductile shear zones and shear bands is^55°relative to the maximum principal stress axis(σ1)and that the kinematic vorticity number(Wk)is^0.94.These preferred orientations should be reflected in the pattern of quartz<c>-fabrics in shear zones and shear bands.Common quartz<c>-fabrics in plane strain can be divided into low-temperature(L)and high-temperature(H)fabrics,with each group showing three patterns.A steady flow with a constant value of Wk≈0.94 gives rise to L-1 and H-1 patterns,which are commonly characterized by a single<c>axis girdle normal to the shear zone and a single<c>-point maximum parallel to the shear zone.Once the conjugate set develops,L-1 and H-1 have opening angles of^70°and^110°,respectively.L-2 and H-2 are asymmetric patterns associated with variable deformation partitioning and vorticity values of0<Wk<0.94.In contrast,L-3 and H-3 are symmetric patterns associated with 100%deformation partitioning and Wk=0.The opening angle in quartz<c>-fabrics is implicitly linked to the temperature during deformation.The opening angle is^70°at low temperature and^110°at high temperature.However,a linear correction between the opening angle and the temperature cannot be established.During deformation partitioning,synthetic shear bands form earlier than antithetic bands and are more easily developed.This may result in opening angles of<70°for low-temperature fabrics and of>110°for high-temperature fabrics.The following criteria can be used to recognize reworked shear zones that have experienced multiple orogenic phases and changes in the stress state:1)the initial Wk is larger or smaller than^0.94;2)the change in Wk is abrupt,rather than progressive;3)inconsistent shear senses are inferred for the different phases of deformation;and4)a negative value of Wk is found in reworked shear zones.
基金the National Natural Science Foundation of China (30270827).
文摘Haynaldia villosa (2n=2X= 14, VV), a relative of wheat, plays important roles in wheat improvement mainly owing to its disease resistance. Powdery mildew resistance gene Pm21 has been successfully transferred into wheat by Cytogenetic Institute, Nanjing Agricultural University, China, and is widely used in the current wheat breeding programs. In this research, our objective is to further transfer and utilize the beneficial genes such as eye-spot resistance, yellow rust resistance, and gene of the tufted bristles on the glume ridge (a remarkable morphology) mapped on 2V of Haynaldia villosa. A disomic addition line with gametocidal chromosome 3C ofAegilops triuncialis added in Norin-26 was crossed to the wheat-H, villosa disomic substitution 2V(2D) and the hybrid F1 was then self-crossed. Chromosome C-banding, genomic in situ hybridization (GISH), and meiotic analysis in combination with molecular markers were applied to detect the chromosome variations derived from hybrids Fz and F3. To date, four translocations including one small segmental translocation T6BS·6BL-2VS, two whole arm translocations (preliminarily designed as T3DS·2VL and T2VS.7DL) and one intercalary translocation T2VS·2VL-W-2VL, one deletion Del. 2VS·2VL-, one monotelosomic Mt2VS, and one isochromosome 2VS·2VS line have been developed and characterized. One wheat SSR marker Xwmc25.120 tagging 2VS and one wheat STS marker NAU/STSBCD135-1 (2BL) tagging 2VL were successfully used to confirm the alien chromosome segments involved in the seven lines. The tufted bristles on the glume ridge appeared in lines T2VS-7DL, Mt2VS, 2VS-2VS as well as the parent DS2V(2D), whereas in T3DS·2VL, this trait did not appear. The gene controlling the tufted bristles was located on 2VS. Gametocidal chromosome 3C ofAegilops triuncialis could successfully induce chromosome 2V structural changes.
基金funded through an NSF Doctoral Dissertation Improvement Grant(DEB-1406989)funded through NIH award number P20GM103638
文摘Background: The Great Plains of the United States includes a large number of hybrid and contact zones between bird species. The amount of gene flow between sister species in these zones ranges from very rare hybridization events to widespread and prevalent introgression. Some of these avian systems have been studied extensively, while others have been indeterminate of whether hybridization exists in areas of sympatry. Using genomic-level approaches allows investigation of genomic patterns of hybridization and gene flow between species—or lack thereof.Methods: We investigated a narrow zone of sympatry in Nebraska, USA between pewee species(Contopus sordidulus and C. virens), for which no hybridization has been confirmed. We used thousands of single nucleotide polymorphisms to identify potential hybridization and investigate genomic patterns of differentiation between these two species.Results: We found evidence of multiple hybrid individuals in the contact zone. Little genomic variation was fixed between species, but a large proportion had differentiated allele frequencies between species. There was a positive relationship between genetic differentiation and chromosome size.Conclusions: We provided the first conclusive evidence of hybridization between C. sordidulus and C. virens, in a region where secondary contact likely occurred due to human disturbance and habitat modification. The genomic patterns of differentiation affirm that these species split in the relatively recent past. Finally, the relationship of chromosome size and genetic differentiation may have resulted from differential rates of chromosomal recombination in songbirds and genetic differentiation between species largely due to genetic drift(possibly in concert with selection).
文摘Background: Over 1100 genes have been annotated for human chromosome 9, including disease genes implicated in inflammation, atherosclerosis, cancer and neurodegeneration. The serine palmitoyltransferase-1, SPTLC1, gene is at the 9q22.2 cytogenetic band, a high G+C content region with common genetic alterations sufficient to modify cellular behavior. The sequence is highly conserved among diverse species from bacteria to humans, including a recently discovered 126 nucleotide alternate open reading frame, AltORF. The protein encoded by the reading frames has domains of biological interest and considerable overlapping molecular functions associated with cellular behavior and cancer progression. Methods: Here we examined molecular features of SPTLC1 in a group of inflammation associated cancer cell lines SKN-SH, MDA-PCa, Glioma LN18, PC3 and 647V. Subcellular localization of SPTLC1 was assessed by immunofluorescence microscopy and recombinant green fluorescent protein expression. In addition, PCR, DNA sequencing and bioinformatics analysis were used for molecular profiling of the SPTLC1 genomic and reverse transcribed cDNA fragments. Results: SPTLC1 is detected in all cell lines examined, with intense peri-nuclear staining, consistent with localization in the cytoplasm. Genomic DNA sample, but not the cD NA of SKN cells could be amplified with an AltORF primer set. The PC3 and MDA-PCa cancer cell lines which are both of prostate origin, show differences in SPTLC1 PCR amplification. Similar levels of SPTLC1 AltORF transcripts were detected by quantitative RT-PCR in all cell lines, except the PC3 cell line with low transcript level whose cDNA did not generate nucleotide base sequence information. Conclusions: This is the first reported transcriptional expression of the SPTLC1 AltORF for the inflammation associated human cancer cell lines. Interestingly, it is proximate of oncogenic cancer susceptibility genes and distal of tumor suppressor genes, the high content of short nucleotide repeats in the SPTLC1 AltORF sequence suggesting the region may be genetically unstable. This nominal functional genomics report on the human SPTLC1 AltORF will contribute to compiling a more detailed SPTLC1 gene ontology and is expected to help shed more insight into unique molecular attributes of SPTLC1 in the context of cancer cell behavior, malignant progression and the design of treatment for inflammation associated cancers.
文摘We analyze correlations and patterns of oxidative activity of 3D DNA at DNA fluorescence in complete sets of chromosomes in neutrophils of peripheral blood. Fluorescence of DNA is registered by method of flow cytometry with nanometer spatial resolution. Experimental data present fluorescence of many ten thousands of cells, from different parts of body in each population, in various blood samples. Data is presented in histograms as frequency distributions of flashes in the dependence on their intensity. Normalized frequency distribution of information in these histograms is used as probabilistic measure for definition of Shannon entropy. Data analysis shows that for this measure of Shannon entropy common sum of entropy, i.e. total entropy E, for any histogram is invariant and has identical trends of changes all values of E (r) = lnr at reduction of rank r of histogram. This invariance reflects informational homeostasis of chromosomes activity inside cells in multi-scale networks of entropy, for varied ranks r. Shannon entropy in multi-scale DNA networks has much more dense packing of correlations than in “small world” networks. As the rule, networks of entropy differ by the mix of normal D 2 and abnormal D > 2 fractal dimensions for varied ranks r, the new types of fractal patterns and hinges for various topology (fractal dimension) at different states of health. We show that all distributions of information entropy are divided on three classes, which associated in diagnostics with a good health or dominants of autoimmune or inflammatory diseases. This classification based on switching of stability at transcritical bifurcation in homeostasis regulation. We defined many ways for homeostasis regulation, coincidences and switching patterns in branching sequences, the averages of Hölder for deviations of entropy from homeostasis at different states of health, with various saturation levels the noises of entropy at activity of all chromosomes in support regulation of homeostasis.
基金supported by Chongqing Normal University Fund (XLY012)Natural Science Foundation of Chongqing Science and Technology Commission (CSTC 2006BB1260)
文摘Objeclive The aim of this study was to investigate R-band of Cervus nippon hortulorum chromosomes and to provide references for genetic variation and gene location of Cervus nippon hortulorum. [Metbod] Cell division was synchronized by the pepripheral blood lymphocyte culture and the excessive dosage of thymine deoxyribonucleoside, and R-band of Cervus nippon hortulorum chromosomes was also analyzed by RBG-banding technique. Result The number of haploid chromosome banding increased to 400. The R-band of No. 1, No. 2, No. 3, No. 4, chromosome X and Y were almost just opposite to the high-resolution G band of them. The terminal of chromosomes except No. 21, No. 24 and No. 28 were all pos- itive deeply stained. E Conclusion] R-band of Cervus nippon hortulorum chromosomes can be manifested by RBG-binding technique.