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1.
The complete mitochondrial DNA (mtDNA) molecule of Sumatran orangutan, plus the complete mitochondrial control region of
another Sumatran specimen and the control regions and five protein-coding genes of two specimens of Bornean orangutan were
sequenced and compared with a previously reported complete mtDNA of Bornean orangutan. The two orangutans are presently separated
at the subspecies level. Comparison with five different species pairs—namely, harbor seal/grey seal, horse/donkey, fin whale/blue
whale, common chimpanzee/pygmy chimpanzee, and Homo/common chimpanzee—showed that the molecular difference between Sumatran and Bornean orangutan is much greater than that between
the seals, and greater than that between the two chimpanzees, but similar to that between the horse and the donkey and the
fin and blue whales. Considering their limited morphological distinction the comparison revealed unexpectedly great molecular
difference between the two orangutans. The nucleotide difference between the orangutans is about 75% of that between Homo and the common chimpanzee, whereas the amino acid difference exceeds that between Homo and the common chimpanzee. On the basis of their molecular distinction we propose that the two orangutans should be recognized
as different species, Pongo pygmaeus, Bornean orangutan, and P. abelii, Sumatran orangutan.
Received: 15 May 1996 / Accepted: 21 June 1996 相似文献
2.
Trichoderma harzianum is the collective name of a set of asexual fungal strains which exhibit heterogeneity in genome structure, DNA sequence and
behavior. Contour-clamped homogeneous field (CHEF) electrophoresis of the chromosomes of ten isolates of T. harzianum revealed six clearly distinct electrophoretic karyotypes. Of the ten isolates analyzed, four (GH12, G109, Y and YF) could
be classified in a single group with identical karyotypes, while the strains T35 and 315 formed a second group. The genome
size characteristic of the different isolates fell into a broad range varying from 29.6 to 56.1 Mb. Gene assignments to the
resolved chromosomes showed that all genes analyzed were localized on equivalent chromosomes in the isolates belonging to
the same group. Analysis of randomly amplified polymorphic DNAs from the ten isolates confirmed the classification into groups
and allowed us to distinguish between isolates T35 and 315, as well as between isolates GH12, G109, Y and YF. Direct confrontation
assays using isolates of the same group showed compatible interactions, whereas the same experiment carried out with isolates
of different groups showed an incompatible interaction characterized by an area of cell damage. Microscopic observation of
the compatible interactions showed hyphal fusions between the isolates, similar to those described for vegetative compatible
groups in other fungi. The molecular karyotypes correlated well with the compatibility of the isolates. In addition, we have
evaluated both electrophoretic karyotype and randomly amplified polymorphic DNAs analysis as criteria for grouping isolates
within the genus according to their capacity for biocontrol of plant pathogens.
Received: 27 July 1996 / Accepted: 23 April 1997 相似文献
3.
Genome size was determined, by nuclear Feulgen staining and image analysis, in 46 accessions of 31 species of Peronosporales (Oomycota), including important plant pathogens such asBremia lactucae, Plasmopara viticola, Pseudoperonospora cubensis,andPseudoperonospora humuli.The 1C DNA contents ranged from 0.046 (45.6 Mb) to 0.163 pg (159.9 Mb). This is 0.041- to 0.144-fold that ofGlycine max(soybean, 1C = 1.134 pg), which was used as an internal standard for genome size determination. The linearity of Feulgen absorbance photometry method over this range was demonstrated by calibration ofAspergillusspecies (1C = 31–38 Mb) againstGlycine,which revealed differences of less than 6% compared to the published CHEF data. The low coefficients of variation (usually between 5 and 10%), repeatability of the results, and compatibility with CHEF data prove the resolution power of Feulgen image analysis. The applicability and limitations of Feulgen photometry are discussed in relation to other methods of genome size determination (CHEF gel electrophoresis, reassociation kinetics, genomic reconstruction) that have been previously applied to Oomycota. 相似文献
4.
Pulsed-field gel electrophoresis (PFGE) of linearized,
full-length chromosomal DNA was used to estimate the genome sizes of three
species of sulfate-reducing bacteria. Genome sizes of Desulfovibrio
desulfuricans, Desulfovibrio vulgaris, and Desulfobulbus
propionicus were estimated to be 3.1, 3.6, and 3.7 Mb, respectively.
These values are double the genome sizes previously determined for two
Desulfovibrio species by two-dimensional agarose gel electrophoresis
of DNA cut with restriction enzymes. PFGE of full-length chromosomal DNA
could provide a generally applicable method to rapidly determine bacterial
genome size and organization.
Received: 1 October 1996 / Accepted: 5 November 1996 相似文献
5.
We have initiated work towards the construction of YAC clone contigs across a repeat sequence island region on the mouse
X Chromosome (Chr). The repeat sequence island region—the 141 island—located at band A3 contains 50 copies of a localized
long complex repeat unit (LCRU). We have isolated 87 YAC clones from the 141 island and have used a dual faceted approach
towards the construction of contigs across the repeat sequence island. First, we have identified YAC clones originating from
the same region of the island by the identification of commonly held LCRU restriction site variants. Second, we have constructed
rare cutter restriction maps of each YAC clone. Taken together, we have been able to assemble one large contig of 2.8 Mb and
a number of smaller contigs. In total, contigs covering 5Mb of the island region have been identified. The island region would
appear to represent a major component of the A3 Giemsa dark band on the mouse X Chr.
Received: 1 September 1995 / Accepted: 11 December 1995 相似文献
6.
We produced electrophoretic karyotypes of the reference strain E150 and of seven other isolates from different geographical
origins to study the genomic organization of the dimorphic yeast Yarrowia lipolytica. These karyotypes differed in the number and size of the chromosomal bands. The karyotype of the reference stain E150 consisted
of five bands of between 2.6 and 4.9 Mb in size. This strain contained at least five rDNA clusters, from 190 to 620 kb in
size, which were scattered over most of the chromosomes. The assignment of 43 markers, including rRNA genes and three centromeres,
to the E150 bands defined five linkage groups. Hybridization to the karyotypes of other isolates with pools of markers of
each linkage group showed that linkage groups I, II, IV and V were conserved in the strains tested whereas group III was not
and was split between at least two chromosomes in most strains. Use of a meganuclease I-SceI site targeted to one locus of E150 linkage group III showed that two chromosomes actually comigrated in band III of this
strain. Our results are compatible with six chromosomes defining the haploid complement of strains of Y. lipolytica and that, despite an unprecedented chromosome length polymorphism, the overall structure of the genome is conserved in different
isolates.
Received: 27 March 1997; in revised form: 8 July 1997 / Accepted: 9 July 1997 相似文献
7.
Mieczysław Śmiech Zbigniew Rusinowski Stefan Malepszy Katarzyna Niemirowicz-Szczytt 《Acta Physiologiae Plantarum》2000,22(3):299-303
The selection of TSWV resistant individuals can be facilitated by molecular markers. RAPD analysis was carried out on three
forms (Stevens × Rodade — resistant; Rey de los Tempranos — moderately tolerant; Potentat — susceptible) with the use of 271
primers. Out of 271 primers 28 generated stable polymorphism and so they were tested for linkage to resistance gene. Bulk
segregant analysis (BSA) was applied to F2 segregating progeny developed from resistant × susceptible parents. As a result, 5 primers enabling us to distinguish between
resistant and susceptible forms were detected. Only one of them had previously been reported by Chague et al. (1996). The analysis should be repeated on a larger population to confirm the results obtained. 相似文献
8.
The genome size of the phytoseiid Metaseiulus (=Typhlodromus or Galendromus) occidentalis (Nesbitt) needs to be estimated before the whole nuclear genome can be sequenced. Two different procedures were used to estimate
the genome size of M. occidentalis; (1) flow cytometry (Marescalchi et al. in Genome 33:789–793, 1990) and (2) quantitative real-time PCR (qRT-PCR) (Wilhelm et al. in Nucleic Acids Res 31:e56, 2003). Fluorescence intensity of propidium iodide-stained nuclei of M. occidentalis was measured by flow cytometry using females, males, and eggs. Only the eggs yielded peaks, which ranged in size from 35
to 160 Mb, with a tall peak of 140 Mb in 1-day-old eggs and 65 Mb in 2-day-old eggs, respectively. However, the peaks are
broad and do not provide an accurate estimate. The qRT-PCR procedure required single-copy nuclear gene sequences from this
phytoseiid. This was accomplished by designing degenerate primers, amplifying the Actin and EF1α sequences from M. occidentalis, and then designing M. occidentalis-specific primers that amplified a unique sequence. The standard qRT-PCR protocol was inefficient and amplification failed
frequently, so we developed a high-fidelity qRT-PCR protocol, which utilizes a mix of two DNA polymerases (Taq and a proof-reading Tgo or ACCUZYME) to consistently amplify sequences. This allowed us to estimate the nuclear genome size of M. occidentalis as 88–90 ± 5 Mb. When compared to other arthropod genomes, this appears to be very small. 相似文献
9.
A. I. Agulnik C. E. Bishop J. L. Lerner S. I. Agulnik V. V. Solovyev 《Mammalian genome》1997,8(2):134-138
Mammalian evolution is believed to be male driven because the greater number of germ cell divisions per generation in males
increases the opportunity for errors in DNA replication. Since the Y Chromosome (Chr) replicates exclusively in males, its
genes should also evolve faster than X or autosomal genes. In addition, estimating the overall male-to-female mutation ratio
(αm) is of great importance as a large αm implies that replication-independent mutagenic events play a relatively small role in evolution. A small αm suggests that the impact of these factors may, in fact, be significant. In order to address this problem, we have analyzed
the rates of evolution in the homologous X-Y common SMCX/SMCY genes from three different species—mouse, human, and horse. The SMC genes were chosen because the X and Y copies are highly homologous, well conserved in evolution, and in all probability functionally
interchangeable. Sequence comparisons and analysis of synonymous substitutions in approximately 1kb of the 5′ coding region
of the SMC genes reveal that the Y-linked copies are evolving approximately 1.8 times faster than their X homologs. The male-to-female
mutation ratio αm was estimated to be 3. These data support the hypothesis that mammalian evolution is male driven. However, the ratio value
is far smaller than suggested in earlier works, implying significance of replication-independent mutagenic events in evolution.
Received: 18 April 1996 / Accepted: 4 October 1996 相似文献
10.
Koretsugu Ogata Rustem I. Aminov Takafumi Nagamine Mutsumi Sugiura Kiyoshi Tajima Makoto Mitsumori Tsutomu Sekizaki Hiroshi Kudo Hajime Minato Yoshimi Benno 《Current microbiology》1997,35(1):22-27
The genomic cleavage map of the type strain Fibrobacter succinogenes S85 was constructed. The restriction enzymes AscI, AvrII, FseI, NotI, and SfiI generated DNA fragments of suitable size distribution that could be resolved by pulsed-field gel electrophoresis (PFGE).
An average genome size of 3.6 Mb was obtained by summing the total fragment sizes. The linkages between the 15 AscI fragments of the genome were determined by combining two approaches: isolation of linking clones and cross-hybridization
of restriction fragments. The genome of F. succinogenes was found to be represented by the single circular DNA molecule. Southern hybridization with specific probes allowed the
eight genetic markers to be located on the restriction map. The genome of this bacterium contains at least three rRNA operons.
PFGE of the other three strains of F. succinogenes gave estimated genome sizes close to that of the type strain. However, RFLP patterns of these strains generated by AscI digestion are completely different. Pairwise comparison of the genomic fragment distribution between the type strain and
the three isolates showed a similarity level in the region of 14.3% to 31.3%. No fragment common to all of these F. succinogenes strains could be detected by PFGE. A marked degree of genomic heterogeneity among members of this species makes genomic RFLP
a highly discriminatory and useful molecular typing tool for population studies.
Received: 23 October 1996 / Accepted: 31 December 1996 相似文献
11.
The most common isochromosome found in humans involves the long arm of the X, i(Xq), and is associated with a subset of Turner
syndrome cases. To study the formation and behavior of isochromosomes in a more tractable experimental system, we have developed
a somatic cell hybrid model system that allows for the selection of mono- or dicentric isochromosomes involving the short
arm of the X, i(Xp). Simultaneous positive and negative counterselection of a mouse/human somatic cell hybrid containing a
human X chromosome, selecting for retention of the UBE1 locus in Xp but against the HPRT locus in Xq, results in a variety of abnormalities of the X chromosome involving deletions of Xq. We have generated 70 such
”Pushmi-Pullyu” hybrids derived from seven independent X chromosomes. Cytogenetic analysis of these hybrids using fluorescence
in situ hybridization showed i(Xp) chromosomes in ∼19% of the hybrids. Southern blot and polymerase chain reaction analyses
of the Pushmi-Pullyu hybrids revealed a distribution of breakpoints along Xq. The distance between the centromeres of the
dicentric i(Xp)s generated ranged from ∼2 Mb to ∼20 Mb. To examine centromeric activity in these dicentric i(Xp)s, we used
indirect immunofluorescence with antibodies to centromere protein E (CENP-E). CENP-E was detected at only one of the centromeres
of a dicentric i(Xp) with ∼2–3 Mb of Xq DNA. In contrast, CENP-E was detected at both centromeres of a dicentric i(Xp) with
∼14 Mb of Xq DNA. Two other dicentric i(Xp) chromosomes were heterogeneous with respect to centromeric activity, suggesting
that centromeric activity and chromosome stability of dicentric chromosomes may be more complicated than previously thought.
The Pushmi-Pullyu model system presented in this study may provide a tool for examining the structure and function of mammalian
centromeres.
Received: 15 December 1998; in revised form: 2 March 1999 / Accepted: 5 April 1999 相似文献
12.
D. J. Wolff Karen M. Gustashaw Vickie Zurcher Lara Ko Wendy White Lester Weiss Daniel L. Van Dyke Stuart Schwartz Huntington F. Willard 《Human genetics》1997,100(2):256-262
High resolution cytogenetics, microsatellite marker analyses, and fluorescence in situ hybridization were used to define
Xq deletions encompassing the fragile X gene, FMR1, detected in individuals from two unrelated families. In Family 1, a 19-year-old
male had facial features consistent with fragile X syndrome; however, his profound mental and growth retardation, small testes,
and lover limb skeletal defects and contractures demonstrated a more severe phenotype, suggestive of a contiguous gene syndrome.
A cytogenetic deletion including Xq26.3–q27.3 was observed in the proband, his phenotypically normal mother, and his learning-disabled
non-dysmorphic sister. Methylation analyses at the FMR1 and androgen receptor loci indicated that the deleted X was inactive
in > 95% of his mother’s white blood cells and 80–85% of the sister’s leukocytes. The proximal breakpoint for the deletion
was approximately 10 Mb centromeric to FMR1, and the distal breakpoint mapped 1 Mb distal to FMR1. This deletion, encompassing
∼13 Mb of DNA, is the largest deletion including FMR1 reported to date. In the second family, a slightly smaller deletion
was detected. A female with moderate to severe mental retardation, seizures, and hypothyroidism, had a de novo cytogenetic
deletion extending from Xq26.3 to q27.3, which removed ∼12 Mb of DNA around the FMR1 gene. Cytogenetic and molecular data
revealed that ∼50% of her white blood cells contained an active deleted X. These findings indicate that males with deletions
including Xq26.3–q27.3 may exhibit a more severe phenotype than typical fragile X males, and females with similar deletions
may have an abnormal phenotype if the deleted X remains active in a significant proportion of the cells. Thus, important genes
for intellectual and neurological development, in addition to FMR1, may reside in Xq26.3–q27.3. One candidate gene in this
region, SOX3, is thought to be involved in neuronal development and its loss may partly explain the more severe phenotypes
of our patients.
Received: 19 December 1996 / Accepted: 13 March 1997 相似文献
13.
G. R. Brown J. E. Carlson 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1997,95(1-2):1-9
Molecular cytogenetics is a convenient tool to investigate the organization and evolution of plant genomes. In coniferous
trees of the Pinaceae, cytogenetic data is rudimentary since individual chromosomes are difficult to distinguish and karyotypes
of related species are poorly differentiated. We determined the chromosomal locations of ribosomal RNA genes in white spruce
(Picea glauca) and Sitka spruce (Picea sitchensis) using fluorescence in situ hybridization. The biotin-labeled DNA probes consisted of the 5s ribosomal DNA (rDNA) amplified from white spruce using the polymerase chain reaction and a heterologous 18s-5.8s-26s rDNA sequence. The 5s rDNA was present only on chromosome 5 at a single locus and near to an 18s-5.8s-26s rDNA locus in both species. Additional 18s-5.8s-26s rDNA loci were found at interstitial sites on six and four chromosomes of white and Sitka spruce, respectively, providing
potentially useful interspecific differences. Progress in karyotyping both species is presented. A molecular analysis of 5s rDNA of white spruce revealed the presence of two classes of repeating units, one of 221 bp corresponding to the PCR amplification
product, and another of approximately 600 bp. The nucleotide sequence and copy number of the 221-bp class is reported.
Received: 17 September 1996/Accepted: 20 December 1996 相似文献
14.
Pulse field gel electrophoresis karyotypes of 41 strains of the genus Debaryomyces, including 35 strains confirmed as D. hansenii species by D1/D2 ribosomal DNA sequence analysis, were performed. Electrophoretic karyotypes of the 41 strains exhibited
4 to 10 chromosomal bands ranging between 0.7 Mb and 4.2 Mb. Among D. hansenii species, the patterns of strains obtained from the CBS collection and cheese isolates differed strongly from D. hansenii var. hansenii CBS767T. Both D. hansenii var. hansenii and D. hansenii var. fabryii showed chromosome length polymorphism. Electrophoretic karyotypes of the D. hansenii strains were analyzed by Southern hybridization with various species-specific probes isolated from D. hansenii var. hansenii CBS767T. Repeated sequences including the F01pro, M18pro, the Ty1-copia retrotransposon Tdh5 and hypothetical telomeric sequence hybridized to several chromosomal bands, while a D1/D2 probe derived
from the large ribosomal sub-unit hybridized only to the largest chromosome. Unique probes such as those hybridizing to actin
ACT1, glycerol-3-phosphate dehydrogenase GPD1 and β-glucosidase LAC4 encoding genes were assigned to specific chromosomal bands of D. hansenii var. hansenii CBS767T. These probes failed to hybridize to D. hansenii var. fabryii strongly suggesting that strains of this variety actually represent a different taxon.
This revised version was published online in August 2006 with corrections to the Cover Date. 相似文献
15.
Pulse field gel electrophoresis karyotypes of 41 strains of the genus Debaryomyces, including 35 strains confirmed as D. hansenii species by D1/D2 ribosomal DNA sequence analysis, were performed. Electrophoretic karyotypes of the 41 strains exhibited
4 to 10 chromosomal bands ranging between 0.7 Mb and 4.2 Mb. Among D. hansenii species, the patterns of strains obtained from the CBS collection and cheese isolates differed strongly from D. hansenii var. hansenii CBS767T. Both D. hansenii var. hansenii and D. hansenii var. fabryii showed chromosome length polymorphism. Electrophoretic karyotypes of the D. hansenii strains were analyzed by Southern hybridization with various species-specific probes isolated from D. hansenii var. hansenii CBS767T. Repeated sequences including the F01pro, M18pro, the Ty1-copia retrotransposon Tdh5 and hypothetical telomeric sequence hybridized to several chromosomal bands, while a D1/D2 probe derived
from the large ribosomal sub-unit hybridized only to the largest chromosome. Unique probes such as those hybridizing to actin
ACT1, glycerol-3-phosphate dehydrogenase GPD1 and β-glucosidase LAC4 encoding genes were assigned to specific chromosomal bands of D. hansenii var. hansenii CBS767T. These probes failed to hybridize to D. hansenii var. fabryii strongly suggesting that strains of this variety actually represent a different taxon.
This revised version was published online in June 2006 with corrections to the Cover Date. 相似文献
16.
The ability to develop type II collagen (CII)-induced arthritis (CIA) in mice is associated with the major histocompatibility
I-A gene and with as yet poorly defined regulatory molecules of the major histocompatibility complex (MHC) class II antigen processing
and presentation pathway. H2-M molecules are thought to be involved in the loading of antigenic peptides into the MHC class
II binding cleft. We sequenced H2-Ma, H2-Mb1, and H2-Mb2 genes from CIA-susceptible and -resistant mouse strains and identified four different Ma and Mb2 alleles and three different Mb1 alleles defined by polymorphic residues within the predicted peptide binding groove. Most CIA-resistant mouse strains share
common Ma, Mb1, and Mb2 alleles. In contrast, H2-M alleles designated Ma-III, Ma-IV, Mb1-III, and Mb2-IV could be exclusively identified in the CIA-susceptible H2
r
and H2
q
haplotypes, suggesting that allelic H2-M molecules may modulate the composition of different CII peptides loaded onto MHC
class II molecules, presumably presenting “arthritogenic” epitopes to T lymphocytes.
Received: 8 December 1995 / Revised: 16 January 1996 相似文献
17.
Contour clamped homogeneous electric field (CHEF) gel electrophoresis was used to obtain electrophoretic karyotypes from nine Mucorstrains representing five different species (M. bainieri, M. circinelloides, M. mucedo, M. plumbeus and M. racemosus). The chromosomal banding patterns revealed high variability among the isolates. The sizes of the DNA in the Mucor chromosomes were estimated to be between 2.5 and 8.7 Mb. The total genome sizes were calculated to be between 30.0 and 44.7 Mb. The applicability of these electrophoretic karyotypes for the investigation of genome structure, for strain identification and for species delimitation is considered. 相似文献
18.
General diffusion pores and specific porin channels from outer membranes of gram-negative bacteria were reconstituted into
lipid bilayer membranes. The current noise of the channels was investigated for the different porins in the open state and
in the ligand-induced closed state using fast Fourier transformation. The open channel noise exhibited 1/f-noise for frequencies up to 200 Hz. The 1/f-noise was investigated using the Hooge formula (Hooge, Phys. Lett.
29A: 139–140 (1969)), and the Hooge parameter α was calculated for all bacterial porins used in this study. The 1/f-noise was in part caused by slow inactivation and activation of porin channels. However, when care was taken that during
the noise measurement no opening or closing of porin channels occurred, the Hooge Parameter α was a meaningful number for a given channel. A linear relationship was observed between α and the single-channel
conductance, g, of the different porins. This linear relation between single-channel conductance and the Hooge parameter α could be qualitatively explained by assuming that the passing of an ion through a bacterial porin channel is—to
a certain extent—influenced by nonlinear effects between channel wall and passing ion.
Received: 8 May 1996/Revised: 27 January 1997 相似文献
19.
Barbara A. Lawrence Jennifer Polse Ana DePina Mary M. Allen Nancy H. Kolodny 《Current microbiology》1997,34(5):280-283
The identity of a number of phosphorus-containing
metabolites present in Synechocystis sp. PCC 6308 has been confirmed
by 31P NMR spectroscopy. The presence of D-ribulose
1,5-bisphosphate (RuBP); DL-glyceraldehyde 3-phosphate (GlyP); D(−)
3-phosphoglyceric acid (3PGA); D-ribulose 5-phosphate (Ru5P);
6-phosphogluconic acid (6PGA); phosphoenolpyruvate (PEP); inorganic phosphate
(Pi); uridine diphosphoglucose (UDPG); ADP and ATP were demonstrated by the
pH dependence of their 31P NMR chemical shifts in spectra of
perchloric acid cell extracts. Intracellular pH of cells was determined to be
7.5–7.7.
Received: 20 September 1996 / Accepted: 26 October 1996 相似文献
20.
Cytogenetically undetectable deletions are suspected to be an important cause of mental retardation and developmental delay,
as suggested by the observation that about 7% of children with undiagnosed mental retardation have rearrangements affecting
the chromosome ends. Screening the whole genome for regions of aneuploidy smaller than 5 Mb is not feasible, but the availability
of a high resolution map of the X chromosome means that it is possible to look for deletions in males by PCR. We have screened
96 affected males and their 96 unaffected fathers with 110 markers distributed across the X chromosome. No deletions were
found in either group. Our results show that the prevalence of deletions greater than 1 Mb in children with mental retardation
is less than 3.9% (95% confidence interval). We conclude that X chromosome deletions in the size range 1–5 Mb are a rare cause
of mental retardation in males.
Received: 22 July 1998 / Accepted: 11 September 1998 相似文献