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PubMed1999

Evolution of a HOXB6 intergenic region within the great apes and humans.

Data accumulated over the past decade from several loci suggest that nonhuman primates have a greater amount of intraspecific genetic variation relative to humans. In phylogenetic reconstructions among primates that are based on genetic data, therefore, it becomes essential to adequately sample the population(s) being analyzed. Inadequate sampling may not only underestimate variation within any given population, but such an underestimate may confound any phylogenetic or population-specific conclusions implied by the data. Here we present inter- and intraspecific data on the molecular evolution of an approximately 1.0 kb intergenic HOXB6 sequence among humans, common chimpanzees, pygmy chimpanzees, gorillas and orangutans. To date, this study represents the most comprehensive investigation of a noncoding nuclear locus among the great apes and humans that examines the nature and amount of intraspecific variation in DNA sequences. Not only do these HOXB6 data continue to support earlier findings that Homo sapiens sapiens has less genetic variation than any great ape species (Ruano et al., 1992; Deinard & Kidd, 1995), but they strongly suggest that a high level of genetic polymorphism existed within the common ancestor of the African ape clade (Homo-Pan-Gorilla). Despite detecting two nucleotide substitutions linking Pan and Homo, we caution against concluding that the HOXB6 data definitively support a Homo-Pan clade to the exclusion of Gorilla. Rather, we believe that taking into consideration the level of genetic polymorphism that is likely to have existed within the common ancestor, the most prudent conclusion that can be made from all available data, including morphological, karyotypic and genetic data, may be that speciation among Homo-Pan-Gorilla is best represented by a "trichotomy".

Animals↗
PubMed1999

A variant of Saccharomyces cerevisiae pep4 strain with improved oligotrophic proliferation, cell survival and heterologous secretion of alpha-amylase.

A variant of Saccharomyces cerevisiae pep4 strain 20B12, with improved oligotrophic proliferation, cell survival and secretion of heterologous mouse alpha-amylase, is described. Previously we reported a procedure to enrich NI transformants that are not inhibited by cytotoxic expression of hepatitis B virus surface antigen in the secretion pathway of the protease-A-deficient (pep4) strain. To use the NI cells as a host for heterologous expression, we tried to amend the introduced pYAS/12S vector and obtain a host strain, NI-C, with stable NI phenotype and trp1 marker restored. Southern analysis of genomic DNA of NI-C suggested that the original pYAS/12S was abnormally rearranged and not completely corrected. Further assay showed that the viability and mitotic ability of the NI-C strain were increased. While using the NI-C strain as host for plasmid transformation and heterologous expression of mouse alpha-amylase, we observed that transformed colonies grew more quickly and secreted more alpha-amylase than general yeast strains. A further test showed that the NI-C strain was able to use mouse alpha-amylase as a positive selection marker to form transformed colonies on nitrogen-starved plates that contain starch as the sole carbon source. The results imply that the NI-C variant is an improved pep4 strain that can be used for heterologous expression and for the development of new selective markers in the yeast transformation system.

Animals↗
PubMed2003

A case report of a novel type of stick use by wild chimpanzees.

We have found evidence that wild chimpanzees used stout sticks to dig into one end of a decayed fallen trunk from the side and a long stick with a frayed end to dig into or brush its stump, in the Moukalaba Reserve, Gabon. This type of stick use by wild chimpanzees has not been recorded in any habitat. This finding should contribute to future studies and discussions of variations in tool use and cultural processes among wild chimpanzees.

Animals↗
PubMed2006

Heterogeneity of Escherichia coli-expressed human muscle creatine kinase.

Creatine kinase (CK) plays an important role in maintaining a constant ATP:ADP ratio during periods of high energy usage. Elevated levels of CK give an early indication of myocardial infarction. The enzyme has four major isozymes with heterogeneity being observed for each of them. In many cases the source of the heterogeneity is unclear. However, some of the isoforms are known to result from exposure to serum proteases, and analysis of the plasma isoforms provides an estimate of the time of onset of the infarction. Somewhat surprisingly, isoelectric focusing (IEF) experiments provided evidence of heterogeneity in human muscle CK (HMCK) expressed in E. coli. To investigate this further, HMCK was purified to apparent homogeneity utilizing Blue Sepharose affinity chromatography and HiPrep Q anion exchange chromatography. Additional purification on a PBE 94 chromatofocusing column resulted in four fractions, three of which, HMCK I - III, were characterized. The three isoforms are all active and have similar kinetic parameters. They exhibited identical bands on SDS PAGE but different anodal mobility on non-denaturing gels. Modification of C-terminal and/or cysteine residues has been ruled out, and deamidation of asparagine or glutamine residue(s) is proposed to be the cause of isoform formation. In addition each of these isoforms showed a similar four-band pattern on a carrier ampholytes-based IEF gel. Two-dimensional IEF analysis showed that an equilibrium was established between the four bands, suggesting that the four components were unstable and generated only when the protein was subjected to IEF.

Cloning, Molecular↗
PubMed2001

CAG repeat instability at SCA2 locus: anchoring CAA interruptions and linked single nucleotide polymorphisms.

Spinocerebellar ataxia 2 (SCA2) is an autosomal dominant neurodegenerative disorder that results from the expansion of a cryptic CAG repeat within the exon 1 of the SCA2 gene. The CAG repeat in normal individuals varies in length from 14 to 31 repeats and is frequently interrupted by one or more CAA triplets, whereas the expanded alleles contain a pure uninterrupted stretch of 34 to 59 CAG repeats. We have previously reported the presence of a limited pool of 'ancestral' or 'at risk' haplotypes for the expanded SCA2 alleles in the Indian population. We now report the identification of two novel single nucleotide polymorphisms (SNPs) in exon 1 of the SCA2 gene and their characterization in 215 normal and 64 expanded chromosomes. The two biallelic SNPs distinguished two haplotypes, GT and CC, each of which formed a predominant haplotype associated with normal and expanded SCA2 alleles. All the expanded alleles segregated with CC haplotype, which otherwise was associated with only 29.3% of the normal chromosomes. CAA interspersion analysis revealed that majority of the normal alleles with CC haplotype were either pure or lacked the most proximal 5' CAA interruption. The repeat length variation at SCA2 locus also appeared to be polar with changes occurring mostly at the 5' end of the repeat. Our results demonstrate that CAA interruptions play an important role in conferring stability to SCA2 repeat and their absence predisposes alleles towards instability and pathological expansion. Our study also provides new haplotypes associated with SCA2 that should prove useful in further understanding the mutational history and mechanism of repeat instability at the SCA2 locus.

Alleles↗
PubMed2003

Compositional evolution of noncoding DNA in the human and chimpanzee genomes.

We have examined the compositional evolution of noncoding DNA in the primate genome by comparison of lineage-specific substitutions observed in 1.8 Mb of genomic alignments of human, chimpanzee, and baboon with 6542 human single-nucleotide polymorphisms (SNPs) rooted using chimpanzee sequence. The pattern of compositional evolution, measured in terms of the numbers of GC-->AT and AT-->GC changes, differs significantly between fixed and polymorphic sites, and indicates that there is a bias toward fixation of AT-->GC mutations, which could result from weak directional selection or biased gene conversion in favor of high GC content. Comparison of the frequency distributions of a subset of the SNPs revealed no significant difference between GC-->AT and AT-->GC polymorphisms, although AT-->GC polymorphisms in regions of high GC segregate at slightly higher frequencies on average than GC-->AT polymorphisms, which is consistent with a fixation bias favoring high GC in these regions. However, the substitution data suggest that this fixation bias is relatively weak, because the compositional structure of the human and chimpanzee genomes is becoming homogenized, with regions of high GC decreasing in GC content and regions of low GC increasing in GC content. The rate and pattern of nucleotide substitution in 333 Alu repeats within the human-chimpanzee-baboon alignments are not significantly affected by the GC content of the region in which they are inserted, providing further evidence that, since the time of the human-chimpanzee ancestor, there has been little or no regional variation in mutation bias.

Alleles↗
PubMed2006

Conservation and divergence of plant microRNA genes.

MicroRNA (miRNA) is one class of newly identified, small, non-coding RNAs that play versatile and important roles in post-transcriptional gene regulation. All miRNAs have similar secondary hairpin structures; many of these are evolutionarily conserved. This suggests a powerful approach to predict the existence of new miRNA orthologs or homologs in other species. We developed a comprehensive strategy to identify new miRNA homologs by mining the repository of available ESTs. A total of 481 miRNAs, belonging to 37 miRNA families in 71 different plant species, were identified from more than 6 million EST sequences in plants. The potential targets of the EST-predicted miRNAs were also elucidated from the EST and protein databases, providing additional evidence for the real existence of these miRNAs in the given plant species. Some plant miRNAs were physically clustered together, suggesting that these miRNAs have similar gene expression patterns and are transcribed together as a polycistron, as observed among animal miRNAs. The uracil nucleotide is dominant in the first position of 5' mature miRNAs. Our results indicate that many miRNA families are evolutionarily conserved across all major lineages of plants, including mosses, gymnosperms, monocots and eudicots. Additionally, the number of miRNAs discovered was directly related to the number of available ESTs and not to evolutionary relatedness to Arabidopsis thaliana, indicating that miRNAs are conserved and little phylogenetic signal exists in the presence or absence of these miRNAs. Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years.

Base Sequence↗
PubMed2004

The two major human metapneumovirus genetic lineages are highly related antigenically, and the fusion (F) protein is a major contributor to this antigenic relatedness.

The growth properties and antigenic relatedness of the CAN98-75 (CAN75) and the CAN97-83 (CAN83) human metapneumovirus (HMPV) strains, which represent the two distinct HMPV genetic lineages and exhibit 5 and 63% amino acid divergence in the fusion (F) and attachment (G) proteins, respectively, were investigated in vitro and in rodents and nonhuman primates. Both strains replicated to high titers (> or =6.0 log(10)) in the upper respiratory tract of hamsters and to moderate titers (> or =3.6 log(10)) in the lower respiratory tract. The two lineages exhibited 48% antigenic relatedness based on reciprocal cross-neutralization assay with postinfection hamster sera, and infection with each strain provided a high level of resistance to reinfection with the homologous or heterologous strain. Hamsters immunized with a recombinant human parainfluenza virus type 1 expressing the fusion F protein of the CAN83 strain developed a serum antibody response that efficiently neutralized virus from both lineages and were protected from challenge with either HMPV strain. This result indicates that the HMPV F protein is a major antigenic determinant that mediates extensive cross-lineage neutralization and protection. Both HMPV strains replicated to low titers in the upper and lower respiratory tracts of rhesus macaques but induced high levels of HMPV-neutralizing antibodies in serum effective against both lineages. The level of HMPV replication in chimpanzees was moderately higher, and infected animals developed mild colds. HMPV replicated the most efficiently in the respiratory tracts of African green monkeys, and the infected animals developed a high level of HMPV serum-neutralizing antibodies (1:500 to 1:1,000) effective against both lineages. Reciprocal cross-neutralization assays in which postinfection sera from all three primate species were used indicated that CAN75 and CAN83 are 64 to 99% related antigenically. HMPV-infected chimpanzees and African green monkeys were highly protected from challenge with the heterologous HMPV strain. Taken together, the results from hamsters and nonhuman primates support the conclusion that the two HMPV genetic lineages are highly related antigenically and are not distinct antigenic subtypes or subgroups as defined by reciprocal cross-neutralization in vitro.

Animals↗
PubMed2005

Genome-wide localization of mobile elements: experimental, statistical and biological considerations.

BACKGROUND: The distribution and location of insertion elements in a genome is an excellent tool to track the evolution of bacterial strains and a useful molecular marker to distinguish between closely related bacterial isolates. The information about the genomic locations of IS elements is available in public sequence databases. However, the locations of mobile elements may vary from strain to strain and within the population of an individual strain. Tools that allow de novo localization of IS elements and are independent of existing sequence information are essential to map insertion elements and advance our knowledge of the role that such elements play in gene regulation and genome plasticity in bacteria. RESULTS: In this study, we present an efficient and reliable method for linear mapping of mobile elements using whole-genome DNA microarrays. In addition, we describe an algorithm for analysis of microarray data that can be applied to find DNA sequences physically juxtaposed with a target sequence of interest. This approach was used to map the locations of the IS5 elements in the genome of Escherichia coli K12. All IS5 elements present in the E. coli genome known from GenBank sequence data were identified. Furthermore, previously unknown insertion sites were predicted with high sensitivity and specificity. Two variants of E. coli K-12 MG1655 within a population of this strain were predicted by our analysis. The only significant difference between these two isolates was the presence of an IS5 element upstream of the main flagella regulator, flhDC. Additional experiments confirmed this prediction and showed that these isolates were phenotypically distinct. The effect of IS5 on the transcriptional activity of motility and chemotaxis genes in the genome of E. coli strain MG1655 was examined. Comparative analysis of expression profiles revealed that the presence of IS5 results in a mild enhancement of transcription of the flagellar genes that translates into a slight increase in motility. CONCLUSION: In summary, this work presents a case study of an experimental and analytical application of DNA microarrays to map insertion elements in bacteria and gains an insight into biological processes that might otherwise be overlooked by relying solely on the available genome sequence data.

DNA Transposable Elements↗
PubMed2001

t(8;21;8)(p23;q22;q22): a new variant form of t(8;21) translocation in acute myeloblastic leukemia with maturation.

The complex variants of t(8;21) involving chromosomes 8 and 21 as well as a variable chromosome account for 1.1-5% of acute myeloid leukemia (AML) patients. This paper reports a case of AML-M2 with t(8;21;8) translocation for the first time. The patient was a female, aged 47 years. Her myelogram was compatible with AML-M2. Chromosome study using R-banding technique revealed a karyotype 46, XX, t(8;8)(p23;q22). Dual-color FISH assay with two probes P1 164(green signal) and YAC 225B8 (red signal) both of which closely located on the 8q showed that one yellow signal consisting of a green signal and a red signal and one red signal appeared on the long and the short arm of the same der(8) chromosome, respectively, further confirming this translocation occurred between both homologous chromosomes 8. RT-PCR analysis detected the AML1/ETO fusion transcript in our patient, thus indicating that this chromosomal aberration was, in fact, a complex three-way rearrangement t(8;21;8)(p23;q22;q22). In conclusion, combining conventional karyotype, FISH or RT-PCR analyses is a rational strategy for identification of the complex variants of t(8;21) translocation.

Bone Marrow Cells↗
PubMed1998

[Study on the relationship between provenance, leaf type and quality in Magnolia officinalis].

An analysis of effective ingredients in 20 to 29 year old Magnolia officinalis of three different leaf types coming from various sources shows that the content of phenols differ extremely significantly in various leaf types which are a key to determination of quality of Magnolia officinalis also varies significantly among different sources which only have a significant effect on the content of magnolol. Varieties and types cultivated in different places are responsible for the variation in content of magnolol. The conclusions obtained from this study coincide with the traditional insight into quality of Magnolia officinalis.

Biphenyl Compounds↗
PubMed2003

[Water storage characteristics of ground covers under three forests in Three Gorges area].

Through water holding experiments and the survey of ground covers under three forests (mixed forest of Quercus variabilis and Pinus massoniana, pure Quercus variabilis forest and pure Pinus massoniana forest) in Three Gorges Area, the hydrological characteristic parameters, e.g., maximum water holding capacity and water absorption speed, were measured. The results showed that the maximum water holding capacity of moss under pure Quercus variabilis forest is the highest (303.1% of its dry weight), that under mixed forest of Quercus variabilis and Pinus massoniana was 283.8%, and that under pure Pinus massoniana forest was 242.3%. The maximum water holding capacity of litter under mixed forest stand of Quercus variabils and Pinus massoniana was 282.2% of its dry weight, that under pure Quercus variabilis forest is 262.5%, that under pure Pinus massoniana forest was 239.3%. The equation between water absorption speed of ground cover and its immersed period could be S = kt(n). The results also showed that when the forests were all in mid-age, the water holding ability of the mosses was higher than that of the litters under the same forest. The ground cover's variation with its immersed period had no relation to forest types.

Absorption↗
PubMed1993

Origin and population structure of the Icelanders.

The Norse and Celtic contributions to the founding population of Iceland have been estimated previously on a pan-Icelandic basis using gene frequency data for the entire island. Accounts of the settlement of Iceland, however, suggest that different regions received different proportions of Norse and Celtic settlers, indicating the need to incorporate geographic variation into Icelandic admixture studies. A formal likelihood ratio test rejects the null hypothesis of regional homogeneity in admixture proportions. Here, regional admixture estimates for Iceland are reported; they are in agreement with the settlement pattern inferred from historical accounts. The western, northern, and southern regions of Iceland exhibit a moderate Celtic component, consistent with historical indications that these regions were settled by Norse Vikings from the British Isles, accompanied by Celtic wives and slaves. Eastern Iceland, believed to have been settled chiefly by Vikings from Scandinavia, is characterized by a large Norse component of admixture. The northwestern peninsula is also found to be predominantly Norse. Regional genetic data are used to elucidate the contemporary population structure of Iceland. The observed structure correlates well with patterns of Icelandic geography, history, economy, marriage, urbanization, and internal migration. The northeastern region is strongly isolated, the urbanized areas of the north and southwest are representative of the overall population, and the remaining regions exhibit small-scale variation about the genetic central tendency. A high level of genetic homogeneity is indicated (RST = 0.0005), consistent with the high internal migration rate of the Icelanders. A regression of mean per-locus heterozygosity on distance from the gene frequency centroid reveals a greater than average external gene flow into the eastern region, whereas the northwestern peninsula has received less than average external gene flow. Iceland is compared with possible founding populations and was found to have diverged markedly from other northern European countries.

Emigration and Immigration↗
PubMed1997

Comparative nuclear and mitochondrial genome diversity in humans and chimpanzees.

Restriction mapping and sequencing have shown that humans have substantially lower levels of mitochondrial genome diversity (d) than chimpanzees. In contrast, humans have substantially higher levels of heterozygosity (H) at protein-coding loci, suggesting a higher level of diversity in the nuclear genome. To investigate the discrepancy further, we sequenced a segment of the mitochondrial genome control region (CR) from 49 chimpanzees. The majority of these were from the Pan troglodytes versus subspecies, which was underrepresented in previous studies. We also estimated the average heterozygosity at 60 short tandem repeat (STR) loci in both species. For a total sample of 115 chimpanzees, d = 0.075 +/0 0.037, compared to 0.020 +/- 0.011 for a sample of 1,554 humans. The heterozygosity of human STR loci is significantly higher than that of chimpanzees. Thus, the higher level of nuclear genome diversity relative to mitochondrial genome diversity in humans is not restricted to protein-coding loci. It seems that humans, not chimpanzees, have an unusual d/H ratio, since the ratio in chimpanzees is similar to that in other catarrhines. This discrepancy in the relative levels of nuclear and mitochondrial genome diversity in the two species cannot be explained by differences in mutation rate. However, it may result from a combination of factors such as a difference in the extent of sex ratio disparity, the greater effect of population subdivision on mitochondrial than on nuclear genome diversity, a difference in the relative levels of male and female migration among subpopulations, diversifying selection acting to increase variation in the nuclear genome, and/or directional selection acting to reduce variation in the mitochondrial genome.

Animals↗
PubMed1999

Multiple endometrial stromal nodules with sparse cysts and glands in the lung--a nodular variation of endometriosis that may mimic metastases of sarcoma.

We report an unusual case of a nodular variation of pulmonary endometriosis. To our knowledge, there is no previous report on a morphological investigation of this entity. The etiology of this rare condition is still a matter of discussion. The well-circumscribed nodular mass is composed of cells identical to, or closely resembling, those of endometrial stroma containing sparse cysts and glands. Immunohistochemically, the cells showed an extensive co-expression of cytokeratin AE1/AE3 and vimentin and were highly positive for progesterone receptor (PRICA) and estrogen receptor (ERICA). Cells lining the cysts and glands as a monolayer were reactive for Ber-Ep4, cytokeratin Pan and cytokeratin AE1/AE3 and negative to all other markers used including PRICA and ERICA. The differential diagnosis of this entity included fibrous tumor of the pleura and metastatic low-grade-endometrial-stromal-sarcoma. The morphological findings are correlated with immunohistochemical studies and results of cell image analysis. This study details the clinicopathological features of the nodular variation of pulmonary endometriosis.

Adult↗
PubMedDate not supplied

Seasonal variation in the testicular volume of capuchin monkeys (Cebus apella) in captivity.

The study of the reproductive strategy developed by different species in order to adapt to their environmental conditions and their meaning in an evolutionary perspective is essential for understanding the mechanisms involved in the process of reproduction. Non-human primates are very interesting models for this purpose. Some species show a typical seasonal reproductive pattern, such as rhesus macaques (Macaca mulatta) [Sade, 1964; Conaway and Sade, 1965] and ring-tailed lemurs (Lemur catta) [Zuckerman, 1953], while others, such as gorillas (Gorilla gorilla) and chimpanzees (Pan troglodytes) [Puschmann, 1975], show relative independence of the environment. Neotropical primates display many different breeding strategies. Female capuchin monkeys (Cebus apella), for instance, having reached puberty, have fertile cycles year-round [Hamlett, 1939; Nagle and Denari, 1983]. Interestingly, there are reports of a clear peak of births in free-living [Hamlett, 1939] and captive colonies [Welker et al., 1983] in the dry season, i.e. May-June in the southern hemisphere. Some authors suggest that a seasonal variation in spermatogenesis could explain the birth peak [Freese and Oppenheimer, 1981]. The aim of this study was to investigate this theory, measuring seasonal variation in total testicular volume in a captive group of male capuchin monkeys and assessing its temporal correlation with the birth season as an indirect indication of variation in male fertility.

Animals↗