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PubMed2001

The temperature dependence for the third shell's Fourier-peak of Nb-EXAFS in KNbO3 as additional source of information on the local atomic structure.

The information on the structure of tetragonal KNbO3 is extracted from the temperature dependence of the third shell's Fourier-peak of Nb-EXAFS. It is shown that this dependence can be explained by two effects: 1) rigid rotations of the O6-octahedron and 2) increase of the third shell's DW-parameter. However, diffraction data on the temperature dependence of the DW-parameter permit us to conclude that the last effect only is sufficient and the O6-octahedron rotation doesn't occur in the high-temperature phases of KNbO3. Using EXAFS it is revealed that in the neighboring cells Nb-atoms are parallel shifted closely to [211] direction in tetragonal phase.

Journal Article↗
PubMed2004

Impacts of gene flow and logging history on the local genetic structure of a scattered tree species, Sorbus torminalis L. Crantz.

Sorbus torminalis L. Crantz is a colonizing tree species usually found at low density in managed European forests. Using six microsatellite markers, we investigated spatial and temporal patterns of genetic structure within a 472-ha population of 185 individuals to infer processes shaping the distribution of genetic diversity. Only eight young stems were found to be the result of vegetative reproduction. Despite high levels of gene flow (standard deviation of gene dispersal = 360 m), marked patterns of isolation by distance were detected, associated with an aggregated distribution of individuals in approximately 100-m patches. This spatial structure of both genes and individuals is likely to result from patterns of seedling recruitment combined with low tree density. Our results suggest that landscape factors and logging cycles markedly shape the distribution of favourable sites for seedling establishment, which are then colonized by sibling cohorts as a result of joint seed transportation by frugivores. These combined genetic and demographic processes result in similar genetic structure both within and among logging units. However, conversion to high forest may enhance genetic structuring.

Age Factors↗
PubMed2005

Local genetic structure in a clonal dioecious angiosperm.

We used seven microsatellite loci to characterize genetic structure and clonal architecture at three different spatial scales (from meters to centimetres) of a Cymodocea nodosa population. C. nodosa exhibits both sexual reproduction and vegetative propagation by rhizome elongation. Seeds remain buried in the sediment nearby the mother plant in a dormant stage until germination. Seed dispersal potential is therefore expected to be extremely restricted. High clonal diversity (up to 67% of distinct genotypes) and a highly intermingled configuration of genets at different spatial scales were found. No significant differences in genetic structure were found among the three spatial scales, indicating that genetic diversity is evenly distributed along the meadow. Autocorrelation analyses of kinship estimates confirmed the absence of spatial clumping of genets at small spatial scale and the expectations of a very restricted seed dispersal (observed dispersal range 1-21 m) in this species.

DNA, Plant↗
PubMed1993

Translational initiation at the coat-protein gene of phage MS2: native upstream RNA relieves inhibition by local secondary structure.

Maximal translation of the coat-protein gene from RNA bacteriophage MS2 requires a contiguous stretch of native MS2 RNA that extends hundreds of nucleotides upstream from the translational start site. Deletion of these upstream sequences from MS2 cDNA plasmids results in a 30-fold reduction of translational efficiency. By site-directed mutagenesis, we show that this low level of expression is caused by a hairpin structure centred around the initiation codon. When this hairpin is destabilized by the introduction of mismatches, expression from the truncated messenger increases 20-fold to almost the level of the full-length construct. Thus, the translational effect of hundreds of upstream nucleotides can be mimicked by a single substitution that destabilizes the structure. The same hairpin is also present in full-length MS2 RNA, but there it does not impair ribosome binding. Apparently, the upstream RNA somehow reduces the inhibitory effect of the structure on translational initiation. The upstream MS2 sequence does not stimulate translation when cloned in front of another gene, nor can unrelated RNA segments activate the coat-protein gene. Several possible mechanisms for the activation are discussed and a function in gene regulation of the phage is suggested.

Base Sequence↗
PubMed1994

The 100 kDa haem:haemopexin-binding protein of Haemophilus influenzae: structure and localization.

All Haemophilus influenzae strains have an absolute requirement for exogenously supplied haem for aerobic growth. A majority of strains of H. influenzae type b (Hib) produce a 100 kDa protein which binds haem: haemopexin complexes. This 100 kDa haem:haemopexin binding protein, designated HxuA, was originally detected on the Hib cell surface. Monoclonal antibody (mAb)-based analyses revealed that the HxuA protein was also present in soluble form in Hib culture supernatants. This soluble HxuA protein exhibited haem:haemopexin-binding activity in a direct binding assay. Nucleotide sequence analysis of the hxuA gene from Hib strain DL42, together with N-terminal amino acid analysis of HxuA protein purified from Hib culture supernatant, revealed that this protein was synthesized as a 101 kDa precursor with a leader peptide that was removed to yield a 99 kDa protein. Southern blot analysis of chromosomal DNA from four Hib and four non-typeable H. influenzae (NTHI) strains detected the presence of a single band in each strain that hybridized a Hib hxuA gene probe. Subsequent analysis of these NTHI strains showed that all four strains released into culture supernatant a haem:haemopexin-binding protein that migrated in SDS-PAGE at a rate similar or identical to that of the Hib HxuA protein. A Hib hxuA mutant was used to screen an NTHI genomic DNA library and an NTHI gene was cloned that complemented the mutation in this Hib strain. Nucleotide sequence analysis of this NTHI gene revealed that it encoded a protein with 87% identity to the Hib HxuA protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1989

Dissection of laminin by cathepsin G into its long-arm and short-arm structures and localization of regions involved in calcium dependent stabilization and self-association.

Native laminin-nidogen complex isolated from mouse Engelbreth-Holm-Swarm tumor was treated with purified cathepsin G or leucocyte elastase, two neutral serine proteases which play a role in inflammatory processes accompanied by degradation of basement membranes. Both enzymes were found to be more active than porcine pancreatic elastase. In the absence of Ca2+, laminin fragments produced by leucocyte elastase resembled those formed by the pancreatic enzyme but at physiological concentrations of Ca2+ cleavage by cathepsin G was much more selective. Initially laminin (900 kDa) was cleaved at two major sites only with similar rates leading to three fragments. Fragment C1-4 (about 550 kDa) comprises the intact three short arms of the molecule and fragment C8-9 (about 350 kDa) contains the entire triple-coiled region by which its three chains are assembled and the major part of the terminal globular domain of the long arm. The remaining C-terminal region of this domain was recovered as fragment C3 of about 50 kDa. Stabilization against proteolytic attack was restricted to the region of fragment C1-4 and only this fragment exhibited strong Ca2+ dependent self-association similar to that of intact laminin or of its complex with nidogen. The associative properties of fragment C1-4 were dramatically diminished upon removal of the tip of one of the short arms comprising fragment 4. In addition, this provides a clear assignment of the important laminin function to a distinct domain in one of its short arms. The new fragment C8-9 may be employed for exploring the properties and possible functions of the upper long-arm region which so far has not been available as a fragment.

Animals↗
PubMed1996

Chromosomal localization, genomic structure and characterization of the human gene and a retropseudogene for 6-pyruvoyltetrahydropterin synthase.

Autosomal recessive mutations in the 6-pyruvoyltetrahydropterin synthase (PTPS) gene are the most common reason for hyperphenylalaninemia due to tetrahydrobiopterin deficiency. We used the previously isolated PTPS cDNA as a probe and identified the human gene, PTS, located on chromosome 11q22.3-q23.3, and a retropseudogene, PTS-P1, assigned to 9p12-p13 (symbols approved by the human genome nomenclature committee). PTS-P1 has 74% similarity to the 3' portion of PTPS cDNA. The PTS gene spans about 8 kb and consists of 6 exons, as revealed by DNA-sequence analysis. This gene structure differs from that published previously which was reported to contain only two exons [Ashida, A., Owada, M. & Hatakeyama, K. (1994) Genomics 24,408-410]. By means of intron-specific primers, we amplified exon 3 from genomic DNA of a PTPS-deficient patient and found a mutation in the 3' acceptor splice site, which is responsible for skipping of exon 3.

Alcohol Oxidoreductases↗
PubMed1994

Tissue-specific expression of the diazepam-binding inhibitor in Drosophila melanogaster: cloning, structure, and localization of the gene.

The diazepam-binding inhibitor (DBI; also called acyl coenzyme A-binding protein or endozepine) is a 10-kDa polypeptide found in organisms ranging from yeasts to mammals. It has been shown that DBI and its processing products are involved in various specific biological processes such as GABAA/benzodiazepine receptor modulation, acyl coenzyme A metabolism, steroidogenesis, and insulin secretion. We have cloned and sequenced the Drosophila melanogaster gene and cDNA encoding DBI. The Drosophila DBI gene encodes a protein of 86 amino acids that shows 51 to 56% identity with previously known DBI proteins. The gene is composed of one noncoding 5' and two coding exons and is localized on the chromosomal map at position 65E. Several transcription initiation sites were detected by RNase protection and primer extension experiments. Computer analysis of the promoter region revealed features typical of housekeeping genes, such as the lack of TATA and CCAAT elements. However, in its low GC content and lack of a CpG island, the region resembles promoters of tissue-specific genes. Northern (RNA) analysis revealed that the expression of the DBI gene occurred from the larval stage onwards throughout the adult stage. In adult flies, DBI mRNA and immunoreactivity were detected in the cardia, part of the Malpighian tubules, the fat body, and gametes of both sexes. Developmentally regulated expression, disappearing during metamorphosis, was detected in the larval and pupal brains. No expression was detected in the adult nervous system. On the basis of the expression of DBI in some but not all tissues with high energy consumption, we propose that in D. melanogaster, DBI is involved in energy metabolism in a manner that depends on the substrate used for energy production.

Amino Acid Sequence↗
PubMed1985

Structure and localization of genes encoding aberrant and normal epidermal growth factor receptor RNAs from A431 human carcinoma cells.

A431 cells have an amplification of the epidermal growth factor (EGF) receptor gene, the cellular homolog of the v-erb B oncogene, and overproduce an aberrant 2.9-kilobase RNA that encodes a portion of the EGF receptor. A cDNA (pE15) for the aberrant RNA was cloned, sequenced, and used to analyze genomic DNA blots from A431 and normal cells. These data indicate that the aberrant RNA is created by a gene rearrangement within chromosome 7, resulting in a fusion of the 5' portion of the EGF receptor gene to an unidentified region of genomic DNA. The unidentified sequences are amplified to about the same degree (20- to 30-fold) as the EGF receptor sequences. In situ hybridization to chromosomes from normal cells and A431 cells show that both the EGF receptor gene and the unidentified DNA are localized to the p14-p12 region of chromosome 7. By using cDNA fragments to probe DNA blots from mouse-A431 somatic cell hybrids, the rearranged receptor gene was shown to be associated with translocation chromosome M4.

Amino Acid Sequence↗
PubMed1980

Physiological effects of hyperthermia: response of capillary blood flow and structure to local tumor heating.

Specific capillary blood flow and small-vessel pathology in animal tumors (rhabdomyosarcoma BA-1112) of WAG/Rij rats were examined following local tumor heating to 40-44.5 degrees C. Blood flow in tumors heated to 40-41 degrees C for 40 minutes was reduced initially by about 50%, but returned to near preheating values within 72 hours, consistent with the histopathological observations indicating small-vessel dilation and temporary congestion. The application of hyperthermia greater than 43 degrees C (for 40 minutes) resulted in the virtual elimination of capillary blood flow, consistent with pathological findings of widespread vessel rupture and hemorrhage in this temperature range.

Animals↗