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Results for “local structure”

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At least 973 records · Page 54Linked to original sources
PubMed1988

Crossover regions in foot-and-mouth disease virus (FMDV) recombinants correspond to regions of high local secondary structure.

The RNA genome of foot-and-mouth disease virus (FMDV) was analysed for the degree of inverted complementarity and thus potential secondary structure using the procedure of Pustell and Kafatos [Nucleic Acids Res (1982) 10: 4765-4782]. Regions of crossover in 42 FMDV recombinants [King et al. (1985) Virus Res 3: 373-384; Saunders et al. (1985) J Virol 56: 921-929] and regions lacking crossovers were assigned an average secondary structure score against which the number of observed recombinants was plotted. In general it was found that the mean value of potential secondary structure is significantly higher in crossover zones than in recombination-free zones. Recombination increased much more steeply with increasing secondary structure in the part of the genome coding for non-structural proteins than in the 5' third of the genome coding for structural proteins.

Aphthovirus↗
PubMed2001

Structure and localization of cyclosporin synthetase, the key enzyme of cyclosporin biosynthesis in Tolypocladium inflatum.

The electron microscopic image of native cyclosporin synthetase molecules showed large globular complexes of 25 nm in diameter, built up by smaller interconnected units. Compartmentation of cyclosporin synthetase and the functionally interconnected D-alanine racemase was revealed after sucrose density gradient centrifugation of subcellular fractions and immunoelectron microscopy. A considerable proportion of cyclosporin synthetase and D-alanine racemase was detected at the vacuolar membrane. The product cyclosporin was localized in the fungal vacuole.

Alanine↗
PubMed1997

Cloning, localization, and structure of new members of the butyrophilin gene family in the juxta-telomeric region of the major histocompatibility complex.

New members of the butyrophilin (BT) gene family have been identified by cDNA and genomic cloning. Six genes are described: BT2. 1, 2.2, 2.3, and BT3.1, 3.2, and 3.3. BT2, BT3, and BT form three distinct subfamilies sharing about 95% amino acid identity at the intra subfamily level and 50% identity at the interfamily level. All the BT2 and BT3 subfamily members map close to BT in the juxta-telomeric region of the major histocompatibility complex. The BT2 members have the canonical structural organization of BT, i.e., two immunoglobulin domains followed by a transmembrane anchor and a B30.2 intracytoplasmic domain. In the BT3 subfamily, only BT3.3 has the structural organization of BT. The two other genes, BT3.1 and BT3.2, code for putative protein without the B30.2 domain. In the case of BT3.2, this is due to an Alu insertion in the B30.2 coding exon, leading to a new polyadenylation site.

Animals↗
PubMed2001

Plasmolipin: genomic structure, chromosomal localization, protein expression pattern, and putative association with Bardet-Biedl syndrome.

Plasmolipin is a membrane protein and belongs to the tetraspan molecule (4TM) family, an expanding group of myelin proteins many of which could be linked to human hereditary demyelinating neuropathies. We have cloned and sequenced the mouse plasmolipin gene, revealing the common organization of the 4TM gene group with four exons and a large first intron. Western blot analysis with an antibody raised against the C-terminal intracellular part of the protein showed that plasmolipin is expressed not only in the nervous system and kidney, but also in a number of other tissues such as thymus, testis, lung, and thyroid gland. By means of radiation hybrid mapping and FISH analysis, we could localize the human plasmolipin gene to Chromosome 16q13 within the putative region of the Bardet-Biedl syndrome type 2 (BBS2) gene locus. BBS2 is a clinically and genetically heterogeneous group of disorders resulting in rod-cone dystrophy, obesity, postaxial polydactyly, renal dysfunction, and mental retardation, which were very recently associated with a novel gene designated BBS2. With respect to intrafamiliar variations in the manifestation of BBS, we suggest that plasmolipin might be either another candidate gene or a modifier of the BBS2 phenotype.

Animals↗
PubMed2003

Gene structure, chromosomal localization, and mutation screening of the human gene for the inner ear protein otospiralin.

Otospiralin is a novel protein of unknown function that is produced by non-sensory cells (fibrocytes) of the inner ear (cochlea and vestibule). We showed that downregulation of otospiralin in guinea pigs leads to deafness and we therefore hypothesized that genetic defects in the otospiralin gene could also cause deafness in humans. In this study, we cloned and localized OTOSP, the human gene for otospiralin. OTOSP spans 1630 nucleotides, contains four exons and codes for a 567-nucleotide cDNA. By fluorescence in situ hybridization and hybrid panel mapping we localized OTOSP on chromosome 2 at position q37.3. There is currently no deafness family linked to this region. We screened OTOSP for mutations in 410 unrelated patients exhibiting various levels of hearing loss. Beside intronic polymorphisms, a rare variant (Pro7Leu) was found in 4 deafness patients and 3 control individuals, indicating that this change is not involved in this condition and excluding OTOSP as a major gene for genetic deafness.

Amino Acid Substitution↗
PubMed2025

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO = 0.333-0.264) and did not reveal population differentiation within our samples (F ST = - 0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗
PubMed1994

The structure and (local) stability constants of borate esters of mono- and di-saccharides as studied by 11B and 13C NMR spectroscopy.

The formation of borate esters of various mono- and di-saccharides in aqueous solution was studied by 11B and 13C NMR spectroscopy. Association constants K(B-L) at a carbohydrate-borate molar ratio of 1:1, pH 7, and 25 degrees C were determined and compared with literature values obtained from potentiometry. The association constants K(B-L) were converted into local association constants Kloc(B-L) by using the distribution of the various anomeric forms in D2O. In this way, values of Kloc(B-L) were obtained, which appear to be characteristic of the configuration concerned. They explain the favourable effect of borate in the alkaline isomerisation of lactose into lactulose. At a low molar ratio (1:3) of carbohydrate-borate, predominantly diborate esters (B-)2L were formed.

Borates↗
PubMed1988

The Drosophila ets-2 gene: molecular structure, chromosomal localization, and developmental expression.

The cellular homologs of the ets gene from the avian erythroblastosis retrovirus E26 have been studied in chickens, humans, mice, and cats. In this report a further evolutionary step is taken by isolating and characterizing a Drosophila ets-related genomic clone. Sequence analysis of this clone has shown it to contain the 3' end of the v-ets gene, called ets-2, corresponding to the last two exons of chicken ets. The predicted amino acid sequence was found to have over 90% homology when compared to that of v-ets. This is the highest level of conservation observed for any previously characterized Drosophila oncogene homolog. Expression of the ets-2 gene occurs throughout development, but is highest during the embryonic and pupal stages. By in situ hybridization, the ets-2 chromosomal position was determined to be 58A/B which corresponds to no known phenotypic mutant. As this is a highly conserved gene, the Drosophila model system should prove useful for the determination of the ets gene function.

Alpharetrovirus↗
PubMed1992

Transcripts of the viroid central conserved region contain the local tertiary structural element found in full-length viroid.

The viroid central conserved region (CCR) is highly conserved among different viroids and is thought to be involved in viroid replication. A novel tertiary structure occurs in the CCR of native circular potato spindle tuber RNAs. To permit more detailed studies of this structural element, a small RNA oligonucleotide containing the CCR of the viroid genome was synthesized. The tertiary structure of these CCR transcripts was examined by UV-crosslinking of the RNA, followed by mapping of the crosslink using limited alkaline digestion and classical RNA secondary analysis. The CCR transcript was found to undergo UV-crosslinking between the same two bases as in full-length viroid, indicating that the tertiary structure is the same and that the CCR transcript will be useful for the affinity purification of host components.

Base Sequence↗
PubMed1992

Three-dimensional structure of (1-36)bacterioopsin in methanol-chloroform mixture and SDS micelles determined by 2D 1H-NMR spectroscopy.

Spatial structures of proteolytic segment A (sA) of bacterioopsin of H. halobium (residues 1-36) solubilized in a mixture of methanol-chloroform (1:1), 0.1 M LiClO4 organic mixture, or in perdeuterated sodium dodecyl sulfate (SDS) micelles, were determined by 2D 1H-NMR techniques. 324 and 400 NOESY cross-peak volumes were measured in NOESY spectra of sA in organic mixture and SDS micelles, respectively. The sA spatial structures were determined by local structure analysis, distance geometry calculation with program DIANA and systematic search for energetically allowed side chain rotamers consistent with NOESY cross-peak volumes. The structures of sA are similar in both milieus and have the right-handed alpha-helical region from Pro8 to Met32 with root mean square deviation (RMSD) of 0.25 A between backbone heavy atoms and fit well with Pro8 to Met32 alpha-helical region in electron cryo-microscopy model of bacteriorhodopsin. The N-terminal region Ala2-Gly6 of sA in organic mixture has a fixed structure of two consecutive gamma-turns as 2 * 2(7)-helix (RMSD of 0.25 A) stabilized by the Thr5 NH...O = C Gln3 and Ile4 NH...O = C Ala2 hydrogen bonds while this region in SDS micelles has disordered structure with RMSD of 1.44 A for backbone heavy atoms. The C-terminal region Gly33-Asp36 of sA is disordered in both milieus. Torsion angles chi 1 of sA were unequivocally determined for 13 (SDS) and 11 (organic mixture) of alpha-helical residues and are identical in both milieus.

Amino Acid Sequence↗
PubMed1994

Localization and structural characterization of an oligosaccharide O-linked to bovine PDC-109. Quantitation of the glycoprotein in seminal plasma and on the surface of ejaculated and capacitated spermatozoa.

PDC-109 (13 kDa) is the most abundant component, and the major heparin-binding protein, of bovine (Bos taurus) seminal plasma. Here, we show that PDC-109 contains a single O-linked oligosaccharide (NeuNAc alpha(2-6)-Gal beta(1-3)-GalNAc-) attached to Thr11. Immunoquantitation of PDC-109 indicates that its concentration in seminal plasma is 15-20 mg/ml. Though PDC-109 is not present on epididymal sperm, ejaculated spermatozoa on average are coated with (9.5 +/- 0.3) x 10(6) molecules of PDC-109/cell. This value remained constant in swim-up sperm and decreased to (7.7 +/- 0.4) x 10(6)/spermatozoon after incubation for 24 h in capacitation medium at 39 degrees C. These data substantiate the hypothesis that PDC-109 may be one of the seminal plasma components that enhance the fertilizing capacity of bull spermatozoa upon interaction with heparin-like glycosaminoglycans present in the female genital tract.

Amino Acid Sequence↗