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PubMed1997

Morphology of the plantar calcaneocuboid ligaments.

The plantar calcaneocuboid ligaments have various configurations and are referred to in the literature by different names. The aims of this study were to classify the form and attachments of the plantar calcaneocuboid ligaments and to determine their dimensions to describe their morphology. The plantar aspects of 59 cadaver feet were dissected to expose the associated ligaments. The long and short plantar ligaments showed several structural variations of shape, band number, and attachments. The variations that were seen have led to confusion in the literature, which needs to be resolved. A new nomenclature is suggested based on the observed morphology. These findings agree with previous reports, and data are also presented that describe the shapes of the ligaments.

Cadaver↗
PubMed2005

Lipopolysaccharide inner core oligosaccharide structure and outer membrane stability in human pathogens belonging to the Enterobacteriaceae.

In the Enterobacteriaceae, the outer membrane is primarily comprised of lipopolysaccharides. The lipopolysaccharide molecule is important in mediating interactions between the bacterium and its environment and those regions of the molecule extending further away from the cell surface show a higher amount of structural diversity. The hydrophobic lipid A is highly conserved, due to its important role in the structural integrity of the outer membrane. Attached to the lipid A region is the core oligosaccharide. The inner core oligosaccharide (lipid A proximal) backbone is also well conserved. However, non-stoichiometric substitutions of the basic inner core structure lead to structural variation and microheterogeneity. These include the addition of negatively charged groups (phosphate or galacturonic acid), ethanolamine derivatives, and glycose residues (Kdo, rhamnose, galactose, glucosamine, N-acetylglucosamine, heptose, Ko). The genetics and biosynthesis of these substitutions is beginning to be elucidated. Modification of heptose residues with negatively charged molecules (such as phosphate in Escherichia coli and Salmonella and galacturonic acid in Klebsiella pneumoniae) has been shown to be involved in maintaining membrane stability. However, the biological role(s) of the remaining substitutions is unknown.

Cell Membrane↗
PubMed2005

Detailed protein sequence alignment based on Spectral Similarity Score (SSS).

BACKGROUND: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. RESULTS: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. CONCLUSION: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an extension to the conventional similarity methods and results indicate that it holds a strong potential for analysis of various biological sequences and structural variations in proteins.

Algorithms↗
PubMed2002

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.

BACKGROUND: Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species. RESULTS: We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes. CONCLUSIONS: This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.

Animals↗
PubMed2024

Identifying inversions with breakpoints in the Dystrophin gene through long-read sequencing: report of two cases.

BACKGROUND: Duchenne Muscular Dystrophy (DMD) is an X-linked disorder caused by mutations in the DMD gene, with large deletions being the most common type of mutation. Inversions involving the DMD gene are a less frequent cause of the disorder, largely because they often evade detection by standard diagnostic methods such as multiplex ligation probe amplification (MLPA) and whole exome sequencing (WES). CASE PRESENTATION: Our research identified two intrachromosomal inversions involving the dystrophin gene in two unrelated families through Long-read sequencing (LRS). These variants were subsequently confirmed via Sanger sequencing. The first case involved a pericentric inversion extending from DMD intron 47 to Xq27.3. The second case featured a paracentric inversion between DMD intron 42 and Xp21.1, inherited from the mother. In both cases, simple repeat sequences (SRS) were present at the breakpoints of these inversions. CONCLUSIONS: Our findings demonstrate that LRS is an effective tool for detecting atypical mutations. The identification of SRS at the breakpoints in DMD patients enhances our understanding of the mechanisms underlying structural variations, thereby facilitating the exploration of potential treatments.

Humans↗
PubMed2025

Identification of a novel non-coding deletion in Allan-Herndon-Dudley syndrome by long-read HiFi genome sequencing.

BACKGROUND: Allan-Herndon-Dudley syndrome (AHDS) is an X-linked disorder caused by pathogenic variants in the SLC16A2 gene. Although most reported variants are found in protein-coding regions or adjacent junctions, structural variations (SVs) within non-coding regions have not been previously reported. METHODS: We investigated two male siblings with severe neurodevelopmental disorders and spasticity, who had remained undiagnosed for over a decade and were negative from exome sequencing, utilizing long-read HiFi genome sequencing. We conducted a comprehensive analysis including short-tandem repeats (STRs) and SVs to identify the genetic cause in this familial case. RESULTS: While coding variant and STR analyses yielded negative results, SV analysis revealed a novel hemizygous deletion in intron 1 of the SLC16A2 gene (chrX:74,460,691 - 74,463,566; 2,876 bp), inherited from their carrier mother and shared by the siblings. Determination of the breakpoints indicates that the deletion probably resulted from Alu/Alu-mediated rearrangements between homologous AluY pairs. The deleted region is predicted to include multiple transcription factor binding sites, such as Stat2, Zic1, Zic2, and FOXD3, which are crucial for the neurodevelopmental process, as well as a regulatory element including an eQTL (rs1263181) that is implicated in the tissue-specific regulation of SLC16A2 expression, notably in skeletal muscle and thyroid tissues. CONCLUSIONS: This report, to our knowledge, is the first to describe a non-coding deletion associated with AHDS, demonstrating the potential utility of long-read sequencing for undiagnosed patients. Although interpreting variants in non-coding regions remains challenging, our study highlights this region as a high priority for future investigation and functional studies.

Humans↗
PubMed1989

Selective suppression of follicle-stimulating hormone secretion in anterior pituitary cells by the gonadal steroid 3 alpha-hydroxy-4-pregnen-20-one.

The effect of 3 alpha-hydroxy-4-pregnen-20-one (3HP), a Sertoli cell steroid, on the secretion of gonadotropins from rat anterior pituitary cells in culture was examined and subsequently compared with the action of other gonadal steroids and steroids structurally related to 3HP. Pituitary cells from randomly cycling, sexually mature female rats were isolated and maintained in culture 72 h before use. On the day of treatment, medium was changed, steroids (10(-16)-10(-4) M) and/or LHRH (10(-8) M) were added, and cells were allowed to incubate for a further 24 h. Medium was then examined for gonadotropin content by RIA. 3HP treatment of anterior pituitary cells resulted in a significant reduction of both basal and LHRH-induced FSH secretion, while LH secretion was unaffected. The lowest effective dose of 3HP (10(-16) M) significantly decreased basal FSH secretion to 65.6% of control levels. The lowest effective dose of 3HP that significantly inhibited (by 31%) LHRH-induced FSH secretion was 10(-14) M 3HP. Maximum suppression by 3HP of basal FSH secretion occurred between 10(-10)-10(-8) M, and maximum suppression of LHRH-induced secretion occurred at 10(-12) M. None of the other gonadal steroids tested (progesterone, testosterone, 5 alpha-dihydrotestosterone, 17 beta-estradiol, 20 alpha-hydroxy-4-pregnen-3-one, and 5 alpha-pregnane-3,20-dione) had a similar selective effect on FSH secretion; progesterone, testosterone, and 17 beta-estradiol actually resulted in increased FSH release, and 5 alpha-pregnane-3,20-dione resulted in significant increase in basal LH. A number of metabolites and structural variations of 3HP were examined in this in vitro system at concentrations of 10(-12)-10(-6) M, and none exhibited a similar selective FSH-suppressing activity as 3HP. The data suggest that the selective FSH-suppressing effect of 3HP seen previously in vivo and here in vitro is due to 3HP itself and not the result of a metabolite of this molecule.

20-alpha-Dihydroprogesterone↗
PubMed1991

A hepatic lipase gene mutation associated with heritable lipolytic deficiency.

Absent hepatic lipase (HL) activity results in dyslipidemia and premature atherosclerosis. DNA sequencing of the HL gene from subjects with heritable HL deficiency identified a new C to T substitution within exon 8 that in the mature enzyme caused a threonine to methionine change at position 383 (T383M). With a rapid DNA detection method we observed that all 6 individuals with complete HL deficiency from 2 families had the T383M mutation. None of 50 random unrelated unaffected subjects had this mutation. We propose that T383M is specific to families with heritable HL deficiency. Furthermore, structural variation at the HL gene, possibly in combination with other factors, appears to be etiologic in HL deficiency.

Adult↗
PubMed1994

Thyrotropic activity of basic isoelectric forms of human chorionic gonadotropin extracted from hydatidiform mole tissues.

hCG is known to have thyroid-stimulating activity and may cause hyperthyroidism in patients with trophoblastic diseases. hCG occurs in normal and molar pregnancy with breaks or nicks in the alpha- or beta-subunit peptide linkage and with substantial heterogeneity in the composition and degree of branching within the oligosaccharide side-chains. The bioactivity of hCG is markedly influenced by these structural variations. We purified hCG from five hydatidiform moles, using chromatofocusing separation after gel filtration. The hCG molecules were fractionated according to their isoelectric points, with a linear pH gradient from 3.2-6.1 and a final 1.0 mol/L NaCl step elution. The hCG immunoreactivity of each fraction was measured by RIA, and the thyroid-stimulating activity of hCG was determined by means of the cAMP response in Chinese hamster ovary cells expressing functional human TSH receptors (Chinese hamster ovary-JP09 cells). The chromatofocusing profile showed that hCG from the moles was eluted in six or seven major peaks at pH 6.1, 5.5, 5.3, 4.8, 3.8, and 3.2 and with 1.0 mol/L NaCl, whereas hCG extracted from serum of hydatidiform moles and standard hCG preparation CR-127 extracted from pregnancy urine showed only small peaks at pH greater than 5.3. Each fraction increased cAMP production significantly in Chinese hamster ovary-JP09 cells. The relative bioactivity/immunoreactivity, represented as the ratio of cAMP/hCG (picomoles per IU), was significantly higher in basic components (pI 6.1, 6.2 +/- 1.2; pI 5.5, 4.4 +/- 2.7; pI 5.3, 5.8 +/- 0.3) than in hCG CR-127 (bioactivity/immunoreactivity, 0.42; P < 0.05). The difference in pI of each hCG isoform was attributable to the extent of sialylation; basic hCG isoforms contained less sialic acid by immunological detection using lectins. These results indicate that isoforms of hCG with more thyrotropic activity were produced by trophoblastic tissues in patients with hydatidiform mole. We speculate that these isoforms of hCG may be responsible for the hyperthyroidism in some patients with hydatidiform moles.

Adult↗
PubMed1995

Identification of alternatively spliced messenger ribonucleic acid encoding truncated growth hormone-releasing hormone receptor in human pituitary adenomas.

The expression of GHRH receptor (GHRH-R) messenger ribonucleic acid (mRNA) was studied in 22 pituitary adenomas and 2 normal anterior pituitaries. Northern blot analysis revealed that GHRH-R mRNA were expressed in all 14 GH-producing adenomas, 1 of 3 ACTH-producing adenomas, the 1 PRL-producing adenoma, 2 of 4 nonfunctioning adenomas, and the 2 normal anterior pituitaries. Their expression levels varied among GH-producing adenomas and were relatively low in GH-nonproducing adenomas. In addition to the major transcript with a molecular mass of 2.0 kilobases (kb), the transcripts were identified at 2.8 and 4.5 kb in some GH-producing adenomas. To examine the structural variations in GHRH-R mRNA in pituitary adenomas, we amplified the complementary DNA fragment encompassing the region from the third cytoplasmic loop to the sixth transmembrane domain of GHRH-R. This region was selected because this region of the G protein-coupled receptor has been known to interact with G protein. Two amplified fragments with the molecular masses of 250 and 810 base pairs were identified by the reverse transcriptase-polymerase chain reaction method. The nucleotide sequence of a smaller fragment, which was the expected size, revealed that no mutations were found in this region in 10 GH-producing adenomas examined. However, a larger fragment contained the currently unidentified insertion. Compared with the genomic DNA sequence, this insertion was found to be generated through alternative splicing. In addition, this variant form contained the premature stop codon in-frame, indicating that it encodes the truncated GHRH-R. This insertion-specific probe could hybridize with 2.8- and 4.5-kb species of GHRH-R mRNA on Northern blot analysis, and these transcripts were expressed mainly in GH-producing adenomas. Finally, study of cell transfection and cAMP measurement revealed that this truncated GHRH-R was unable to transmit GHRH signals. These results suggest that some GH-producing adenomas preferentially express the truncated GHRH-R as a nonfunctioning receptor through alternative splicing.

Adenoma↗
PubMed2000

Solubilization of meso-tetraphenylporphyrin photosensitizers by substitution with fluorine and with 2,3-dihydroxy-1-propyloxy groups.

The tetra(hydroxyphenyl)porphyrins (5,10,15,20-tetrakis(2-hydroxyphenyl)porphyrin (3), 5,10,15,20-tetrakis(3-hydroxyphenyl)porphyrin (4), and 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin (5) and the tetrahydroporphyrins (5,10,15,20-tetrakis(2-fluoro-3-hydroxyphenyl)porphyrin (6), 5,10,15,20-tetrakis(2,4-difluoro-3-hydroxyphenyl)porphyrin (7), and 5,10,15,20-tetrakis(3,5-difluoro-4-hydroxyphenyl)porphyrin (8)) have been reported as potential photosensitizers for photodynamic therapy. In particular, the tetrahydroporphyrin 7, which has been in Phase III clinical trials for three years in the USA and Canada, has shown great promise for primary and recurrent head and neck cancer. It is expected to be on the market soon. A potentially limiting property of compounds 3-8 is their hydrophobicity, which renders them insoluble in aqueous media. We therefore set out to develop an approach for their solubilization in aqueous media. The first attempt was to prepare analogues with fluorine substituents at the positions ortho to each of the four hydroxy groups on the meso-phenyl rings. This was expected to increase the acidity of the ortho hydroxy groups, and therefore the solubility of the compounds in hydroxylic media. This structural alteration resulted in a slight but significant decrease in the partition coefficients. The second attempt was substitution of each of the hydroxy groups on the phenyl rings with 2,3-dihydroxy-1-propyloxy groups. This structural alteration resulted in a substantial decrease in the partition coefficients. To harness the combined effect of these two structural variations porphyrins were prepared containing both 2,3-dihydroxy-1-propyloxy and ortho fluorine groups on the meso-phenyl rings. The partition coefficients decreased by more than two orders of magnitude. The most significant decrease was due to the substitution with 2,3-dihydroxy-1-propyloxy groups, rather than the substitution with fluorine, although fluorination alone contributed significantly. The effect of this method was demonstrated most clearly by comparison of the partition coefficients of meta and para isomers of these porphyrins.

Fluorine↗
PubMed2002

Characterization of two isomeric beta-d-glucosiduronic acids derived from 1,2-diethyl-3-hydroxypyridin-4-one (CP94) in rat liver homogenate incubates.

1,2-Diethyl-3-hydroxypyridin-4-one (CP94) is an orally active iron chelator with potential for use in photodynamictherapy. This investigation reports the formation and characterization of two isomeric glucuronides of CP94 in rat liver homogenate incubates. To assign the glucuronidation sites in the CP94 molecule, two O-methylated derivatives of CP94 have been synthesized. By comparing the spectral characteristics of the CP94 3-O- and 4-O-methyl derivatives with CP94 and the CP94 glucuronides formed during incubation, evidence was obtained which enabled the assignment of these two isomeric glucuronides to the 3-O-glucuronide and 4-O-glucuronide of CP94. It was found that the 3-O-glucuronide was the dominant CP94 metabolite under in-vitro conditions. In an attempt to understand the potential influence of structural variation on the glucuronidation of CP94 analogues, the 1-and 2-monoethyl derivatives of CP94 were investigated. The 2-monoethyl derivative of CP94 yielded only the 3-O-glucuronide in rat liver homogenate incubate, while no glucuronide was formed from the 1-monoethyl derivative. In addition, no glucuronide from the 3-O-methyl or 4-O-methyl derivatives of CP94 could be detected. The relevance of these findings to the development of new 3-hydroxypyridin-4-one iron chelators is discussed.

Animals↗
PubMed1978

The cell surface of Trypanosoma cruzi: cytochemistry and freeze-fracture.

The ultrastructure of epimastigotes of Trypanosoma cruzi, obtained from acellular cultures, and bloodstream trypomastigotes, isolated from infected mice, were studied by thin-sectioning and freeze-fracturing techniques. Epimastigotes showed a thin (5 nm) surface coat when stained with ruthenium red, while the surface coat of trypomastigotes was more prominent (15 nm thick). Both P and E faces of the plasma membrane of T. cruzi had roughly the same number of intramembranous particles (IMP) as seen by freeze-fracture. The plasma membrane of bloodstream trypomastigotes had less IMP than epimastigotes. Several differentiations of the plasma membrane was observed. In epimastigotes a cytostome appears as a particle-poor region delimited by a pallisade-like row of adjacent IMP. Bloodstream trypomastigotes did not have a cytostome. Instead, abundant pinocytic vesicles were observed. At the base of the flagellum of epimastigotes a ciliary necklace was found. At this region, the surface coat was differentiated as long, hair-like projections after staining with ruthenium red. The flagellar membrane had less IMP than the body membrane. Clusters of IMP were present on both faces of the flagellar membrane at the flagellar-body adhesion zone of epimastigotes. Linear arrays of IMP were also seen. In bloostream trypomastigotes clusters of particles were observed both on the flagellar and cell body membranes. Our observations demonstrate the presence of considerable structural variations of the T. cruzi plasma membrane at the two stages of the life cycle studied.

Animals↗
PubMed2003

[Drug binding analysis of human alpha 1-acid glycoprotein using capillary electrophoresis].

Drug-plasma protein binding analysis is indispensable for drug development and clinical use. However, conventional methods for binding analyses were not suitable for small amounts of proteins because of large sample requirements. On the other hand, high-performance frontal analysis/capillary electrophoresis (HPFA/CE) consumes very small sample volumes, and is useful for ligand-binding study of small amounts of proteins. In this study, HPFA/CE was used in a drug-binding study of alpha 1-acid glycoprotein (AGP) subtypes in which plasma concentrations change dynamically to elucidate the effects of structural variation on drug binding. Binding study on desialyrated AGP revealed that (S)-enantiomer selectivity in propranolol-AGP binding was caused by sialic acid residues, while neither sialic acid nor galactose caused the enantioselectivity of verapamil binding to AGP. Biantennary glycans slightly suppressed disopyramide binding to AGP, whereas the glycans did not have any influence on propranolol and verapamil binding. Disopyramide and verapamil were selectively bound to the A variant rather than the F1S variant. The A variant showed larger enantioselective binding to disopyramide, but not to verapamil.

Binding Sites↗
PubMed1998

Comparative mapping of the cri du chat and DiGeorge syndrome regions in the great apes.

Structural variations between great ape and human chromosomes due to pericentric inversions and translocations have created at apparent controversy during the reconstruction of hominoid phylogeny. One such variation involves human chromosome 5, which is equivalent to chromosome 4 in chimpanzee and orangutan but equivalent to segments of chromosomes 4 and 19 in gorilla. Obviously, neither banding patterns nor centromeric indecies in these chromosomes match. The pathological condition of cri du chat syndrome is due to the cytogenetic deletion of band p15.2 of chromosome 5. Is this region involved during pericentric inversion of apes chromosome 4? We used a human cosmid probe for cri du chat syndrome as a phylogenetic marker in search of the aforementioned question. The genomic sequences for cri du chat syndrome region were conserved in chimpanzee (PTR4) and orangutan (PPY4) but displayed a positional divergence in gorilla on chromosome 19(GG019). In addition, we used a human cosmid DNA probe for DiGeorge syndrome which is located on chromosome 22 band q11.2 and was conserved within band 23q11.2 in apes. The loci specific human genomic probes may help to describe the inversions and translocations for other chromosomes.

Animals↗
PubMed2006

Brillouin characterization of holey optical fibers.

We report the results of detailed measurements on the Brillouin frequency shift (BFS), gain bandwidth, and gain coefficients of several small-core holey optical fibers (HFs) of both uniform and axially varying structural characteristics and compare these with measurements on more conventional fibers. Our measurements show that the BFS of HFs is first-order proportional to the modal index for light propagating along the fiber and is thus extremely sensitive to its precise structural parameters. Our results highlight the possibility of using distributed Brillouin scattering measurements to perform nondestructive structural characterization of HFs, and the possibility of producing Brillouin-suppressed HFs using controlled structural variation along the fiber length.

Journal Article↗
PubMed2006

Nonlinear imaging of embedded microstructures inside transparent materials with laser-induced ionization microscopy.

We present a novel nonlinear imaging method that utilizes femtosecond laser-induced plasma emission to probe microscopic structures embedded inside transparent materials. This nonlinear diagnostic tool can resolve either elemental or structural variations of the sample of interest and provide significant improvements over the ordinary linear microscopes by having much higher contrast ratios for the observed areas of different refractive indices. Examples of using this technique to examine the microstructures fabricated by ultrashort laser pulses inside optical glass are presented.

Journal Article↗
PubMed2006

Proteomics: a new diagnostic frontier.

BACKGROUND: Analysis of proteins has been an integral part of the field of clinical chemistry for decades. Recent advances in technology and complete identification of the human genome sequence have opened up new opportunities for analysis of proteins for clinical diagnostic purposes. METHODS: Content of a recent conference of proteomics is summarized. RESULTS: New analytical methods allow the simultaneous analysis of a large number of proteins in biological fluids such as serum and plasma, offering partial views of the complete set of proteins or proteome. Plasma presents many analytical challenges, such as the complexity of components, predominance of a few major components, and the large concentration range of components, but the number of proteins that can be detected in plasma has expanded dramatically from hundreds to thousands. At the same time, there is increased capability to detect structural variations of proteins. Recent studies also identified the presence of complex sets of small protein fragments in plasma. This set of protein fragments, the fragmentome or peptidome, is potentially a rich source of information about physiologic and disease processes. CONCLUSIONS: Advances in proteomics offer great promise for the discovery of markers that might serve as the basis for new clinical laboratory tests. There are many challenges, however, in the translation of newly discovered markers into clinical laboratory tests.

Biomarkers↗