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PubMed1997

The Local Structure of Space-variant Images.

Local image structure is widely used in theories of both machine and biological vision. The form of the differential operators describing this structure for space-invariant images has been well documented. Although space-variant coordinates are universally used in mammalian visual systems, the form of the operators in the space-variant coordinate system has received little attention. In this report we derive the form of the most common differential operators and surface characteristics in the space-variant domain and show examples of their use. The operators include the Laplacian, the gradient and the divergence, as well as the fundamental forms of the image treated as a surface. We illustrate the use of these results by deriving the space-variant form of corner detection and image enhancement algorithms. The latter is shown to have interesting properties in the complex log domain, implicitly encoding a variable grid-size integration of the underlying PDE, allowing rapid enhancement of large scale peripheral features while preserving high spatial frequencies in the fovea. Copyright 1997 Elsevier Science Ltd.

Journal Article↗

PubMed2003

Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide sakacin P and a sakacin P variant that is structurally stabilized by an inserted C-terminal disulfide bridge.

The three-dimensional structures in dodecylphosphocholine (DPC) micelles and in trifluoroethanol (TFE) of the pediocin-like antimicrobial peptide sakacin P and an engineered variant of sakacin P (termed sakP[N24C+44C]) have been determined by use of nuclear magnetic resonance spectroscopy. SakP[N24C+44C] has an inserted non-native activity- and structure-stabilizing C-terminal disulfide bridge that ties the C-terminus to the middle part of the peptide. In the presence of DPC, the cationic N-terminal region (residues 1-17) of both peptides has an S-shaped conformation that is reminiscent of a three-stranded antiparallel beta-sheet and that is more pronounced when the peptide was dissolved in TFE instead of DPC. The four positively charged residues located in the N-terminal part are found pointing to the same direction. For both peptides, the N-terminal region is followed by a well-defined central amphiphilic alpha-helix (residues 18-33), and this in turn is followed by the C-terminal tail (residues 34-43 for sakacin P and 34-44 for sakP[N24C+44C]) that lacks any apparent common secondary structural motif. In the presence of DPC, the C-terminal tails in both peptides fold back onto the central alpha-helix, thereby creating a hairpin-like structure in the C-terminal halves. The lack of long-range NOEs between the beta-sheet Nu-terminal region and the hairpin-like C-terminal half indicates that there is a flexible hinge between these regions. We discuss which implications such a structural arrangement has on the interaction with the target cell membrane.

Amino Acid Sequence↗

PubMed1999

Isoporphycene: The Fourth Constitutional Isomer of Porphyrin with an N(4) Core-Occurrence of E/Z Isomerism.

Liberation of the ligand from the nickel complex 1 obtained by template synthesis yielded isoporphycene (as the octaethyl derivative 2), the first constitutional isomer of porphyrin with an N(4) core for which E/Z isomerism is involved: Compound 2 is present as the E isomer, which is in rapid, presumably acid-catalyzed equilibrium with a small amount (2 %) of the Z isomer. The remaining unknown constitutional isomers of porphyrin are considerably higher in energy than the already rather labile isoporphycene, so that the latter should mark the border of existence for this type of structural variant of porphyrin.

Journal Article↗

PubMed2026

Safe and Stable Germline Transmission of MSTN Mutations in Cattle.

With the global population expected to reach 10 billion by 2050, sustainable livestock production is critical. Gene editing of the myostatin (MSTN) gene represents a promising strategy to enhance muscle growth in cattle. In this study, MSTN-mutated founder (F0) cows were used to generate F1 offspring via ovum pick-up, in vitro fertilization, and embryo transfer. Four F1 calves were born, all confirmed to be heterozygous for the MSTN mutation. Long-term monitoring showed normal growth and no visible health abnormalities. Whole-genome sequencing identified SNPs, INDELs, and structural variants, most with minimal predicted functional effects. Proteomic profiling of Longissimus dorsi muscle quantified 2947 proteins, revealing only subtle expression differences between MSTN-mutated and wild-type cattle. These results demonstrate stable inheritance and confirm that MSTN editing does not disrupt genome integrity or protein expression. Overall, our findings support the safety and utility of MSTN gene editing to improve livestock productivity for future food security.

Animals↗

PubMed2003

Poland anomaly--report of an unusual family.

A family with classical Poland anomaly presenting in the son and a partially affected mother is reported. We hypothesize that Poland anomaly has a multifactorial basis involving vascular compromise in early development. Two possible predisposing factors are aberrant vascular formation and thrombophilia. The investigation of our family has not demonstrated an abnormality in coagulation, therefore, we surmise that an inherited structural variant of blood vessel formation is responsible.

Family Health↗

PubMed2007

Axillary arch in Bulgarian population: clinical significance of the arches.

In order to study the incidence of the axillary arch in the Bulgarian population, we examined the axillary regions of 56 formol-carbol fixed human cadavers and observed two cases with a unilateral axillary arch. In the first case, the variant structure was situated on the right side of a 58-year-old female cadaver. The axillary arch extended from the lateral border of the latissimus dorsi to the posterior layer of the pectoralis major tendon. In the second case, the axillary arch was found on the left side of a 63-year-old male cadaver and had the same attachment points as in the first case. The innervation and blood supply of the arches are discussed. We have also reviewed extensive information concerning the clinical importance of the axillary arch, and for the first time, it was summarized clearly for clinicians. The summary consists of three parts: "diagnosis" of the axillary arch by physical investigation or imaging techniques; the axillary arch and surgical interventions in the region of the axilla; the axillary arch as an entrapment site for the axillary vessels and nerves.

Axilla↗

PubMed1988

Electrophoretic heterogeneity of maize histones.

Histones from maize embryos and seedlings have been isolated using a fast extraction procedure. Three different electrophoretic systems have been applied for the study of the heterogeneity of maize core histones. Electrophoresis in acetic acid/urea polyacrylamide gels, containing high concentrations of urea, resulted in optimum fractionation of the core histones and especially of histone H4. Sodium dodecyl sulfate-containing polyacrylamide gels were not useful for the fractionation of maize histone classes H2a and H2b, nor for the various subfractions of H3 and H4. Gels containing Triton X-100, used for the dimension in two-dimensional electrophoresis proved to be efficient for the separation of all histone classes, as well as their structural variants and chemical modifications. Maize core histones have been oxidized in an attempt to define which of the Triton X-100 resolved subfractions represent oxidation forms.

Cell Nucleus↗

PubMed1988

A second subunit of CD8 is expressed in human T cells.

The CD8 glycoprotein plays important functions in T cell development and in T cell activation. In rodents, CD8 is a heterodimer, consisting of an alpha-chain (Lyt2) and a beta-chain (Lyt3). In humans, only the alpha-chain has been detected, and it has been thought that CD8 consists of homodimers of this protein. We have isolated functional cDNA clones encoding human CD8 beta, and show that the CD8 beta protein is expressed on the surface of CD8+ human T cells. cDNA clones encoding multiple forms of the human CD8 beta-chain have been isolated and characterized. These structural variants, which are likely to arise by alternative splicing, differ in the sequences encoding the cytoplasmic domain, which can consist of 19, 30, or 52 amino acids. One of the cDNAs lacks nucleotide sequences corresponding to a hydrophobic transmembrane domain, and may encode a secreted CD8 beta protein. The protein product of the human CD8 beta gene can be detected by a recently described anti-CD8 monoclonal antibody, 597. Expression of the epitope recognized by this antibody requires co-expression of the CD8 alpha and CD8 beta gene products. About 90% of human CD8 alpha positive thymocytes and peripheral blood lymphocytes express CD8 beta at the cell surface. Expression of the CD8 beta chain is thus conserved between human and rodents, and the variant CD8 beta polypeptides may have distinct roles in T cell function and development.

Antigens, Differentiation, T-Lymphocyte↗

PubMed1992

A confined variable region confers ligand specificity on fibroblast growth factor receptors: implications for the origin of the immunoglobulin fold.

Binding of cellular growth factors to their receptors constitutes a highly specific interaction and the basis for cell and tissue-type specific growth and differentiation. A unique feature of fibroblast growth factor (FGF) receptors is the multitude of structural variants and an unprecedented degree of cross-reactivity between receptors and their various ligands. To examine receptor-ligand specificity within these families of growth factors and receptors, we used genetic engineering to substitute discrete regions between Bek/FGFR2 and the closely related keratinocyte growth factor receptor (KGFR). We demonstrate that a confined, 50 amino acid, variable region within the third immunoglobulin-like domain of Bek and KGFR exclusively determines their ligand binding specificities. Replacing the variable region of Bek/FGFR2 with the corresponding sequence of KGFR resulted in a chimeric receptor which bound KGF and had lost the capacity to bind basic FGF. We present evidence that the two variable sequences are encoded by two distinct exons that map close together in the mouse genome and follow a constant exon, suggesting that the two receptors were derived from a common gene by mutually exclusive alternative mRNA splicing. These results identify the C-terminal half of the third immunoglobulin-like domain of FGF receptors as a major determinant for ligand binding and present a novel genetic mechanism for altering receptor-ligand specificity and generating receptor diversity.

3T3 Cells↗

PubMed2026

Somatic Mitochondrial-Nuclear DNA Transfer in Lymphoproliferative Disorders.

INTRODUCTION: Somatic mitochondrial-nuclear DNA transfer (SMNT) is a process by which mitochondrial DNA (mtDNA), of varying sizes, integrate into the nuclear genome and has been previously reported in solid tumours. METHODS: EuroClonality-NGS DNA Capture sequencing data from 755 lymphoid malignancies and 59 lymphoid cell lines were analysed for SMNT-associated structural variants. RESULTS: Five malignancies (0.66%) harboured SMNTs, predominantly involving IGH genes, with one PTEN gene disruption identified. Breakpoint features supported non-homologous end joining-mediated integration. CONCLUSION: SMNTs are rare but recurrent events in lymphoid malignancies and may represent stable clonal markers for minimal residual disease monitoring. TRIAL REGISTRATION: The authors have confirmed clinical trial registration is not needed for this submission.

Journal Article↗

PubMed2006

Summer changes in cyanobacterial bloom composition and microcystin concentration in eutrophic Czech reservoirs.

In mid-July and August 2003 and 2004, 18 reservoirs in the Czech Republic were sampled for phytoplankton species composition and concentration of intracellular microcystins (MCs). As a consequence of high nutrient loading, most of the reservoirs experienced cyanobacterial blooms of various intensities, with the prevalence of cyanobacteria increasing markedly in August, along with a conspicuous shift in species composition toward dominance of Microcystis spp. Microcystins were detected in 90% of the samples, and their amount also increased considerably in August, reflecting the cyanobacterial biomass. In Microcystis-dominated samples, a significantly higher amount of MCs (p < 0.001) occurred than in samples in which other taxa prevailed. Microcystins were positively correlated with chlorophyll a and cyanobacterial biovolume (p < 0.05, R2 = 0.61 and 0.66, respectively), with the strongest correlation found for Microcystis spp. biovolume (p < 0.001, R2 = 0.87). This taxon was the most important producer of MCs in Czech reservoirs. The main structural variants of MCs were MC-LR, MC-RR, and MC-YR. This study's data also indicate that the relative share of MC variants (MC-LR and MC-RR) varies considerably with time, most likely as a consequence of different species and strain compositions during the summer. This study clearly demonstrates a high prevalence of MC-producing cyanobacteria in Czech reservoirs. Therefore, regular monitoring of these reservoirs is highly desirable in an effort to minimize potential health risks to the human population.

Biomass↗

PubMed1993

Structural heterogeneity of Caucasian N-acetyltransferase at the NAT1 gene locus.

The human N-acetylation polymorphism is a genetic trait phenotypically reflected by differences in N-acetyltransferase (NAT) activity with therapeutic agents (rapid and slow acetylation), but a genetic invariability in N-acetylation of some arylamine drugs is also known. There are two highly similar human NAT genes: NAT1 is thought to encode a genetically invariant protein, whereas NAT2 has conclusively been shown to represent a polymorphic locus. This study demonstrates the presence of discrete NAT1 structural variants among Caucasians. These were detected by direct sequencing of 1.6-kilobase NAT1 fragments generated by the polymerase chain reaction with liver and leukocyte DNA from 13 subjects of established acetylator phenotype and NAT2 genotype. A prominent alteration in one of the variants was obliteration of the consensus polyadenylation signal (AATAAA-->AAAAAA). Several mutations were discernible in all regions of the second variant allele, including silent (codon 153) and nonsilent (Ser-214-->Ala) substitutions in the coding region and deletion of nine bases from an AT-rich segment in the 3' untranslated region. One-half of the unrelated subjects were either homozygous or heterozygous for the mutant NAT1 alleles, both of which obeyed a Mendelian inheritance pattern. These novel results unambiguously show that human NAT1, like NAT2, is a polymorphic locus.

Acetylation↗

PubMed1996

Characterization of the aryl hydrocarbon receptor complex in human B lymphocytes: evidence for a distinct nuclear DNA-binding form.

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) suppresses B lymphocyte proliferation and immunoglobulin production. We previously reported that the aryl hydrocarbon receptor (AhR) complex, composed of the AhR ligand binding subunit and the Ah receptor nuclear translocator (ARNT), was constitutively present in nuclear extracts from two human B lymphocyte cell lines (Biochem. Biophys. Res. Commun. 212, 27-34, 1995). The present study compared the AhR complex in the IM-9 and PJS-91 human B lymphocyte and HepG2 human hepatoma cell lines. AhR mRNA levels in the two lymphocyte cell lines were substantially lower than those in HepG2 cells, as was immunoreactive AhR protein. In contrast, ARNT mRNA and protein were expressed at a high level in all three cell lines. TCDD induction of cytochrome P450 1A1 mRNA and protein was detected in only the PJS-91 lymphocyte cell line, and at a markedly lower level than that in HepG2 cells. In gel shift assays, the cytosolic DNA-binding AhR complex in IM-9 and PJS-91 cells was indistinguishable from that in HepG2 cells. In contrast, the nuclear DNA-binding AhR complex in IM-9 and PJS-91 cells consisted of several closely migrating species, one being recognized by an AhR antibody, while an ARNT antibody reacted with all species. Protein:DNA cross-linking analysis revealed the presence of a novel Mr 100,000 DNA-binding protein in nuclear extracts from IM-9 and PJS-91, but not HepG2, cells that was not recognized by either AhR or ARNT antibodies. These results show that IM-9 and PJS-91 human B cells constitutively express a distinct nuclear DNA-binding form of the AhR complex that may result from the presence of an additional protein or a structural variant of the AhR.

Aryl Hydrocarbon Receptor Nuclear Translocator↗

PubMed1997

The use of sequential high-performance liquid chromatography and capillary zone electrophoresis to separate the glycosylated peptides from recombinant tissue plasminogen activator to a detailed level of microheterogeneity.

The advantage of using the two-dimensional separation method was demonstrated by the separation of the complex tryptic peptides of recombinant human tissue plasminogen activator (rt-PA) glycoprotein. This method hybridizes two analytical methods where fractions containing glycopeptides are collected from reversed-phase high-performance liquid chromatography (RP-HPLC) and separated by capillary zone electrophoresis (CZE). CZE readily resolved carbohydrate structural variants, based on sialic acid content and branching, on the same peptide. Nonglycosylated peptides incidentally collected in the same RP-HPLC fraction were well resolved from the glycopeptides. This combination of RP-HPLC and CZE was able to uniquely resolve all of the peptides and glycopeptide variants in rt-PA. Confirmation of the specific peaks in the CZE was made by matrix-assisted laser-induced ionization time-of-flight mass spectrometry. The advantages and disadvantages of the existing methods for carbohydrate characterization in the biotech industry were compared. The advantage of this approach is to provide a simple extension of the existing tryptic digest protocols to include carbohydrate analysis to a detailed level of microheterogeneity.

Amino Acid Sequence↗

PubMed2027

Nanopore Sequencing for Chikungunya Virus: Principles and Application.

Nanopore sequencing is transforming viral genomics through real-time, portable, long-read analysis of RNA and DNA. Unlike traditional short-read platforms, it detects nucleotide sequences by measuring ionic current changes as nucleic acids pass through nanoscale pores, enabling direct single-molecule sequencing and base modification detection. Its simplicity, flexibility, and capacity for ultra-long reads make it ideal for resolving complex genomic regions, structural variants, and full viral genomes. These advantages have accelerated its use in pathogen surveillance and outbreak response, especially in resource-limited settings. For chikungunya virus (CHIKV), nanopore sequencing allows rapid, culture-independent recovery of complete genomes from clinical and vector samples, enabling real-time tracking of viral diversity, evolution, and spread. Experiences from Ebola, Zika, and COVID-19 have demonstrated the power of portable sequencing, now applied to CHIKV monitoring. Advances in tools such as Guppy, Dorado, Minimap2, and Medaka enhance read quality, consensus accuracy, and downstream analyses. Despite challenges in basecalling and error correction, robust quality control pipelines ensure reliable results. Ongoing improvements in chemistry, flow cell design, and machine learning will further enhance fidelity and throughput, establishing nanopore sequencing as a cornerstone of CHIKV genomic surveillance and epidemic preparedness.

Chikungunya virus↗

PubMed1995

Isolation and characterization of six heat shock transcription factor cDNA clones from soybean.

Thermal stress in soybean seedlings causes the activation of pre-existing heat shock transcription factor proteins (HSFs). Activation results in the induction of DNA binding activity which leads to the transcription of heat shock genes. From a soybean cDNA library we have isolated cDNA clones corresponding to six HSF genes. Two HSF genes are expressed constitutively at the transcriptional level, and the remaining four are heat-inducible. Two of the heat inducible genes are also responsive to cadmium stress. Comparative analysis of HSF sequences indicated higher conservation of the DNA binding domain among plant HSFs than those from yeast or other higher eukaryotes. The putative plant HSF oligomerization domain contains hydrophobic heptapeptide repeats characteristic of coiled coils and seems to exist in two structural variants. The carboxy-terminal domains are reduced in size and the C-terminal heptad repeat is degenerate.

Amino Acid Sequence↗

PubMed1994

Homology-dependent gene silencing in transgenic plants: epistatic silencing loci contain multiple copies of methylated transgenes.

Previous work has shown that two homologous, unlinked transgene loci can interact in plant nuclei, leading to non-reciprocal trans-inactivation and methylation of genes at one locus. Here, we report the structure and methylation of different transgene loci that contain the same construct but are variably able to inactivate and methylate a partially homologous, unlinked target locus. Silencing loci comprised multiple, methylated copies of the transgene construct, whereas a non-silencing locus contained a single, unmethylated copy. The correspondence between strength of silencing activity and copy number/degree of methylation was further demonstrated by producing novel alleles of a strong silencing locus: reducing the transgene copy number and methylation within this silencing locus decreased its ability to inactivate the target locus. The strong silencing locus, which was located close to a telomere, trans-inactivated various structural variants of the original target construct, regardless of their location in the genome. This suggests that the silencing locus can scan the entire genome for homologous regions, a process possibly aided by its telomeric location. Our data support the idea that epistatic trans-inactivation of unlinked, homologous transgenes in plants results from a pre-existing epigenetic difference between transgene loci, which is subsequently equalized by "epigene conversion" involving DNA-DNA pairing.

Alleles↗

PubMed1986

De novo 21/21 translocation Down syndrome. Studies of parental origin of the translocation and acrocentric associations in parents.

Among ten families with de novo 21/21 translocation Down syndrome (tDS), four were informative, according to the studies of structural variants of chromosome 21, about the origin of the aberrant chromosome. In three of these, the translocation originated in the paternal and in one in the maternal gametogenesis. The parents with meiotic failure were compared with 20 control individuals (10 males and 10 females). There were no significant differences between them in the association coefficient of chromosome 21 and in the frequency of 21-21 associations. Similar results were obtained previously with the entire sample of tDS parents. The results obtained, unless they reflect too small a sample, suggest that the origin of the aberrant chromosome is not related to an increased chromosome 21 association tendency. It could be supposed that in the case of an apparent 21/21 translocation, the 21q isochromosome, morphologically indistinguishable from the Robertsonian translocation, is in question. The Ag-NOR negative acrocentrics in the tDS parents reappeared in the probands confirming the heritability of that nucleolus organizer regions (NOR) trait.

Chromosome Banding↗