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At least 1,351 records · Page 75Linked to original sources
PubMed2004

Androgen dependent development of a modified anal fin, gonopodium, as a model to understand the mechanism of secondary sexual character expression in vertebrates.

Male external genitalia show structural variations among species. Androgenic hormones are essential for the morphological specification of male type copulatory organs, while little is known about the developmental mechanisms of such secondary sexual characters. Western mosquitofish Gambusia affinis may offer a clue to the sexual differentiation researches, because they show a prominent masculine sexual character for appendage development, anal fin to gonopodium (GP) transition, and its formation could be induced in early juvenile fry by exogenously supplied androgens. We show that GP development is promoted by androgen dependent augmentation of sonic hedgehog (Shh) expression. Two AR cDNAs were cloned and identified as ARalpha and ARbeta from western mosquitofish. Both ARs were predominantly expressed in the distal region of outgrowing anal fin rays. Exposure of fry to androgen caused anal fin outgrowth concomitant with the Shh induction in the distal anal fin ray epithelium. When AR signaling was inhibited by its antagonist flutamide in fry, the initial induction of the Shh was suppressed accompanying retarded anal fin outgrowth. Similar suppression of anal fin outgrowth was induced by treatment with cyclopamine, an inhibitor of Shh signaling. These observations indicate that androgen dependent Shh expression is required for anal fin outgrowth leading to the formation of a genital appendage, the GP in teleost fishes. Androgen-induced GP formation may provide insights into the expression mechanism regulating the specification of sexual features in vertebrates.

Amino Acid Sequence↗
PubMed2004

Cloning, genomic organization, expression, and effect on beta-casein promoter activity of a novel isoform of the mouse Oct-1 transcription factor.

The ubiquitously expressed transcription factor Oct-1, a member of the POU domain factors, is involved in the regulation of expression of many tissue-specific and house-keeping genes. Multiple alternatively spliced isoforms of Oct-1 have been identified in human and mouse cells. The expression patterns of these isoforms and the analysis of their genomic organization and structure have suggested that the structural variation of Oct-1 isoforms may be important in conferring target and tissue specificity to its transcriptional activity. In this study, we have cloned and sequenced a new mouse Oct-1 isoform, named mOct-1Z. This novel isoform differs markedly at the C-terminus from the previously identified Oct-1 isoforms A, B, and C. It is generated by alternative splicing from the Oct-1 gene and its transcript exhibits a frameshift followed by an early stop codon, thus, its predicted protein has a distinct, much shorter C-terminal tail. However, this truncated isoform could still effectively bind to a consensus Oct-1 motif oligonucleotide and, like Oct-1B, activated the basal promoter activity of the mouse beta-casein gene. Oct-1Z is another ubiquitously expressed Oct-1 isoform, its transcript being detected in all mouse tissues examined, including the mammary gland, liver, lung, kidney, spleen, small intestine mucosa, uterus, and ovary.

5' Flanking Region↗
PubMed2006

Monitoring small molecule diffusion into hydrogels at various temperatures by fluorescence technique.

Steady state fluorescence technique was used to study small molecule diffusion into polyacrylamide (PAAm) gels at various temperatures. Pyranine (P(y)), dissolved in water was introduced as a probe and fluorescence emission (I(p)) from P(y) was monitored during diffusion. Scattered light intensities, I(sc) from PAAm gel was also monitored to observe structural variations during diffusion process. Increase in I(p) intensity was attributed to P(y) diffusion into PAAm gel. On the other hand decrease in I(sc) intensity was interpreted as the variation of the spatial heterogeneities in the system. Li-Tanaka and Fickian models were used to quantify the swelling and diffusion experiments and diffusion coefficients were produced in both cases. Related activation energies were also calculated from the corresponding physical processes.

Biophysics↗
PubMed2005

Molecular modeling study of the aggregation behavior of nickel(II), cobalt(II), lead(II) and zinc(II) bis(2-ethylhexyl) phosphate complexes.

The physiochemical nature of the metal-extractant species in organic solvent has been a matter of debate over liquid-liquid extraction of transition metals by bis(2-ethylhexyl) phosphate. The aggregation behavior of nickel(II), cobalt(II), lead(II), and zinc(II) bis(2-ethylhexyl) phosphate have been investigated using molecular modeling. The recently confirmed "open" water channels rodlike reversed micelles which is in contact with the nonaqueous solvent rather than in an inner core (or "closed" water channel) of the nickel-extractant species by Ibrahim and Neuman appears to be a unique structure for such species. Lead-, cobalt- and zinc-extractant species behave in a different manner. The cobalt-extractant species form rodlike reversed micelles, but does not show the formation of any open water channel. The zinc- and lead-extractant species form ellipsoidal (or deformed spherical) reversed micelles with fewer water molecules located at the core of the micelles which is in accord with the conventional view of reversed micelles. The structural variations of the reversed micelles for the metal extracted species are in accord with the known extraction behavior of such metals when using HDEHP.

Journal Article↗
PubMed2006

When being straight bends rules: a rationale for the linear FeNO unit in the low-spin square-pyramidal {FeNO}7 tetracyanonitrosylferrate(2-) anion.

All low-spin S=1/2 heme-NO complexes feature FeNO angles of about 140 degrees . In contrast, the square-pyramidal [Fe(CN)(4)(NO)](2-) complex features an exactly linear {FeNO}(7) unit. We have sought here to determine a possible, simple molecular orbital (MO) rationale for these structural variations. A DFT-based (DFT=density functional theory) MO analysis shows that the linearity of the latter stems from the greater pyramidalization of the Fe center, relative to nitrosylheme, which results in significant differences in d orbital hybridization. Thus, the singly occupied molecular orbital (SOMO) of [Fe(CN)(4)(NO)](2-) , while primarily Fe dz2-based, also has a significant amount of 4p(z) character, which makes it less stereochemically active, accounting for the linearity of the FeNO unit.

Ferric Compounds↗
PubMed2005

Cell cycle regulation of breast cancer cells through estrogen-induced activities of ERK and Akt protein kinases.

The proliferative effect of estrogens on breast cancer cell (BCC) is mainly mediated through estrogen receptors (ER). Non-transcriptional effects of estrogens, exerted through activation of several protein kinases, may also contribute to BCC proliferation. However, the relative contribution of these two responses to BCC proliferation is not known. We characterized a novel estrogenic receptor ligand which possess Akt and ERK activating properties distinct from that of 17beta-estradiol. Early and delayed waves of activation of these kinases were detected upon estrogenic challenge of BCC, but only molecules able to promote a significant, delayed activation of ERK-induced BCC proliferation. Estrogen-induced cell cycle progression was not sensitive to the inhibition of ERK-regulating kinases MEK1 and 2. ERalpha was found to be necessary, but not sufficient for kinases activation. Thus, estrogens elicit a distinct pattern of early and delayed activation of ERK and Akt, and early protein kinase activation is probably not involved in BCC proliferation. Structural variations in the estrogen molecule may confer novel biological properties unrelated to estrogen-dependent transcriptional activation.

Breast Neoplasms↗
PubMed2005

Chromosomal fragility, structural rearrangements and mobile element activity may reflect dynamic epigenetic mechanisms of importance in neurobehavioural genetics.

Advances in human genome analyses have not yet allowed identification of specific genetic mechanisms underlying the expression of human neurobehavioural disorders. There is an increasing awareness that several genes may contribute to behavioural phenotypes and these genes appear to interact in as yet undetermined ways. It has been suggested that the problem needs elucidation from an epigenetic, gene expression perspective. Cytogenetic instability manifesting as chromosomal fragile sites, translocations, duplications, deletions and inversions, when co-occurring with neurobehavioural disorders, may offer a doorway to the investigation of such chromatin level, regulatory region, epigenetic processes. Due to earlier indications of non-specificity of chromosomal aberrations, poor phenotype:genotype correlations and a shift to analysing candidate coding regions on high resolution map level, the only utility of chromosomal breakpoints came to be seen as harbouring possible candidate genes of interest when segregating together with particular neurobehavioural disorders. More recent findings of the expression of highly specific subsets of fragile sites in association with Tourette and Rett syndromes need to be extended to other neurobehavioural disorders to ascertain whether observed patterns can be considered representative of 'chromatin endophenotypes' correlating with discrete sets of neurobehavioural symptoms. Environmental/epigenetic factors could affect the chromatin characteristics of the genome arising through DNA strand breakage, mobile element activity and retroinsertion, establishing new architectural features of regulatory control networks very rapidly in comparison to coding region evolution rates. Microarray-based techniques for the genome-wide mapping of in vivo protein-DNA interactions offer increasingly comprehensive views of genetic and epigenetic regulatory networks. It may be informative to include functionally significant chromatin structural variation analyses when considering candidate genes for neurobehavioural disorders.

Cell Cycle↗
PubMed2005

Mycobacterial trehalose-containing glycolipid with immunomodulatory activity on human CD4+ and CD8+ T-cells.

Protection against Mycobacterium tuberculosis is based on cell-mediated immunity, most importantly involving CD4+ and CD8+ T-cell subsets. One of the key features of the tubercle bacillus is its cell envelope, characterized by extremely abundant and specific lipids. The cell-surface glycolipid 2,3-di-O-acyl-trehalose (DAT) has been consistently found in M. tuberculosis strains. In this study, analysis of proliferation, activation markers and cytokine release was performed in human peripheral blood mononuclear cells (PBMC) activated in the presence and absence of DAT. We present evidence that mycobacterial DAT is able to reduce antigen-induced proliferation of human CD4+ and CD8+ T-cell subsets. We show that the effect is associated with a decrease of cells expressing the T-cell surface activation markers CD25 and CD69, and down-modulation of IL-2, IL-12, TNF-alpha and IL-10 cytokines. Data indicating that fine acyl chain structural variations in the trehalose-containing lipid may be involved in the degree of immune modulation are also presented.

Adult↗
PubMed2005

Convergence of auditory-nerve fiber projections onto globular bushy cells.

Globular bushy cells are a key element of brainstem circuits that mediate the early stages of sound localization. Many of their physiological properties have been attributed to convergence of inputs from the auditory nerve, many of which are large with complex geometry, but the number of these terminals contacting individual cells has not been measured directly. Herein we report, using cats as the experimental model, that this number ranged greatly (9-69) across a population of 12 cells, but over one-half of the cells (seven of 12) received between 15 and 23 inputs. In addition, we provide the first measurements of cell body surface area, which also varies considerably within this population and is uncorrelated with convergence. For one cell, we were able to document axonal structure over a distance greater than 100 microm, between the soma and the location where the axon expanded to its characteristic large diameter. These data were combined with accumulated physiological information on vesicle release, receptor kinetics and voltage-gated ionic conductances, and incorporated into computational models for four cells that are representative of the structural variation within our sample population. This predictive model reveals that basic physiological features, such as precise first spike latencies and peristimulus time histogram shapes, including primary-like with notch and onset-L, can be generated in these cells without including inhibitory inputs. However, phase-locking is not significantly enhanced over auditory-nerve fibers. These combined anatomical and computational approaches reveal additional parameters, such as active zone density, nerve terminal size, numbers and sources of inhibitory inputs and their activity patterns, that must be determined and incorporated into next-generation models to understand the physiology of globular bushy cells.

Action Potentials↗
PubMed2006

Peroxidase activity can dictate the in vitro lignin dehydrogenative polymer structure.

The objective of this study was to assess the influence of the peroxidase/coniferyl alcohol (CA) ratio on the dehydrogenation polymer (DHP) synthesis. The soluble and unsoluble fractions of horseradish peroxidase (HRP)-catalyzed CA dehydrogenation mixtures were recovered in various proportions, depending on the polymerization mode (Zutropf ZT/Zulauf ZL) and HRP/CA ratio (1.6-1100purpurogallin U mmol(-1)). The ZL mode yielded 0-57%/initial CA of unsoluble condensed DHPs (thioacidolysis yields <200micromolg(-1)) with a proportion of uncondensed CA end groups increasing with the HRP/CA ratio (7.2-55.5%/total uncondensed CA). Systematically lower polymer yields (0-49%/initial CA) were obtained for the ZT mode. In that mode, a negative correlation was established between the beta-O-4 content (thioacidolysis yields: 222-660micromolg(-1)) and the HRP/CA ratio. In both modes, decreasing the HRP/CA ratio below 18Ummol(-1) favoured an end-wise polymerization process evidenced by the occurrence of tri-, tetra- and pentamers involving at least one beta-O-4 bond. At low ratio, the unsoluble ZT DHP was found to better approximate natural lignins than DHPs previously synthesized with traditional methods. Besides its possible implication in lignin biosynthesis, peroxidase activity is a crucial parameter accounting for the structural variations of in vitro DHPs.

Benzocycloheptenes↗
PubMed2026

The current and future perspective of ChickenGTEx project and its applications in precision breeding.

The Chicken Genotype-Tissue Expression (ChickenGTEx) project was established to systematically characterize the regulatory landscape of the chicken genome and to accelerate the translation of functional genomics into precision breeding. By integrating whole-genome sequencing with multi-tissue transcriptomic profiling, ChickenGTEx provides a comprehensive atlas of gene expression regulation across diverse tissues and physiological systems. Current findings demonstrate that complex production traits are governed by coordinated regulatory networks rather than isolated loci, with substantial contributions from tissue-specific gene expression, structural variation, and genotype-by-sex interactions. Sex-dependent regulatory effects further refine the genetic architecture of metabolic, immune, and reproductive traits, highlighting the importance of incorporating sex as a biological variable in genomic analyses. Application of integrative omics frameworks within elite layer populations has revealed multilayer regulatory mechanisms underlying extended laying performance, feed efficiency, metabolic health, and eggshell quality. By partitioning phenotypic variance into genetic, regulatory, and host-microbiome components, these approaches move beyond association-based mapping toward causal inference and biological interpretation. Importantly, validated regulatory loci identified through ChickenGTEx and related analyses provide actionable markers for genomic selection and rational targets for precision genome modification. Looking forward, continued expansion of regulatory atlases, incorporation of single-cell and longitudinal data in diverse environmental conditions, and integration of functional annotation into breeding pipelines will further enhance prediction accuracy and sustainable genetic improvement. The ChickenGTEx project thus represents a foundational platform bridging functional genomics and practical poultry breeding.

Animals↗
PubMed2005

On interpretation of a missing spectral band; IR spectra of acidic salts of benzohydroxamic acid.

Using solid benzohydroxamic acid (BHA) as a model compound for its salts, a broad absorption at 2730 cm(-1) was generally agreed to represent the nu(OH) band of the OH... ON bonds. The absence of nu(OH) band in the IR region 3600-1700 cm(-1) was taken to indicate the absence of OH groups in the solid salts. The same argument and conclusion was erroneously accepted for lithium (LiBHA) and potassium (KBHA) salts of BHA which are not "normal" but acid salts and do contain OH groups. X-ray diffraction results allow explanation of this discrepancy. The lithium and potassium acid salts have much shorter OH... ON bridges (O...O distances of 247 and 245 pm, respectively) than the model compound (258 pm). Accordingly, the nu(OH...O) bands in the acidic salts are shifted into the crowded 1600-700 cm(-1) interval. Obviously, interpretation of a missing spectral band in terms of molecular structure can be misleading when the models do not include all possible structural variations.

Crystallography, X-Ray↗
PubMed2026

The SMN locus in the T2T era: Structure, gene conversion, and clinical implications.

Long-read sequencing, paralog-aware variant calling, and telomere-to-telomere (T2T) human genome assemblies now enable the resolution of copy-, haplotype-, and nucleotide-level complexities in segmentally duplicated loci, which were previously inaccessible with short-read sequencing. In this review, we highlight how current technologies and analysis methods reveal extensive diversity in copy number (CN), structure, and gene conversion within the spinal muscular atrophy-associated survival motor neuron (SMN) locus. We summarize how understanding population-level structural variation could be translated into clinical practice, where a nucleotide-level view of the SMN locus may refine prognostic accuracy beyond SMN2 CN and explain variable treatment responses. Finally, we discuss how the approaches and methodologies required to study the SMN locus may be applied elsewhere, providing a scaffold to characterize other complex human genetic regions.

Humans↗
PubMed2005

Norovirus and its histo-blood group antigen receptors: an answer to a historical puzzle.

Recent findings demonstrate that human histo-blood group antigens (HBGAs) serve as receptors for norovirus infection. The recognition of human HBGAs by noroviruses is a typical protein-carbohydrate interaction, in which the protruding domain of the viral capsid protein forms an interface with the oligosaccharide side-chains of the antigens, with a wide diversity among different strains. The human HBGA system is also highly polymorphic and is controlled by multiple gene families with silent alleles. The presence of such diversified molecules on the cell surfaces indicates a possible host defense mechanism against the changing external environment. As mild pathogens that replicate possibly only in the intestinal tract, noroviruses have developed unique strategies to overcome the host defense system. This has been shown by their genetic and structural variations, which explains why norovirus-associated diseases are so common and widespread in every population worldwide.

Blood Group Antigens↗
PubMed2024

Ribosomes unraveled: The path from variant to impact.

In this issue of Cell Genomics, Rothschild et&#xa0;al.1 reveal how ribosomal RNA diversity impacts ribosome structure and its implications for health and disease. Their innovative methodologies uncover distinct ribosome subtypes with significant structural variations and expression patterns. This work reveals connections to tissue-specific biology and cancer, positing new research avenues.

Ribosomes↗
PubMed2026

Protocol for haplotype-resolved structural variant detection via long-read sequencing using cuteHap.

Long-read sequencing technologies have revolutionized human genome exploration at an unparalleled resolution, particularly facilitating the analysis of structural variation (SV) at haplotype resolution. Here, we present a protocol for using cuteHap, a robust framework for haplotype-aware SV detection through phased alignment reads generated by diverse long-read sequencing platforms. We describe procedures for single-nucleotide variant (SNV) calling, read phasing, SV calling, and genotyping. We also establish a benchmarking pipeline to evaluate the detected SV callsets. For complete details on the use and execution of this protocol, please refer to Cao et al.1.

Bioinformatics↗
PubMed2004

What is the evidence that oxcarbazepine and carbamazepine are distinctly different antiepileptic drugs?

Oxcarbazepine (OXC, Trileptal) is a modern antiepileptic drug (AED) used as both monotherapy and adjunctive therapy for the treatment of partial seizures with or without secondary generalization in adults and children above 4 years (USA) or 6 years (Europe) of age. Although OXC has been developed through structural variation of carbamazepine (CBZ) with the intent to avoid metabolites causing side effects, significant differences have emerged between the two drugs. The mechanism of action of OXC involves mainly blockade of sodium currents but differs from CBZ by modulating different types of calcium channels. In contrast to CBZ, which is oxidized by the cytochrome P-450 system, OXC undergoes reductive metabolism at its keto moiety to form the monohydroxy derivative (MHD), which is glucuronidated and excreted in the urine. The involvement of the hepatic cytochrome P-450-dependent enzymes in the metabolism of OXC is minimal. Although it does not prevent interaction with oral contraceptives, it explains why OXC can be more effectively combined with other AEDs such as valproate compared with CBZ. Switching from CBZ to OXC normalized CBZ-associated thyroid and sexual hormone abnormalities and pathological lipid values in small patient samples. OXC is often better tolerated than CBZ and causes fewer rashes than CBZ. Add-on or substitution treatment with OXC was effective in controlled trials even when CBZ did not achieve sufficient seizure control. This constitutes compelling clinical evidence that OXC and CBZ are distinctly different medications. From postmarketing experience in over 1,000,000 patient years, OXC had an advantageous risk-benefit balance also in comparison to other new AEDs. OXC should be preferred over CBZ and other older AEDs because of its proven efficacy and excellent side effect profile in children, adolescents, and adults with partial seizures.

Animals↗
PubMed1991

Endoscopic laser-assisted lacrimal surgery.

Since Sept. 1, 1989, we have successfully performed 20 video-endoscopic, transnasal, laser-assisted lacrimal procedures on 18 patients ranging in age from 3 to 88 years. This technique avoided a cutaneous scar and caused less surgical trauma and bleeding than that seen in conventional lacrimal surgery, which shortened postoperative recovery time and lessened postoperative pain. With minor modifications in surgical technique, both dacryocystorhinostomy and conjunctivodacryocystorhinostomy were performed with either the potassium titanyl phosphate or carbon dioxide lasers. The use of the video endoscope allowed laser surgery to be performed across a broad range of intranasal structural variations and provided an excellent medium for teaching this new technique.

Adolescent↗