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PubMed1976

A critical review of the 'neugliederung' concept in relation to the development of the vertebral column.

The literature on the early embryonic development of the vertebral column in various animal species was analyzed to evaluate so many unrelated or contradictory observations. The recurring problems are described. One of the first was the lack of correspondence between the metameric boundaries of the 'primitive vertebral bodies' arising from the somites and those of the adult vertebral bodies, as presumably shown by their relationship to the vertebral processes and spinal nerves. A century ago, Remak introduced the concept of 'Neugliederung', according to which the ultimate vertebral body boundaries are determined by a shift of a half segment in comparison with the earlier segment boundaries. Another question was about the nature of the structures the primitive segments give rise to (axial skeletal tissue and/or muscular tissue and/or nervous tissue), which led to the fundamental problem which system (skeleton or musculature) retains its segmentation. The observation of what was called the intervertebral fissure led to a far-reaching modification of the 'Neugliederung' concept, making a regrouping of parts of the primitive vertebral bodies both possible and probable. The functional necessity for the alternation of muscle and skeleton primordia was also assumed. Although the difference in rostro-caudal level between the boundaries of the somites and the definitive vertebral bodies, measured for instance in relation to the position of the intersegmental vessels, does not support a resegmentation of the vertebral column, because the somite is not a precursor of the adult vertebra, few authors have rejected this view. Subsequently, the discussion focussed on the problem of a) the animal species in which and b) the time at which the intervertebral fissure occurs, and the relationship of this fissure to the primitive vertebral cavity. Under the influence of comparative embryology, a number of authors concentrated mainly on identifying certain embryonic primordia as homologues of phylogenetic vertebral elements, and also on attempting to determine the recombination by which such elements could form a definitive vertebra. According to these authors, not only the vertebral bodies but also the arches and ribs undergo a 'Neugliederung'. Another variant of the 'Neugliederung' concept envisages a gradual shift of the original boundaries of the somites with respect to the transverse level of the definitive vertebrae with or without migration of cellular material. A critical consideration of the concepts at issue, and notably of the 'Neugliederung' concept, is presented. Certain phenomena held to be pillars of the 'Neugliederung' theory could not be confirmed. The functional interpretation of the resegmentation was also reduced to its proper proportions by the analysis. A development of the axial skeleton without resegmentation is just as conceivable in functional terms as one in which resegmentation occurs. A functionally meaningful relationship between muscles and skeletal elements is possible in both cases...

Animals↗
PubMed2000

Is a mutator analogous to the Ig hypermutator of the sheep ileal Peyer's patch active on MHC class I genes in the germ line?

Polymorphic sequence variation in the peptide-binding domains of MHC class I molecules appears to have been driven largely by the constructive action of natural selection on the specificity of the peptide-binding groove. Similar features are displayed by the variable domains of immunoglobulins generated in the sheep ileal Peyer's patch, but in this case there is evidence that the action of a targeted hypermutator acting on a selected substrate rather than antigen-driven selection is responsible for the pattern of variation in the system. Such a hypermutator acting in the germ line would not only mimic the action of natural selection but also, by convergent mutation, generate similar patterns of variation in unrelated alleles that could be interpreted as evidence for short-tract gene conversion. We analyzed human class I MHC alleles in the light of these data, but failed to find evidence of the action of a similar hypermutator. A search for other mutationally driven patterns of variation also failed, even in hypervariable residues from parsimonious phylogenies. Single-nucleotide variation at these residues is also frequent in recent allelic variants, but the data are as consistent with short-tract gene conversion as with base mutation. We conclude that the patterns of allelic variation in MHC molecules are not driven by mutational pressure, but rather by conventional mutational processes, accompanied by short-tract gene conversion and intense natural selection.

Alleles↗
PubMed1993

Tamoxifen resistance in breast cancer.

Tamoxifen (TAM) resistance is the underlying cause of treatment failure in many breast cancer patients receiving TAM. The mechanism(s) involved in TAM resistance are poorly understood. A variety of mechanisms have been proposed but only limited evidence exists to substantiate them. Studies have now shown that in many patients TAM resistance is not related to the down regulation or loss of estrogen receptors (ER). Variant ER have been identified, but their significance clinically remains to be proven. Since breast cancer cells secrete several estrogen-regulated growth factors and growth inhibitors that may have autocrine or paracrine activity, altered growth factor production is another possible mechanism for TAM resistance. Tissue-specific transcription activating factors that may alter how the signal induced by TAM binding to the receptor is interpreted by the cell also require further investigation. An increase in antiestrogen binding sites (AEBS), which could effectively partition TAM and reduce its concentration at the ER has also been proposed as a potential mechanism. Pharmacologic mechanisms, such as a shift in metabolism toward the accumulation of estrogenic metabolites, are supported by recent data demonstrating metabolite E and bisphenol in tumors from TAM-resistant patients. Furthermore, a decrease in tumor TAM accumulation and an altered metabolite profile have been reported in TAM-resistant breast tumors grown in nude mice. These and other studies suggest that TAM resistance may be multifactorial in nature, but definitive identification of mechanisms that are operative in clinical TAM resistance requires further study.

Animals↗
PubMed2025

Whole-genome phenotype prediction with machine learning: open problems in bacterial genomics.

MOTIVATION: How can we identify causal genetic mechanisms governing bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype yield high accuracy scores. However, attempts to extract meaningful interpretations from the predictive models are found to be corrupted by falsely identified 'causal' features. Relying solely on pattern recognition and correlations is unreliable, significantly so in bacterial genomics settings where high-dimensionality and spurious associations are the norm. Though it is not yet clear whether we can overcome this hurdle, significant efforts are being made towards discovering potential high-risk bacterial genetic variants. In view of this, we set up open problems surrounding phenotype prediction from bacterial whole-genome datasets and extending those approaches to learning causal effects, and discuss challenges that impact the reliability of a machine's decision-making when faced with datasets of this nature. RESULTS: We identify major sources of non-injectivity in the formulation of the genotype-to-phenotype mapping function-linkage-disequilibrium, limited sampling, information loss in representations, unmeasured confounders and observational noise-and analyse their implications for machine learning applications. Using a collection of 4,140 Staphylococcus aureus isolates, we illustrate challenges surrounding the defined open problems. AVAILABILITY AND IMPLEMENTATION: Raw sequencing data are available from the European Nucleotide Archive (ENA) under project accessions ERP001012, PRJEB3174, PRJEB2655, PRJEB2756, and PRJEB2944. Assemblies and annotations were generated with the Sanger bacterial pipeline (https://github.com/sanger-pathogens/vr-codebase) and unitigs extracted using DBGWAS (https://gitlab.com/leoisl/dbgwas).

Machine Learning↗
PubMed1974

Isoallele frequencies in very large populations.

The frequencies of electrophoretically distinguishable allelic forms of enzymes may be very different from the corresponding frequencies of structurally distinct forms, because many sequence variants may have identical electrophoretic charge. In large populations such frequencies will be determined largely by the number of amino acid sites that are free to vary. The number of distinguishable electrophoretic variants will remain fairly small. Beyond some limiting size, no further effect of population size on allele frequencies is expected, so isolated large populations will have closely similar allele frequencies if polymorphism is due largely to mutation and drift. The most common electrophoretic alleles are expected to be flanked by the next most common, with the rarer alleles increasingly distal. Neither strong selection nor mutation/drift interpretations of enzyme polymorphism are yet disproven, nor is any point between these extremes.

Alleles↗
PubMed1996

Novel HLA-B alleles, B*8201, B*3515 and B*5106, add to the complexity of serologic identification of HLA types.

Three class I alleles, B*8201, B*3515 and B*5106, have been described using DNA and cDNA sequencing. The B*8201 allele is most structurally related to B*5602, differing from it by 14 nucleotide substitutions resulting in 5 amino acid differences. The other two alleles, B*3515 and B*5106, differ from their most closely related HLA-B alleles by 2-3 nucleotide substitutions resulting in 1-2 amino acid substitutions, respectively. The majority of nucleotide substitutions marking these new alleles are observed in other HLA-B alleles suggesting that gene conversion and/or reciprocal recombination have created this diversity. All of the amino acid substitutions are predicted to alter the antigen binding site of the HLA-B molecule. The newly defined HLA-B allelic products were originally defined by their unusual serologic reactivity patterns. The B*8201 allelic product is serologically typed as a B "blank" or as a variant of B22 or B45. These patterns and the serologic reactivity of the other newly described allelic products are consistent with the protein sequence homology among specific HLA-B molecules. While serology remains a powerful tool for detecting HLA diversity, alleles generated by events resulting in the sharing of HLA sequence polymorphisms among alleles at a locus will continue to create complexity in the interpretation of typing results.

Alleles↗
PubMed2025

New Genetic Loci Implicated in Cardiac Morphology and Function Using Three-Dimensional Population Phenotyping.

BACKGROUND: Cardiac remodeling occurs in the mature heart and is a cascade of adaptations in response to stress, which are primed in early life. A key question remains as to the processes that regulate the geometry and motion of the heart and how it adapts to stress. METHODS: We performed spatially resolved phenotyping using machine learning-based analysis of cardiac magnetic resonance imaging in 47 549 UK Biobank participants. We analyzed 16 left ventricular spatial phenotypes, including regional myocardial wall thickness and systolic strain in both circumferential and radial directions. In up to 40 058 participants, genetic associations across the allele frequency spectrum were assessed using genome-wide association studies with imputed genotype participants, and exome-wide association studies and gene-based burden tests using whole-exome sequencing data. We integrated transcriptomic data from the GTEx project and used pathway enrichment analyses to further interpret the biological relevance of identified loci. To investigate causal relationships, we conducted Mendelian randomization analyses to evaluate the effects of blood pressure on regional cardiac traits and the effects of these traits on cardiomyopathy risk. RESULTS: We found 42 loci associated with cardiac structure and contractility, many of which reveal patterns of spatial organization in the heart. Whole-exome sequencing revealed 3 additional variants not captured by the genome-wide association study, including a missense variant in CSRP3 (minor allele frequency 0.5%). The majority of newly discovered loci are found in cardiomyopathy-associated genes, suggesting that they regulate spatially distinct patterns of remodeling in the left ventricle in an adult population. Our causal analysis also found regional modulation of blood pressure on cardiac wall thickness and strain. CONCLUSIONS: These findings provide a comprehensive description of the pathways that orchestrate heart development and cardiac remodeling. These data highlight the role that cardiomyopathy-associated genes have on the regulation of spatial adaptations in those without known disease.

Humans↗
PubMed2004

Genetic variation and lactose intolerance: detection methods and clinical implications.

The maturational decline in lactase activity renders most of the world's adult human population intolerant of excessive consumption of milk and other dairy products. In conditions of primary or secondary lactase deficiency, the lactose sugars in milk pass through the gastrointestinal tract undigested or are partially digested by enzymes produced by intestinal bacterial flora to yield short chain fatty acids, hydrogen, carbon dioxide, and methane. The undigested lactose molecules and products of bacterial digestion can result in symptoms of lactose intolerance, diarrhea, gas bloat, flatulence, and abdominal pain. Diagnosis of lactose intolerance is often made on clinical grounds and response to an empiric trail of dietary lactose avoidance. Biochemical methods for assessing lactose malabsorption in the form of the lactose breath hydrogen test and direct lactase enzyme activity performed on small intestinal tissue biopsy samples may also be utilized. In some adults, however, high levels of lactase activity persist into adulthood. This hereditary persistence of lactase is common primarily in people of northern European descent and is attributed to inheritance of an autosomal-dominant mutation that prevents the maturational decline in lactase expression. Recent reports have identified genetic polymorphisms that are closely associated with lactase persistence and nonpersistence phenotypes. The identification of genetic variants associated with lactase persistence or nonpersistence allows for molecular detection of the genetic predisposition towards adult-onset hypolactasia by DNA sequencing or restriction fragment length polymorphism analysis. The role for such genetic detection in clinical practice seems limited to ruling out adult-onset hypolactasia as a cause of intolerance symptoms but remains to be fully defined. Attention should be paid to appropriate interpretation of genetic detection in order to avoid potentially harmful reduction in dairy intake or misdiagnosis of secondary lactase deficiency.

Adult↗
PubMed2002

Construct conversions caused by simultaneous co-transfection: "GFP-walking".

Several GFP variants have been developedfor multicolor labeling in vivo. Here we report that simultaneous co-transfection of fluorescent protein chimeras can give false-positive results caused by the conversion of spectral properties. Under standard transfection conditions, approximately 8% of cells produce false-positive results, but, depending on the conditions, up to 26% of the cells permanently express altered fusion proteins. This compromises the interpretation of the results. The conversion is independent of transfection methods or cell types. Our results show that the effect is based on homologous recombination/repair/replication process events that occur between the nucleotide sequences of the fluorescent proteins. Consecutive transfection or low sequence similarities avoided recombination. The appearance of conversion facilitates exchanges of spectral properties infusion proteins, the creation of libraries, or the assembly of DNA fusion constructs in vivo. The detailed quantification of the conversion rate allows the investigation of recombination/repair/replication processes in general.

Animals↗
PubMed1997

[Patient outcome--towards a definition and classification of nursing care outcome].

Within the context of the desired unambiguousness in definitions and classifications of the nursing terminology, this literature research attempts to inventory the divergent meanings in recent professional nursing literature of the concept 'patient outcome', as well as the classifications used. Data analysis and interpretation was carried out by means of analytic induction. The results clearly show the ambiguousness of the concept. Nursing literature appears to pay little attention to the study of the structure of (the) patient outcome(s). Then, the context in which the patient outcome has to be situated appears to be described in many divergent ways. Finally, classifications of patient outcomes are found in many variants. This report concludes with suggestions for an unequivocal definition of patient outcome, as well as for the construction of (a) classification(s) of patient outcomes.

Data Collection↗
PubMed2003

Association between a promoter variant in the monoamine oxidase A gene and schizophrenia.

Monoaminergic transmission has been implicated in the pathophysiology of schizophrenia. We investigated a putative functional promoter polymorphism in the monoamine oxidase A (MAOA) gene in schizophrenic patients (n=133) and control subjects (n=377). In men, there was an association between the less efficiently transcribed alleles and schizophrenia (chi(2)=4.01, df=1, p<0.05). In women, no significant differences were found. The present results support the involvement of the MAOA gene in men with schizophrenia in the investigated Swedish population but should be interpreted with caution until replicated.

Adult↗
PubMedDate not supplied

Hepatic metastases from the spindle cell variant of medullary thyroid carcinoma: report of a case with diagnosis by fine needle aspiration biopsy.

BACKGROUND: The liver is a common site of neuroendocrine tumors (NTs) metastatic from primaries in the gastrointestinal tract, pancreas, biliary system and lungs. Medullary thyroid carcinoma (MTC) is also a potential source of metastases of NTs. Their metastases to the liver are frequent and can appear several years after the primitive tumor. Although a wide variety of cytomorphologic features are normally exhibited by MTC in smears, a spindle-shaped cell pattern can predominate, complicating the correct interpretation of a metastasis. CASE: A 63-year-old man presented with multiple liver nodules two years after a total thyroidectomy for MTC. Fine needle aspiration biopsy smears of the liver revealed neoplastic cells occurring in loose groupings or lying singly, most of them with a spindle shape and elongated nucleus with the characteristic "salt and pepper" chromatin pattern of a neuroendocrine tumor. Cytoplasmic dendritic processes and intranuclear inclusions were frequently seen. The cytomorphologic features of the tumor were essentially the same as those of the primary MTC. Immunoreactivity for calcitonin confirmed the diagnosis. CONCLUSION: In fine needle aspiration biopsy of liver masses, knowledge of the spindle pattern of the NT is important in order to achieve a correct diagnosis when metastases are the first manifestation of an occult primary tumor. Among neuroendocrine tumors, MTC must be included in the differential diagnosis.

Biopsy, Needle↗
PubMed2004

PC-3 cells with enhanced androgen receptor signaling: a model for clonal selection in prostate cancer.

BACKGROUND: Two sublines of the human prostate cancer cell line, PC-3, which is widely used as a model of prostate cancer progression, have been reported: PC-3(AR-) that do not express androgen receptor (AR), and PC-3AR+ that have measurable AR RNA but little protein. METHODS: We assayed the geneotype, karyotype, AR expression, and physical characteristics of the two PC-3 sublines, and compared their ability to elicit a transactivation response from ectopic AR in the presence and absence of specific AR coregulators. RESULTS: PC-3(AR-) and PC-3AR+ cells are genotypically and karyotypically similar, but exhibit salient differences in their morphology, growth rate, and expression of AR RNA. Whereas endogenous AR expression in PC-3AR+ cells does not result in sufficient protein to confer androgen responsiveness in culture, ectopic AR consistently elicited a much greater transactivation response in PC-3AR+ than in PC-3(AR-) cells, without altered sensitivity to activation by native ligand or AR coregulators including GRIP1, BRCA1, and Zac1. Moreover, phenotypic differences of AR variants implicated in prostate cancer susceptibility and progression were only observed in PC-3AR+ cells. Higher levels of known AR coregulator proteins detected in PC-3AR+ compared with PC-3(AR-) cells likely contribute to these differences. CONCLUSIONS: These studies provide new evidence that the androgen-signaling axis can be sensitized in prostate cancer cells, and have important implications for the analysis and interpretation of AR structure and function in in vitro cell systems.

Cell Division↗
PubMed2001

Metastatic brain tumours from oesophageal carcinoma: neuro-imaging and clinicopathological characteristics in Japanese patients.

BACKGROUND: Since metastatic brain tumours from esophageal carcinoma are essentially rare, previous reports have not determined the common neuro-radiological findings and its clinical aspects. FINDINGS: We report the neuro-imaging and clinicopathological features of our 8 metastatic brain tumours from an esophageal site. Histologically, 6 of our 8 patients had squamous cell carcinoma and 2 had small cell carcinoma, a rare variant form. Both histological types mainly exhibited cystic lesions with a thin enhanced rim on magnetic resonance images (MRI, 4 of 6 squamous cell carcinomas and 1 of 2 small cell carcinomas). Combination therapy (irradiation and chemotherapy) after surgical treatment, the number of metastatic brain tumours, and the interval between their appearance and the diagnosis of the primary lesion could be prognostic factors in our series. INTERPRETATION: Among Japanese, the vast majority of primary esophageal cancers are squamous cell carcinomas. Therefore, MRI findings of a cystic tumour with a thin enhanced rim may alert one to the possibility of a metastatic brain tumour from the esophagus.

Aged↗
PubMed2005

Comparison of different kinds of probes used for analysis of variant telomeric sequences.

In this work we aimed to compare and critically evaluate results obtained by different types of probes used for hybridisation to detect variant telomeric sequences with respect to their reliability and information value. Using slot-blot hybridisation we investigated three types of probes (oligonucleotides, cloned fragments and concatenated probes) under various conditions of hybridisation and washing. The concatenated probes exhibited the highest specificity although all three types are suitable for hybridisation of telomeric sequences under appropriate experimental conditions. We demonstrate how understanding generated from these data enables interpretation of hybridisation patterns of oligonucleotide probes to genomic DNAs.

Base Sequence↗
PubMed2004

[Semantic dementia: clinical profile and cognitive-neuropsychological relevance].

Semantic Dementia (SD) represents a rare variant of presenile primary degenerative diseases of "frontotemporal lobar degenerations" (FTLD). SD is characterized by anterior-temporal atrophy and a selective semantic deficit. Neuropsychological impairment either bears on fluent aphasia with marked naming and comprehension difficulties or on a disorder of object recognition or on both. Behavioural alterations such as stereotyped behaviour and change in food preference become prominent as the disease progresses and are interpreted as a correlative for the pathological spreading to frontal structures. Since SD is often misclassified as Alzheimer's disease (AD), but calls for a different management, diagnostic consensus criteria by Neary and colleagues are depicted. The neuropsychological profile is described in detail and complemented by a case report. Implications from the dissociation of disturbed memory systems of SD (semantic) and AD (episodic) for models of long-term memory are discussed in terms of connectivity in the medial temporal lobe. SD can contribute to a better understanding of the structure and organisation of the semantic system.

Cognition↗
PubMedDate not supplied

Polymorphisms and inheritance patterns of tetrazolium oxidase and octanol dehydrogenase in the house fly.

Zymogram analyses suggested the existence of two autosomal codominant alleles each at loci controlling the production of tetrazolium oxidase (To1) and octanol dehydrogenase (Odh1) in Texas house flies; an additional variant of the To1 locus was detected in a population from South Dakota. The allozymes of both systems may be dimeric as indicated by the presence of possible heteropolymers in flies heterozygous for To1 and Odh1 allels. Apparent nonsegregating isozymes of To and Odh (To2 and Odh2) were also noted in the zymograms of Texas flies. Some banding forms in the Odh gels could not be interpreted genetically.

Alcohol Oxidoreductases↗
PubMed2004

Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination.

We introduce a conceptually novel method for intracellular fluxome profiling from unsupervised statistical analysis of stable isotope labeling. Without a priori knowledge on the metabolic system, we identified characteristic flux fingerprints in 10 Bacillus subtilis mutants from 132 2H and 13C tracer experiments. Beyond variant discrimination, independent component analysis automatically mapped several fingerprints to their metabolic determinants. The approach is flexible and paves the way to large-scale fluxome profiling of any biological system and condition.

Amino Acids↗