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PubMed1999

The correlation between morphological and phylogenetic classification of myxobacteria.

In order to determine whether morphological criteria are suitable to affiliate myxobacterial strains to species, a phylogenetic analysis of 16S rDNAs was performed on 54 myxobacterial strains that represented morphologically 21 species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of 'Corallococcus', previously 'Chondrococcus', within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium ('Sorangium') cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria ('Polyangium thaxteri' Pl t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947T and Angiococcus disciformis An d1), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material.

Bacterial Typing Techniques↗
PubMed1983

Candidate counterparts of Sézary cells and adult T-cell lymphoma-leukaemia cells in normal peripheral blood: an ultrastructural study with the immunogold method and monoclonal antibodies.

The ultrastructural and immunologic features of normal convoluted T-lymphocytes were studied with a panel of monoclonal antibodies and the immunogold technique and these were compared with cells from patients with Sézary syndrome (SS) and adult T-cell lymphoma-leukaemia (ATLL). According to the characteristics of the nucleus, two distinct T-cell subtypes, representing 2-4% of normal peripheral blood lymphocytes were recognized: (i) a cerebriform lymphocyte ('Sézary-like') characterized by narrow and deep nuclear indentations, closely resembling the cells of SS, and (ii) a convoluted or polylobated lymphocyte ('ATLL-like'), with shorter and broader nuclear indentations than those seen in SS, that resemble the cells of ATLL. Both types of lymphocytes were positive with the monoclonal antibodies OKT3, OKT4, OKT17 and FMC3 and were negative with OKT8, OKM1 and FMC4 (anti-HLA-Dr) as SS and ATLL cells. A difference was observed with the expression of the anti-T monoclonal antibody 3Al: Sézary-like lymphocytes, like SS and ATLL cells, were 3Al negative whilst ATLL-like lymphocytes were 3Al positive. The close morphological and membrane phenotype similarities observed between these two types of lymphocytes and the cells from SS and ATLL suggest that they may well represent the normal counterparts of the malignant T cells in both conditions.

Antibodies, Monoclonal↗
PubMed2006

Carcinoid tumor arising in a duplication cyst of the duodenum.

Reported herein is a case of carcinoid tumor arising in a duplication cyst of the duodenum in a 34-year-old woman. Ultrasonography at a health check-up revealed a 10 cm cystic mass located in the retroperitoneum adjacent to the third portion of the duodenum. Macroscopically, it had a smooth surface without communication with other organs and was filled with brownish necrotic fluid. More than half of the inner wall was occupied by a white, irregular, and solid nodule, which protruded into the lumen. The nodule was diagnosed as a carcinoid tumor invasive to the deep muscular layer. The non-neoplastic cyst wall had bowel structures including mucosa, submucosa and double layers of smooth muscle, indicating that the lesion was a duodenal duplication cyst. Most of the mucosa was eroded by marked inflammation. The remaining mucosa consisted of various types of epithelium, the major type having the nature of primitive gastric mucosa. Of interest was the presence of hamartomatous components in the wall. Furthermore, the non-neoplastic mucosal lining cells around the carcinoid tumor expressed neuroendocrine antigens and had minimal proliferative activity, suggesting that part of the cyst wall provided a microenvironment for accelerated differentiation of epithelial cells to an endocrine phenotype and transformation to neoplasia.

Adult↗
PubMed2025

CNV-Finder: Streamlining Copy Number Variation Discovery.

Copy Number Variations (CNVs) play pivotal roles in the etiology of complex diseases and are variable across diverse populations. Understanding the association between CNVs and disease susceptibility is significant in disease genetics research and often requires analysis of large sample sizes. One of the most cost-effective and scalable methods for detecting CNVs is based on normalized signal intensity values, such as Log R Ratio (LRR) and B Allele Frequency (BAF), from Illumina genotyping arrays. In this study, we present CNV-Finder, a novel pipeline integrating deep learning techniques on array data, specifically a Long Short-Term Memory (LSTM) network, to expedite the large-scale identification of CNVs within predefined genomic regions. This facilitates efficient prioritization of samples for time-consuming or costly subsequent analyses such as Multiplex Ligation-dependent Probe Amplification (MLPA), short-read, and long-read whole genome sequencing. We incorporate four genes to establish our methods-Parkin (PRKN), Leucine Rich Repeat And Ig Domain Containing 2 (LINGO2), Microtubule Associated Protein Tau (MAPT), and alpha-Synuclein (SNCA)-which may be relevant to neurological diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Progressive Supranuclear Palsy (PSP), or related disorders such as essential tremor (ET). By training our models on expert-annotated samples and validating them across diverse cohorts, including those from the Global Parkinson's Genetics Program (GP2) and additional dementia-specific databases, we demonstrate the efficacy of CNV-Finder in accurately detecting deletions and duplications. Our pipeline outputs app-compatible files for visualization within CNV-Finder's interactive web application. This interface enables researchers to review predictions and filter displayed samples by model prediction values, LRR range, and variant count in order to explore or confirm results. Our pipeline integrates this human feedback to enhance model performance and reduce false positive rates. Through a series of comprehensive analyses and validations using visual inspection, MLPA, short-read, and long-read sequencing data, we demonstrate the robustness and adaptability of CNV-Finder in identifying CNVs with regions of varied size, probe density, and noise. Our findings highlight the significance of contextual understanding and human expertise in enhancing the precision of CNV identification, particularly in complex genomic regions like 17q21.31. The CNV-Finder pipeline is a scalable, publicly available resource for the scientific community, available on GitHub (https://github.com/GP2code/CNV-Finder; DOI 10.5281/zenodo.14182563). CNV-Finder not only expedites accurate candidate identification but also significantly reduces the manual workload for researchers, enabling future targeted validation and downstream analyses in regions or phenotypes of interest.

Copy Number Variation (CNV)↗
PubMed2000

Drosophila endosomal proteins hook and deep orange regulate synapse size but not synaptic vesicle recycling.

To study the function of endosomes at synapses we analyzed the localization and function of two Drosophila endosomal proteins, Hook and Deep orange (Dor), at the larval neuromuscular junction. Hook, a negative regulator of endocytic trafficking, and Dor, a positive regulator of endocytic trafficking, are highly enriched at synapses, especially close to postsynaptic membranes. Mutations in hook (hk) and dor do not affect synaptic vesicle recycling, as assessed by electrophysiological analysis of synaptic transmission and behavioral studies of double mutants with shi(ts) mutations that alter vesicle recycling. However, hk and dor mutations alter the number of presynaptic varicosities (synapse size) in opposing ways. Synapse size is increased in hk(11) mutants and is decreased in dor(4) mutants. Double mutants for dor and hk show a dor-like phenotype. These effects on synapse size parallel known functions of Hook and Dor in endocytosis and strongly indicate a role for endocytic trafficking in the regulation of synapse size in vivo. Our observations suggest a model in which Hook and Dor function in later stages of endocytosis is essential for regulating synaptic plasma membrane composition but not synaptic vesicle recycling.

Animals↗
PubMed1997

Failed cell migration and death of purkinje cells and deep nuclear neurons in the weaver cerebellum.

The mouse neurological mutant weaver has an atrophic cerebellar cortex with deficits in both Purkinje and granule cell number. Although granule cells are known to die postnatally shortly after their final cell division, the cause of the Purkinje cell deficit (cell death vs lack of production) is unknown. We report here a quantitative analysis of large cerebellar neurons of the weaver mutant during postnatal development. We explored the hypothesis that the cells of the entire cerebellar anlage were affected by the mutation by including in our study the neurons of the deep cerebellar nuclei (DCN). Our analysis reveals that in homozygous weaver mutants (1) the DCN are displaced laterally, display an abnormal anatomy, and suffer a 20-25% decrease in neuron number; (2) this numerical deficit is located in medial regions, similar to the localization of cortical deficits in both Purkinje and granule cells; (3) pyknotic figures are present in the juvenile DCN and in the Purkinje cell layer; and (4) the majority of cell death in these populations occurs not in medial regions where the numerical deficits are observed, but rather laterally where adult cell number is nearly normal. These results lead us to propose that the complete weaver phenotype includes a failure of the cell movements that lead to the fusion of the bilateral cerebellar anlage, and that this failure to migrate properly leaves some of the Purkinje cells and DCN neurons in a position where they are unable to make appropriate connections, leading to their death. In addition to implications for normal development, these observations suggest that weaver effects on the cerebellum can be unified into one consolidated model in which failure of cell movement affects all major cerebellar neurons.

Animals↗
PubMed1999

Well-differentiated adenocarcinoma, gastric foveolar type, of the extrahepatic bile ducts: A previously unrecognized and distinctive morphologic variant of bile duct carcinoma.

Two examples of a rare but distinctive morphologic variant of extremely well-differentiated adenocarcinoma of the extrahepatic bile ducts are reported. One tumor arose in the common bile duct of a 51-year-old man; the other arose in the common hepatic duct of a 27-year-old man. Both tumors were composed predominantly (>95%) of gastric foveolar-type epithelium. Because of their bland nuclear features, low mitotic index, and focal polypoid and lobular architecture, they were initially confused with adenomas. Foci of less-differentiated adenocarcinoma and perineural invasion present in the deep portions of the tumors facilitated recognition. The neoplastic cells and extracellular mucin were periodic acid-Schiff- and alcian blue-positive. By immunohistochemistry, the tumor cells expressed cytokeratins 8 and 20 as well as cathepsin D, as reported in normal foveolar cells. Likewise, p53 overexpression was documented immunohistochemically in both adenocarcinomas, which also stained with the Ki-67 antibody. Despite the well-differentiated nature of the neoplasms and their deceptively benign microscopic appearance, one patient developed recurrence and liver metastasis 5 years after surgery. The other patient is disease-free 2 years following a segmental resection of the common hepatic duct, cystic duct, and gallbladder. The cell phenotype of these tumors can be explained by the ability of the bile duct epithelium to differentiate along gastric cell lines.

Adenocarcinoma↗
PubMed2000

Idiomarina gen. nov., comprising novel indigenous deep-sea bacteria from the Pacific Ocean, including descriptions of two species, Idiomarina abyssalis sp. nov. and Idiomarina zobellii sp. nov.

Two bacterial strains, KMM 227T and 231T, were isolated from seawater samples collected from the north-western Pacific Ocean at a depth of 4000-5000 m and were characterized using polyphasic taxonomy. Both were Gram-negative, psychrotolerant, heterotrophic, aerobic and required NaCl for growth (0.6-15.0%). The temperature for growth was 4-30 degrees C. Both strains were rod-shaped, with a single flagellum. However, strain KMM 231T revealed a single long fimbrium. Cellular fatty acids detected in the isolates were predominantly odd-numbered and iso-branched, with 15 and 17 carbons (ca. 70%). Also present were saturated and monounsaturated straight-chain fatty acids. Results of phylogenetic analyses, employing three tree-making methods, strongly indicated that the two strains formed a distinct lineage within a clade containing the genera Alteromonas, Colwellia and Pseudoalteromonas, in the gamma-Proteobacteria. The two strains shared 16S rDNA sequence similarity of 96.9% and genomic DNA relatedness of 27%; the latter was determined by dot-blot hybridization. The strains were differentiated by the presence of fimbria, production of chitinase, ability to grow on 15% NaCl and BIOLOG profiles. Given the polyphasic evidence accumulated in this study, it is proposed that the two deep-sea isolates be classified in the genus Idiomarina gen. nov., as Idiomarina abyssalis sp. nov. (type strain is KMM 227T) and Idiomarina zobellii sp. nov. (type strain is KMM 231T).

Base Composition↗
PubMed1993

Duplication 9q34-->qter identified by chromosome painting.

We have studied an infant with multiple anomalies and a 46,XY,12p+ karyotype. Parental chromosomes were normal, and it was not possible to determine the identity of the extra material on chromosome 12 cytogenetically. Chromosome painting with probes from a chromosome 9 library identified this material as coming from chromosome 9, and cytogenetics established the duplication as 9q34-->qter. Comparison of this patient with others reported with partial dup(9q) documented excellent concordance of minor anomalies, most notably dolichocephaly, "deep-set" eyes, short horizontal palpebral fissures, beaked nose, micrognathia, arachnodactyly, and developmental delay. Identification of cytogenetically indeterminate abnormalities by molecular cytogenetics is very important, as it permits prognosis to be offered for families of newborn infants with unbalanced karyotypes.

Abnormalities, Multiple↗
PubMed1982

De novo interstitial deletion in the long arm of chromosome 9: a new chromosome syndrome.

An infant with an interstitial deletion 46,XY, del(9)(pter leads to q22::q32 leads to qter) is described. Clinical features included abnormal craniofacies with hypotelorism, narrow palpebral fissures, sclerocornea, deep vertical groove, and supraorbital ridge hypoplasia. There was unilateral preaxial polydactyly and toe syndactyly. Generalised hirsutism was noted. The infant had surgery for duodenal atresia but died at the age of 3 months. Unilateral renal dysplasia and accessory spleens were found at necropsy.

Abnormalities, Multiple↗
PubMed1990

Differentiation of crypt epithelium in human palatine tonsils: the microenvironment of crypt epithelium as a lymphoepithelial organ.

The differentiation of the keratinocytes of the human palatine tonsils were studied by means of light and electron microscopy and immunohistochemistry using a polyclonal (K) and two monoclonal antikeratin antibodies (PKK1, PKK2). In the surface epithelium, the basal cells, cuboidal or columnar in shape, undergo progressive terminal differentiation and are transformed into the flattened cells of the upper layers. K reacts with both the basal and spinous layers, while PKK1 and PKK2 mark exclusively the basal layer. In the neck portion of the crypt, cavities containing one or aggregated lymphocytes with amorphous substances are observed in the spinous layer. The cavities are surrounded by elongated cytoplasmic processes of transformed epithelial cells bearing surface microvilli. These transformed epithelial cells display intense PKK1- and PKK2-positive reactions, whereas other conventional polygonal cells in the vicinity remain PKK1- and PKK2-negative as do those in the surface epithelium. In the deep portion of the crypt, where numerous lymphocytes invade the epithelium, the epithelial cells are transformed into star-shaped reticulum cells showing PKK1- and PKK2-positive reactions. The extended and branched cytoplasmic processes interconnect with one another constituting a complex network of reticulum cells, the well known reticulation of the crypt epithelium. Ten-nm filaments are usually oriented parallel to the longitudinal axis of transformed epithelial cells. Our observations suggest that the cell-shape transformation, i.e., from conventional polygonal epithelial cells into epithelial reticulum cells, occurs when the epithelial cells are in close contact with the infiltrating lymphocytes, and that this transformation is accompanied by a change in keratin phenotype.

Adolescent↗
PubMed1994

Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds.

A polyphasic approach was used in which genotypic and phenotypic properties of a gram-negative, obligately anaerobic, rod-shaped bacterium isolated from a black anoxic freshwater mud sample were determined. Based on these results, the name Holophaga foetida gen. nov., sp. nov. is proposed. This microorganism produced dimethylsulfide and methanethiol during growth on trimethoxybenzoate or syringate. The only other compounds utilized were pyruvate and trihydroxybenzenes such as gallate, phloroglucinol, or pyrogallol. The aromatic compounds were degraded to acetate. Although comparison of the signature nucleotide pattern of the five established subclasses of Proteobacteria with the 16S rDNA sequence of Holophaga foetida revealed a relationship to members of the delta-subclass, the phylogenetic position within the radiation of this class is so deep and dependent upon the number and selection of reference sequences that its affiliation to the Proteobacteria must be considered tentative. The type strain is H. foetida strain TMBS4 (DSM 6591).

Acetates↗
PubMed1991

Expression of type 1 blood group precursor in human gastric carcinoma.

The surface epithelium of normal gastric mucosa from patients with gastric adenocarcinoma expressed the type 1 blood group precursor only in Lewis (Le) non-secretor individuals, Le a+b- (se/se, Le/-) and Le a-b- (se/se, le/le). In secretors, the superficial mucosa was negative. Deep areas of the mucosa showed no type 1 precursor regardless of secretor status. Expression of type 1 precursor was anomalously found in neoplastic cells in 14 of 16 Le a-b+ (secretors) patients and in 4 of 5 Le a-b- (secretors) patients. The 1 Le a-b- non-secretor carcinoma expressed type 1 precursor strongly. 6 of 8 Le a+b- non-secretor carcinomas showed positivity for the monoclonal antibody K-21. Thus the type 1 precursor reacted with the non-neoplastic gastric surface of non-secretors but not with those of secretors, and also with most gastric adenocarcinoma regardless of secretor status and Lewis phenotype.

Adenocarcinoma↗
PubMed2002

Transepithelial migration of Toxoplasma gondii is linked to parasite motility and virulence.

After oral ingestion, Toxoplasma gondii crosses the intestinal epithelium, disseminates into the deep tissues, and traverses biological barriers such as the placenta and the blood-brain barrier to reach sites where it causes severe pathology. To examine the cellular basis of these processes, migration of T. gondii was studied in vitro using polarized host cell monolayers and extracellular matrix. Transmigration required active parasite motility and the highly virulent type I strains consistently exhibited a superior migratory capacity than the nonvirulent type II and type III strains. Type I strain parasites also demonstrated a greater capacity for transmigration across mouse intestine ex vivo, and directly penetrated into the lamina propria and vascular endothelium. A subpopulation of virulent type I parasites exhibited a long distance migration (LDM) phenotype in vitro, that was not expressed by nonvirulent type II and type III strains. Cloning of parasites expressing the LDM phenotype resulted in substantial increase of migratory capacity in vitro and in vivo. The potential to up-regulate migratory capacity in T. gondii likely plays an important role in establishing new infections and in dissemination upon reactivation of chronic infections.

Animals↗
PubMed1990

Diversity and origin of Desulfovibrio species: phylogenetic definition of a family.

The different nutritional properties of several Desulfovibrio desulfuricans strains suggest that either the strains are misclassified or there is a high degree of phenotypic diversity within the genus Desulfovibrio. The results of partial 16S rRNA and 23S rRNA sequence determinations demonstrated that Desulfovibrio desulfuricans ATCC 27774 and "Desulfovibrio multispirans" are closely related to the type strain (strain Essex 6) and that strains ATCC 7757, Norway 4, and El Agheila Z are not. Therefore, these latter three strains of Desulfovibrio desulfuricans are apparently misclassified. A comparative analysis of nearly complete 16S rRNA sequences in which we used a least-squares analysis method for evolutionary distances, an unweighted pair group method, a signature analysis method, and maximum parsimony was undertaken to further investigate the phylogeny of Desulfovibrio species. The species analyzed were resolved into two branches with origins deep within the delta subdivision of the purple photosynthetic bacteria. One branch contained five deep lineages, which were represented by (i) Desulfovibrio salexigens and Desulfovibrio desulfuricans El Agheila Z; (ii) Desulfovibrio africanus; (iii) Desulfovibrio desulfuricans ATCC 27774, Desulfomonas pigra, and Desulfovibrio vulgaris; (iv) Desulfovibrio gigas; and (v) Desulfomicrobium baculatus (Desulfovibrio baculatus) and Desulfovibrio desulfuricans Norway 4. A correlation between 16S rRNA sequence similarity and percentage of DNA relatedness showed that these five deep lineages are related at levels below the minimum genus level suggested by Johnson (in Bergey's Manual of Systematic Bacteriology, vol. 1, 1984). We propose that this branch should be grouped into a single family, the Desulfovibrionaceae. The other branch includes other genera of sulfate-reducing bacteria (e.g., Desulfobacter and Desulfococcus) and contains Desulfovibrio sapovorans and Desulfovibrio baarsii as separate, distantly related lineages.

Base Sequence↗
PubMed1994

Malignant mesenchymomas of soft tissue associated with numerous osteoclast-like giant cells mimicking the so-called giant cell variant of "malignant fibrous histiocytoma".

Three cases of malignant mesenchymoma with numerous osteoclast-like giant cells, arising in deep soft tissue, and which mimicked the so-called giant cell variant of "malignant fibrous histiocytoma" have been studied. All three neoplasms arose in adults; two patients were male and one was female. Two tumours arose in the thigh, and one in the right shoulder. Two patients died within 2 years of the primary excision while the third is alive and well at 2.5 years. Histologically, one case showed leiomyosarcoma plus liposarcoma, one leiomyosarcoma plus osteosarcoma, and one tumour consisted of liposarcoma plus osteosarcoma; all components were assessed morphologically as high-grade malignant. All three cases showed prominent osteoclast-like giant cells in the leiomyosarcomatous or osteosarcomatous areas, thereby closely mimicking the phenotype of so-called giant cell variant of "malignant fibrous histiocytoma". We discuss briefly differences in soft tissue sarcomas demonstrating this distinctive osteoclast-rich phenotype.

Adult↗
PubMed2001

Endometrial carcinoma: association of steroid hormone receptor expression with low angiogenesis and bcl-2 expression.

In endometrial tissues, malignant change may be accompanied by a loss of hormone dependence which is, usually, reflected in a parallel loss of oestrogen and progesterone receptors (ER and PR). In this study, the steroid receptor status of 164 endometrial carcinomas was related to intratumoural angiogenesis and the apoptotic proteins bcl-2 and p53. Relationships to conventional histopathological features and patient survival were also sought. Immunohistochemistry was performed on formalin-fixed, paraffin-embedded tissues. The mean follow-up was 55 months (range 19-167 months). Specific nuclear staining for ER and PR was detected in 35% and 32% of endometrial carcinomas, respectively, and was very commonly co-expressed (P<0.0001). The failure of demonstrating a steroid receptor complement in endometrial neoplasms was, in general terms, an adverse prognostic sign. Thus, ER or PR loss was significantly associated with non-endometrioid carcinomas (ER P=0.01; PR P=0.004) and with deep myometrial invasion (ER P<0.0002), high intratumoural angiogenesis (PR P<0.01) and the absence of bcl-2 expression (PR P<0.005). There was a trend for patients with ER or simultaneous ER/PR expression to have an improved survival, but this association did not reach the level of statistical significance. In multivariate analysis (all stages), tumour cell type (endometrioid versus non-endometrioid carcinomas) and stage of disease were the only variables associated with prognosis (P=0.01 and P<0.0001, respectively), with tumour cell type retaining its independent prognostic value and within stage-I endometrial carcinomas (P=0.02). It is suggested that the loss of steroid hormone receptors in endometrial carcinomas is associated with a more aggressive phenotype and the switching-on of angiogenic pathways.

Adenocarcinoma↗
PubMed2006

The distribution of myofibroblasts and CD34-positive stromal cells in normal renal pelvis and ureter and their cancers.

In this article, we examined the distribution of myofibroblasts and CD34-positive stromal cells in normal renal pelvis and ureter and their cancers using immunohistochemistry. Eighteen tumors and normal tissues apart from the main tumor were examined. In the wall of normal renal pelvis and ureter, no myofibroblasts were observed through all layers, but CD34-positive stromal cells were observed in the deep area of lamina propria, muscular layer and adventitia. In the stroma of renal pelvic and ureteral cancers, myofibroblasts were distributed in fifteen tumors and were absent in three tumors. All three tumors containing no myofibroblasts in the stroma were non-invasive type and all invasive cancers contained myofibroblasts in the stroma. CD34-positive stromal cells were consistently absent in the stroma of cancers, irrespective of the invasiveness. Finally, myofibroblasts are major stromal components in renal pelvic and ureteral cancers, particularly in invasive cancers, and CD34-positive stromal cells are consistently absent or lost in the stroma of their cancers. These findings suggest that the invasion of renal pelvic and ureteral cancers may cause the phenotypic change of stromal cells.

Aged↗