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PubMed2001

Craniofacial and cutaneous findings expand the phenotype of hereditary neuralgic amyotrophy.

BACKGROUND: Hereditary neuralgic amyotrophy (HNA) is an autosomal-dominant disorder associated with recurrent, episodic, painful, brachial neuropathy. The gene for HNA has been mapped to chromosome 17q25. Characteristic features including hypotelorism, short stature, and cleft palate occur in some patients. OBJECTIVE: To further characterize the clinical, neurologic, and craniofacial features in 27 patients from seven families with HNA. METHODS: Medical history, physical examination, and facial measurements were obtained. Facial measurements were also made on 60 healthy controls. RESULTS: Twenty-five patients had an average of three attacks of brachial neuritis. The right arm was involved more frequently. Cleft palate was present in four individuals. Facial measurements showed significant hypotelorism in HNA patients versus controls. Unusual skin folds and creases were observed on the necks of several individuals as well as on the scalp of one man: cutis verticis gyrata. In three families, deep skin creases were present on the limbs of infants and toddlers who were subsequently affected with HNA. CONCLUSIONS: The phenotypic consequences of the mutant hereditary neuralgic atrophy gene may include a wider spectrum than previously appreciated and involve nonneural tissue.

Adolescent↗
PubMed1997

Transforming growth factor-beta predominantly stimulates phenotypically changed chondrocytes in osteoarthritic human cartilage.

OBJECTIVE: One of the most prominent alterations that characterizes osteoarthritic cartilage damage is a reduction of proteoglycan content, reflecting an imbalance between synthesis and release of proteoglycans. Both synthesis and release depend on the activity of cartilage cells. Chondrocytes in the upper layer of moderately osteoarthritic human knee cartilage appear to be phenotypically altered, including diminished proteoglycan synthesis. Transforming growth factor-beta (TGF-beta) as a multifunctional growth factor has differential effects believed to depend on the differentiation stage of the target cells. We tested the effect of TGF-beta on phenotypically altered chondrocytes in osteoarthritic cartilage. METHODS: Human articular cartilage was cultured 4 days with or without TGF-beta. Proteoglycan synthesis was determined by (35)SO4(2-) incorporation (biochemically and by autoradiography) for the upper and deep layer separately. RESULTS: Osteoarthritic cartilage proved more sensitive to TGF-beta than normal cartilage. Proteoglycan synthesis of osteoarthritic cartilage was stimulated significantly more by 5 ng/ml TGF-beta than normal cartilage. For normal cartilage this increase was equally divided among the upper and deeper layer of the explants. For osteoarthritic cartilage the increase in proteoglycan synthesis could largely be attributed to the upper layer. Autoradiography revealed that the relative (35)SO4(2-) incorporation in the cell clusters, present in the upper layer of osteoarthritic cartilage, was significantly increased upon the addition of TGF-beta. CONCLUSION: Osteoarthritic cartilage is more sensitive to TGF-beta than normal cartilage because phenotypically changed chondrocytes in the damaged upper layer of osteoarthritic cartilage are more sensitive to TGF-beta than chondrocytes in the more intact deep layer and are more sensitive than the chondrocytes of normal cartilage. TGF-beta appears to redifferentiate the phenotypically altered chondrocytes in osteoarthritic cartilage.

Aged↗
PubMed1990

Neuronal lineages in chimeric mouse forebrain are segregated between compartments and in the rostrocaudal and radial planes.

On the basis of neuronal phenotypes and the mode of development of the mammalian forebrain, the cerebral cortex can be subdivided into deep versus superficial layers, and the striatum into patch versus matrix compartments. Interspecific chimeric Mus musculus----Mus caroli mice were used to determine the contribution of lineage to cellular position within these forebrain compartments. Statistical analysis revealed evidence of both spatial and compartmental lineage segregation. A significant difference in genotype ratio depending on chimeric specimen was observed between areas (regardless of compartment) that were separated by greater than 300 microns in the rostrocaudal plane. Differences were observed between early-born (striatal patch and deep cortex) versus late-born (striatal matrix and superficial cortex) neurons, but not between neurons of cortex as a whole versus neurons of striatum as a whole. The difference between early- and late-born neurons was primarily due to the difference between deep and superficial cortical neurons. On a finer scale of analysis, differences in genotype ratios were seen between radially aligned deep versus superficial cortical compartments, in both the neuronal and glial populations. This evidence is consistent with an early positional and compartmental segregation of forebrain progenitor cells.

Analysis of Variance↗
PubMed2024

Central conducting lymphatic anomaly: from bench to bedside.

Central conducting lymphatic anomaly (CCLA) is a complex lymphatic anomaly characterized by abnormalities of the central lymphatics and may present with nonimmune fetal hydrops, chylothorax, chylous ascites, or lymphedema. CCLA has historically been difficult to diagnose and treat; however, recent advances in imaging, such as dynamic contrast magnetic resonance lymphangiography, and in genomics, such as deep sequencing and utilization of cell-free DNA, have improved diagnosis and refined both genotype and phenotype. Furthermore, in vitro and in vivo models have confirmed genetic causes of CCLA, defined the underlying pathogenesis, and facilitated personalized medicine to improve outcomes. Basic, translational, and clinical science are essential for a bedside-to-bench and back approach for CCLA.

Cell-Free Nucleic Acids↗
PubMed2003

Descent with modification: the unity underlying homology and homoplasy as seen through an analysis of development and evolution.

Homology is at the foundation of comparative studies in biology at all levels from genes to phenotypes. Homology is similarity because of common descent and ancestry, homoplasy is similarity arrived at via independent evolution. However, given that there is but one tree of life, all organisms, and therefore all features of organisms, share some degree of relationship and similarity one to another. That sharing may be similarity or even identity of structure and the sharing of a most recent common ancestor--as in the homology of the arms of humans and apes--or it may reflect some (often small) degree of similarity, such as that between the wings of insects and the wings of birds, groups whose shared ancestor lies deep within the evolutionary history of the Metazoa. It may reflect sharing of entire developmental pathways, partial sharing, or divergent pathways. This review compares features classified as homologous with the classes of features normally grouped as homoplastic, the latter being convergence, parallelism, reversals, rudiments, vestiges, and atavisms. On the one hand, developmental mechanisms may be conserved, even when a complete structure does not form (rudiments, vestiges), or when a structure appears only in some individuals (atavisms). On the other hand, different developmental mechanisms can produce similar (homologous) features. Joint examination of nearness of relationship and degree of shared development reveals a continuum within an expanded category of homology, extending from homology --> reversals --> rudiments --> vestiges --> atavisms --> parallelism, with convergence as the only class of homoplasy, an idea that turns out to be surprisingly old. This realignment provides a glimmer of a way to bridge phylogenetic and developmental approaches to homology and homoplasy, a bridge that should provide a key pillar for evolutionary developmental biology (evo-devo). It will not, and in a practical sense cannot, alter how homoplastic features are identified in phylogenetic analyses. But seeing rudiments, reversals, vestiges, atavisms and parallelism as closer to homology than to homoplasy should guide us toward searching for the common elements underlying the formation of the phenotype (what some have called the deep homology of genetic and/or cellular mechanisms), rather than discussing features in terms of shared or independent evolution.

Animals↗
PubMed2002

Salinisphaera shabanensis gen. nov., sp. nov., a novel, moderately halophilic bacterium from the brine-seawater interface of the Shaban Deep, Red Sea.

A novel, moderately halophilic bacterium was isolated from the brine-seawater interface of the Shaban Deep, northern Red Sea. A polyphasic approach was used for the taxonomic characterization of this isolate, with the phenotypic and phylogenetic data clearly showing the distinctiveness of this bacterium. Cells of isolate E1L3A were Gram-negative, monotrichous cocci that showed a remarkable physiological flexibility, as could be seen by the quite broad growth ranges for oxygen, temperature, NaCl, and, to a smaller degree, pH. In addition, it was able to grow from atmospheric pressure up to 15 MPa, making it a piezotolerant bacterium. Phylogenetically, strain E1L3A represents a new, deeply branching lineage within the gamma-Proteobacteria, as determined by 16S rRNA gene sequence analysis. No close relatives are known so far, with sequence similarity to other cultivated members of the gamma-Proteobacteria being lower than 88%. The creation of the new genus Salinisphaera and the new species Salinisphaera shabanensis (DSM 14853; JCM 11575) for this new and highly versatile microorganism is therefore proposed.

Base Composition↗
PubMed2002

A novel polymer produced by a bacterium isolated from a deep-sea hydrothermal vent polychaete annelid.

AIMS: The objective of the present work was to describe an aerobic, mesophilic and heterotrophic marine bacterium, designated HYD657, able to produce an exopolysaccharide (EPS). It was isolated from a East Pacific Rise deep-sea hydrothermal vent polychaete annelid. METHODS AND RESULTS: This micro-organism, on the basis of the phenotypical features and genotypic investigations, can be clearly assigned to the Alteromonas macleodii species and the name A. macleodii subsp. fijiensis biovar deepsane is proposed. Optimal growth occurs between 30 and 35 degrees C, at pH between 6.5 and 7.5 and at ionic strengths between 20 and 40 g x l(-1) NaCl. The G + C content of DNA was 46.5%. This bacterium excreted, under laboratory conditions, an EPS consisting of glucose, galactose, rhamnose, fucose and mannose as neutral sugars along with glucuronic and galacturonic acids and a diacidic hexose identified as a 3-0-(1 carboxyethyl)-D-glucuronic acid. Its average molecular mass was 1.6 x 10(6) Da. CONCLUSIONS: The bacterium HYD657, for which the name A. macleodii subsp. fijiensis biovar deepsane is proposed, produces an unusual EPS in specific medium. SIGNIFICANCE AND IMPACT OF THE STUDY: Due to its interesting biological activities, applications have been found in cosmetics. Its probable contribution to the filamentous microbial mat in the Alvinella pompejana microenvironment can be also mentioned.

Alteromonas↗
PubMed2000

[A study on biological characteristics of normal adult human nasal septal chondrocytes cultured in vitro].

OBJECTIVE: To study the characteristics of normal adult human nasal chondrocytes cultured in vitro. METHOD: The adult human nasal septal chondrocytes were cultured in vitro. The changes of cellular morphology from primary to subculture were investigated; to observe the proliferation of chondrocytes by the growth curve and the survive rate of chondrocytes; and to determine the biologic synthesis of the chondrocytes by toluidine blue, alkaline phosphatase staining and type II collagen immunohistochemistry reaction. The survive rate of the nasal septal chondrocytes was observed after being frozen (-196 degrees C). RESULT: The morphology of the primary chondrocytes maintained the spherical shape, and some became polygonal shape after 4 days. Most of the chondrocytes transformed into the shape of the fibroblast cell since the fifth generation. The number of the chondrocytes (2th generation) after being cultured in vitro for 5 days was approximately 4 fold of that of the plating. The phenotype of the chondrocytes was maintained in the first 4 generation, the survive rate of the chondrocytes suscitating from being frozen (-196 degrees C) was 93%. CONCLUSION: The normal adult nasal septal chondrocytes cultured in monolayer in vitro maintained the specific chondrocytes phenotype in the first 4 generation, the growth was normal, and could survive in the condition of deep-frozen.

Adult↗
PubMed2026

DeepPlaque: a scalable multimodal platform for Aβ pathology and cell analysis in Alzheimer's disease.

Histological analysis is essential for understanding disease pathology and the microenvironment, particularly in Alzheimer's disease (AD), characterized by beta-amyloid (Aβ) plaques that exist as diffuse, fibrillar, and core species, with distinct toxicity levels. However, accurate classification of Aβ plaque types in postmortem brain tissues and profiling of surrounding cells present significant challenges. To address these challenges, we developed "DeepPlaque", an integrated system featuring "PlaqueNet", a deep learning model for automated classification of Aβ plaque species from diverse imaging platforms. DeepPlaque includes automated workflows for cellular phenotyping and proteomic profiling through targeted laser microdissection. PlaqueNet achieves expert-level accuracy (AUC > 90%) in classifying the 3 major Aβ plaque species, supporting consistent and large-scale annotation. By integrating spatial cellular phenotyping with laser microdissection, DeepPlaque enables high-throughput proteomic analysis of Aβ plaque niches, revealing that microglia are more abundant around core and fibrillar Aβ plaques, with increased expression of apolipoprotein E and amyloid precursor protein in core Aβ plaques. This customizable platform enhances the molecular and cellular characterization of Aβ plaque-associated environments, providing critical insights into AD pathology.

Alzheimer Disease↗
PubMed2003

Comparison of eight phenotypic methods for subspecies characterization of thermophilic Campylobacter spp. isolated from pig liver.

Four hundred pork livers from bacon pigs (37 herds) obtained at six pig-processing plants were studied to assess the Campylobacter contamination rate. Deep tissue areas were sampled immediately after evisceration. Approximately 6% of livers were infected with Campylobacter spp., including Campylobacter coli (67%), Campylobacter jejuni (30%), and Campylobacter lari (3%). The 60 resulting isolates (39 C. coli isolates, 19 C. jejuni isolates, and 2 C. lari isolates) employed in this study were characterized at the subspecies level in a comparison of eight phenotyping schemes, including four biotyping, two serotyping, and two phage-typing schemes. The Skirrow-Benjamin biotyping scheme produced two biotypes for C. jejuni, i.e., biotype 2 (95%) and biotype 1 (5%). The Lior biotyping scheme subdivided C. coli into biotype 1 (41%) and biotype 2 (59%), while biotype 4 was the dominant type (95%) for C. jejuni. The Roop scheme allowed further differentiation of C. coli into three biovars, i.e., biovar 1 (57%), biovar 2 (40%), and biovar 3 (3%), and it subdivided C. jejuni into two biotypes, i.e., biovar 1 (95%) and biovar 2 (5%). Preston biotyping produced the largest degree of subspecies differentiation, with 18 C. coli biotypes and 7 C. jejuni biotypes being identified. The most common were biotypes 2650 and 6030, representing 18 and 42% of all C. coli and C. jejuni isolates, respectively. The Penner-Hennessy serotyping scheme successfully serotyped 89% of the isolates, with 10 serotypes being identified; 30% of the serotypeable isolates were accounted for by Penner 23, followed by Penner 20 (16%) and Penner 39 (14%). The Lior serotyping scheme successfully serotyped only 45% of the strains, and eight serogroups were identified, with Lior 36 (31%), Lior 20 (23%), and Lior 5 being the most frequent. The Preston scheme and the Khakhria-Lior phage-typing scheme were able to type 16 and 25% of the isolates, respectively. The Preston scheme produced three phage groups, i.e., 69 (56%), 90 (22%), and 116 (22%), and the Khakhria-Lior scheme also produced three phage types, i.e., 44 (40%), 27 (33%), and 37 (20%), as well as atypical lysis patterns (7%). The results of this study demonstrate the role of Preston biotyping in the phenotyping of isolates, particularly in diagnostic laboratories that have no access or limited access to molecular typing equipment.

Animals↗
PubMed1997

Prenatal diagnosis of partial trisomy 12 and partial trisomy 21 due to a 3:1 segregation of maternal reciprocal translocation t(12;21) (p13.3;q21).

We describe the prenatal diagnosis and fetal phenotype of partial trisomy 12 (p13.3-pter) and partial trisomy 21 (pter-q21) due to a 3:1 segregation with tertiary aneuploidy transmitted from a maternal reciprocal translocation 12;21. Genetic amniocentesis of a 39-year-old gravida 2, para 1 woman at 19 weeks' gestation due to advanced maternal age revealed an unusual karyotype of 47,XY,+der(21)t(12;21)(p13.3;q21)mat. The pregnancy was terminated at 24 gestational weeks. The proband postnatally displayed by dysmorphic features of a round flat face with prominent cheeks and high forehead, upward slanting palpebral fissures, epicanthic folds, hypertelorism, a short nose, a broad and depressed nasal bridge, anteverted nares, a deformed philtrum, an open mouth, thin upper vermilion and broad everted lower lip, low-set ears with prominent anthelix and deep concha, broad hands with simian creases, a short neck, and cryptorchidism. The association of the involved chromosomal segments with the phenotype of Down's syndrome and trisomy 12p syndrome is discussed.

Adult↗
PubMed2025

APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19.

MOTIVATION: Computational analyses of bulk and single-cell omics provide translational insights into complex diseases, such as COVID-19, by revealing molecules, cellular phenotypes, and signalling patterns that contribute to unfavourable clinical outcomes. Current in silico approaches dovetail differential abundance, biostatistics, and machine learning, but often overlook nonlinear proteomic dynamics, like post-translational modifications, and provide limited biological interpretability beyond feature ranking. RESULTS: We introduce APNet, a novel computational pipeline that combines differential activity analysis based on SJARACNe co-expression networks with PASNet, a biologically informed sparse deep learning model, to perform explainable predictions for COVID-19 severity. The APNet driver-pathway network ingests SJARACNe co-regulation and classification weights to aid result interpretation and hypothesis generation. APNet outperforms alternative models in patient classification across three COVID-19 proteomic datasets, identifying predictive drivers and pathways, including some confirmed in single-cell omics and highlighting under-explored biomarker circuitries in COVID-19. AVAILABILITY AND IMPLEMENTATION: APNet's R, Python scripts, and Cytoscape methodologies are available at https://github.com/BiodataAnalysisGroup/APNet.

COVID-19↗
PubMed1988

High level expression of fms proto-oncogene mRNA is observed in clinically aggressive human endometrial adenocarcinomas.

Six micron paraffin sections of paraformaldehyde-fixed endometrial currettings of 21 benign and neoplastic endometrial specimens were assayed for tumor cell-specific oncogene expression by in situ hybridization with probes for six oncogenes, beta-actin, and the E. coli plasmid pBR322. In the benign hyperplasias and invasive adenocarcinomas, multiple oncogenes, including erbB, fms, c-myc, and Ki-ras were expressed at significant levels. For the adenocarcinomas, statistical analysis demonstrated that high levels of expression of fms-complementary mRNA correlated strongly with clinicopathologic features (high FIGO histologic grade, high FIGO clinical stage, deep myometrial penetration) predictive of aggressive clinical behavior and poor outcome. The authors discuss the role which M-CSF receptor (the fms gene product) and locally-produced M-CSF may play in the development of the observed aggressively-malignant phenotypes. They also propose that pre-hysterectomy assay of fms gene expression in endometrial currettings in FIGO Stage I patients might be clinically useful to help identify preoperatively those patients with deep myometrial penetration or other locoregional spread.

Adenocarcinoma↗
PubMed2002

"Staphylococcus pettenkoferi," a novel staphylococcal species isolated from clinical specimens.

In this report we describe a novel species of coagulase-negative novobiocin susceptible staphylococci obtained from an epidemiologically unrelated blood culture and a wound infection. These isolates significantly differed from all other validated Staphylococcus species based on phenotypic characteristics and 16S rRNA gene sequencing. Both isolates had identical 16S rRNA sequences and phylogenetic trees constructed from evolutionary distances showed that this species formed a distinct and deep subline that was most closely related to members of the Staphylococcus saprophyticus cluster group (S. kloosii, S. gallinarum, S. arlettae, S. saprophyticus, S. xylosus, S. equorum, S. succinus and S. cohnii) and Staphylococcus auricularis. Furthermore these strains could each be distinguished from all other staphylococci based on at least one phenotypic trait. Therefore we propose the designation of "Staphylococcus pettenkoferi" a novel species of coagulase-negative staphylococci.

Adult↗
PubMed2003

[Clinical phenotype of Charcot-Marie-Tooth disease (CMT) and familial amyloid polyneuropathy (FAP)].

A nationwide study of CMT and FAP has been performed. In FAP TTR Met30 families with late onset, neuropathy showed male preponderance, low penetrance, little relationship to endemic foci, sensorimotor symptoms beginning distally in the lower extremities with disturbance of both superficial and deep sensation, and relatively mild autonomic symptoms, consistent with pathological findings. In contrast, families with early onset showed higher penetrance, concentration in endemic foci, predominant loss of superficial sensation, severe autonomic dysfunction. Demyelinating versus axonal phenotypes are major issues in CMT. CMT1A duplication caused mainly demyelinating phenotype, while axonal features were variably present. In CMT1B, two distinctive phenotypic subgroups were present: one showed exclusively axonal features; and another was exclusively demyelinating. CMTX showed intermediate slowing of MCV, predominantly axonal features, and relatively mild demyelinating pathology. Differing from CMT1B, these axonal and demyelinating features were concomitantly present in individual patients in variable extent. Median nerve MCVs were well maintained independently of age, disease duration, and severity of clinical and pathologic abnormalities. Amplitude of CMAPs was correlated significantly with distal muscle strength, indicating that clinical weakness results from reduced numbers of functional large axons, not from demyelination. CMT patients with demyelinating and/or axonal features, together with FAP patients with axonal feature and scattered distribution, are supposed to increase according to the development of genetic diagnosis for hereditary neuropathy that verifies late-onset, de novo and asymptomatic patients.

Adult↗
PubMed1995

Further delineation of the partial proximal trisomy 10q syndrome.

We report on a girl with a partial duplication of the proximal part of the long arm of chromosome 10, confirmed by chromosome painting. The phenotypic findings are compared to those found in six other published cases with the same karyotype. Recognition of a specific partial proximal trisomy 10q syndrome seems to be possible, consisting of mild to moderate developmental delay, postnatal growth retardation, microcephaly, prominent forehead, small and deep set eyes, epicanthus, upturned nose, bow shaped mouth, micrognathia, thick and flat helices of the ears, and long, slender limbs. Severe ocular malformations are possibly part of the syndrome. No major phenotypic differences were seen between patients with a duplication of segment 10q11-->10q22 and patients with a duplication of 10q21-->10q22.

Adenosine Kinase↗
PubMed2002

The relationship between metal concentrations and phenotypes in the Baltic clam Macoma balthica (L.) from the Gulf of Gdansk, southern Baltic.

Soft tissue accumulated concentrations of nine metals (V, As, Se, Ag, Cd, Pb, Mn, Cu and Zn) were studied in two main phenotypes (1) according to external shell colour (white and pink), and (2) according to shell shape (shell with a rounded posterior end--"regular" and with an elongate posterior end and a notable flexure--"irregular") of the Baltic clam Macoma balthica from southern Baltic Sea off Poland. No differences in metal concentrations were observed between colour-based phenotypes. By contrast, "irregular" clams exhibited generally higher concentrations of all elements in their tissues than "regular" bivalves. This finding provides the first reference on a potential linkage of shell deformation with tissue metal concentrations within one entire population of clams living in the same habitat. Different ability of metal handling in the shape-based phenotypes is presumably related to different physiological capacity of the bivalves induced by the selection effect of specific environmental conditions. It is suggested that unfavourable conditions in deep waters of the Gulf of Gdansk (e.g. hypoxia/anoxia, hydrogen sulphide, elevated bioavailability of metals) induces, in a certain part of the population, morphological deformation of shell (thereby leading to irregular shape) and in parallel physiological adaptations which result in greater sensitivity to trace metals of "irregular" clams. This hypothesis however, requires further investigation with special focus on genetic divergences between phenotypes because till now we cannot exclude the co-occurrence of two types (semi-species) of clams in the Gulf: an Atlantic type and a Baltic type. Genetic analysis with a use of DALP technique revealed strong intrapopulational polymorphism but no fingerprints or intraspecific polymorphism characterising any of the phenotypes considered (both colour- and shape-based). Since eight polymorphic loci were clearly identified further studies of population genetic structure hold optimistic promise.

Adaptation, Physiological↗
PubMed2006

Dermacoccus barathri sp. nov. and Dermacoccus profundi sp. nov., novel actinomycetes isolated from deep-sea mud of the Mariana Trench.

The taxonomic positions of two actinobacterial strains isolated from Mariana Trench sediment were established using a combination of genotypic and phenotypic data. The strains, isolates MT2.1(T) and MT2.2(T), formed a distinct phyletic line in the Micrococcineae 16S rRNA gene tree together with Dermacoccus abyssi NCIMB 14084(T). The isolates had chemical and phenotypic properties typical of members of the genus Dermacoccus and could be distinguished sharply from one another and from the type strains of Dermacoccus abyssi and Dermacoccus nishinomiyaensis using DNA-DNA relatedness data. A range of phenotypic properties served to distinguish the two novel strains from one another and from the type strains of established Dermacoccus species. The G+C contents of the DNAs of strains MT2.1(T) and MT2.2(T) were 66.8 and 69.1 mol%, respectively. It is evident that the two isolates merit recognition as novel species within the genus Dermacoccus. The names proposed for these taxa are Dermacoccus barathri sp. nov. (type strain MT2.1(T)=DSM 17574(T)=NCIMB 14081(T)) and Dermacoccus profundi sp. nov. (type strain MT2.2(T)=DSM 17575(T)=NCIMB 14126(T)) [corrected]

Actinomycetales↗