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PubMed2026

ClearDepthIAS enables automated high-throughput quantification of roots in soil-grown taproot crops.

Understanding root system architecture is critical for improving crop productivity and resilience, yet phenotyping root traits such as root growth angle and rooting depth remains technically challenging, especially at high throughput. Here, we present ClearDepthIAS, a high-throughput imaging and analysis platform that enables nondestructive, automated quantification of root architecture traits in taproot system crops. By capturing and stitching 360° images of roots growing along the transparent walls of pots and applying deep learning-based segmentation (ClearDepth-WRT), we measured wall root shallowness (WRS)-a proxy for root growth angle-with high precision. We demonstrated for the tap root systems of soybean and canola that the system accurately detects root tips, quantifies their vertical distribution, and extracts biologically meaningful traits such as root area, distribution indices, and growth angles. Validation experiments in canola and soybean demonstrated that WRS can correlate with root crown architecture in mature plants, both in greenhouse and field settings. Furthermore, WRS and root distribution indices derived from ClearDepthIAS are predictors of early root architecture and can be correlated with root biomass distribution across soil depths under field conditions; however, environmental interactions may influence these relationships and weaken or even negate such correlations, as observed when comparing field to field variation in root system architecture. Our system enables efficient phenotyping of genetically diverse populations, with medium to high trait heritability, supporting its utility for genome-wide association studies and breeding. ClearDepthIAS accelerates the development of root ideotypes for improved resource acquisition and carbon sequestration, offering a scalable tool for supporting climate-resilient agriculture.

Plant Roots↗

PubMed1998

A new L527R mutation of the betaIGH3 gene in patients with lattice corneal dystrophy with deep stromal opacities.

Mutations in the betaIGH3 gene on chromosome 5q31 cause five distinct autosomal dominant corneal dystrophies: granular Groenouw type I, Reis-Bücklers', lattice type I and IIIA. and Avellino corneal dystrophies. We present here a new mutation of the betaIGH3 gene in patients with late-onset lattice corneal dystrophy manifest as a deep stromal opacity. To test the previously reported R124C, R124H, P501T, R555W, and R555Q mutations of the betaIGH3 gene, 30 patients and 11 normal relatives from 16 independently ascertained families with lattice corneal dystrophy, 49 patients and 12 normal relatives from 40 independently ascertained families with other corneal dystrophies, and 40 unrelated normal volunteers, were analyzed. A L527R (CTG/CGG) mutation of the betaIGH3 gene was found in 6 unrelated patients with lattice corneal dystrophy. A retrospective review of the patients' records showed that the opacities were deep in the stromal layer and of late onset. The mutation was a heterozygous single base-pair transversion from T to G of the second nucleotide position of codon 527. This caused the substitution of arginine for leucine. These six patients did not have mutations in codons 124, 501, or 555. The L527R mutation was not detected in the other corneal dystrophies or 40 normal volunteers. Although phenotypic variations in the size and shape of the deposits were found, all patients with the L527R mutation showed deposits deep in the stromal layer. We conclude that there are now at least six different mutations that have been detected in the betaIGH3 gene on chromosome 5q31 and that lead to corneal dystrophy.

Aged↗

PubMed2005

First report of a partial trisomy 3q12-q23 de novo--FISH breakpoint determination and phenotypic characterization.

We present a 1-year-old boy with mild mental retardation, postnatal growth retardation, and facial dysmorphisms such as frontal bossing, laterally accentuated bushy eyebrows, deep set eyes with long lashes, hypertelorism, and a broad nasal bridge. Except for hip dysplasia, no congenital malformations were detected. By conventional cytogenetics a derivative chromosome 3 de novo was diagnosed which was identified as tandem dup(3)(q12q23) by fluorescence in situ hybridization (FISH) applying arm specific paints and eight different YAC-probes. The duplicated segment lies proximally from the reported dup(3q) syndrome critical region, thus explaining the absence of characteristic phenotypic features of dup(3q) syndrome. To our knowledge this is the first report of a patient with pure trisomy of this proximal region of the long arm of chromosome 3.

Chromosome Disorders↗

PubMed2026

Detection of antibiotic heteroresistance in clinical microbiology: current and emerging methodologies.

BACKGROUND: Antibiotic heteroresistance (HR) is characterised by the coexistence of susceptible and resistant subpopulations within an apparently isogenic bacterial isolate. Because routine antimicrobial susceptibility testing (AST) primarily assesses the dominant population, HR may escape detection, potentially leading to discrepancies between laboratory susceptibility categorisation and the underlying bacterial population structure. OBJECTIVES: To provide a critical and practice-oriented evaluation of current and emerging methodologies for HR detection and to discuss their strengths, limitations, and potential for clinical implementation. SOURCES: Narrative review based on PubMed searches, complemented by screening of key reference lists and relevant EUCAST and CLSI documents. Peer-reviewed literature was prioritised. CONTENT: Phenotypic approaches, particularly population analysis profiling, remain the reference method for HR definition, but their labour-intensive workflows, long turnaround times, and limited standardisation restrict routine implementation. Alternative strategies, including modified AST assays, metabolic assays, and single-cell platforms, offer gains in speed or throughput but require broader validation. Molecular approaches such as quantitative PCR, droplet digital PCR, targeted deep sequencing, and whole-genome sequencing improve detection of minority resistance determinants. Emerging computational frameworks, including machine learning models integrating phenotypic and genomic data, represent a promising frontier for scalable HR prediction. IMPLICATIONS: Available evidence supports the clinical relevance of HR, although its association with adverse outcomes varies across bacterial species and antibiotic classes. Harmonised methodologies and clinically validated interpretive criteria are needed to support integration of HR assessment into routine diagnostics. Prospective multicentre studies and further standardisation, including engagement with EUCAST and CLSI, will be important to advance clinical implementation.

Antimicrobial resistance↗

PubMed1991

Diversity of ultrastructure in different phenotypes of cultured microvessel endothelial cells isolated from bovine corpus luteum.

Five different types of cultured microvessel endothelial cells defined by use of light microscopy and scanning electron microscopy in a preceding study were investigated by transmission electron microscopy. Type-1 cells displayed a deep invagination of the cell membrane or a single cilium. Granules of low electron density were abundant. A perinuclear ring of intermediate filaments occurred. Cultures of type-2 cells were subdivided into phenotype A, reminiscent of cell-type 1, and into phenotype B, assumed to be vascular smooth muscle cells. Many highly electron-dense granules appeared in late postconfluent cultures of both phenotypes. Cell-type 3 was conspicuous because of a large intracytoplasmic vacuole. Lysosomes with curvilinear bodies were found in cell-types 3 and 4. Both cell types developed a peripheral regular network of microfilaments. Cell-type 5 showed vesiculation of the rough endoplasmic reticulum, lipid droplets and a peripheral felt-like belt of microfilaments. Tubular forms seen in late postconfluent cultures of cell-types 1 to 3 displayed a core of extracellular matrix. Pseudotubular forms of cell-type 4 contained apoptotic bodies. Thus, as seen at the ultrastructural level, different features are maintained by cultured microvessel endothelial cells, suggesting that they have different inherent properties.

Animals↗

PubMed1990

Enzymatic profiles of 11 barophilic bacteria under in situ conditions: evidence for pressure modulation of phenotype.

Barophilic bacteria are microorganisms that grow preferentially (facultative barophiles) or exclusively (obligate barophiles) under elevated hydrostatic pressure. Barophilic bacteria have been isolated from a variety of deep-sea environments. Attempts to characterize these organisms have been hampered by a lack of appropriate methodologies. A colorimetric method for the detection of 19 constitutively expressed enzymes under in situ conditions of pressure and temperature has been devised, using a simple modification of the commercially available API ZYME enzyme assay kit. By using this method, enzyme profiles of 11 barophilic isolates, including an obligate barophile, were determined. Nine of the 10 facultatively barophilic isolates examined exhibited a change of phenotype in at least one enzyme reaction when tested at 1 atm (1 atm = 101.29 kPa), compared with results obtained under in situ pressure. The assay is simple and rapid and allows for direct determination of enzyme activity under conditions of high pressure and low temperature.

Atmospheric Pressure↗

PubMed1993

Interstitial duplication of 7(q22-->q34).

We report on a 3-year-old boy with an interstitial duplication of 7(q22-->q34), confirmed with fluorescent in-situ hybridization. He had post-natal growth retardation, developmental delay, frontal and parietal bossing, deep-set eyes, strabismus, bilateral optic nerve hypoplasia, and mild dilatation of the cerebral ventricles. His phenotype was not significantly different from that of the three previously reported patients with interstitial duplication of the smaller segment 7(q22-->q31).

Abnormalities, Multiple↗

PubMed2026

Form and function of actin impacts actin health and aging.

The actin cytoskeleton is a fundamental and highly conserved structure that functions in diverse cellular processes, yet its direct contribution to organismal aging remains unclear. Here, we systematically interrogated how genetic and pharmacologic perturbations of actin structure and function influence lifespan and various hallmarks of aging in Caenorhabditis elegans. Whole-animal and tissue-specific knockdown of actin and key actin-binding proteins (ABPs)-arx-2 (Arp2/3), unc-60 (cofilin), and lev-11 (tropomyosin)-led to premature disruption of filament organization, reduced lifespan, and tissue-specific physiological defects. Actin dysfunction also displayed a more "aged" transcriptome using previously validated transcriptomics clocks, and broadly exacerbated many age-associated phenotypes, including mitochondrial dysfunction, lipid dysregulation, loss of proteostasis, impaired autophagy, and intestinal barrier failure. Pharmacological destabilization with Latrunculin A mirrored genetic knockdowns, while mild stabilization with Jasplakinolide modestly extended lifespan, emphasizing that optimal and finely tuned actin function is critical for healthy aging. Finally, analysis of human genome-wide association data revealed that common ACTB polymorphisms correlate with differences in age-related decline in gait speed, suggesting some links between aging and actin across organisms. Taken together, our results provide a comprehensive and publicly accessible resource that maps, for the first time, how changes in actin integrity correlate with diverse aging phenotypes across tissues. This descriptive framework is intended to enable future mechanistic discovery by offering a deep, unbiased dataset that can be integrated with emerging studies to define how actin dynamics can potentially influence aging.

actin↗

PubMed1997

Transfer of Blastobacter natatorius (Sly 1985) to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov.

The budding bacterium Blastobacter natatorius belongs to the alpha-4 group of the Proteobacteria and clusters phylogenetically on a deep branch with Sphingomonas capsulata, with which it shares 93.9% 16S rRNA sequence similarity. On phylogenetic, phenotypic, and chemotaxonomic grounds a proposal is made to transfer B. natatorius to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov.

Gram-Negative Aerobic Bacteria↗

PubMed2004

High factor VIII levels in venous thromboembolism show linkage to imprinted loci on chromosomes 5 and 11.

High factor VIII (FVIII) levels are known to be a risk factor for deep venous thrombosis, but the mechanisms responsible for high FVIII levels remain unclear. Here, a new phenotype "FVIII level residuum" (FVIII-R) was defined in order to eliminate the impact of common determinants on FVIII levels. We studied 13 families of patients with thrombosis and reproducibly high FVIII levels of unknown origin. Since familial clustering was evident, we looked for a possible genetic basis. A genome scan was performed with 402 evenly spaced microsatellite markers. A quantitative linkage analysis using variance component methods showed suggestive evidence for linkage of FVIII-R with a locus on chromosome 8 (logarithm of odds [LOD] = 2.1). In addition, we performed parametric exploratory linkage analysis of dichotomized FVIII-R, taking a parent-of-origin effect into account. Single-trait-locus MOD-score analysis showed suggestive evidence for linkage under an imprinting model at chromosomes 5 and 11. Furthermore, a 2-trait-locus analysis under a multiplicative model for the loci of chromosomes 5 and 11 yielded a remarkable LOD of 4.44. It confirmed the finding of paternal imprinting, obtained by single-trait-locus analysis, at both loci. Our results suggest that high FVIII levels in venous thromboembolism represent a complex trait caused by several genetic factors.

Chromosomes, Human, Pair 11↗

PubMed1993

Expression of relB transcripts during lymphoid organ development: specific expression in dendritic antigen-presenting cells.

We have studied the expression of the relB gene during mouse development using in situ hybridization and immunocytochemical analysis. The results show that the expression of the relB gene is highly restricted to a subpopulation of cells that colonize the lymphoid tissues and that appear very late during the process of hematopoietic diversification. RNA transcripts of relB are very low or undetectable in early and late embryos. Low relB expression is observed in the thymus at late stages of embryogenesis but rapidly increases after birth. In adult lymphoid tissues, relB is detected in the medullary region of the thymus, the periarterial lymphatic sheaths of the spleen, and the deep cortex of the lymph nodes, which correspond to the regions where T cells of mature phenotype and interdigitating dendritic cells are present. Using double immunofluorescent labeling of thymic cell suspensions, we have identified the interdigitating dendritic cells as the target of RelB expression. These cells are part of a system of antigen-presenting cells that function in the induction of several immune responses, such as, tolerance, sensitization of MHC-restricted T cells, rejection of organ transplants and formation of T-dependent antibodies. Our observations indicate that RelB may play a particular role in the signal transduction pathway that regulate dendritic cell differentiation and its cellular responses.

Animals↗

PubMed2005

Deep venous thrombosis: behaviour of the polymorphonuclear leukocyte integrin pattern at baseline and after in vitro activation.

In a group of 18 subjects with acute deep venous thrombosis (DVT), evidenced by clinical examination and echo-color-Doppler, we examined the phenotypical expression of the polymorphonuclear leukocyte (PMN) beta2-integrins (CD11a, CD11b, CD11c, CD18), obtained by using a flow cytofluorimeter. The evaluation was performed before and after in vitro activation (prolonged for 5 and 15 minutes) with 4-phorbol 12-myristate 13-acetate (PMA) and N-formyl-methionyl-leucyl-phenylalanine (fMLP). In DVT subjects, at baseline, the phenotypical expression of CD11b was decreased and that of CD11c was increased when compared with normal controls; no difference was found in CD11a and CD18 expression. In normal subjects PMN activation with both activators led to a constant increase of all PMN adhesion molecules; in DVT subjects CD11b, CD11c and CD18 increased, while CD11a expression did not show any change. These data indicate the presence of a functional alteration in circulating PMN cells from patients with DVT.

Adult↗

PubMed2004

Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough.

A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16 : 1omega7c, 15 : 0 iso, 16 : 0 and 13 : 0 iso. The G+C content of the DNA was 44.9 mol%. On the basis of 16S rRNA gene sequences, strain LT13a(T) was shown to belong to the gamma-Proteobacteria, being closely related to Shewanella putrefaciens (98 %), Shewanella oneidensis (97 %) and Shewanella baltica (96 %). Levels of DNA homology between strain LT13a(T) and S. putrefaciens, S. oneidensis and S. baltica were <20 %, indicating that strain LT13a(T) represents a novel species. Genetic evidence and phenotypic characteristics showed that isolate LT13a(T) constitutes a novel species of the genus Shewanella. Because of the deep origin of the strain, the name Shewanella profunda sp. nov. is proposed, with LT13a(T) (=DSM 15900(T)=JCM 12080(T)) as the type strain.

Anaerobiosis↗

PubMed1993

An unusual patient with the neonatal Marfan phenotype and mitochondrial complex I deficiency.

We report the case of a 16-month-old male with the neonatal appearance of Marfan syndrome (NMS), with dolichocephaly, a long midface, deep-set eyes, arachnodactyly, dislocated lenses and carciovascular abnormalities. The presence of persistent lactic acidosis led to studies which disclosed mitochondrial complex I deficiency. We speculate that this unusual association may be due to the combination of an inherited mutation affecting complex I activity along with a de novo mutation disrupting the corresponding locus and an adjacent NMS locus on the homologous autosome. The possibility that the phenotype observed in this patient is directly due to the mitochondrial defect cannot be excluded.

Electron Transport Complex I↗

PubMed1988

Frequency and characteristics of plasmids in bacteria isolated from deep-sea amphipods.

Bacterial strains isolated from deep-sea amphipods were identified, classified, and screened for plasmid content. Plasmids were common, with 11 of 16 isolates carrying one or more plasmids; these ranged in size from 2.9 to 63 megadaltons. Several of the strains demonstrated distinctly different phenotypic traits yet contained plasmids of the same molecular weight. Results of agarose gel electrophoresis, DNA hybridization, and restriction analysis indicate that the plasmids detected in these deep-sea isolates are identical, suggesting that transmission may occur in the deep-sea environment and that plasmids are common in some deep-sea habitats.

Journal Article↗

PubMed2002

Characterization of subpopulated articular chondrocytes separated by Percoll density gradient.

The aim of this study was to develop a method for fractionation of articular chondrocytes from the entire thickness of the tissue. Isolated chondrocytes from rabbit articular cartilage fractionated by centrifugation in a discontinuous Percoll gradient resulted in four cell fractions with two differing properties. The lowest-density fraction consisted mainly of large cells with small nuclei proliferated actively, maintained the chondrocytic phenotype, and secreted larger amounts of proteoglycan. In contrast, the highest-density fraction consisted of small cells with large nuclei proliferated slowly, did not express the chondrocytic phenotype, and produced larger amounts of interleukin 1-induced nitric oxide. Comparing our results with other previous reports, we find that fraction 1 cells are likely originated from the deep layer of the articular cartilage, whereas fraction 4 cells are tentatively categorized as chondrocytes from the superficial layer of cartilage. Centrifugal fractionation of articular chondrocytes via Percoll density gradient permits clear separation of these heterogeneous cells into different phenotypic populations and allows distinguishing of cells from the different layers of articular cartilage. This simple novel method will provide ready separation of articular chondrocytes for the investigation of the pathogenesis of articular cartilage.

Alkaline Phosphatase↗

PubMed2003

Isolation of extremophiles with the detection and retrieval of Shewanella strains in deep-sea sediments from the west Pacific.

Tests to detect the presence of piezophilic Shewanella strains in the deep-sea sediments of the west, mid- and east Pacific at different depths were done by amplification of previously identified pressure-regulated operons (ORF1,2 and ORF3). The operon fragments were detected in all the deep-sea sediment samples, indicating the broad presence of piezophilic deep-sea Shewanella species or related species in the deep-sea sediments across the Pacific. Extremophiles were isolated from the deep-sea sediment of the west Pacific under atmospheric pressure. Two psychrophilic/psychrotrophic strains, WP2 and WP3, were assigned to the Shewanella genus as determined by their 16S rDNA sequences. WP2 and WP3 were both capable of amplifying pressure-regulated operons; the sequences of the pressure-regulated operons of WP2 and WP3 share high identity between each other, but have more differences from those of S. benthica and S. violacea. The major fatty acids of WP2 and WP3 are 3OH-i-13:0, 14:0, i-15:0, 16:0, 16:1, 18:1, and 20:5. Combined phenotypic analysis, 16S rDNA sequences, and DNA-DNA hybridization results suggest that WP2 and WP3 are two new deep-sea Shewanella species.

Amino Acid Sequence↗

PubMed2006

Intestinal crypt properties fit a model that incorporates replicative ageing and deep and proximate stem cells.

A model of intestinal crypt organization is suggested based on the assumption that stem cells have a finite replicative life span. The model assumes the existence in a crypt of a quiescent ('deep') stem cell and a few more actively cycling ('proximate') stem cells. Monte Carlo computer simulation of published intestinal crypt mutagenesis data is used to test the model. The results of the simulation indicate that stabilization of the crypt mutant phenotype following treatment with external mutagen is consistent with a stem cell replicative life span of about 40 divisions for mouse colon and 90-100 divisions for mouse small intestine, corresponding to a deep stem cell cycle time of about 3.9 and 8.5 weeks for colon and small intestine, respectively. Simulation of the data obtained for human colorectal crypts suggests that the proximate stem cell cycle time is about 80 h, assuming a replicative life span of 50-150 divisions, and that the deep stem cell divides approximately every 30 weeks.

Animals↗