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PubMed2022

TTC5 syndrome: Clinical and molecular spectrum of a severe and recognizable condition.

Biallelic mutations in the TTC5 gene have been associated with autosomal recessive intellectual disability (ARID) and subsequently with an ID syndrome including severe speech impairment, cerebral atrophy, and hypotonia as clinical cornerstones. A TTC5 role in IDs has been proposed based on the physical interaction of TTC5 with p300, and possibly reducing p300 co-activator complex activity, similarly to what was observed in Menke-Hennekam 1 and 2 patients (MKHK1 and 2) carrying, respectively, mutations in exon 30 and 31 of CREBBP and EP300, which code for the TTC5-binding region. Recently, TTC5-related brain malformation has been linked to tubulinopathies due to the function of TTC5 in tubulins' dynamics. We reported seven new patients with novel or recurrent TTC5 variants. The deep characterization of the molecular and phenotypic spectrum confirmed TTC5-related disorder as a recognizable, very severe neurodevelopmental syndrome. In addition, other relevant clinical aspects, including a severe pre- and postnatal growth retardation, cryptorchidism, and epilepsy, have emerged from the reversal phenotype approach and the review of already published TTC5 cases. Microcephaly and facial dysmorphism resulted in being less variable than that documented before. The TTC5 clinical features have been compared with MKHK1 published cases in the hypothesis that clinical overlap in some characteristics of the two conditions was related to the common p300 molecular pathway.

Exons↗

PubMed1992

Differences between the deep pores of K+ channels determined by an interacting pair of nonpolar amino acids.

The pore of a chimeric K+ channel, CHM, differed from its parental host channel, Kv2.1, by 9 amino acids. Four were located in a putative deep region and 5 in a nearby outer mouth. Point reversions were without restorative effects, and reversions V369I or L374V in the deep pore produced novel phenotypes. Among double mutations, only V369I and L374V were effective in restoring the Kv2.1 pore phenotype. Adding a change in charge at Q382K in the outer pore fully restored the parental phenotype. Thus, the pore appears to have an inner, deep region where ions such as K+ and TEA+ may be regulated by nonpolar residues and an outer region where ions may be regulated by charged residues.

Amino Acid Sequence↗

PubMed1989

Expression of type 1 and type 2 blood group-related antigens in normal and neoplastic gastric mucosa.

The distribution of the blood group-related antigens type 1 (Lewis(a) [Le(a)], Lewis(b) [Le(b)]) and type 2 (H type 2, Y) has been examined in histologically normal and malignant mucosa of 40 surgical specimens of patients with adenocarcinoma of the stomach, with the use of a panel of monoclonal antibodies. Patients' Lewis phenotype and secretor status are correlated to the authors' findings. The surface epithelium of normal pyloric and fundic mucosa expressed the Lewis isoantigen (Le(a) in Le[a+b-] phenotype and Le(b) in Le[a-b+] phenotype), whereas the deep areas of this mucosa no showed the Le(a), Le(b) antigens and expressed the Y and H type 2 antigens whatever the secretor status of patients. Nineteen of 24 patients with Le(a-b+) phenotype showed anomalous expression of Lea antigen in neoplastic cells. In three of them, this alteration was found in tumor adjacent mucosa. No expression of Le(a) or Le(b) antigens was found in tumors or normal mucosa from Le(a-b-) phenotype patients.

Antibodies, Monoclonal↗

PubMed2005

Inheritance and genetic mapping of tuber eye depth in cultivated diploid potatoes.

Tuber eye depth of the potato (Solanum tuberosum L.) is an important trait for the processing quality and appearance of potatoes. In the present study, we used a cultivated diploid potato family (12601) of 107 plants to dissect the mode of inheritance and to map the gene(s) controlling the trait. The family segregated for both eye depth (deep vs shallow) and tuber shape (round vs long) traits. The deep eye (Eyd) phenotype was found to be associated with round tubers (Ro) in most progeny clones. Further evaluation of this population with molecular markers including simple sequence repeats, amplified fragment length polymorphism, and sequence-characterized amplified regions revealed that the primary locus for eye depth is located on chromosome 10. This map location was confirmed by evaluating a second diploid family (12586). The results of this study led to the following conclusions: (1) there is a major locus controlling the eye depth trait; (2) deep eye (Eyd) is dominant to shallow (eyd); (3) the Eyd/eyd locus is located on chromosome 10; and (4) the Eyd/eyd locus is closely linked with the major locus for tuber shape (Ro/ro), at a distance of about 4 cM.

Agriculture↗

PubMed1997

Activation of the metaphase checkpoint and an apoptosis programme in the early zebrafish embryo, by treatment with the spindle-destabilising agent nocodazole.

We have studied the developmental activation of the metaphase checkpoint, and the consequences of activating this checkpoint, in the zebrafish embryo. (1) Treatment with nocodazole (a microtubule destabiliser) before mid-blastula transition (MBT) produces complete destruction of all nuclei in the deep cell layer of the embryo. In contrast, nocodazole treatment after MBT efficiently produces metaphase arrest in this cell layer. Thus, the metaphase checkpoint becomes activated at MBT. (2) Although a metaphase arrest is induced by nocodazole, it is not induced by paclitaxel (a microtubule stabiliser). Thus the metaphase checkpoint appears to sense a destabilisation, but not a stabilisation, of spindle microtubules. (3) Metaphase-arrested cells (in nocodazole) can be driven into the next interphase by adding the Ca2+-specific ionophore A23187. Thus, a Ca2+-signalling pathway lies downstream of, or parallel to, the metaphase checkpoint. (4) After mid-gastrula stage, treatment with nocodazole produces DNA fragmentation in all three cell layers. In the enveloping epithelial monolayer (EVL), this is associated with a classical apoptotic phenotype. In the deep layer, it is associated with an unusual, highly condensed nuclear state that is entered directly from metaphase arrest. Thus, after the mid-gastrula stage, the embryo responds to nocodazle by undergoing apoptosis. (5) Nocodazole-induced apoptosis in the deep cell layer can be blocked by the caspase-1,4,5 inhibitors Ac-YVAD-CHO and Ac-YVAD-CMK. This suggests that a homologue of the C. elegans ced-9-ced-4-ced-3 pathway is involved in control over apoptosis in the early zebrafish embryo.

Amino Acid Chloromethyl Ketones↗

PubMed2002

Patterns of genetic and phenotypic variation in Iris haynei and I. atrofusca (Iris sect. Oncocyclus = the royal irises) along an ecogeographical gradient in Israel and the West Bank.

Iris haynei and I. atrofusca are two closely related narrow endemics distributed vicariously along an ecogeographical north-south gradient in Israel and the West Bank. To obtain baseline information of the taxonomic status, conservation and population history of these taxa, we investigated patterns of phenotypic variation and the partitioning of genetic variation within and among populations using dominant random amplified polymorphic DNA (RAPD) markers. Multivariate (principal components analysis) and taxonomic distance analyses based on morphometric traits from eight populations revealed no unambiguous separation into two distinct groups. Results of genetic analyses for nine populations differed only slightly when either allele- or marker-based approaches were employed. Mean within-population diversity was high (0.258 for Nei's expected heterozygosity), but there was no significant relationship between genetic diversity and either population size or latitude. Although the range-wide estimate of GST ( approximately 0.20) revealed relatively high differentiation among populations this value was inflated because of a small, but significant, component of molecular variance among regions viz. taxa ( approximately 5%). Limited long-distance dispersal capabilities in conjunction with a linearized habitat distribution are proposed to contribute to the approximate isolation by distance pattern observed. It also appears that extant populations are currently deviating from equilibrium conditions because of primary divergence of a formerly more widespread ancestral population. Given the absence of deep genetic and phenotypic subdivision among northern (I. haynei) vs. central/southern (I. atrofusca) populations, we argue for a revision of their species status. Nonetheless, we recommend conservation attention to these geographically differentiated segments as separate management units, which can be seen as an instructive example of incipient species formation.

Conservation of Natural Resources↗

PubMed1998

The phylogeny of unicellular, extremely halotolerant cyanobacteria.

We examined the morphology, physiology, and 16S rRNA gene sequences of three culture collection strains and of ten novel isolates of unicellular cyanobacteria from hypersaline environments. The strains were morphologically diverse, with average cell widths ranging from 2.8 to 10.3 micron. There were single-celled, colonial, and baeocyte-forming strains. However, morphological traits were markedly variable with culture conditions. In contrast, all strains displayed extreme halotolerance (growing close to optimally at above 12% salinity); all were obligately marine, euryhaline, and moderately thermophilic; and all shared a suite of chemotaxonomic markers including phycobilins, carotenoids, and mycosporine-like amino acids. 16S rRNA gene sequence analysis indicated that the strains were related to each other. Sequence similarity analysis placed the strains in a monophyletic cluster (which we named the Halothece cluster) apart from all cultured or uncultured, not extremely halotolerant cyanobacteria whose 16S rRNA gene sequences are available in public nucleotide sequence databases. This represents the first case in which a phylogenetically coherent group of cyanobacteria can be defined on the basis of physiology. The Halothece cluster contained two subclusters that may be divergent at the generic level, one encompassing 12 strains (spanning 5% 16S rRNA gene sequence divergence and named the Euhalothece subcluster), and a single deep-branching isolate. Phenotypic characterization of the isolates, including morphological, physiological, and chemotaxonomic traits, did not distinguish these subclusters and only weakly suggested the existence of two separate clades, one encompassing strains of small cell size (cell width < 5 m) and another one encompassing strains of larger cell size.

Bacterial Proteins↗

PubMed1997

Mice lacking p35, a neuronal specific activator of Cdk5, display cortical lamination defects, seizures, and adult lethality.

The adult mammalian cortex is characterized by a distinct laminar structure generated through a well-defined pattern of neuronal migration. Successively generated neurons are layered in an "inside-out" manner to produce six cortical laminae. We demonstrate here that p35, the neuronal-specific activator of cyclin-dependent kinase 5, plays a key role in proper neuronal migration. Mice lacking p35, and thus p35/cdk5 kinase activity, display severe cortical lamination defects and suffer from sporadic adult lethality and seizures. Histological examination reveals that the mutant mice lack the characteristic laminated structure of the cortex. Neuronal birth-dating experiments indicate a reversed packing order of cortical neurons such that earlier born neurons reside in superficial layers and later generated neurons occupy deep layers. The phenotype of p35 mutant mice thus demonstrates that the formation of cortical laminar structure depends on the action of the p35/cdk5 kinase.

Animals↗

PubMed1996

A diagnostic molecular marker for zebra mussels (Dreissena polymorpha) and potentially co-occurring bivalves: mitochondrial COI.

We report diagnostic differences in the nucleotide sequences of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from the zebra mussel (Dreissena polymorpha) and potentially co-occurring bivalves: the quagga mussel (Dreissena bugensis); the Asiatic clam (Corbicula fluminea), the dark false mussel (Mytilopsis leucophaeata), and the wedge clam (Rangia cuneata). The COI sequence of the deep-water "profunda" phenotype of the quagga mussel was nearly identical to that of shallow-water quagga mussels. Restriction fragment length polymorphisms (RFLPs) in this portion of COI produced species-specific differences in fragment numbers and sizes that could be used as diagnostic markers to distinguish the free-living larvae produced by these bivalves.

Animals↗

PubMed2003

Rheinheimera pacifica sp. nov., a novel halotolerant bacterium isolated from deep sea water of the Pacific.

An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, non-pigmented bacterium, KMM 1406(T), was isolated from a sample of Pacific deep sea water and investigated for phenotypic characteristics, chemotaxonomic features and phylogenetic relationships. The deep-sea isolate exhibited growth in 0-8 % (w/v) NaCl and at 4-37 degrees C, hydrolytic activity on gelatin, Tween 80 and starch and lack of D-glucose utilization. The major fatty acids were C(16 : 0), C(16 : 1)omega9c, C(17 : 1)omega8c and C(18 : 1)omega7c. The DNA G+C content was 49.6 mol%. 16S rRNA gene sequence analysis revealed that strain KMM 1406(T) was related closely to Rheinheimera baltica DSM 14885(T) within the gamma-Proteobacteria, with 96.8 % sequence similarity. On the basis of phenotypic and molecular data, a novel species, Rheinheimera pacifica sp. nov., is proposed. The type strain is KMM 1406(T) (=IAM 15043(T)=JCM 12090(T)=NRIC 0539(T)=CCUG 46544(T)).

Chromatiaceae↗

PubMed1983

[Heart surgery in a female patient with blood group Oh (Bombay phenotype)].

A 62-year-old woman with stenosing coronary artery disease had the rare blood group Oh (Bombay phenotype). After prophylactic deep-freeze conservation of autologous blood, direct myocardial revascularization was successfully accomplished under extracorporeal circulation. Three deep-freeze units of erythrocyte concentrates were used. Both operation and postoperative wound healing progressed without complication.

ABO Blood-Group System↗

PubMed1997

Alterations affecting the p53 control pathway in bilharzial-related bladder cancer.

Bilharzial-related bladder carcinoma (BBC) is the most common malignant neoplasm in Egypt, also occurring with a high incidence in other regions of the Middle East and East Africa. The clinical and pathological features of BBC are different than those described for the conventional transitional cell carcinoma of the bladder, including the high incidence of squamous cell carcinoma reported in BBC and the fact that over 90% of BBC cases at presentation are advanced-stage tumors (P3 and P4). This study was conducted to better define the phenotypic alterations associated with BBC affecting the p53 cell cycle control pathway, including altered patterns of expression of downstream effector proteins such as mdm2 and p21/WAF1. A well-characterized cohort of 125 patients affected with bilharzial-related bladder tumors was studied. Tumors were classified as squamous carcinomas (n = 68), transitional cell carcinomas (n = 55), or adenocarcinomas (n = 2). The products encoded by TP53, mdm2, and p21/WAF1 genes were analyzed by immunohistochemistry. Furthermore, the patterns of expression of these molecules were correlated with the Ki67 proliferative index. In addition, the microanatomical distribution of programmed cell death was assessed in a subset of tumors, using the so-called terminal deoxynucleotidyl transferase-mediated nick end labeling method. p53 nuclear overexpression was identified in 25 (20%) of 125 cases. Nuclear overexpression of mdm2 was detected in 74 (59.2%) of 125 cases. There was a statistically significant association between coexpression of both p53 and mdm2 and detection of lymph node metastases (P = 0.04). p21/WAF1 expression was detected in 87 (72%) of 121 evaluable cases. A high Ki67 proliferative index was observed in 99 (86%) of 115 evaluable cases. There was a statistically significant association between high Ki67 proliferative index and mdm2-positive phenotype (P = 0.005) and deep muscle invasion (P3b; P = 0.026) as well as lymph node metastases (P = 0.039). Apoptosis was observed in terminally differentiated tumor cells identified in the superficial layers of well-differentiated squamous carcinoma or exfoliating cells in transitional lesions. However, only rare apoptotic tumor cells were found in basal or suprabasal layers as well as in the invasive elements of the neoplasms studied. These results suggest that the frequency of p53 nuclear overexpression in BBC is lower than that reported for conventional transitional cell carcinoma. Nevertheless, tumors with p53 alterations have a greater propensity to progress. The prominent number of cases displaying an mdm2-positive phenotype suggests that this may be an early incident in BBC and should be regarded as a potential oncogenic phenomenon. This is supported by the significant correlation between high Ki67 proliferative index and mdm2 overexpression. The association of an aggressive clinical course with the coexpression of both p53 and mdm2 products might be viewed as a cooperative effect that develops in tumor progression.

Adenocarcinoma↗

PubMed2026

Spectral Transforms as a Tool to Optimize Digital Phenotyping in Biological Images.

Modern livestock breeding has mastered genotyping. Genome-wide association studies, genomic selection, and SNP arrays enable genetic merit prediction at lower cost. However, phenotyping remains the bottleneck, as manual measurement is slow, expensive, subjective, and unable to capture spatial or temporal trait organization. Digital phenotyping via artificial intelligence could resolve this, but deep learning requires thousands of labelled examples, impractical when phenotyping cost itself limits datasets to hundreds of individuals. This creates a paradox: AI could accelerate phenotyping but requires large numbers of samples to train the models. Here, we demonstrate that integrating computer vision with machine learning offers sample-efficient digital phenotyping using eggshell colour as a model system. Rather than learning features from scratch (deep learning), we engineer physically motivated features via Wavelet transforms that decompose images into multi-scale spatial components. Wavelet features captured 14.2 percentage points more variance (R2 = 0.976 vs. 0.834, p < 0.001) than standard colorimetry, with 50% better sample efficiency (achieving at n = 60 what colorimetry required n = 120). Variance decomposition revealed 77% of discriminative capacity derives from spatial patterns (bands, spots, gradients) invisible to scalar averages. Additionally, we identified "cryptic phenotypes" (3.3%) where spatial patterns contradicted average colour, cases where colorimeters failed but Wavelets succeeded. The underlying principle-that spatial decomposition can recover organizational information lost by scalar averaging-may be applicable to other traits with spatial or temporal structure, such as marbling, dermatitis, or pigmentation rhythms, although whether comparable performance gains would be observed remains to be tested empirically. Hence, for breeding programs implementing genomic selection, computer vision-based digital phenotyping captures complex trait variation without massive training datasets, addressing the bottleneck that increasingly limits genetic progress as genotyping becomes trivial.

Wavelet transform↗

PubMed2002

[Biology of periodontal regeneration: a review and a hypothesis for future researches].

Since the end of the seventies several studies have been carried out about the possibility of regeneration of periodontal osseous defects. The results of such researches supported by histological tests allowed to establish which surgical techniques could yield periodontal regeneration in a predictable way. In spite of a quite large diffusion of these sugical techniques in the treatment of periodontal osseous defects, some biological aspects of periodontal regeneration are still unknown. The most important among them is the origin and the differentiation pathway of the synthetic cells that shall provide for the reconstruction of the deep periodontium. Particularly, the phenotypic pattern and the origin of cementoblasts are not clear. Our researches focused on pericytes, a mesenchyma-derived cell population with remarkable differentiation capacities which have a microvascular location. We considered the hypothesis that pericytes could play an important role in regeneration of the alveolar bone, of the cementum and of the periodontal ligament. Should pericytes be actually the precursors of osteoblatsts, fibroblasts and cementoblasts involved in periodontal regeneration, new therapies, such as cultivated cells reimplantation or the targeted use of growth factors could be feasible. Future researches shall verify these observations.

Alveolar Bone Loss↗

PubMed2002

[Maternal toxoplasma infection and mosaic trisomy 8 syndrome].

INTRODUCTION: Mosaic trisomy 8 syndrome shows significant phenotypic variability. High forehead, deep set eyes, wide base of the nose, upturned tip of the nose, protruding lips, prominent ears, strabism, corpus callosum agenesia, deep plantar furrow and variable degree of psychomotor retardation are present in most patients. PATIENTS/METHODS: The authors describe a patient with severe motor and mental retardation, optic disc hypoplasia, cardiomyopathy and partial extrahepatic bile-duct atresia, who's mother was treated for toxoplasma infection in her pregnancy. Perinatal infection of the child was ruled out by the documentation of decreasing IgG values in the mother and newborn and normal IgM levels in the newborn. RESULTS: Facial characteristics and the bilateral deep plantar furrow raised the possibility of trisomy 8 syndrome. Routine chromosomal analysis and fluorescent in situ hybridization studies revealed a normal cell line, mosaic trisomy 8 in 13% of the cells, and a pericentric marker 8 ring chromosome in 27% of the cells. CONCLUSION: The authors suggest that the periconceptional toxoplasma infection may play a role in the occurrence of the mosaic trisomy presenting with cardiomyopathy and partial bile-duct atresia previously undescribed in this syndrome.

Bile Ducts↗

PubMed1997

Nitric oxide production by superficial and deep articular chondrocytes.

OBJECTIVE: Chondrocytes have been shown to produce large amounts of nitric oxide (NO) when appropriately stimulated with proinflammatory cytokines or bacterial lipopolysaccharide (LPS). In view of recent observations underscoring profound phenotypic differences between superficial and deep articular chondrocytes, these studies investigated NO production, inducible NO synthase (iNOS) activity, and messenger RNA (mRNA) expression of superficial and deep cartilage explants and cells. METHODS: Superficial and deep bovine and human articular cartilage explants and isolated bovine chondrocytes were cultured in the presence of stimulating cytokines or LPS. NO was measured by the Griess reagent. Inducible NOS activity was quantitated by conversion of L-14 C-arginine to L-14C-citrulline. Inducible NOS mRNA expression was quantitated by reverse transcription-polymerase chain reaction (RT-PCR) and in situ hybridization. RESULTS: Superficial bovine cartilage explants stimulated with interleukin-1 alpha, LPS, or tumor necrosis factor alpha for 24 and 48 hours produced significantly more NO than did deep explants with all stimulants and at both times. Similar results were obtained with stimulated isolated superficial and deep cells. NO synthase activity, measured by the conversion of L-14C-arginine to L-14C-citrulline, paralleled NO production. Comparable results were obtained using explants from a normal human donor. Semiquantitation of iNOS mRNA by RT-PCR showed significantly larger amounts of PCR products in superficial cells and superficial explants. These results were confirmed by in situ hybridization of explants and isolated cells. CONCLUSION: Increased NO production at the cartilage surface-synovial fluid interface may play an important role in the modulation of cartilage damage in inflammatory arthritis.

Animals↗

PubMed2000

Charged residues between the selectivity filter and S6 segments contribute to the permeation phenotype of the sodium channel.

The deep regions of the Na(+) channel pore around the selectivity filter have been studied extensively; however, little is known about the adjacent linkers between the P loops and S6. The presence of conserved charged residues, including five in a row in domain III (D-III), hints that these linkers may play a role in permeation. To characterize the structural topology and function of these linkers, we neutralized the charged residues (from position 411 in D-I and its homologues in D-II, -III, and -IV to the putative start sites of S6) individually by cysteine substitution. Several cysteine mutants displayed enhanced sensitivities to Cd(2+) block relative to wild-type and/or were modifiable by external sulfhydryl-specific methanethiosulfonate reagents when expressed in TSA-201 cells, indicating that these amino acids reside in the permeation pathway. While neutralization of positive charges did not alter single-channel conductance, negative charge neutralizations generally reduced conductance, suggesting that such charges facilitate ion permeation. The electrical distances for Cd(2+) binding to these residues reveal a secondary "dip" into the membrane field of the linkers in domains II and IV. Our findings demonstrate significant functional roles and surprising structural features of these previously unexplored external charged residues.

Animals↗

PubMed1998

The morphological and spectral phenotype of apoptosis in HeLa cells varies following exposure to UV-C and the addition of inhibitors of ICE and CPP32.

Numerous extra- and intracellular factors, including UV radiation, can initiate a programme of cell death by apoptosis. While apoptosis is commonly defined morphologically, the relationships between morphology and molecular events are not well established. To investigate these relationships in HeLa cells, eight morphometric criteria for cell proliferation and damage and 10 criteria for apoptotic phenotype were examined using light microscopy, and corroborated by ultrastructure and spectral imaging. They were identified (1) during a time course after irradiation with 0, 10 or 30 J/m2 UV-C; (2) after separation of apoptotic from normal cells on a Percoll gradient; and (3) after irradiation with UV-C plus perturbation of the apoptotic pathway by treatment with inhibitors of two caspases, ICE and CPP32. The number of cells in apoptosis increased in a dose-dependent manner after UV-C treatment. Centrifugation of irradiated cells on a Percoll gradient increased the collection of apoptotic cells tenfold. The stereotypical apoptotic phenotype, in which cells have deep cytoplasmic blebbing and highly condensed DNA, comprised only a few percent of all apoptosis, and was rarely seen in groups receiving caspase inhibitors. The most common apoptotic phenotype was a rounded cell with large spherical nucleolus and associated DNA. After treatment with UV-C plus inhibitors the apoptotic index was decreased by about 30% compared to UV-C radiation alone. These apoptotic cells had dark spherical cytoplasm with small blebs, greatly increased numbers of cytoplasmic ribosomes, abundant nucleolar material with a large separate granular component, and chromatin condensed at the nuclear membrane. Using the technique of spectral imaging, it was found that the spectrum obtained from the granular component of the nucleolus, which was elevated in apoptotic cells treated with UV-C plus inhibitors, was similar to the dense accumulation of ribosomes in the apoptotic cytoplasm. The data indicate that spectral imaging may be a useful tool for identifying and characterizing variations in the apoptotic process, and that the caspase inhibitors used here do not completely abolish UV-C induced apoptosis, but rather alter its incidence and progression.

Amino Acid Chloromethyl Ketones↗