In recent years, due to the increasing concerns about their negative impact on wildlife and possible toxicity to living organisms (including humans), microplastics have become the subject of intense ...investigations. In the ocean, microplastics can be easily ingested by numerous marine organisms because of their small size (<5 mm). The Northwest African upwelling system is an important fishery area, and the present study is the first one in the region to reveal the presence of microplastic particles in the digestive tract of Atlantic chub mackerel (Scomber colias). From the 120 examined fish gastrointestinal tracts, 78.3% contained some type of microplastics, 74.2% contained fibres, 17.5% plastic fragments, and 16.7% paint. More studies are needed on fish, but S. colias is a candidate for being a good indicator of microplastic contamination in the region.
•Ingestion of microplastics by fish around the Canary Islands was documented for the first time.•Microplastics were found in the digestive tract of 78.4% of the sampled fish.•Fibres comprised 74.2% of the microplastics found.•We hypothesize that high fibres incidence may be related to untreated wastewater discharges.•Scomber colias could be a good indicator of microplastic contamination in the region.
Respiration quotient variability Romero-Kutzner, V.; Packard, T. T.; Berdalet, E. ...
Marine ecology. Progress series (Halstenbek),
01/2015, Letnik:
519
Journal Article
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Respiratory metabolism was compared between 2 different physiological states of acetate- and pyruvate-grown cultures of Pseudomonas nautica and Vibrio natriegens. Here, we analyze 35 h and 520 h ...experiments in which time-courses of protein, pyruvate, acetate, respiratory CO₂ production (RCO₂), respiratory O₂ consumption (RO₂), isocitrate dehydrogenase (IDH) activity, and potential respiration (Φ) were measured. Respiratory quotients (RQs) were calculated as the ratio of the respiration rates (RCO₂/RO₂). Such RQs are widely used in ocean ecosystem models, in calculations of carbon flux, and in evaluations of the ocean’s metabolic balance. In all the cultures, the RQ tended to increase. In the case of P. nautica on acetate, the RQ rose nearly an order of magnitude from values below 1 during carbon-substrate sufficiency to values close to 10 during carbon-substrate deficiency. In all the cultures, the respiration rates during the growth period paralleled the biomass increase, but after the substrates were exhausted, the respiration rates fell. In contrast, through this same transition period, the IDH activity and the Φ remained relatively high for the first 10 h of carbon-substrate deprivation, and then, these enzyme activities fell slowly, along with the biomass, as the carbon-substrate deprivation continued. The nutritional state of the bacteria affected the RQ, rendering the RQ variable for physiological and ecological purposes. These results argue that ecosystem models, oceanographic calculations of carbon flux, and evaluations of the ocean’s metabolic balance that are influenced by bacterial metabolism need to be reconsidered in light of RQ variability.
We present a correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to ...subnanometer. It utilizes a chemically accurate force field and thermodynamic sampling to improve the real-space correlation between the modeled structure and the cryo-EM map. Our framework employs a gradual increase in resolution and map-model agreement as well as simulated annealing, and allows fully automated refinement without manual intervention or any additional rotamer- and backbone-specific restraints. Using multiple challenging systems covering a wide range of map resolutions, system sizes, starting model geometries and distances from the target state, we assess the quality of generated models in terms of both model accuracy and potential of overfitting. To provide an objective comparison, we apply several well-established methods across all examples and demonstrate that CDMD performs best in most cases.
The concept of biomedical significance of the functional pairing between tissue lectins and their glycoconjugate counterreceptors has reached the mainstream of research on the flow of biological ...information. A major challenge now is to identify the principles of structure–activity relationships that underlie specificity of recognition and the ensuing post-binding processes. Toward this end, we focus on a distinct feature on the side of the lectin, i.e. its architecture to present the carbohydrate recognition domain (CRD). Working with a multifunctional human lectin, i.e. galectin-3, as model, its CRD is used in protein engineering to build variants with different modular assembly. Hereby, it becomes possible to compare activity features of the natural design, i.e. CRD attached to an N-terminal tail, with those of homo- and heterodimers and the tail-free protein. Thermodynamics of binding disaccharides proved full activity of all proteins at very similar affinity. The following glycan array testing revealed maintained preferential contact formation with
N
-acetyllactosamine oligomers and histo-blood group ABH epitopes irrespective of variant design. The study of carbohydrate-inhibitable binding of the test panel disclosed up to qualitative cell-type-dependent differences in sections of fixed murine epididymis and especially jejunum. By probing topological aspects of binding, the susceptibility to inhibition by a tetravalent glycocluster was markedly different for the wild-type vs the homodimeric variant proteins. The results teach the salient lesson that protein design matters: the type of CRD presentation can have a profound bearing on whether basically suited oligosaccharides, which for example tested positively in an array, will become binding partners in situ
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When lectin-glycoconjugate aggregates (lattices) are formed, their structural organization will depend on this parameter. Further testing (ga)lectin variants will thus be instrumental (i) to define the full range of impact of altering protein assembly and (ii) to explain why certain types of design have been favored during the course of evolution, besides opening biomedical perspectives for potential applications of the novel galectin forms.
Discoveries on involvement of glycan-protein recognition in many (patho)physiological processes are directing attention to exploring the significance of a fundamental structural aspect of sugar ...receptors beyond glycan specificity, i.e., occurrence of distinct types of modular architecture. In order to trace clues for defining design-functionality relationships in human lectins, a lectin's structural unit has been used as source material for engineering custom-made variants of the wild-type protein. Their availability facilitates comparative analysis toward the stated aim. With adhesion/growth-regulatory human galectin-1 as example, the strategy of evaluating how changes of its design (here, from the homodimer of non-covalently associated domains to (i) linker-connected di- and tetramers and (ii) a galectin-3-like protein) affect activity is illustrated by using three assay systems of increasing degree of glycan complexity. Whereas calorimetry with two cognate disaccharides and array testing with 647 (glyco)compounds disclosed no major changes, galectin histochemical staining profiles of tissue sections that present natural glycome complexity revealed differences between wild-type and linker-connected homo-oligomers as well as between the galectin-3-like variant and wild-type galectin-3 for cell-type positivity, level of intensity at the same site and susceptibility for inhibition by a bivalent glycocompound. These results underscore the strength of the documented approach. Moreover, they give direction to proceed to (i) extending its application to other members of this lectin family, especially galectin-3 and (ii) then analyzing impact of architectural alterations on cell surface lattice formation and ensuing biosignaling systematically, considering the variants' potential for translational medicine.
The myosin-directed chaperone UNC-45B is essential for sarcomeric organization and muscle function from Caenorhabditis elegans to humans. The pathological impact of UNC-45B in muscle disease remained ...elusive. We report ten individuals with bi-allelic variants in UNC45B who exhibit childhood-onset progressive muscle weakness. We identified a common UNC45B variant that acts as a complex hypomorph splice variant. Purified UNC-45B mutants showed changes in folding and solubility. In situ localization studies further demonstrated reduced expression of mutant UNC-45B in muscle combined with abnormal localization away from the A-band towards the Z-disk of the sarcomere. The physiological relevance of these observations was investigated in C. elegans by transgenic expression of conserved UNC-45 missense variants, which showed impaired myosin binding for one and defective muscle function for three. Together, our results demonstrate that UNC-45B impairment manifests as a chaperonopathy with progressive muscle pathology, which discovers the previously unknown conserved role of UNC-45B in myofibrillar organization.
•The dicentric chromosome assay is the gold standard for biodosimetry.•It is now possible to adapt this assay to an automated imaging cytometry method.•We examined chromosome isolation methods and ...analyzed them on an imaging cytometer.•Mono- and dicentric chromosomes can be differentiated by imaging cytometry.•A dose response curve was generated using this technology.
The dicentric chromosome assay (DCA), which involves counting the frequency of dicentric chromosomes in mitotic lymphocytes and converting it to a dose-estimation for ionizing radiation exposure, is considered to be the gold standard for radiation biodosimetry. Furthermore, for emergency response, the DCA has been adapted for triage by simplifying the scoring method 1. With the development of new technologies such as the imaging flow cytometer, it may now be possible to adapt this microscope-based method to an automated cytometry method. This technology allows the sensitivity of microscopy to be maintained while adding the increased throughput of flow cytometry. A new protocol is being developed to adapt the DCA to the imaging cytometer in order to further increase the rapid determination of a biological dose.
Peripheral blood mononuclear cells (PBMC) were isolated from ex vivo irradiated whole blood samples using a density gradient separation method and cultured with PHA and Colcemid. After 48h incubation, the chromosomes were isolated, stained for DNA content with propidium iodide (PI) and labelled with a centromere marker. Stained chromosomes were then analyzed on the ImageStream× (EMD-Millipore, Billerica, MA).
Preliminary results indicate that individual chromosomes can be identified and mono- and dicentric chromosomes can be differentiated by imaging cytometry. A dose response curve was generated using this technology. The details of the method and the dose response curve are presented and compared to traditional microscope scoring.
Imaging cytometry is a new technology which enables the rapid, automated analysis of fluorescently labelled chromosomes. Adapting the dicentric assay to this technology has the potential for high throughput analysis for mass casualty events.
Background Follicular lymphomatoid papulosis (LyP) describes a variant of LyP with perifollicular infiltrates and some degree of folliculotropism of CD30+ atypical lymphocytes. So far, only a few ...cases of follicular LyP have been described. Objective Our goal was to study the clinicopathologic features of follicular LyP in a series of 11 cases (9 male, 2 female; age range 7-78 years, mean age 50 years). Methods In all, 113 cases of LyP were reviewed to select cases showing follicular involvement. Histology was correlated with the clinical data to exclude cases of CD30+ anaplastic large-cell lymphoma or folliculotropic mycosis fungoides. Results Six cases were classified as type C and 4 as type A, whereas the remaining case manifested epidermotropism of small lymphocytes in a background of a typical type A lesion (overlapping type A/B). Perifollicular infiltrates of CD30+ atypical lymphoid cells were seen in all 11 cases, with infiltration of the follicular epithelium in 8 cases. Hyperplasia of the follicular epithelium was observed in 4 cases; ruptured hair follicles, in 3 cases; and follicular mucinosis, in 2 cases. In addition to hair follicle infiltration, atypical cells were recognized within sebaceous glands in 2 lesions. New findings were presence of numerous intrafollicular neutrophils in 2 patients, who clinically had pustules in addition to papules. Other histopathological features encountered included perieccrine infiltration (n = 5), focal subcutaneous involvement (n = 4), granulomatous inflammation (n = 3), epidermal hyperplasia (n = 2), and 1 each of infiltration of muscle bundles, numerous eosinophils in the infiltrate, and angiocentricity. Limitations This was a retrospective study. Conclusions Follicular LyP is a variant of LyP with involvement of hair follicles, mostly in the form of perifollicular infiltrate with variable degree of folliculotropism. Other changes including hyperplasia of the follicular epithelium, rupture of hair follicle, and follicular mucinosis are less common. Rarely, intrafollicular pustules can be seen in the follicular epithelium; such lesions manifest clinically as pustules.
Multiple studies have compared the performance of artificial intelligence (AI)–based models for automated skin cancer classification to human experts, thus setting the cornerstone for a successful ...translation of AI-based tools into clinicopathological practice.
The objective of the study was to systematically analyse the current state of research on reader studies involving melanoma and to assess their potential clinical relevance by evaluating three main aspects: test set characteristics (holdout/out-of-distribution data set, composition), test setting (experimental/clinical, inclusion of metadata) and representativeness of participating clinicians.
PubMed, Medline and ScienceDirect were screened for peer-reviewed studies published between 2017 and 2021 and dealing with AI-based skin cancer classification involving melanoma. The search terms skin cancer classification, deep learning, convolutional neural network (CNN), melanoma (detection), digital biomarkers, histopathology and whole slide imaging were combined. Based on the search results, only studies that considered direct comparison of AI results with clinicians and had a diagnostic classification as their main objective were included.
A total of 19 reader studies fulfilled the inclusion criteria. Of these, 11 CNN-based approaches addressed the classification of dermoscopic images; 6 concentrated on the classification of clinical images, whereas 2 dermatopathological studies utilised digitised histopathological whole slide images.
All 19 included studies demonstrated superior or at least equivalent performance of CNN-based classifiers compared with clinicians. However, almost all studies were conducted in highly artificial settings based exclusively on single images of the suspicious lesions. Moreover, test sets mainly consisted of holdout images and did not represent the full range of patient populations and melanoma subtypes encountered in clinical practice.
•We analysed studies comparing artificial intelligence (AI)–based skin cancer classifiers with clinicians.•All 19 included studies showed superior or equivalent performance of AI.•Studies were often carried out in artificial settings, with little external testing.•To enhance clinical relevance of reader studies, less artificial settings are vital.•Future comparisons should be validated with the use of external test sets.
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•Bivalency is integrated into a heterobifunctional galectin inhibitor.•Testing this lectin inhibitor on a tissue-based platform is optimized.•2-Colour fluorescence microscopy ...determines relative inhibitory capacity.•Analysis of clinical specimens opens biomedical perspectives.
Pairing glycans with tissue lectins controls multiple effector pathways in (patho)physiology. A clinically relevant example is the prodegradative activity of galectins-1 and -3 (Gal-1 and -3) in the progression of osteoarthritis (OA) via matrix metalloproteinases (MMPs), especially MMP-13. The design of heterobifunctional inhibitors that can block galectin binding and MMPs both directly and by preventing their galectin-dependent induction selectively offers a perspective to dissect the roles of lectins and proteolytic enzymes. We describe the synthesis of such a reagent with a bivalent galectin ligand connected to an MMP inhibitor and of two tetravalent glycoclusters with a subtle change in headgroup presentation for further elucidation of influence on ligand binding. Testing was performed on clinical material with mixtures of galectins as occurring in vivo, using sections of fixed tissue. Two-colour fluorescence microscopy monitored binding to the cellular glycome after optimization of experimental parameters. In the presence of the inhibitor, galectin binding to OA specimens was significantly reduced. These results open the perspective to examine the inhibitory capacity of custom-made ditopic compounds on binding of lectins in mixtures using sections of clinical material with known impact of galectins and MMPs on disease progression.
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