AlphaFind: discover structure similarity across the proteome in AlphaFold DB.

AlphaFind is a web-based search engine that provides fast structure-based retrieval in the entire set of AlphaFold DB structures. Unlike other protein processing tools, AlphaFind is focused entirely on tertiary structure, automatically extracting the main 3D features of each protein chain and using a machine learning model to find the most similar structures. This indexing approach and the 3D feature extraction method used by AlphaFind have both demonstrated remarkable scalability to large datasets as well as to large protein structures. The web application itself has been designed with a focus on clarity and ease of use. The searcher accepts any valid UniProt ID, Protein Data Bank ID or gene symbol as input, and returns a set of similar protein chains from AlphaFold DB, including various similarity metrics between the query and each of the retrieved results. In addition to the main search functionality, the application provides 3D visualizations of protein structure superpositions in order to allow researchers to instantly analyze the structural similarity of the retrieved results. The AlphaFind web application is available online for free and without any registration at https://alphafind.fi.muni.cz.

Comparison of single and double pulse laser-induced breakdown spectroscopy for the detection of biomolecules tagged with photon-upconversion nanoparticles.

BACKGROUND: Laser-induced breakdown spectroscopy (LIBS) is a well-recognized analytical technique used for elemental analysis. This method is gaining considerable attention also in biological applications thanks to its ability for spatial mapping and elemental imaging. The implementation of LIBS in the biomedical field is based on the detection of metals or other elements that either naturally occur in the samples or are present artificially. The artificial implementation of nanoparticle labels (Tag-LIBS) enables the use of LIBS as a readout technique for immunochemical assays. However, one of the biggest challenges for LIBS to meet immunoassay readout standards is its sensitivity. RESULTS: This paper focuses on the improvement of LIBS sensitivity for the readout of nanoparticle-based immunoassays. First, the LIBS setup was optimized on photon-upconversion nanoparticle (UCNP) droplets deposited on the microtiter plate wells. Two collection optics systems were compared, with single pulse (SP) and collinear double pulse (DP) LIBS arrangements. By deploying the second laser pulse, the sensitivity was improved up to 30 times. The optimized SP and DP setups were then employed for the indirect detection of human serum albumin based on immunoassay with UCNP-based labels. Compared to our previous LIBS study, the detection limit was enhanced by two orders of magnitude, from 10 ng mL-1 to 0.29 ng mL-1. In addition, two other immunochemical methods were used for reference, based on the readout of upconversion luminescence of UCNPs and absorbance measurement with enzyme labels. Finally, the selectivity of the assay was tested and the practical potential of Tag-LIBS was demonstrated by the successful analysis of urine samples. SIGNIFICANCE AND NOVELTY: In this work, we improved the sensitivity of the Tag-LIBS method by combining new labels based on UCNPs with the improved collection optics and collinear DP configuration. In the instrumental setup optimization, the DP LIBS showed better sensitivity and signal-to-noise ratio than SP. The optimizations allowed the LIBS readout to surpass the sensitivity of enzyme immunoassay, approaching the qualities of upconversion luminescence readout, which is nowadays a state-of-the-art readout technique.

The Development of Dentin Microstructure Is Controlled by the Type of Adjacent Epithelium.

Considerable amount of research has been focused on dentin mineralization, odontoblast differentiation, and their application in dental tissue engineering. However, very little is known about the differential role of functionally and spatially distinct types of dental epithelium during odontoblast development. Here we show morphological and functional differences in dentin located in the crown and roots of mouse molar and analogous parts of continuously growing incisors. Using a reporter (DSPP-cerulean/DMP1-cherry) mouse strain and mice with ectopic enamel (Spry2+/- ;Spry4-/- ), we show that the different microstructure of dentin is initiated in the very beginning of dentin matrix production and is maintained throughout the whole duration of dentin growth. This phenomenon is regulated by the different inductive role of the adjacent epithelium. Thus, based on the type of interacting epithelium, we introduce more generalized terms for two distinct types of dentins: cementum versus enamel-facing dentin. In the odontoblasts, which produce enamel-facing dentin, we identified uniquely expressed genes (Dkk1, Wisp1, and Sall1) that were either absent or downregulated in odontoblasts, which form cementum-facing dentin. This suggests the potential role of Wnt signalling on the dentin structure patterning. Finally, we show the distribution of calcium and magnesium composition in the two developmentally different types of dentins by utilizing spatial element composition analysis (LIBS). Therefore, variations in dentin inner structure and element composition are the outcome of different developmental history initiated from the very beginning of tooth development. Taken together, our results elucidate the different effects of dental epithelium, during crown and root formation on adjacent odontoblasts and the possible role of Wnt signalling which together results in formation of dentin of different quality. © 2021 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

Laser-induced breakdown spectroscopy as a straightforward bioimaging tool for plant biologists; the case study for assessment of photon-upconversion nanoparticles in Brassica oleracea L. plant.

The main purpose of this work is to thoroughly describe the implementation protocol of laser-induced breakdown spectroscopy (LIBS) method in the plant analysis. Numerous feasibility studies and recent progress in instrumentation and trends in chemical analysis make LIBS an established method in plant bioimaging. In this work, we present an easy and straightforward phytotoxicity case study with a focus on LIBS method. We intend to demonstrate in detail how to manipulate with plants after exposures and how to prepare them for analyses. Moreover, we aim to achieve 2D maps of spatial element distribution with a good resolution without any loss of sensitivity. The benefits of rapid, low-cost bioimaging are highlighted. In this study, cabbage (Brassica oleracea L.) was treated with an aqueous dispersion of photon-upconversion nanoparticles (NaYF4 doped with Yb3+ and Tm3+ coated with carboxylated silica shell) in a hydroponic short-term toxicity test. After a 72-hour plant exposure, several macroscopic toxicity end-points were monitored. The translocation of Y, Yb, and Tm across the whole plant was set by employing LIBS with a lateral resolution 100 µm. The LIBS maps of rare-earth elements in B.oleracea plant grown with 50 µg/mL nanoparticle-treated and ion-treated exposures showed the root as the main storage, while the transfer via stem into leaves was minimal. On the contrary, the LIBS maps of plants exposed to the 500 µg/mL nanoparticle-treated and ion-treated uncover slightly different trends, nanoparticles as well as ions were transferred through the stem into leaves. However, the main storage organ was a root as well.

Methodology for the Implementation of Internal Standard to Laser-Induced Breakdown Spectroscopy Analysis of Soft Tissues.

The improving performance of the laser-induced breakdown spectroscopy (LIBS) triggered its utilization in the challenging topic of soft tissue analysis. Alterations of elemental content within soft tissues are commonly assessed and provide further insights in biological research. However, the laser ablation of soft tissues is a complex issue and demands a priori optimization, which is not straightforward in respect to a typical LIBS experiment. Here, we focus on implementing an internal standard into the LIBS elemental analysis of soft tissue samples. We achieve this by extending routine methodology for optimization of soft tissues analysis with a standard spiking method. This step enables a robust optimization procedure of LIBS experimental settings. Considering the implementation of LIBS analysis to the histological routine, we avoid further alterations of the tissue structure. Therefore, we propose a unique methodology of sample preparation, analysis, and subsequent data treatment, which enables the comparison of signal response from heterogenous matrix for different LIBS parameters. Additionally, a brief step-by-step process of optimization to achieve the highest signal-to-noise ratio (SNR) is described. The quality of laser-tissue interaction is investigated on the basis of the zinc signal response, while selected experimental parameters (e.g., defocus, gate delay, laser energy, and ambient atmosphere) are systematically modified.

Influence of sample surface topography on laser ablation process.

In this work we discuss how sample surface topography can significantly influence the laser ablation (LA) process and, in turn, the analytical response of the LA Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) method. Six different surface topographies were prepared on a certified aluminium alloy sample BAM 311 and SRM NIST 610 to investigate the phenomenon. All the samples were repetitively measured by LA-ICP-MS using a spot by spot analysis. The effect of laser fluence in the range of 1-13 J/cm2 was studied. For majority of measured isotopes, the ICP-MS signal was amplified with roughening of the sample surface. A stronger effect was observed on the Al alloy sample, where the more than sixty-time enhancement was achieved in comparison to the polished surface of the sample. Since the effect of surface topography is different for each analyte, it can be stated that surface properties affect not only the ICP-MS response, but also elemental fractionation in LA. The presented results show that different surface topographies may lead to misleading data interpretation because even when applying ablation preshots, the signal of individual elements changes. The utmost care must be taken when preparing the surface for single shot analysis or chemical mapping. On the other hand, by roughening the sample surface, it is possible to significantly increase the sensitivity of the method for individual analytes and supress a matrix effect.

Could mechanical thrombectomy replace thrombolysis in the treatment of acute and subacute limb ischemia?

Acute limb ischemia is a vascular emergency defined as a sudden decrease in limb perfusion associated with a risk of loss of viability of the affected extremity. Surgical treatment (Fogarty thromboembolectomy) is indicated only in suprainguinal occlusions. Other cases of acute and subacute limb ischemia should be managed percutaneously. Catheter-based treatment involves local thrombolysis and percutaneous mechanical thrombectomy (PMT). There are several devices in use for PMT; of them, the Rotarex system appears to be the most useful. There are no randomized studies comparing thrombolysis and PMT. Only indirect comparison is possible. The immediate and long-term results of PMT using the Rotarex device are probably more favorable than those following thrombolysis. Particularly for older and polymorbid patients, it may be significant that PMT, in comparison with thrombolysis, can restore blood flow faster and in one session; no contraindications for PMT in contrast to potentially life-threatening complications in thrombolysis exist, and there is also no need for observation in intensive care unit after PMT. Hospital stay after PMT is shorter. There is only one exception when thrombolysis cannot be replaced by Rotarex PMT - in the case of crural arteries involvement - due to the catheter size. In our opinion, PMT is superior to thrombolysis in the treatment of acute and subacute limb ischemia. Thrombolysis should be considered only in special cases, e.g. in crural arteries occlusions or in failure of mechanical thrombectomy.

Feasibility of Nanoparticle-Enhanced Laser Ablation Inductively Coupled Plasma Mass Spectrometry.

Nanoparticles (NPs) applied to the surface of some solids can increase signals in inductively coupled plasma mass spectrometry (ICPMS). Drops containing 20 and/or 40 nm nanoparticles of Ag and/or Au were deposited on metallic and ceramic/glass samples, and after being dried, both the samples treated with NPs and plain targets were ablated by one pulse per spot. The laser ablation ICPMS (LA-ICPMS) signals were enhanced for metallic samples modified with NPs in comparison to signals produced at the plain, untreated surface. Maps of LA-ICPMS signals recorded for several laser fluences show that the NP-induced signal enhancement exceeds even 2 orders of magnitude for metallic samples. No enhancement was achieved for nonconductive samples. This enhancement is limited to the peripheral annular region of the dried droplet area where NPs are concentrated due to the "coffee stain" effect. Ablation crater profilometric inspection revealed a more uniform material rearrangement over the NP-treated surface compared with the ablated plain target. However, besides a smoother crater bottom, no other evidence of an NP-enhancing effect was noticed, although an increased ablation rate was anticipated. Limits of detection dropped by 1 order of magnitude for the minor elements in the presence of NPs. Observed phenomena depend only on the NP surface concentration but not on the material or size of the NPs. An electron microprobe study of the collected ablation aerosol has shown that aerosol particles consisting of target material are aggregated around the NPs. The hypothesis is that such aggregates exhibit better transport/vaporization efficiency, thus enhancing signals for metallic samples. A detailed study of the suggested mechanism will be continued in ongoing work.

Multivariate classification of echellograms: a new perspective in Laser-Induced Breakdown Spectroscopy analysis.

In this work, we proposed a new data acquisition approach that significantly improves the repetition rates of Laser-Induced Breakdown Spectroscopy (LIBS) experiments, where high-end echelle spectrometers and intensified detectors are commonly used. The moderate repetition rates of recent LIBS systems are caused by the utilization of intensified detectors and their slow full frame (i.e. echellogram) readout speeds with consequent necessity for echellogram-to-1D spectrum conversion (intensity vs. wavelength). Therefore, we investigated a new methodology where only the most effective pixels of the echellogram were selected and directly used in the LIBS experiments. Such data processing resulted in significant variable down-selection (more than four orders of magnitude). Samples of 50 sedimentary ores samples (distributed in 13 ore types) were analyzed by LIBS system and then classified by linear and non-linear Multivariate Data Analysis algorithms. The utilization of selected pixels from an echellogram yielded increased classification accuracy compared to the utilization of common 1D spectra.

Optimization of liquid jet system for laser-induced breakdown spectroscopy analysis.

A complex optimization of geometrical and temporal parameters of a jet system (developed in Laser-induced breakdown spectroscopy (LIBS) laboratory of Brno University of Technology) for direct elemental analysis of samples in a liquid state of matter using LIBS was carried out. First, the peristaltic pump was synchronized with the flashlamp of the ablation laser, which reduced variation of the ablated sample amount. Also, the fluctuation of the laser ray angle incident on the jet surface was diminished. Such synchronization reduced signal standard deviations and thus increased repeatability of the measurements. Then, laser energy and distance of the focusing lens from the sample were optimized. The gate delay time and the gate width were optimized for single pulse (SP) experiments; the gate delay time and the inter-pulse delay were optimized for the use of double pulse (DP) variant. Results were assessed according to the highest signal to noise ratios and the lowest relative standard deviations of the signal. The sensitivity of the single pulse and the double pulse LIBS for the detection of heavy metals traces, copper (Cu i at 324.754 nm) and lead (Pb i at 405.781 nm), in aqueous solution of copper (ii) sulfate and lead (ii) acetate, was estimated in terms of limits of detection (LODs). As a result, sensitivity improvement of DP LIBS system was observed, the LOD of Cu obtained with DP was calculated 40% lower than LOD gained from SP technique.

Percutaneous mechanical thrombectomy in the treatment of acute and subacute occlusions of the peripheral arteries and bypasses.

BACKGROUND: The aim of this prospective single-centre study was to analyse the immediate results, failures and complications of percutaneous mechanical thrombectomy using the Rotarex catheter in the treatment of acute and subacute occlusions of peripheral arteries and bypasses, as well as to evaluate long-term outcomes of this method. PATIENTS AND METHODS: Patients with acute (duration of symptoms < 14 days) or subacute (duration of symptoms > 14 days and < 3 months) occlusions of peripheral arteries and bypasses were selected consecutively for treatment. The cohort consisted of 113 patients, aged 18-92 years (median 72 years). In all, 128 procedures were performed. RESULTS: Angiographic success was obtained in 120 interventions (93.8%). Reasons for failures were rethrombosis of a partially recanalised segment in six procedures, and embolism into crural arteries in one intervention--percutaneous aspiration thromboembolectomy (PAT) and/or thrombolysis were ineffective in all these cases. Breakage of the Rotarex catheter happened in one procedure. Embolisation into crural arteries as a transitory complication solvable with PAT and/or thrombolysis occurred in four cases. Rethrombosis was more frequent in bypasses than in native arteries (p = 0.0069), in patients with longer occlusions (p = 0.026) and those with poorer distal runoff (p = 0.048). Embolisation happened more often in patients with a shorter duration of symptoms (p = 0.0001). Clinical success was achieved in 82.5%. Major amputation was performed in 10% of cases. Cumulative patency rates were 75% after one month, 71% after six months, 38% after 12 months, 33% after 18 months and 30% after 24, 30, 36 and 42 months. CONCLUSIONS: Rotarex thrombectomy has excellent immediate results with a low rate of failures and complications. In comparison to thrombolysis, it enables the fast and efficient treatment of acute and subacute occlusions of peripheral arteries in one session.

Algal biomass analysis by laser-based analytical techniques--a review.

Algal biomass that is represented mainly by commercially grown algal strains has recently found many potential applications in various fields of interest. Its utilization has been found advantageous in the fields of bioremediation, biofuel production and the food industry. This paper reviews recent developments in the analysis of algal biomass with the main focus on the Laser-Induced Breakdown Spectroscopy, Raman spectroscopy, and partly Laser-Ablation Inductively Coupled Plasma techniques. The advantages of the selected laser-based analytical techniques are revealed and their fields of use are discussed in detail.