<p><strong>Scientists at IOCB Prague are uncovering new details of gene transcription. They have identified a previously unknown molecular mechanism by which the transcription of genetic information from deoxyribonucleic acid (DNA) into ribonucleic acid (RNA) can be initiated. The researchers focused on a specific class of molecules known as alarmones, which are found in cells across a wide range of organisms and whose levels often increase under conditions of cellular stress. The results were published in the prestigious scientific journal </strong><i><strong>Nature Chemical Biology</strong></i><strong>.</strong></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_bc2bfffa6c.jpg" alt="IOCB Prague/Tomáš Belloň: Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription: Dr. Hana Cahová, head of the Chemical Biology of Nucleic Acids research group." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_bc2bfffa6c.jpg 234w," sizes="100vw" width="2000" height="1335"></p><div><p>Molecules of ribonucleic acid can carry a variety of chemical modifications at one end, known as caps. In eukaryotic organisms, including human cells, the best-known cap plays an important role in RNA stability and in regulating its subsequent fate. In recent years, however, it has become clear that alternative, non-canonical RNA caps also exist, although their formation and the mechanisms by which they are attached to RNA remain only partially understood. These include alarmone caps, formed by dinucleoside polyphosphate molecules, that protect cellular RNA at moments when the cell is under threat.</p><p>In their study,<strong> </strong><a target="_blank" rel="noopener noreferrer" href="https://cahova.group.uochb.cz/en"><strong>Dr. Hana Cahová</strong></a> and colleagues examined bacterial RNA polymerase and investigated how this enzyme can initiate transcription using dinucleoside polyphosphates (NpNs) instead of the standard RNA building blocks. For the first time, the scientists described, at the atomic level, how RNA bearing an alarmone cap can be generated directly at the initiation of gene transcription. They also observed that NpNs bind through a different type of base pairing than is typically observed.</p><p>The work was significantly shaped by <strong>Valentina Serianni from Hana Cahová’s team</strong>, who demonstrated the ability of dinucleoside polyphosphates to initiate gene transcription, and by <strong>Jana Škerlová</strong>, who focused on the structural analysis of RNA polymerase. Using cryogenic electron microscopy data, she showed how dinucleoside polyphosphate molecules bind within the active site of RNA polymerase – that is, the core of the enzyme where genetic information is transcribed. Together, their findings help to elucidate the processes that accompany the transcription of genetic information from DNA to RNA.</p><p>Hana Cahová adds: <i>“We’re describing something that truly occurs in cells and that we’re now able to observe directly at the level of individual molecules. This allows us to answer fundamental questions about cellular processes, such as how cells adapt to stress. RNA plays a central role in this, as it carries the cascade of information underlying any cellular response – for example, to threatening conditions caused by nutrient deprivation or temperature shock.”</i></p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_2_0fe88ff9e9.jpg" alt="IOCB Prague/Tomáš Belloň: Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription: Dr. Tomáš Kouba, head of the Cryogenic Electron Microscopy core facility." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_2_0fe88ff9e9.jpg 234w," sizes="100vw" width="2000" height="1335"></p><div><p>Cryogenic electron microscopy (cryo-EM) was central to the project. This part of the work was led by<strong> Dr. Tomáš Kouba</strong>, one of the authors of the study. <i>“Cryogenic electron microscopy allows us to freeze biological molecules in a state very close to their natural form and then determine their three-dimensional structure. This makes it possible to look directly into the active centers of enzymes and observe their function down to the atomic level,”</i> he explains.</p><p>Last year, IOCB Prague opened a new <a target="_blank" rel="noopener noreferrer" href="https://cryoem.group.uochb.cz/en"><strong>cryo-EM center</strong></a><strong> </strong>that is unique within the Czech research environment. State-of-the-art cryogenic electron microscopes are housed in a specially designed building and enable the study of biological processes with exceptional structural precision.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_3_4d881e7a58.jpg" alt="IOCB Prague: Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription: This work shows how NpnNs initiate bacterial transcription. Cryo-EM reveals how nucleobases pair with the template: one in canonical and one in reverse Watson–Crick mode, providing a structural basis for their function as non-canonical RNA caps." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_UOCHB_Vyzkum_z_UOCHB_odhaluje_dosud_nepoznany_zpusob_prepisu_geneticke_informace_3_4d881e7a58.jpg 245w," sizes="100vw" width="2000" height="1077"></p><blockquote><h4><strong>The Original article</strong></h4><h4><a target="_blank" rel="noopener noreferrer" href="https://www.nature.com/articles/s41589-025-02134-5"><strong>Molecular insight into 5′ RNA capping with Np<sub>n</sub>Ns by bacterial RNA polymerase</strong></a></h4><p>Valentina M. Serianni, Jana Škerlová, Anna Knopp Dubánková, Anton Škríba, Hana Šváchová, Tereza Vučková, Anatolij Filimoněnko, Milan Fábry, Pavlína Řezáčová, Tomáš Kouba &amp; Hana Cahova&nbsp;</p><p>Nat. Chem. Biol. 21 (2026)</p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1038/s41589-025-02134-5">https://doi.org/10.1038/s41589-025-02134-5</a></p><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6></blockquote><h4><strong>Abstract</strong></h4><p>RNA capped with dinucleoside polyphosphates has been discovered in bacteria and eukaryotes only recently. The likely mechanism of this specific capping involves direct incorporation of dinucleoside polyphosphates by RNA polymerase as noncanonical initiating nucleotides. However, how these compounds bind into the active site of RNA polymerase during transcription initiation is unknown. Here, we explored transcription initiation in vitro, using a series of DNA templates in combination with dinucleoside polyphosphates and model RNA polymerase from <i>Thermus</i> <i>thermophilus</i>. We observed that the transcription start site can vary on the basis of the compatibility of the specific template and dinucleoside polyphosphate. Cryo-electron microscopy structures of transcription initiation complexes with dinucleoside polyphosphates revealed that both nucleobase moieties can pair with the DNA template. The first encoded nucleotide pairs in a canonical Watson–Crick manner, whereas the second nucleobase pairs noncanonically in a reverse Watson–Crick manner. Our work provides a structural explanation of how dinucleoside polyphosphates initiate RNA transcription.</p></div></div>

Research from IOCB Prague reveals a previously unknown mechanism of genetic transcription

<p><strong>In the week from February 9, the following webinars await you in the field of atomic and molecular spectroscopy and spectrometry</strong></p><blockquote><h4><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinars"><strong>👉 DETAILS AND REGISTRATION IN THE WEBINARS SECTION</strong></a></h4><p><strong>👉 Search and filter in the largest global database</strong> with over <strong>5 000 GC, LC, MS and spectroscopy webinars</strong>.</p></blockquote><h5><strong>1. Thermo Fisher Scientific: Process Raman – A Reliable and Versatile Tool for Downstream Process Monitoring and Control for mAb Production</strong></h5><ul><li>Tu, 10.2.2026 16:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5808">Registration</a></li></ul><p>The presentation highlights how process Raman spectroscopy offers several advantages over traditional in-line UV-Vis analysis for process monitoring and metabolite production control.</p><h5><strong>2. Bruker: Meet Compact-Q DEER Spectrometer – Your Gateway to Quantum Innovation</strong></h5><ul><li>Tu, 10.2.2026 17:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5757">Registration</a></li></ul><p>Discover how the Compact-Q DEER spectrometer enables high-fidelity qubit characterization and control, combining advanced microwave architecture, AWGs, and cryogen-free operation.</p><h5><strong>3. Agilent Technologies: Novel Advancements in Trace Level Determination and Long-Term Stability of Metals in TMAH and UPW Matrices</strong></h5><ul><li>Tu, 10.2.2026 21:30 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/3733">Registration</a></li></ul><p>Explore novel approaches for trace-level metal determination and long-term stability assessment in TMAH and ultrapure water matrices.</p><h5><strong>4. AZoM: From First to Best – Introducing the Litesizer DIF Series</strong></h5><ul><li>We, 11.2.2026 15:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5765">Registration</a></li></ul><p>Join this live webinar introducing the new Litesizer DIF series of laser diffraction particle size analyzers.</p><h5><strong>5. Anton Paar: Polymer Rheology – Rotational and Transient Measurements on a Polymer Melt</strong></h5><ul><li>We, 11.2.2026 18:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5786">Registration</a></li></ul><p>Learn how rotational and transient viscosity measurements on rotational rheometers reveal polymer melt flow behavior, from method setup and accessories to data interpretation.</p><h5><strong>6. Milestone: Practical Guidance to Improve the Journey from Sample to Heavy Metals Analysis for Environmental Labs</strong></h5><ul><li>Th, 12.2.2026 16:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/5803">Registration</a></li></ul><p>Improve heavy metals analysis in environmental laboratories with practical tips on reagents, filtration, cleaning, and workflow optimization to enhance data quality and efficiency.</p><h5><strong>7. Agilent Technologies: Moving from R&amp;D and Limited QC on a UV-Vis-NIR Instrument to Large-Scale QC Using an Autosampler</strong></h5><ul><li>Th, 12.2.2026 20:00 CET</li><li><a target="_blank" rel="noopener noreferrer" href="https://icpms.labrulez.com/webinar/2104">Registration</a></li></ul><p>This presentation covers key aspects of adding and using an autosampler to maximize UV-Vis-NIR QC workflows when scaling from R&amp;D to routine quality control.</p>

Webinars LabRulezICPMS Week 07/2026

<p><strong>LA-ICP-MS imaging, particularly in TOF mode, provides rapid, high-resolution elemental maps of complex geological materials, but quantitative accuracy is often limited by heterogeneous mineralogy. This study introduces a workflow using UMAP for unsupervised dimensionality reduction combined with k-means clustering to segment mineral phases directly from per-pixel elemental data.</strong></p><p>Cluster compositions are matched to known minerals based on stoichiometry, allowing phase-specific normalization and reducing quantification errors by up to 60%. Validated on dawsonite-bearing sandstones, the approach enables consistent phase-resolved geochemical comparisons across depth profiles and establishes UMAP as a practical tool for accurate, interpretable multielement imaging.</p><blockquote><h4><strong>The original article</strong></h4><h4><a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05398"><strong>Mineral Phase-Resolved Quantification in LA-ICP-MS Imaging</strong></a></h4><p>Barbara Umfahrer, Jakub Buday, Pavel Pořízka, Jozef Kaiser, Paolo S. Garofalo*, and Detlef Günther*</p><p>Anal. Chem. 2026, 98, 1, 581–589</p><p><a target="_blank" rel="noopener noreferrer" href="https://doi.org/10.1021/acs.analchem.5c05398">https://doi.org/10.1021/acs.analchem.5c05398</a></p><h6>licensed under <a target="_blank" rel="noopener noreferrer" href="https://creativecommons.org/licenses/by/4.0/"><strong>CC-BY 4.0</strong></a></h6></blockquote><p><strong>Selected sections from the article follow. Formats and hyperlinks were adapted from the original.</strong></p><p>Since its introduction in 1985, <a href="javascript:void(0);">(1)</a> Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) has matured into a routine technique for both qualitative and quantitative elemental analysis, finding use in diverse fields such as geology, <a href="javascript:void(0);">(2−4)</a> biology, <a href="javascript:void(0);">(5,6)</a> materials science, <a href="javascript:void(0);">(7)</a> and cultural heritage. <a href="javascript:void(0);">(8,9)</a> Especially in comparison to liquid analysis techniques, the method excels through minimal sample preparation, negligible sample destruction, and low limits of detection, which enable trace element analysis. However, besides the availability of standard reference materials, a longstanding challenge of quantitative LA-ICP-MS is the need for a suitable internal standard to account for variations in ablation rate and transport efficiency, as well as instrumental drift. <a href="javascript:void(0);">(10)</a> Developed for applications in geological matrices, this requirement was elegantly circumvented by Liu et al. <a href="javascript:void(0);">(11)</a> through 100 wt % normalization, which assumes that all detected elements form oxides summing up to 100 wt %. This approach was conceptually inspired by the summed-spectrum normalization calibration procedure introduced by Leach and Hieftje in 2000, which emphasized the use of total signal intensities for robust internal standardization. <a href="javascript:void(0);">(12)</a> The 100 wt % normalization strategy was subsequently extended to the bulk analysis of carbonates. <a href="javascript:void(0);">(13)</a></p><p>Concurrently, the advent of time-of-flight (TOF) mass analyzers and the development of fast-washout laser ablation cells <a href="javascript:void(0);">(14−16)</a> have transformed LA-ICP-MS into a powerful imaging tool, capable of generating spatial maps across a variety of sample matrices at high data acquisition rates. <a href="javascript:void(0);">(17−19)</a> Furthermore, in comparison to, e.g., X-ray fluorescence spectroscopy (XRF) or Scanning Electron Microscopy with Energy-Dispersive X-ray Spectroscopy (SEM-EDS), LA-ICP-MS offers a high depth resolution of approximately 0.2 μm on glass, enabling precise measurement of fine-scale structures not only laterally but also in depth. <a href="javascript:void(0);">(18)</a> However, as the volume and complexity of these elemental images have grown according to the progressive advancement of the method itself, now consisting of gigabytes of data produced within minutes, manual data interpretation has become increasingly impractical. To uncover meaningful details and patterns, researchers have applied multivariate methods such as Principal Component Analysis (PCA) and k-means clustering to reduce dimensionality and delineate distinct regions within the images. <a href="javascript:void(0);">(20−23)</a> The nonlinear dimensionality reduction technique Uniform Manifold Approximation and Projection (UMAP), <a href="javascript:void(0);">(24)</a> which supports data interpretation with its capability to capture and separate subtle local structures, has first been employed to LA-ICP-MS bulk analysis data in 2024, where it was used to classify pyrite samples and discriminate between Pb and Zn deposit types. <a href="javascript:void(0);">(25,26)</a> In combination with elemental imaging, UMAP has recently been applied to biological tissue data sets as an exploratory analysis tool, <a href="javascript:void(0);">(27)</a> further enhancing the ability to visualize and interpret complex elemental distributions.</p><p>Despite these advances, no existing approach combines the unsupervised segmentation of mineral phases by UMAP with phase-specific normalization. In this study, we introduce a UMAP-driven workflow that (1) automatically segments distinct mineralogical phases within fine-grained geological matrices and (2) applies phase-specific 100 wt % normalization (e.g., oxide <a href="javascript:void(0);">(11)</a> or carbonate <a href="javascript:void(0);">(13)</a>), thereby improving quantification accuracy and enabling phase-specific quantitative interpretation of mineral distributions in complex matrices.</p><h4><strong>Materials and Methods</strong></h4><h5><strong>LA-ICP-TOFMS Imaging</strong></h5><p>LA-ICP-TOFMS analyses were performed using a 193 nm ArF excimer laser (GeoLas C, Lambda Physik, Göttingen, Germany) coupled to an ICP-TOFMS instrument (icpTOF 2R, TOFWERK AG, Thun, Switzerland). Ablation was conducted in the modified parallel flow ablation cell (MPFAC) <a href="javascript:void(0);">(16,34)</a> under a He atmosphere (99.999%, Linde Gas Schweiz AG, Dagmersellen, Switzerland) with Ar (99.996%, Linde Gas Schweiz AG) used as the carrier gas. A piezoelectrically driven xyz translational stage (1 nm resolution, SmarAct GmbH, Oldenburg, Germany) enabled precise sample positioning. Laser, stage movement, and ICP-TOFMS data acquisition were synchronized using a custom-built imaging control system. <a href="javascript:void(0);">(19)</a> The system was optimized each day based on maximum sensitivity while ensuring a <sup>238</sup>U<sup>+</sup>/<sup>232</sup>Th<sup>+</sup> intensity ratio of 1.0 to 1.1 on NIST SRM 610 and a <sup>232</sup>Th<sup>16</sup>O<sup>+</sup>/<sup>232</sup>Th<sup>+</sup> rate of below 0.5%.</p><h5><strong>LIBS Imaging</strong></h5><p>The LIBS analyses were performed on a Firefly system (Lightigo, Czech Republic). The laser (1064 nm, 5 mJ, pulse duration ∼10 ns, diameter 6 mm, operating at 50 Hz) was focused on the sample with a singlet lens (focal length 50 mm) to a 30 μm spot. The spatial resolution of the acquired elemental maps, with a size of about 16 mm × 26 mm, was 20 μm. Plasma radiation is collected by a multifiber configuration with a collimator and an optical fiber (400 μm core diameter), which delivered the light to several Czerny–Turner spectrometers (resolution 0.25–0.4 nm). The spectral range of the spectrometers is 180–850 nm. The radiation is collected 1.5 μs after ablation, with a gate width of 15 μs.</p><p>Data processing was done with Python 3.11.8 in the Spyder environment and included background correction and per-pixel z-score normalization.</p><h4><strong>Results and Discussion</strong></h4><h5><strong>LIBS and XRD Measurements</strong></h5><p>To assess whether carbonate-based normalization <a href="javascript:void(0);">(13)</a> is warranted, first, large-scale LIBS elemental intensity maps of the samples across about a third of the thin sections were acquired. <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05398#fig1">Figure 1</a> reveals the results for “Layer 2” of the Poggio del Gatto sandstone for selected elements. A complete mapping of all four thin sections can be found in <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5c05398/suppl_file/ac5c05398_si_001.pdf">Figures S3 and S6</a> in the Supporting Information. The maps reveal that C is strongly enriched in fracture veins as well as in finer-grained domains within the matrix and correlates with Ca, indicating carbonate minerals rather than oxides. Bulk XRD analysis identifies calcite alongside quartz, plagioclase, white mica, and kaolinite. These complementary observations confirm calcite as a major phase and thus justify the need for performing the 100 wt % normalization on a carbonate basis for pixels representing calcite.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Anal_Chem_2026_98_1_581_589_Figure_1_LIBS_elemental_intensity_maps_of_the_data_set_from_Layer_2_of_the_Poggio_del_Gatto_sandstone_mounted_on_a_microscope_slide_73ada1b7b8.jpg" alt="Anal. Chem. 2026, 98, 1, 581–589: Figure 1. LIBS elemental intensity maps of the data set from “Layer 2” of the Poggio del Gatto sandstone mounted on a microscope slide, depicting calcite veins and fine-grained structures within the matrix, underlining the need for carbonate-based normalization for specific pixels. Emission lines for evaluation are shown in the corresponding subfigure title. The epoxy used to fix the thin section on the slide is visible along the margin." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Anal_Chem_2026_98_1_581_589_Figure_1_LIBS_elemental_intensity_maps_of_the_data_set_from_Layer_2_of_the_Poggio_del_Gatto_sandstone_mounted_on_a_microscope_slide_73ada1b7b8.jpg 245w," sizes="100vw" width="2088" height="414"></p><h5><strong>Renormalization Based on Carbonates</strong></h5><p>Applying an oxide-based normalization to carbonate samples will introduce composition-dependent biases that cannot immediately be generalized as a singular numerical value. The difference between the molecular masses of carbonate CO<sub>3</sub><sup>2–</sup> and its oxide equivalent O<sup>2–</sup> yields an intrinsic bias on the order of a factor of about two, depending on the stoichiometry. Once this data is renormalized to a total of 100 wt %, the magnitude of the error becomes highly dependent on the specific elemental composition of the sample. An exemplary calculation illustrating this effect for a representative calcite pixel is provided in <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/suppl/10.1021/acs.analchem.5c05398/suppl_file/ac5c05398_si_001.pdf">Table S2</a>, yielding a relative error of 79%. In practice, this error varies across the image according to the local phase composition. <a target="_blank" rel="noopener noreferrer" href="https://pubs.acs.org/doi/10.1021/acs.analchem.5c05398#fig6">Figure 6</a> illustrates the impact of normalization approaches for layer 2 of the samples as well as the spatial distribution of the resulting relative error. The figure presents Ca and Si elemental maps in two rows, while the first three columns compare different normalization strategies: normalization based on all oxides, normalization based on all carbonates, and a pixel-wise normalization guided by mineral phase identification, as outlined in the workflow proposed in this study. The final column displays the relative error between the bulk oxide- or carbonate-based normalization and the pixel-wise, phase-informed normalization.</p><p><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/Anal_Chem_2026_98_1_581_589_Figure_6_Comparison_of_normalization_strategies_for_Ca_and_Si_LA_ICP_TOFMS_elemental_maps_in_Layer_2_ce3a0c1a5c.jpg" alt="Anal. Chem. 2026, 98, 1, 581–589: Figure 6. Comparison of normalization strategies for Ca and Si LA-ICP-TOFMS elemental maps in “Layer 2” of the Poggio del Gatto sandstone. Rows show Ca (top) and Si (bottom); columns compare (1) oxide-based normalization, (2) carbonate-based normalization, (3) pixel-wise, phase-informed normalization (this study), and (4) relative error between the first two and the phase-informed approach." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_Anal_Chem_2026_98_1_581_589_Figure_6_Comparison_of_normalization_strategies_for_Ca_and_Si_LA_ICP_TOFMS_elemental_maps_in_Layer_2_ce3a0c1a5c.jpg 202w," sizes="100vw" width="2088" height="1622"></p><p>For Ca (in this matrix primarily associated with calcite, a dominant carbonate phase in our samples), the relative error depicted quantifies the effect of applying oxide-based normalization across the entire image. This results in a systematic overestimation of the Ca concentration by approximately 60%. Conversely, for Si─in this matrix found mainly in quartz and various plagioclase phases─the error is shown for applying carbonate-based normalization across an oxidic matrix. In such cases, the Si concentrations are underestimated by roughly 10% to 40%, depending on the mineral phase.</p><p>These findings highlight that using a single normalization scheme across heterogeneous samples introduces substantial quantification errors. To mitigate this, the pixel-wise phase segmentation enabled by the proposed UMAP-based workflow offers a significant advantage, especially in fine-grained matrices. In short, phase-aware, pixel-wise normalization combines the strengths of both normalization approaches and proves to be highly beneficial.</p><h4><strong>Conclusion</strong></h4><p>This study demonstrates that phase-specific normalization, guided by unsupervised phase segmentation of LA-ICP-MS images, can substantially improve the accuracy of elemental quantification in fine-grained geological matrices. Rather than relying on a single global assumption (e.g., all oxides or all carbonates), the workflow adapts normalization to the actual mineralogy, minimizing systematic errors and enabling phase-resolved geochemical interpretation.</p><p>The segmentation step, based on UMAP embedding and <i>k</i>-means clustering, is fully unsupervised. However, the subsequent matching of clusters to specific minerals still relies on a limited set of preidentified stoichiometries and is therefore not yet fully unsupervised. Expansion to larger stoichiometric databases could help overcome this limitation and move toward automated mineral classification. A key challenge remains the similarity of cation ratios in certain mineral groups, which may still require complementary data to ensure robust assignments.</p><p>Overall, beyond the specific case of the Poggio del Gatto sandstone presented in this study, this work provides a framework for quantitative elemental imaging of complex geological samples and is readily transferable to other contexts that require spatially resolved composition-aware normalization. This contribution adds a practical implementation to a growing literature that already uses multivariate statistics to unlock the immense information depth of LA-ICP-TOFMS.</p>

Mineral Phase-Resolved Quantification in LA-ICP-MS Imaging

Article

Webinars

Scientific article

Science and research

Video

The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB Prague) is a leading scientific institution in the Czech Republic, recognized internationally. Its primary mission is basic research in the fields of chemical biology and medicinal chemistry, organic and material oriented chemistry, chemistry of natural compounds, biochemistry and molecular biology, physical chemistry, theoretical chemistry, and analytical chemistry. 

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences

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Agilent Technologies

<p><strong>Two years have passed since we hosted our first microplastics symposium.</strong></p>
<p>Since then, the microplastic landscape has witnessed significant developments—the impending release of the first ISO standard and ongoing advancements in SOPs. We are pleased that we can bring you together with experts in our field.</p>
<p>This digital conference aims to explore various crucial topics related to the analysis of microplastics, covering areas such as sampling, sample preparation, analysis, and evaluation.</p>
<h3><strong>Highlights – Why you should attend</strong></h3>
<h5><strong>Stay updated on microplastic analysis</strong></h5>
<p>Gain insight into the latest advancements and challenges in microplastic analysis. This seminar covers essential aspects such as sampling, sample preparation, and analysis techniques like spectroscopy (ICP-MS) and chromatography (pyr/TED-GC/MS). </p>
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<p>Discover the wide range of applications beyond microplastic analysis that can be addressed with a QCL-based IR imaging system like the LDIR 8700. Get an overview of its potential in areas such as materials, bio, and pharmaceuticals.</p>
<h5><strong>Take part in a live demo</strong></h5>
<p>Witness a live demonstration of an automatic microplastic analysis workflow. Experience firsthand how these techniques and technologies come together to address real-world challenges. Engage with Agilent experts who will answer any questions you may have.</p>
<h5><strong>Showcase your expertise</strong></h5>
<p>Actively participate by presenting your work and contributions in techniques like TED-GC/MS, pyr-GC/MS, and ICP-MS, which are crucial for microplastic analysis. Alternatively, highlight your knowledge of the versatile LDIR 8700 system, showcasing its applications in pharmaceuticals, material analysis, or bio sectors.</p>
<h3><strong>Agenda</strong></h3>
<h5><strong>09:00 Welcome Introduction &amp; Video of Geoff Winkett , Agilent Technologies</strong></h5>
<h5><strong>9:10 The World of Microplastics Up to Date an Overview</strong></h5>
<ul>
<li>Andreas Kerstan (Agilent Technologies)</li>
</ul>
<h5><strong>09:30 Hot news on Agilent LDIR, new developments, and future perspective</strong></h5>
<ul>
<li>Wesam Alwan , Darren Robey (Agilent Technologies)</li>
</ul>
<h5><strong>09:50 Release of Plastic Additives and Microplastic Particles from Different Consumer Products into Water under Accelerated UV Weathering Conditions</strong></h5>
<ul>
<li>Lars Hildebrandt (Scientist, Helmholtz Zentrum Hereon)</li>
</ul>
<p>Photodegradation of plastic products is known to accelerate weathering and the resulting release of chemical additives and particles to the environment, however these processes are complex. Here, eight different plastic consumer products were leached in double distilled water under exposure to strong ultraviolet (UV) light for ten days, and the chemical composition of the leachates was compared to their respective dark controls. The leachates and plastic particles were investigated with a wide battery of chemical analytical tools to broadly characterize the underlying processes and possible hazards. These covered (a) metal(loid) analysis, (b) microplastic analysis, (c) analysis of &gt;70 organic target analytes and (d) nontargeted screening of the extracts.</p>
<h5><strong>10:10 Identification of Polymers Using Machine Learning</strong></h5>
<ul>
<li>Xin Tian (Scientific Researcher, KWR NL)</li>
</ul>
<p>Microplastics and other polymers are found in the environment. For this reason, it is important to have reliable methods to identify them. Methods used to detect nano- and microplastics in the environment include Fourier-transform infrared (FTIR) spectroscopy, Raman spectroscopy, laser-directed infrared (LDIR) spectroscopy and thermogravimetric analysis (TGA)/pyrolysis. These measurement techniques can provide a lot of information, but sometimes require a database with a lot of high-quality data to compare measurement results. Machine learning (especially classification models) can help improve data processing and accuracy.</p>
<p>Recent research has looked at how machine learning can help improve the accuracy of identification with infrared spectroscopy. Different computer models were tested and examined to see if the accuracy increases and if it does not require an unreasonable amount of computing power and time. This research focused on finding an effective method for identifying polymers in the environment based on their mid-infrared spectroscopic signals.</p>
<p>Polymers are identified by infrared spectroscopy by comparing their spectra with spectra in a database/library. This works well for new polymers, which are clean and barely degraded. Since polymers from the environment are actually degraded, comparing their infrared spectra with spectra in the library is difficult. This is because the spectra in the library often have large deviations from the spectra of the measured polymers. Increasing the number of spectra in the library is not possible because the number of spectra of environmentally degraded polymers is almost infinite. The study therefore looked at whether the problem of small data sets can be addressed using machine learning. The research presents a data enrichment technique to generate spectra of degraded polymers from single spectra of a limited number of samples. Four models were tested using these spectra to identify polymers. The study shows that all the models achieve high success rates, thereby facilitating the identification of polymers from environmental samples. Moreover, the research shows that it is not necessarily the most advanced computer model (particularly deep neural network models) that yields the best results.</p>
<h5><strong>10:30 From the River to the Sea: Microplastics in Sediments of the Thames River</strong></h5>
<ul>
<li>Friederike Strock (Postdoc, German Federal Institute of Hydrology)</li>
</ul>
<p>Microplastics have been investigated for over 45 years especially in the marine environment, but only in the past years research has started to focus on freshwater environments. In the frame of the H2020 LABPLAS project, sediments along the course of the Thames river in its freshwater and estuarune part were studied in order to better understand the sources, transport, distribution and impacts of plastic pollution and to detect the amount of plastics transport via the rivers into the sea.</p>
<p>In the frame of the project, a winter and a summer campaign were conducted 2022 and samples taken from 6 sites within the study area. Sediment samples were taken with a Van Veen grabber from the edge of the river, wet sieved into different compartments (10 100 µm, 100 1000 µm, &gt;1000 µm), density separated and the organic matter digested. The plastics from the sediments were characterized with a Laser Direct Infrared (LDIR). The preliminary results reveal that microplastics are present in all samples. The amount of particles varies significantly between the sampling sites showing the importance of industrial emissions and cities.</p>
<h5><strong>10:50 Good Laboratory Practices to Characterize Microplastics Using Quantum-Cascade Laser Reflectance Absorbance Spectrometry</strong></h5>
<ul>
<li>Jose Manuel Andrade Garda (Professor Analytical Chemistry, University of A Corunna)</li>
</ul>
<p>The nowadays broad societal interest in microplastic pollution demands urgent responses and actions. For these be possible politicians must set rules which, in turn, are not possible at all without sound scientific data. Unfortunately, there is a general feeling that the experimental results obtained so far are not still fully comparable and, further, that the monitoring field where hundreds or samples are taken is not being fully considered. Scientific studies and future regulations depend critically on a reliable identification of the polymers (if any) that constitute the suspicious particles under study. Out of the various analytical techniques to characterize them a novel one based on reflectance-absorbance spectrometry, commercialized as LDIR, outstands. It uses a tuneablemid-IR quantum cascade laser (QCL) to imaging a reflective microscopy slide or a metal-coated filter in a remarkable small timeframe. This communication is meant to present best practice guides to overcome some obstacles/difficulties in routine measurements, and open a path for field monitoring; among them: the adequacy of the spectral range, the variation of the peak&#39;s intensities with the size of the particles; the speed of the analysis as a function of the instrumental setup; the criterion to identify unknown spectra (a tiered approach is finally suggested); and how to differentiate fibers and fragments semiautomatically. Also, an empirical dependence of the depth of penetration of the QCL laser in common plastic particles is approached first time.</p>
<h5><strong>11:10 Chemical Characterization of Microplastics using Pyrolysis-Gas Chromatography-Mass Spectrometry (Py-GC-MS)</strong></h5>
<ul>
<li>Soledad Muniategui-Lorenzo (Pull Professor of Analytical Chemistry, University of A Corunna)</li>
</ul>
<p>The implementation of monitoring programs for Microplastics requires reliable and standardisedmethods. Fourier Transform Infrared (FTIR) and Raman spectroscopy techniques are the most commonly used for Microplastics analysis. However, thermal analytical techniques are currently gaining popularity. This presentation focuses on the potential of mass-based thermal analytical techniques, in particular, Pyrolysis coupled with Gas Chromatography-Mass Spectrometry (Py-GC-MS), for the accurate qualitative and quantitative analysis of microplastics in environmental matrices. It outlines some advantages and good laboratory practices of this approach, the importance of method normalisation, and how it can provide detailed information on polymers and plastic additives.</p>
<h5><strong>11:20 Analysis of Fibrous Microplastics Using Laser Direct Infrared Imaging</strong></h5>
<ul>
<li>Monique Greiner (Research Associate, Hohenstein Laboratories)</li>
</ul>
<p>In the research field of microplastics the identification of their source is important in order to develop strategies to minimize the pollution. A major percentage of microplastics originates from textiles. One pathway into the environment are washing procedures because the textiles release fibers during the process. Therefore our aim was to find a fast and easy way to identify fibers. In our presentation we want to give insights in our approach to the analysis of fibrous microplastics with the LDIR 8700. We will talk about our strategies, the results we achieved and difficulties we faced.</p>
<h5><strong>11:40 Looking beyond the Polymer: Using Thermal Desorption GC MS to expand our understanding of Microplastics</strong></h5>
<ul>
<li>Jan Peter Mayser (Market Specialist, Markes International)</li>
</ul>
<p>Detecting and analysingmicroplastics in the environment is challenging. The method must be able to detect and distinguish between a large variety of polymers. Additives, such as hardeners, flame retardants and preservatives, used during the manufacturing process and other compounds, that can adhere to the surfaces of microplastics from their environment, can affect their toxicity assessment. These additives could be used to link the microplastics found in the environment to their original use or potentially even back to the manufacturer.</p>
<p>In this study, various salts were sampled and filtered and analyzed for their microplastic content. TD–GC–MS was used to identify and measure which concentration of the plastic PS, PET, PVC and Nylon 6 had been incorporated into the crystalline structure of the salt during evaporation. By using direct desorption and backflushing technology, a large sample size could be easily isolated from the lab environment during analysis while ensuring a large range of volatile organic compounds (VOCs) including the marker compounds for four polymers could be trapped and analyzed.</p>
<p>The VOC-profile of the microplastics not only gave information about the polymer and its concentration within the sample, but further information about the toxicity could be extracted. This enabled the determination and tentative identification of additional compounds in the samples, such as dimethyl ether, acrolein and cyclopentane. These are used in the process of manufacturing plastics, so could assist with identifying the source of the plastics. For the four analysed polymers distinct marker compounds could be identified and calibration curves determined for each polymer. In all of the real-world salt samples microplastics were identified, highlighting the ubiquitous nature of the microplastic contamination.</p>
<p>This further information about the origin of the polymer, as well as the origin of the microplastic particles can be gathered by investigating the full VOC-profile obtained by TD-GC-MS. This allows both additional polymer information and particle source characterization.</p>
<h5><strong>12:00 Tiny Problems</strong></h5>
<ul>
<li>Roxana Sühring (Assistant Professor in Analytical Environmental Chemistry, Toronto Metropolitan University)</li>
</ul>
<p>Microplastics have been on the front page of newspapers, a dominant topic for environmental research (and funding), and a recent focus for regulatory action across the globe. Their potential impacts have been classed as a planetary boundary threat and new studies are published daily, reporting microplastics virtually anywhere on the planet. But despite numerous publications, there are still a lot of open questions on how to effectively and reproducibly characterize microplastics. How can microplastic characterization be automized? What is the impact of additives or weathering on the characterization accuracy?</p>
<p>In this presentation I will provide an overview and the first results of a research collaboration between Agilent technologies and the Emerging contaminants lab at Toronto Metropolitan University that works on addressing some of these questions. Our research aims to create a versatile microplastic library using weathered and new plastics commonly found in the environment. This library will additionally be used as a training set for developing automated particle characterization for the LDIR.</p>
<h5><strong>12:20 Identification of Microplastic Particles in Soil Using LDIR</strong></h5>
<ul>
<li>Martine Graf, PhD (Student &amp; Senior Technician, Bangor University)</li>
</ul>
<p>The use of agricultural plastic has become increasingly concerning in an environmental setting in recent years; in Europe alone, an estimated 2.5 million tones of plastic mulch films are used each year. The use of mulch films for crop production has been promoted by governments worldwide due to its many benefits, however the removal of these films from the soil can be difficult due to their poor mechanical strength and fragmentation, and barriers such as poor incentives for farmers and underdeveloped infrastructure for collection and disposal. The latter often leading to the films being discarded or incinerated along field margins, or ploughed back into the fields, leading to an accumulation of plastic legacy in soil. To evaluate the microplastic pollution levels in agricultural soils, we are i ) conducting a global soil survey in all partner countries; ii) assessing the degradation and fragmentation of conventional and biodegradable plastic mulch films in soil, and measuring the resulting microplastic production rate; and iii) measure the degradation and movement of microplastic in soil after repeated application. Microplastics are extracted from soil using targeted methods for different polymer types, and analysed using fluorescent microscopy, FTIR spectroscopy, and LDIR spectroscopy.</p>
<h5><strong>12:40 Wrap up and open discussion</strong></h5>


Agilent Technologies: Agilent Microplastics Virtual Symposium 2023

Agilent Microplastics Virtual Symposium 2023

Explore various crucial topics related to the analysis of microplastics, covering areas such as sampling, sample preparation, analysis, and evaluation.

<p><strong>Join Us For This Innovative Oligo Virtual Event</strong></p>
<p><strong>Join some or all of the sessions over 13 &amp; 14 March.</strong></p>
<p>In recent years a renewed interest in synthetic oligonucleotides has been piqued due to their potential in biochemical research and for therapeutic applications. This popularity has meant a growing need to develop robust approaches for analysis and purification of oligos, alongside an increased understanding of this class of compounds.</p>
<p>Across 2 days this educational virtual event will share key learnings around the analysis of synthetic oligonucleotides, providing expert insights from research discovery to production QA/QC. We invite you to join along with other scientists in this important field to revisit oligo fundamentals, discover tips and tricks, ask questions to experts, and discuss recent innovations in this fast-moving environment.</p>
<h4><strong>Agenda:</strong></h4>
<h4><strong>Day 2</strong></h4>
<h5><strong>10:00 - More details to follow</strong></h5>
<h5><strong>10:45 - Oligonucleotide and Biopharmaceuticals Raw Materials Identification by Raman SORS and UV-VIS Thermal Melt Identification</strong></h5>
<ul>
<li>Paolo Scardina, Spectroscopy Product Specialist, Agilent Technologies</li>
</ul>
<h5><strong>11:30 - Analysis of Elemental Impurities in Synthetic Oligonucleotides by ICP-MS</strong></h5>
<ul>
<li>Sebastien Sannac, Atomic Spectroscopy Product Specialist, Agilent Technologies</li>
</ul>
<h5><strong>11:55 - Exploring the Applications and Innovations of Gas Chromatography-Mass Spectrometry (GC-MS) in Biopharmaceuticals</strong></h5>
<ul>
<li>Soma Dasgupta, Applications Engineer, Agilent</li>
</ul>
<h5><strong>12:20 - Oligonucleotide Purity Analysis - Oligo Pro II</strong></h5>
<ul>
<li>Leslie Friedmann, Product Manager, Agilent Technologies</li>
</ul>
<h5><strong>13:05 - End of presentations</strong></h5>


Agilent: OligoConnect: Linking Science, Innovation, and Therapeutics

OligoConnect: Linking Science, Innovation, and Therapeutics (Day 2)

Across 2 days this educational virtual event will share key learnings around the analysis of synthetic oligonucleotides.

OligoConnect: Linking Science, Innovation, and Therapeutics

<p><strong>As cosmetic formulations grow more complex and regulations tighten, ensuring product safety, compliance, and sustainability requires advanced analytical solutions. This webinar brings together expert-led sessions and real-world insights that cover three key challenges: raw material testing, nanoparticle characterization, and fragrance allergen analysis.</strong></p><ul><li><strong>New Standard XP CEN ISO/TS 19590:2024</strong> – <strong>Characterization of Nano-Objects Using Single Particle ICP-MS. Application to Cosmetics</strong>: Explore the ISO/TS 19590:2024 standard, and hear from guest speaker Mathieu Menta (UT2A) who will present its applications in cosmetics, highlighting both technical and regulatory perspectives.</li><li><strong>Raw Material Testing Through Bags &amp; Closed Containers with the Vaya Handheld Raman System:</strong> Discover how innovative spatially offset Raman spectroscopy (SORS) technology &nbsp;allows non-destructive identification &nbsp;through transparent and opaque packaging—eliminating sampling waste, improving productivity, and supporting ISO 22716 GMP compliance and sustainable practices.</li><li><strong>Analysis of Fragrance Allergens: Following European Regulation 2023/1545:</strong> Learn how Agilent’s GC/TQ workflow helps cosmetics manufacturers comply with new allergen regulations by reliably identifying and quantifying fragrance allergens—even in complex formulations—while minimizing false results.</li></ul><h5><strong>Key learning objectives:</strong></h5><ul><li>Learn how to verify raw materials directly through packaging using Raman spectroscopy to eliminate sampling and reduce waste</li><li>Apply ISO/TS 19590:2024 for accurate characterization of nanoparticles in cosmetic formulations using single-particle ICP-MS</li><li>Gain practical insights from a customer case on implementing spICP-MS for nano-object analysis under real regulatory and quality constraints</li><li>Quantify fragrance allergens in complex cosmetic matrices with high selectivity and sensitivity using GC/TQ</li><li>Enhance analytical workflows by minimizing sample handling, reducing false identifications, and improving compliance with current regulations</li></ul><h5><strong>Who should attend?</strong></h5><ul><li>QC/QA professionals in cosmetics and pharmaceuticals</li><li>Regulatory and compliance managers</li><li>Analytical scientists, chemists and lab managers</li><li>R&amp;D teams</li><li>Anyone involved in nanoparticle characterization, raw material verification, or cosmetic testing</li></ul><blockquote><p><strong>Presenter:</strong> Hansel Koelblen (Application Engineer - GC &amp; GC/MS, Agilent Technologies)</p><p>Hansel has worked with GCMS instrument for almost 10 years. He joined Agilent in 2017, first as a Field Service Engineer and now holds the position of France GC &amp; GC/MS Application Engineer.</p><p><strong>Presenter: </strong>Thibault Brule (Product Specialist – Molecular Spectroscopy, Agilent Technologies)</p><p>Thibault Brule is Molecular Spectroscopy Product Specialist. He joined Agilent Technologies on November 2024. His main role is to provide applicative and technical support to the network on UV-Vis-NIR, FTIR and Raman spectroscopies.</p><p><strong>Presenter: </strong>Yolande Abdelnour (Product Specialist - Atomic Spectroscopy, Agilent Technologies)</p><p>Yolande Abdelnour holds a Ph.D. in Chemical and Plasma Process Engineering from “Ecole Supérieure de Chimie” in Paris and “University of Paris Sorbonne”. She worked as a research engineer at “Photowatts” for 3 years and then joined Varian in 1997 as European ICP-MS product specialist. Since 2010, she occupies within Agilent Technologies the position of Product Specialist for the Atomic Spectroscopy techniques including Atomic Absorption, Microwave Plasma, Inductively Coupled Plasma coupled to Optical Emission Spectroscopy, Single Quad and Triple Quad Mass Spectrometry.</p><p><strong>Presenter: </strong>Mathieu Menta (Application Engineer, Ultra- Trace Analyses Aquitaine (UT2A) - Pau)</p><p>Mathieu Menta is Applications Engineer at UT2A since 2011. He is responsible for the physico-chemical characterization of nanomaterials and the speciation of trace elements by elemental mass spectrometry. He is also involved in project management and quality assurance. He has co-authored several scientific publications, notably on the quantification of nanoparticles in food, cometics ans pharmaceutics using spICP-MS and on the rapid and accurate determination of elemental impurities in pharmaceutical products using a combination of standard addition and isotope dilution methods</p></blockquote>

Agilent Technologies: Characterization in Cosmetics: Nano-Objects ISO 19590:2024, Raw Material & Fragrance Allergens

Characterization in Cosmetics: Nano-Objects ISO 19590:2024, Raw Material & Fragrance Allergens

Ensure safety and compliance in cosmetics with insights on raw materials, nanoparticles, and allergens. Discover cutting-edge tools like ICP-MS and Raman SORS.

ICPMS webinars focusing on ICP/MS - page 1