Identification of Plant Compounds with Mass Spectrometry Imaging (MSI).

The presence and localization of plant metabolites are indicative of physiological processes, e.g., under biotic and abiotic stress conditions. Further, the chemical composition of plant parts is related to their quality as food or for medicinal applications. Mass spectrometry imaging (MSI) has become a popular analytical technique for exploring and visualizing the spatial distribution of plant molecules within a tissue. This review provides a summary of mass spectrometry methods used for mapping and identifying metabolites in plant tissues. We present the benefits and the disadvantages of both vacuum and ambient ionization methods, considering direct and indirect approaches. Finally, we discuss the current limitations in annotating and identifying molecules and perspectives for future investigations.

The Open SprayBot: A high-throughput paper spray mass spectrometry platform for disease screening.

Newborn disease screening increases survival, improves quality of life and reduces treatment costs for healthcare systems. Mass spectrometry (MS) is an effective method for metabolic screening. However, conventional analytical methods require biofluid handling and cooling conditions during transport, making the logistics difficult and expensive, especially for remote regions. 'Paper-spray' (PS) ionization generates a charged solvent spray from samples deposited on paper strips. Therefore, samples can be applied on a suitable matrix and shipped as dried spots to diagnostic laboratories with standard postal or messenger services. We built a robotic platform, the 'Open SprayBot', to automatically analyze paper-deposited samples via PS-MS and increase the sample throughput. The system is operated via RUMBA32 and Arduino Mega boards. A commercial syringe pump and power supply provide solvent application and electrical current required for PS-MS. The usability of the Open SprayBot was demonstrated by quantifying palmitoyl-l-carnitine, a common biomarker in newborn screening.

An intense 60-day weight-loss course leads to an 18 kg body weight reduction and metabolic reprogramming of soldiers with obesity.

Soldiers of the Mexican Army with obesity were subjected to an intense 60-day weight-loss course consisting of a controlled diet, daily physical training, and psychological sessions. The nutritional treatment followed the European Society of Cardiology (ESC) recommendations, incorporating elements of the traditional milpa diet in the nutritional intervention. The total energy intake was reduced by 200 kcal every 20 days, starting with 1,800 kcal and ending with 1,400 kcal daily. On average, the participants reduced their body weight by 18 kg. We employed an innovative approach to monitor the progress of the twelve soldiers who completed the entire program. We compared the untargeted metabolomics profiles of their urine samples, taken before and after the course. The data obtained through liquid chromatography and high-resolution mass spectrometry (LC-MS) provided insightful results. Classification models perfectly separated the profiles pre and post-course, indicating a significant reprogramming of the participants' metabolism. The changes were observed in the C1-, vitamin, amino acid, and energy metabolism pathways, primarily affecting the liver, biliary system, and mitochondria. This study not only demonstrates the potential of rapid weight loss and metabolic pathway modification but also introduces a non-invasive method for monitoring the metabolic state of individuals through urine mass spectrometry data.

Malignant Peripheral Nerve Sheath Tumor, a Heterogeneous, Aggressive Cancer with Diverse Biomarkers and No Targeted Standard of Care: Review of the Literature and Ongoing Investigational Agents.

BACKGROUND: Malignant peripheral sheath tumor (MPNST) is a rare, aggressive form of soft-tissue sarcoma that presents a unique set of diagnostic and treatment challenges and is associated with major unmet treatment medical needs. OBJECTIVE: The chief aim of this review is to consider the epidemiology, histology, anatomic distribution, pathologic signaling pathways, diagnosis, and management of MPNST, with a focus on potential targeted therapies. A subordinate objective was to establish benchmarks for the antitumor activity of such treatments. RESULTS: MPNST has an incidence of 1:100,000 in the general population and 1:3500 among patients with the inherited condition of neurofibromatosis-1. Spindle-cell sarcomas of neural-crest origin, MPNSTs are frequently situated in the extremities and pelvis/trunk, often at the confluence of large nerve roots and bundles. Highly copy-number aberrant and enriched in chromosome 8, MPNSTs have a complex molecular pathogenesis that likely involves the interplay of multiple signaling pathways, including Ras/AKT/mTOR/MAPK, EGFR, p53, PTEN, and PRC2, as well as factors in the tumor microenvironment. A combination of magnetic resonance imaging (MRI) and positron emission tomography with 18F-fluorodeoxyglucose (FDG-PET) enables comprehensive assessment of both morphology and metabolism, while MRI- and ultrasound-guided core needle biopsy can confirm histopathology. Although surgery with wide excisional margins is now the chief curative approach to localized disease, MPNST-specific survival has not improved in decades. For advanced and metastatic MPNST, radiation and chemotherapy (chiefly with anthracyclines plus ifosfamide) have somewhat promising but still largely uncertain treatment roles, chiefly in local control, downstaging, and palliation. No single druggable target has emerged, no objective responses have been observed with a number of targeted therapies (cumulative disease control rate in our review = 22.9-34.8%), and combinatorial approaches directed toward multiple signal transduction mechanisms are hallmarks of ongoing clinical trials. CONCLUSIONS: Despite advances in our understanding of the genetics and molecular biology of MPNST, further research is warranted to: (1) unravel the complex pathogenesis of this condition; (2) improve diagnostic yield; (3) delineate the appropriate roles of chemotherapy and radiation; and (4) develop a targeted therapy (or combination of such treatments) that is well tolerated and prolongs survival.

Nanoscale, surface-confined phase separation by electron beam induced oxidation.

Electron-assisted oxidation of Co-Si-based focused electron beam induced deposition (FEBID) materials is shown to form a 2-4 nm metal oxide surface layer on top of an electrically insulating silicon oxide layer less than 10 nm thick. Differences between thermal and electron-induced oxidation on the resulting microstructure are illustrated.

The DNA methyltransferase inhibitor decitabine blunts the response to a high-animal fat and protein diet in mice.

Increasing evidence hints that DNA hypermethylation may mediate the pathogenic response to cardiovascular risk factors. Here, we tested a corollary of that hypothesis, that is, that the DNA methyltransferase inhibitor decitabine (Dec) ameliorates the metabolic profile of mice fed a moderately high-animal fat and protein diet (HAFPD), a proxy of cardiovascular risk-associated Western-type diet. HAFPD-fed mice were exposed to Dec or vehicle for eight weeks (8W set, 4-32/group). To assess any memory of past exposure to Dec, we surveyed a second mice set treated as 8W but HAFPD-fed for further eight weeks without any Dec (16W set, 4-20/group). In 8W, Dec markedly reduced HAFPD-induced body weight gain in females, but marginally in males. Characterization of females revealed that Dec augmented skeletal muscle lipid content, while decreasing liver fat content and increasing plasma nonesterified fatty acids, adipose insulin resistance, and-although marginally-whole blood acylcarnitines, compared to HAFPD alone. Skeletal muscle mitochondrial DNA copy number was higher in 8W mice exposed to HAFPD and Dec, or in 16W mice fed HAFPD only, relative to 8W mice fed HAFPD only, but Dec induced a transcriptional profile indicative of ameliorated mitochondrial function. Memory of past Dec exposure was tissue-specific and sensitive to both duration of exposure to HAFPD and age. In conclusion, Dec redirected HAFPD-induced lipid accumulation toward the skeletal muscle, likely due to augmented mitochondrial functionality and increased lipid demand. As caveat, Dec induced adipose insulin resistance. Our findings may help identifying strategies for prevention and treatment of lipid dysmetabolism.

Volatile Semiochemicals Emitted by Beauveria bassiana Modulate Larval Feeding Behavior and Food Choice Preference in Spodoptera frugiperda (Lepidoptera: Noctuidae).

Beauveria bassiana is an entomopathogenic fungus that parasitizes and kills insects. The role of volatile organic compounds (VOCs) emitted by B. bassiana acting as semiochemicals during its interaction with lepidopterans is poorly explored. Here, we studied the effect of VOCs from B. bassiana and 3-methylbutanol (as a single compound) on the feeding behavior of L2 larvae of Spodoptera frugiperda in sorghum plants. Additionally, we assessed whether fungal VOCs induce chemical modifications in the plants that affect larval food preferences. Metabolomic profiling of plant tissues was performed by mass spectrometry and bioassays in a dual-choice olfactometer. The results showed that the larval feeding behavior was affected by the B. bassiana strain AI2, showing that the insect response is strain-specific. Furthermore, 80 µg of 3-methylbutanol affected the number of bites. The larval feeding choice was dependent on the background context. Fragment spectra and a matching precursor ion mass of 165.882 m/z enabled the putative identification of 4-coumaric acid in sorghum leaves exposed to fungal VOCs, which may be associated with larval deterrent responses. These results provide valuable insights into the bipartite interaction of B. bassiana with lepidopterans through VOC emission, with the plant as a mediator of the interaction.

Technical Note: mzML and imzML Libraries for Processing Mass Spectrometry Data with the High-Performance Programming Language Julia.

Julia combines the virtues of high-level and low-level programming languages: The code is human-readable, and the performance of the created binaries competes with machine-orientated compilers. Thus, Julia is popular in "Big Data" sciences. Reading mass spectrometry (MS) data with Julia was impossible until now due to missing libraries. Here, we present a Julia library for importing mass spectrometry (MS) data in HUPO standard mzML and imzML formats and demonstrate its function with direct and ambient ionization MS, liquid chromatography-MS, and MS imaging data on standard platforms (Windows, Linux, and Mac OS). The processing speed of Julia for reading imzML MS imaging files was up to 214 times faster than the comparable code in R. Julia can remove bottlenecks for computationally demanding tasks in large-scale MS-Omics and MS imaging data processing workflows and supports their agile development. In addition, time-critical and complex data evaluation tasks become possible, such as following the real-time monitoring of biological processes and pattern recognition in large MS imaging projects. Our mzML/imzML libraries and code examples are available under the terms of the MIT license from https://github.com/CINVESTAV-LABI/julia_mzML_imzML.

Multi-Stimuli Operando Transmission Electron Microscopy for Two-Terminal Oxide-Based Devices.

The integration of microelectromechanical systems (MEMS)-based chips for in situ transmission electron microscopy (TEM) has emerged as a highly promising technique in the study of nanoelectronic devices within their operational parameters. This innovative approach facilitates the comprehensive exploration of electrical properties resulting from the simultaneous exposure of these devices to a diverse range of stimuli. However, the control of each individual stimulus within the confined environment of an electron microscope is challenging. In this study, we present novel findings on the effect of a multi-stimuli application on the electrical performance of TEM lamella devices. To approximate the leakage current measurements of macroscale electronic devices in TEM lamellae, we have developed a postfocused ion beam (FIB) healing technique. This technique combines dedicated MEMS-based chips and in situ TEM gas cells, enabling biasing experiments under environmental conditions. Notably, our observations reveal a reoxidation process that leads to a decrease in leakage current for SrTiO3-based memristors and BaSrTiO3-based tunable capacitor devices following ion and electron bombardment in oxygen-rich environments. These findings represent a significant step toward the realization of multi-stimuli TEM experiments on metal-insulator-metal devices, offering the potential for further exploration and a deeper understanding of their intricate behavior.

Weld-free mounting of lamellae for electrical biasing operando TEM.

Recent advances in microelectromechanical systems (MEMS)-based substrates and sample holders for in situ transmission electron microscopy (TEM) are currently enabling exciting new opportunities for the nanoscale investigation of materials and devices. The ability to perform electrical testing while simultaneously capturing the wide spectrum of signals detectable in a TEM, including structural, chemical, and even electronic contrast, represents a significant milestone in the realm of nanoelectronics. In situ studies hold particular promise for the development of Metal-Insulator-Metal (MIM) devices for use in next-generation computing. However, achieving successful device operation in the TEM typically necessitates meticulous sample preparation involving focused ion beam (FIB) systems. Conducting contamination introduced during the FIB thinning process and subsequent attachment of the sample onto a MEMS-based chip remains a formidable challenge. This article delineates an improved FIB-based sample preparation methodology that results in good electrical connectivity and operational functionality across various MIM devices. To exemplify the efficacy of the sample preparation technique, we demonstrate preparation of a clean cross section extracted from a Au/Pt/BaSrTiO3/SrMoO3 tunable capacitor (varactor). The FIB-prepared TEM lamella mounted on a MEMS-based chip showed current levels in the tens of picoamperes range at 0.1 V. Furthermore, the electric response and current density of the TEM lamella device closely align with macro-scale devices. These samples exhibit comparable current densities to their macro-sized counterparts thus validating the sample preparation process and confirming device connectivity. The simultaneous operation and TEM characterization of electronic devices enabled by this process enables direct correlation between device structure and function, which could prove pivotal in the development of new MIM systems.

Backcrossing Modulates the Metabolic Profiles of Anthocyanin-Pigmented 'Vitamaize' Lines Derived from Elite Maize Lines.

Vitamaize lines (VMLs) were created by backcrossing the pigmented aleurone trait into Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) maize lines (CMLs). This study evaluates metabolic differences between the VMLs and their original CMLs. Direct infusion mass spectrometry (DIMS) analyses, carotenoid profiling, total anthocyanins content (TAC) determination, and biochemical evaluation of the quality protein maize (QPM) endosperm trait allowed a comprehensive chemical characterization of the maize lines. DIMS data indicate higher hexoses and trigonelline content for most VMLs; the carotenoid profile revealed a decrease in ß-cryptoxanthin to less than half of the original parent content for two VMLs but an augmentation for one VML. The pigmented aleurone VMLs did not inherit the complex QPM endosperm trait of the QPM CMLs. Except for anthocyanin accumulation, no other metabolites were consistently modified across all the backcross-generated maize lines with a pigmented aleurone trait. These findings suggest using genetic or metabolic markers rather than morphological or visual traits for future breeding programs.

Texture Transfer in Dielectric Layers via Nanocrystalline Networks: Insights from in Situ 4D-STEM.

Transition metal oxide dielectric layers have emerged as promising candidates for various relevant applications, such as supercapacitors or memory applications. However, the performance and reliability of these devices can critically depend on their microstructure, which can be strongly influenced by thermal processing and substrate-induced strain. To gain a more in-depth understanding of the microstructural changes, we conducted in situ transmission electron microscopy (TEM) studies of amorphous HfO2 dielectric layers grown on highly textured (111) substrates. Our results indicate that the minimum required phase transition temperature is 180 °C and that the developed crystallinity is affected by texture transfer. Using in situ TEM and 4D-STEM can provide valuable insights into the fundamental mechanisms underlying the microstructural evolution of dielectric layers and could pave the way for the development of more reliable and efficient devices for future applications.

LOX1- and PLP1-dependent transcriptional reprogramming is essential for injury-induced conidiophore development in a filamentous fungus.

IMPORTANCE: In addition to being considered a biocontrol agent, the fungus Trichoderma atroviride is a relevant model for studying mechanisms of response to injury conserved in plants and animals that opens a new landscape in relation to regeneration and cell differentiation mechanisms. Here, we reveal the co-functionality of a lipoxygenase and a patatin-like phospholipase co-expressed in response to wounding in fungi. This pair of enzymes produces oxidized lipids that can function as signaling molecules or oxidative stress signals that, in ascomycetes, induce asexual development. Furthermore, we determined that both genes participate in the regulation of the synthesis of 13-HODE and the establishment of the physiological responses necessary for the formation of reproductive aerial mycelium ultimately leading to asexual development. Our results suggest an injury-induced pathway to produce oxylipins and uncovered physiological mechanisms regulated by LOX1 and PLP1 to induce conidiation, opening new hypotheses for the novo regeneration mechanisms of filamentous fungi.

Pillar Growth by Focused Electron Beam-Induced Deposition Using a Bimetallic Precursor as Model System: High-Energy Fragmentation vs. Low-Energy Decomposition.

Electron-induced fragmentation of the HFeCo3(CO)12 precursor allows direct-write fabrication of 3D nanostructures with metallic contents of up to >95 at %. While microstructure and composition determine the physical and functional properties of focused electron beam-induced deposits, they also provide fundamental insights into the decomposition process of precursors, as elaborated in this study based on EDX and TEM. The results provide solid information suggesting that different dominant fragmentation channels are active in single-spot growth processes for pillar formation. The use of the single source precursor provides a unique insight into high- and low-energy fragmentation channels being active in the same deposit formation process.

The plant organellar primase-helicase directs template recognition and primosome assembly via its zinc finger domain.

BACKGROUND: The mechanisms and regulation for DNA replication in plant organelles are largely unknown, as few proteins involved in replisome assembly have been biochemically studied. A primase-helicase dubbed Twinkle (T7 gp4-like protein with intramitochondrial nucleoid localization) unwinds double-stranded DNA in metazoan mitochondria and plant organelles. Twinkle in plants is a bifunctional enzyme with an active primase module. This contrast with animal Twinkle in which the primase module is inactive. The organellar primase-helicase of Arabidopsis thaliana (AtTwinkle) harbors a primase module (AtPrimase) that consists of an RNA polymerase domain (RPD) and a Zn + + finger domain (ZFD). RESULTS: Herein, we investigate the mechanisms by which AtTwinkle recognizes its templating sequence and how primer synthesis and coupling to the organellar DNA polymerases occurs. Biochemical data show that the ZFD of the AtPrimase module is responsible for template recognition, and this recognition is achieved by residues N163, R166, and K168. The role of the ZFD in template recognition was also corroborated by swapping the RPDs of bacteriophage T7 primase and AtPrimase with their respective ZFDs. A chimeric primase harboring the ZFD of T7 primase and the RPD of AtPrimase synthesizes ribonucleotides from the T7 primase recognition sequence and conversely, a chimeric primase harboring the ZFD of AtPrimase and the RPD of T7 primase synthesizes ribonucleotides from the AtPrimase recognition sequence. A chimera harboring the RPDs of bacteriophage T7 and the ZBD of AtTwinkle efficiently synthesizes primers for the plant organellar DNA polymerase. CONCLUSIONS: We conclude that the ZFD is responsible for recognizing a single-stranded sequence and for primer hand-off into the organellar DNA polymerases active site. The primase activity of plant Twinkle is consistent with phylogeny-based reconstructions that concluded that Twinkle´s last eukaryotic common ancestor (LECA) was an enzyme with primase and helicase activities. In plants, the primase domain is active, whereas the primase activity was lost in metazoans. Our data supports the notion that AtTwinkle synthesizes primers at the lagging-strand of the organellar replication fork.

A Review of the Current State of Magnetic Force Microscopy to Unravel the Magnetic Properties of Nanomaterials Applied in Biological Systems and Future Directions for Quantum Technologies.

Magnetism plays a pivotal role in many biological systems. However, the intensity of the magnetic forces exerted between magnetic bodies is usually low, which demands the development of ultra-sensitivity tools for proper sensing. In this framework, magnetic force microscopy (MFM) offers excellent lateral resolution and the possibility of conducting single-molecule studies like other single-probe microscopy (SPM) techniques. This comprehensive review attempts to describe the paramount importance of magnetic forces for biological applications by highlighting MFM's main advantages but also intrinsic limitations. While the working principles are described in depth, the article also focuses on novel micro- and nanofabrication procedures for MFM tips, which enhance the magnetic response signal of tested biomaterials compared to commercial nanoprobes. This work also depicts some relevant examples where MFM can quantitatively assess the magnetic performance of nanomaterials involved in biological systems, including magnetotactic bacteria, cryptochrome flavoproteins, and magnetic nanoparticles that can interact with animal tissues. Additionally, the most promising perspectives in this field are highlighted to make the reader aware of upcoming challenges when aiming toward quantum technologies.

Myeloid leukemia vulnerabilities embedded in long noncoding RNA locus MYNRL15.

The noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While lncRNA dysregulation has been reported in myeloid malignancies, their functional relevance remains to be systematically interrogated. We performed CRISPRi screens of lncRNA signatures from normal and malignant hematopoietic cells and identified MYNRL15 as a myeloid leukemia dependency. Functional dissection suggests an RNA-independent mechanism mediated by two regulatory elements embedded in the locus. Genetic perturbation of these elements triggered a long-range chromatin interaction and downregulation of leukemia dependency genes near the gained interaction sites, as well as overall suppression of cancer dependency pathways. Thus, this study describes a new noncoding myeloid leukemia vulnerability and mechanistic concept for myeloid leukemia. Importantly, MYNRL15 perturbation caused strong and selective impairment of leukemia cells of various genetic backgrounds over normal hematopoietic stem and progenitor cells in vitro, and depletion of patient-derived xenografts in vivo.

Guided analysis of ambient ionization mass spectrometry data with the MQ_Assistant.

RATIONALE: Ambient ionization mass spectrometry (AIMS) delivers realistic data from samples in their native state. In addition, AIMS methods reduce time and costs for sample preparation and have less environmental impact. However, AIMS data are often complex and require substantial processing before interpretation. METHODS: We developed an interactive R script for guided mass spectrometry (MS) data processing. The "MQ_Assistant" is based on MALDIquant, a popular R package for MS data processing. In each step, the user can try and preview the effect of chosen parameters before deciding on the values with the best result and proceeding to the next stage. The outcome of the MQ_Assistant is a feature matrix that can be further analyzed in R and statistics tools such as MetaboAnalyst. RESULTS: Using 360 AIMS example spectra, we demonstrate the step-by-step processing for creating a feature matrix. In addition, we show how to visualize the results of three biological replicates of a plant-microbe interaction between Arabidopsis and Trichoderma as a heatmap using R and upload them to MetaboAnalyst. The final parameter set can be saved for reuse in MALDIquant workflows of similar data. CONCLUSIONS: The MQ_Assistant helps novices and experienced users to develop workflows for (AI)MS data processing. The interactive procedure supports the quick finding of appropriate settings. These parameters can be exported and reused in future projects. The stepwise operation with visual feedback also suggests the use of the MQ_Assistant in education.

Transduction of Single Nanomechanical Pillar Resonators by Scattering of Surface Acoustic Waves.

One of the challenges of nanoelectromechanical systems (NEMS) is the effective transduction of the tiny resonators. Vertical structures, such as nanomechanical pillar resonators, which are exploited in optomechanics, acoustic metamaterials, and nanomechanical sensing, are particularly challenging to transduce. Existing electromechanical transduction methods are ill-suited as they put constraints on the pillars' material and do not enable a transduction of freestanding pillars. Here, we present an electromechanical transduction method for single nanomechanical pillar resonators based on surface acoustic waves (SAWs). We demonstrate the transduction of freestanding nanomechanical platinum-carbon pillars in the first-order bending and compression mode. Since the principle of the transduction method is based on resonant scattering of a SAW by a nanomechanical resonator, our transduction method is independent of the pillar's material and not limited to pillar-shaped geometries. It represents a general method to transduce vertical mechanical resonators with nanoscale lateral dimensions.