Robert Winkler

Center for Research and Advanced Studies of the National Polytechnic Institute | Cinvestav · LANGEBIO - Laboratorio Nacional de Genómica para la Biodiversidad

Mass spectrometry imaging (MSI) is of high and growing interest in life science research, but the investment for necessary equipment is often prohibitive for small research groups. Therefore, we developed a basic MSI system from low cost 'Plug and Play' components, which are connected to the Universal Serial Bus (USB) of a standard computer. Our op...

Low-temperature plasma (LTP) ionization represents an emerging technology in ambient mass spectrometry (AIMS). LTP enables the solvent-free direct detection of a broad range of molecules and mass spectrometry imaging (MSI). The low energy consumption and modest technical requirements of these ion sources favors their employment in mobile applicatio...

Building novel analytical systems requires various elements: Sensors, a sampling system and data evaluation software. For emerging technologies, such as ambient ionization mass spectrometry (AIMS), the assembly of a functional prototype is often more time-consuming than developing the actual probes. The modification of commercial platforms for test...

Today we have five types of timber tracking tools available. Each has its own strengths and limitations (see the Timber Tracking Tool Infogram), but together they offer a broad range of methods that can assist us in identifying the botanical as well as the geographic origin (provenance) of most kinds of timber samples, even those smaller than 1 cm³...

Living organisms constantly interact with their environment, including through the exchange of gases. Respiration and the release and uptake of volatile organic compounds (VOCs) create dynamic microenvironments in biological systems. Studying the kinetics of volatiles in biological systems requires expensive instruments, and data analysis is challe...

Metabolomics database of Mexico

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 interactiv...

Volatile organic compounds (VOCs) comprises a broad class of small molecules (up to ~300 g/mol) produced by biological and non-biological sources. VOCs play a vital role in an organism’s metabolism during its growth, defense, and reproduction. The well-known 6-pentyl-α-pyrone (6-PP) molecule is an example of a major volatile biosynthesized by Trich...

En el examen predoctoral-también conocido como 'rigurosum', 'candidatura', o PreDoc-se evalúan el conocimiento y las habilidades de un candidato para desarrollarse como un investigador independiente con el título académico de Doctor. Como el prestigio de un programa doctoral de una institución depende de la calidad de sus egresados, el examen predo...

Plant metabolites are the basis of human nutrition and have biological relevance in ecology. Farmers selected plants with favorable characteristics since prehistoric times and improved the cultivars, but without knowledge of underlying mechanisms. Understanding the genetic basis of metabolite production can facilitate the successful breeding of pla...

Mucoralean fungi from the genus Rhizopus are common inhabitants of terrestrial ecosystems, being some pathogens of animals and plants. In this study, we analyzed the symbiotic and toxinogenic potential of Rhizopus species derived from agricultural soils dedicated to the production of papaya ( Carica papaya L.) in Mexico. Four representative strains...

Background: Metabolic reconfiguration in plants is a hallmark response to insect herbivory that occurs in the attack site and systemically in undamaged tissues. Metabolomic systemic responses can occur rapidly while the herbivore is still present and may persist in newly developed tissue to counterattack future herbivore attacks. This study analyz...

Microbial volatile organic compounds may act as semiochemicals, inciting different behavioral responses in insects. Beauveria bassiana is an entomopathogenic fungus, and physiological and environmental factors are positively related to fungal virulence. In this study, we examined the volatile profiles produced by eight B. bassiana strains, isolated...

Circadian clocks are important for an individual’s fitness, and recent studies have underlined their role in the outcome of biological interactions. However, the relevance of circadian clocks in fungal-fungal interactions remains largely unexplored. We sought to characterize a functional clock in the biocontrol agent Trichoderma atroviride to asses...

Soldiers in active military service need optimal physical fitness for successfully carrying out their operations. Therefore, their health status is regularly checked by army doctors. These inspections include physical parameters such as the body-mass index (BMI), functional tests, and biochemical studies. If a medical exam reveals an individual’s e...

Hepatocarcinoma is one of the main causes of cancer-related deaths worldwide. Maize peptides have emerged a novel group of anticancer peptides to investigate. In this study, we evaluated the cytotoxic activity of α-zein hydrolysates obtained by three enzymatic treatments on HepG2 cells (T: trypsin, C: chymotrypsin, and TC: both enzymes). Their cyto...

Mass fingerprinting is a fast and straightforward approach for analyzing the chemical composition of biological materials. This chapter details how to generate mass fingerprints from diverse food sources, from the extraction of metabolites to data analysis, using different mass spectrometry (MS) methods. We cover four high-throughput ionization tec...

The localization of metabolites in plant tissues is often related to their biological function and biosynthesis. Mass spectrometry imaging (MSI) provides comprehensive information about the distribution of known and unknown compounds in tissues. In this protocol, we describe the use of laser desorption low-temperature plasma (LD-LTP) ionization MSI...

Cisplatin (CP) is an antineoplastic agent used to treat solid tumors, that has high nephrotoxicity caused by physiologic, hemodynamic, and biochemical alterations. Some studies have shown that naturally derived bioactive compounds in CP-induced nephrotoxicity reduce the side effects of this antineoplastic drug. Pitaya is an endemic fruit from Mexic...

Coffee is one of the most valued consumer products. Surprisingly, there is limited scientific knowledge about the biochemical processes during the storage of green coffee that affects its sensory quality. This review analyzes the impact of the different variables involved in the green coffee storage on quality from a chemical point of view. Further...

Ambient ionisation mass spectrometry (AIMS) enables studying biological systems in their native state and direct high-throughput analyses. The ionisation occurs in the physical conditions of the surrounding environment. Simple spray or plasma-based AIMS devices allow the desorption and ionisation of molecules from solid, liquid and gaseous samples....

Most of the plant species found in the high mountain ecosystems of the tropics is unique and exceptional, because they have developed complex adaptations to survive in extreme environmental conditions, such as high levels of UVR and low temperatures of these ecological environments. In an exploratory study carried out on some plants of this ecosyst...

Moringa oleifera is a highly versatile plant with potential use in the agro-food and biochemical industry. The goals of this study were to evaluate the effect of chemical fertilization and vermicompost on plant growth, and to analyze the metabolomic profile of M. oleifera crops cultivated over agricultural and native soils. The extracts were obtain...

The ATP-dependent chromatin remodeling factor CHD1 is essential for the assembly of variant histone H3.3 into paternal chromatin during sperm chromatin remodeling in fertilized eggs. It remains unclear, however, if CHD1 has a similar role in normal diploid cells. Using a specifically tailored quantitative mass spectrometry approach, we show that Ch...

Caracterización del metabolismo de especies terrestres y marinas de México

The Physalis genus includes species of commercial importance due to their ornamental, edible and medicinal properties. These qualities stem from their variety of biologically active compounds. We performed a metabolomic analysis of three Physalis species, i.e., P. angulata, P. grisea, and P. philadelphica, differing in domestication stage and culti...

Bromelia karatas L. is a plant species from the Americas. The presence of proteases in fruits of B. karatas has been reported but scarcely studied in detail. Proteolytic enzymes from Ananas comosus have displayed antifungal and antibacterial activity. Thus, novel proteases present in B. karatas may be useful as a source of compounds against microor...

Abstract: Transcription factors are important regulators of gene expression. They can orchestrate the activation or repression of hundreds or thousands of genes and control diverse processes in a coordinated way. This work explores the effect of a master regulator of plant development, BOLITA (BOL), in plant metabolism, with a special focus on spec...

Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differential mass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficient dis...

Motivation Machine learning algorithms excavate important variables from big data. However, deciding on the relevance of identified variables is challenging. The addition of artificial noise, ‘decoy’ variables, to raw data, ‘target’ variables, enables calculating a false-positive rate (FPR) and a biological relevance probability (BRp) for each vari...

Hemileia vastatrix is a fungus associated with coffee leaf rust, the most destructive disease of Coffea arabica. The objective of this work was to evaluate the antifungal activity of alcoholic extracts from roots of Baccharis salicina and to determine the metabolites present in these fractions. Antifungal activity was evaluated under in vitro condi...

Air, water, and soil are essential for terrestrial life, but pollution, overexploitation, and climate change jeopardize the availability of these primary resources. Thus, assuring human health and food production requires efficient strategies and technologies for environmental protection. Knowing key parameters such as soil moisture, air, and water...

3D-printing is revolutionizing the rapid prototyping in analytical chemistry. In the last years, we observed the development of 3D-printed components for ion studies, such as ion sources, ion transfer and ion mobility spectrometry (IMS) devices. Often, 3D-printed gadgets add functions to existing mass spectrometry (MS) systems. Custom adapters impr...

Machine learning algorithms excavate important variables from biological big data . However, deciding on the biological relevance of identified variables is challenging. The addition of artificial noise, ‘decoy’ variables, to raw data, ‘target’ variables, enables calculating a false-positive rate (FPR) and a biological relevance probability (BRp) f...

Comparing multiple label-free shotgun proteomics datasets requires various data processing and formatting steps, including peptide-spectrum matching, protein inference, and quantification. Finally, the compilation of results files into a format that allows for downstream analyses. ProtyQuant performs protein inference and quantification calculation...

div>Air, water, and soil are essential for terrestrial life, but pollution, overexploitation, and climate change jeopardize the availability of these primary resources. Thus, assuring human health and food production requires efficient strategies and technologies for environmental protection. Knowing key parameters such as soil moisture, air, and w...

Hybrid maize (Zea mays L.) is one of the major grains used as food for humans and animals. Besides carbohydrates and amino acids, maize contains micronutrients such as vitamins and phytochemicals with health-promoting effects. In a current maize breeding program, the phytochemical profiles of 35 maize hybrids grown in three significant agroecologie...

p>Comparing multiple label-free shotgun proteomics datasets requires various data processing and formatting steps, including peptide-spectrum matching, protein inference, and quantification. Finally, the compilation of results files into a format that allows for downstream analyses. ProtyQuant performs protein inference and quantification calculati...

Peroxidases (PODs) have many biological functions during the plant life cycle. In maize kernels, endosperm PODs have been identified as biochemical contributors to resistance against Sitophilus zeamais, but their identities have not been determined. In this study, we identified these PODs and determined whether their contributions are basal or indu...

Biofertilizer production and application for sustainable agriculture is already a reality. The methods for biofertilizers delivery in crop fields are diverse. Although foliar spray is gaining wide acceptance, little is known about the influence that the biochemical features of leaves have on the microbial colonization. Arthrobacter agilis UMCV2 is...

div>Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differential mass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficien...

Arbuscular mycorrhizal fungi (AMF) colonization, sampled at 32–50 days post-inoculation (dpi), was significantly reduced in a suppressor of prosystemin-mediated responses2 (spr2) mutant tomato plants impaired in the ω−3FATTY ACIDDESATURASE7 (FAD7) gene that limits the generation of linolenic acid and, consequently, the wound-responsive jasmonic aci...

Thin-layer chromatography (TLC) is a classic method for the separation and analysis of complex mixtures. Biological assays, chemical derivatisation and spectroscopy techniques are compatible with TLC and provide extra information about isolated compounds. However, coupling TLC to mass spectrometry is hampered by the difficulty to desorb the analyte...

Metabolomics and proteomics allow deep insights into the chemistry and physiology of biological systems. This book expounds open-source programs, platforms and programming tools for analysing metabolomics and proteomics mass spectrometry data. In contrast to commercial software, open-source software is created by the academic community, which facil...

The evaluation of metabolomics data sets involves multiples steps of data processing, statistical analysis and interpretation. XCMS is a commonly employed program for analyzing metabolomics data. It exists in two distinct variants: XCMS/R and XCMS Online. XCMS/R is a package for the statistics and graphics language R which requires manual coding, a...

The installation of software, especially open source, can be cumbersome because of the differences in the target operating systems. Thus, installation issues are a major obstacle for the distribution of novel programs. Possible workarounds for this situation include (1) the development of web-services (e.g., XCMS Online; see Chapter 8), (2) defined...

The last chapter provides a short evaluation of the state-of-the-art in processing mass spectrometry data with open-source software. The community has reached a critical mass and is using modern concepts of software design and distribution. Future advancements are expected in the analysis of multidimensional datasets, the integration of Omics data...

Genetic improvement of coffee plants represents a great challenge for breeders. Conventional breeding takes a too long time for responding timely to market demands, climatic variations and new biological threads. The correlation of genetic markers with the plant phenotype and final product quality is usually poor. Additionally, the creation and use...

Iron is an essential plant micronutrient. It is a component of numerous proteins and participates in cell redox reactions; iron deficiency results in a reduction in nutritional quality and crop yields. Volatiles from the rhizobacterium Arthrobacter agilis UMCV2 induce iron acquisition mechanisms in plants. However, it is not known whether microbial...

Mass spectrometry research laboratories reported multiple probes for ambient ionization in the last years. Combining them with a mechanical moving stage enables automated sampling and imaging applications. We developed a robotic platform, which is based on RepRap 3D-printer components, and therefore easy to reproduce and to adopt for custom prototy...

Background: different Solanaceae and Erythroxylaceae species produce tropane alkaloids. These alkaloids are the starting material in the production of different pharmaceuticals. The commercial demand for tropane alkaloids is covered by extracting them from cultivated plants. Datura stramonium is cultivated under greenhouse conditions as a source o...

Direct-injection electron spray ionization mass spectrometry (DIESI-MS) can be used to quantify the whole set of positive and negative ions in complex biological samples. A cherry tomato cultivar was grown inside a greenhouse in soil pots supplemented with different nitrogen sources. Organic cultivation increased fruit dry matter while conventional...

Interest in the plant gender Moringa oleifera has grown in recent years as it is a plant that can potentially provide a good amount of nutrients necessary for human consumption. Thus, humans could benefit from nutrient enrichment in this plant and produce foods with high protein content. Protein and metabolite content is influenced by soil type, or...

The sensorial quality of coffee can be impaired by prolonged storage. Aged coffee presents an off-note taste which is called “rested coffee flavor.” This quality reduction is accompanied by changes of the lipid profiles. Therefore, we tested the suitability of MALDI-ToF mass fingerprinting to discriminate between unrested (“fresh”) and rested Colom...

Background: Understanding of iron oxide nanoparticles (IONP) interaction with the body milieu is crucial to guarantee their efficiency and biocompatibility in nanomedicine. Polymer coating to IONP, with polyethyleneglycol (PEG) and polyvinylpyrrolidone (PVP), is an accepted strategy to prevent toxicity and excessive protein binding. Aim: The aim...

The chapter describes principles of LTP ionization sources, and the state of the art in food and ambient applications using LTP.

Abstract Mass spectrometry imaging (MSI) using laser ablation (LA) inductively coupled plasma (ICP) is an innovative and exciting methodology to perform highly sensitive elemental analyses. LA-ICP-MSI of metals, trace elements or isotopes in tissues has been applied to a range of biological samples. Several LA-ICP-MSI studies have shown that metals...

A previous study with spr2 mutant tomato plants which are negatively affected in the synthesis of jasmonic acid (JA), suggested that JA regulates the arbuscular mycorrhizal fungi (AMF) colonization via the control of carbon (C) partitioning. Although this and other studies have suggested the important positive role played by JA in the regulation of...

A previous study with spr2 mutant tomato plants which are negatively affected in the synthesis of jasmonic acid (JA), suggested that JA regulates the arbuscular mycorrhizal fungi (AMF) colonization via the control of carbon (C) partitioning. Although this and other studies have suggested the important positive role played by JA in the regulation of...

Crataegus is distributed worldwide and presents a phenotypic diversity in size, shape, color and aroma of the fruit. The objective of this study was to identify genotypes of Crataegus with a similar profile of volatile compounds by means of a metabolomic study. In addition, the content of pigment was evaluated to contribute to the agronomic, medici...

The response to injury represents an important strategy for animals and plants to survive mechanical damage and predation. Plants respond to injury by activating a defense response that includes the production of an important variety of compounds that help them withstand predator attack and recover from mechanical injury (MI). Similarly, the filame...

Genetic improvement of coffee plants represents a great challenge for breeders. Conventional breeding takes a too long time for responding timely to market demands, climatic variations and new biological threads. The correlation of genetic markers with the plant phenotype and final product quality is usually poor. Additionally, the creation and use...

Las variedades de café resistentes a plagas y enfermedades como uso alternativo para mantener su producción, deben adaptarse a las condiciones edafológicas de las regiones cultivadas, presentar un rendimiento de producción adecuado (kg/ha) y contener marcadores químicos de calidad, que impacten en el perfil aromático y sensorial en su bebida. El ob...

The goal of this research was to identify major compounds of the aerial parts of M. parvifolia (Benth.) Parra-Os., that could enhance its possible application as additive in dermocosmetic products, as well as evaluate the antioxidant properties. The extracts agreed with the broad-spectrum UVB/UVA absorption detected and could act as broad-spectrum...

Fungi, like other organisms, have natural predators, including fungivorous nematodes and arthropods that use them as an important food source. Thus, they require mechanisms to detect and respond to injury. Trichoderma atroviride responds to mycelial injury by rapidly regenerating its hyphae and developing asexual reproduction structures. Whether th...