Biological Research Research Articles

Thin microporous polydimethylsiloxane membrane prepared by phase separation and its applications for cell culture

Animal experiments are often required for biological studies. However, in vitro cell culture models, such as cell-culture inserts and microphysiological systems, can provide a suitable alternative, making them essential tools in cell biology research, including the simulation of an organ environments closely related to the human body. Cell-culture inserts with porous membranes assist in recreating in vivo cell culture environments to study and process cell-culture assays. However, conventional cell culture membranes typically made of polyethylene terephthalate or polycarbonate cannot accommodate cell types that require deformable substrates. As such, this paper introduced a novel approach using spin-casting-assisted polymer-blend phase separation to create thin, flexible, and highly porous membranes for cell culture applications. Polydimethylsiloxane (PDMS) was selected as the material for the porous membrane, and polystyrene (PS) was used as a counter pair to induce phase separation with PDMS. PDMS facilitated the necessary reversible deformations during cell culture owing to its low elastic modulus. The thickness of the membrane and connectivity of the phase-separated PS domains can be adjusted, facilitating the fine-tuning of the pore size and density to improve the membrane performance. Therefore, this study successfully fabricated thin microporous PDMS membranes with improved performance over standard membranes for cell-culture inserts, namely a higher porosity, flexibility, and softness. The results of this study can enhance cell culture methodologies and contribute to a deeper understanding of cellular processes.

Tyrp1 is the mendelian determinant of the Axolotl (Ambystoma mexicanum) copper mutant

Several dozen Mendelian mutants have been discovered in axolotl (Ambystoma mexicanum) populations, including several that affect pigmentation. Four recessive mutants have been described in the scientific literature and genes for three of these have been identified. Here we describe and genetically dissect copper, a mutant with an albino-like phenotype known only from the pet trade. We performed a cross segregating copper and wildtype color phenotypes and used bulked segregant RNA-Seq to identify a region on chromosome 6 that was enriched for single-nucleotide polymorphisms (SNPs) between the color phenotypes. This region included Tyrosinase-like Protein 1 (Tyrp1), a melanin synthesis protein that when mutated, is associated with lighter than black melanin coloration in animal models and oculocutaneous albinism in humans. Inspection of RNA-Seq reads identified a single nucleotide deletion that is predicted to change the coding frame, introduce a premature stop codon in exon 6 and yield a truncated Tyrp1 protein in copper individuals. Using CRISPR-Cas9 editing, we show that wildtype Tyrp1 crispants exhibit copper pigmentation, thus confirming Tyrp1 as the copper locus. Our results suggest that commercial and hobbyist axolotl populations may harbor useful mutants for biological research.

Next-generation red ultra-bright fluorescent dyes for nuclear imaging and peripheral blood leukocytes sorting.

The nucleus is a membrane-bound organelle in eukaryotic cells and plays a crucial role in cellular processes. Visualizing nuclear morphology is essential for investigating nuclear functions and understanding the relationship between nuclear morphological alterations and multiple diseases. Fluorescent dyes have been developed to visualize nuclear morphology, but the selection of red nuclear-labeling fluorescent dyes remains limited (high price, unknown structure, or high toxicity). Herein, we have developed a red ultra-bright nuclear-targeted dye, BPC1, through the engineering of unsymmetrical cyanine dyes derived from D-π-A systems. BPC1 exhibits ultrahigh fluorescence brightness and exceptional cell permeability, and selectively stains nuclear DNA rather than mitochondrial DNA, enabling the visualization of the nucleus in diverse cells at extremely low doses (100 nM) and laser power (0.8 μW). Furthermore, BPC1 is utilized for nuclear staining in blood cells, aiding in the distinct visualization of the white blood cell nucleus and facilitating the identification and enumeration of various leukocyte types. Our study implies considerable commercial potential for BPC1 and underscores its capacity to serve as a powerful tool in life sciences and cell biology research.

Novel cell spheroid culture method using Medaka dried fish powder

Highly biocompatible microcarriers are culture materials designed to enhance the efficiency of cell spheroid culture. Typically, collagen or specially processed plastic materials serve as these microcarriers. In the context of cultured-cell-based food production, however, both collagen and plastic materials present challenges regarding their cost-effectiveness and edibility. A notable issue with collagen, especially when derived from fish scales, is its low denaturation temperature, making it unsuitable for use with mammalian cells unless cross-linked. To address this issue, our research pivoted towards utilizing dried fish, a rich source of proteins including collagen. For this study, Medaka fish were selected. The fish were dried, ground into fine particles, and then impregnated with ethanol to create dried fish powder (DFP). Its efficacy was then evaluated as a microcarrier in spheroid cultures. The results revealed that DFP supports the adhesion and proliferation of various cell types, including human epidermal cells, human malignant melanoma cells, mouse fibroblasts, mouse endothelial cells and fish fibroblasts. Furthermore, Western blot analysis was used to verify the expression of mitogen-activated protein kinase-related proteins in both human epidermal cells and mouse fibroblasts cultured with DFP. This fish-derived powdered microcarrier offers a cost-effective production method requiring only a few steps. Its affordability and high performance as a carrier position it as a potentially revolutionary material for use in biological research and food production science.

TCR3d 2.0: expanding the T cell receptor structure database with new structures, toolsand interactions.

Recognition of antigens by T cell receptors (TCRs) is a key component of adaptive immunity. Understanding the structures of these TCR interactions provides major insights into immune protection and diseases, and enables design of therapeutics, vaccinesand predictive modeling algorithms. Previously, we released TCR3d, a database and resource for structures of TCRs and their recognition. Due to the growth of available structures and categories of complexes, the content of TCR3d has expanded substantially in the past 5 years. This expansion includes new tables dedicated to TCR mimic antibody complex structures, TCR-CD3 complexesand annotated Class I and II peptide-MHC complexes. Additionally, tools are available for users to calculate docking geometries for input TCR and TCR mimic complex structures. The core tables of TCR-peptide-MHC complexes have grown by 50%, and include binding affinity data for experimentally determined structures. These major content and feature updates enhance TCR3d as a resource for immunology, therapeuticsand structural biology research, and enable advanced approaches for predictive TCR modeling and design. TCR3d is available at: https://tcr3d.ibbr.umd.edu.

Genome-Wide Identification of the bHLH Gene Family in Rhododendron delavayi and Its Expression Analysis in Different Floral Tissues.

The bHLH genes play a crucial role in plant growth, development, and stress responses. However, there is currently limited research on bHLH genes in the important horticultural plant Rhododendron delavayi Franch. In this study, we conducted a comprehensive genome-wide identification and in-depth analysis of the bHLH gene family in R. delavayi using bioinformatics approaches. A total of 145 bHLH family members were identified, encoding proteins ranging from 98 to 3300 amino acids in length, with molecular weights ranging from 11.44 to 370.51 kDa and isoelectric points ranging from 4.22 to 10.80. These 145 bHLH genes were unevenly distributed across 13 chromosomes, with three bHLH genes located on contig 52. Chromosome 8 contained the highest number of bHLH family members with 19 genes, while chromosomes 9 and 13 had the lowest, with 7 genes each. Phylogenetic analysis revealed a close evolutionary relationship between bHLH genes in R. delavayi and Arabidopsis thaliana. Subcellular localization analysis indicated that most bHLH genes were located in the nucleus. Promoter analysis of R. delavayi bHLH genes revealed the presence of various cis-regulatory elements associated with light responses, methyl jasmonate responses, low-temperature responses, and coenzyme responses, suggesting that bHLH genes are involved in multiple biological processes in R. delavayi. Through transcriptome analysis, we identified three key functional genes-Rhdel02G0041700, Rhdel03G0013600, and Rhdel03G0341200-that may regulate flower color in R. delavayi. In conclusion, our study comprehensively identified and analyzed the bHLH gene family in R. delavayi and identified three bHLH genes related to flower color, providing a foundation for molecular biology research and breeding in R. delavayi.

Canada's contributions to RNA research: past, present, and future perspectives.

The field of RNA research has provided profound insights into the basic mechanisms modulating the function and adaption of biological systems. RNA has also been at the center stage in the development of transformative biotechnological and medical applications, perhaps most notably was the advent of mRNA vaccines that were critical in helping humanity through the Covid-19 pandemic. Unbeknownst to many, Canada boasts a diverse community of RNA scientists, spanning multiple disciplines and locations, whose cutting-edge research has established a rich track record of contributions across various aspects of RNA science over many decades. Through this position paper, we seek to highlight key contributions made by Canadian investigators to the RNA field, via both thematic and historical viewpoints. We also discuss initiatives underway to organize and enhance the impact of the Canadian RNA research community, particularly focusing on the creation of the not-for-profit organization RNA Canada ARN. Considering the strategic importance of RNA research in biology and medicine, and its considerable potential to help address major challenges facing humanity, sustained support of this sector will be critical to help Canadian scientists play key roles in the ongoing RNA revolution and the many benefits this could bring about to Canada.

I’m not half and half: navigating being a “both” in discipline-based education research

Introduction and methodsThrough years of conversations, three discipline-based education researchers used a duoethnographic process to interrogate their own discipline-based education research (DBER) identities. We present a description of how these individuals navigate being a “both,” gathered through reflections, discussions, and deeper research to explore perspectives of our professional identities and what we perceive those identities look like to our peers, supervisors, and trainees.ResultsOur own definitions and eventually realized identities as a “both” emerged through this research process. We envision that science faculty have multiple roles, demands, and identities; at the most basic level, they are “both” an educator and a researcher. In the unique case of discipline-based education research (i.e., scholars studying the teaching and learning of science often in science departments), some faculty find an overlap between complementary yet sometimes competing research agendas (i.e., biology research (BR) and discipline-based education research (DBER)), of which they do “both.”DiscussionThis article has two key contributions. First, it articulates this side-glancing process of our navigation of being a DBER “both,” leveraging each of our unique perspectives and the literature. Second, it represents how such an exploration may be useful to other interdisciplinary researchers in understanding and embracing all parts of their identities.

Exploring the use of deep learning models for accurate tracking of 3D zebrafish trajectories.

Zebrafish are ideal model organisms for various fields of biological research, including genetics, neural transmission patterns, disease and drug testing, and heart disease studies, because of their unique ability to regenerate cardiac muscle. Tracking zebrafish trajectories is essential for understanding their behavior, physiological states, and disease associations. While 2D tracking methods are limited, 3D tracking provides more accurate descriptions of their movements, leading to a comprehensive understanding of their behavior. In this study, we used deep learning models to track the 3D movements of zebrafish. Videos were captured by two custom-made cameras, and 21,360 images were labeled for the dataset. The YOLOv7 model was trained using hyperparameter tuning, with the top- and side-view camera models trained using the v7x.pt and v7.pt weights, respectively, over 300 iterations with 10,680 data points each. The models achieved impressive results, with an accuracy of 98.7% and a recall of 98.1% based on the test set. The collected data were also used to generate dynamic 3D trajectories. Based on a test set with 3,632 3D coordinates, the final model detected 173.11% more coordinates than the initial model. Compared to the ground truth, the maximum and minimum errors decreased by 97.39% and 86.36%, respectively, and the average error decreased by 90.5%.This study presents a feasible 3D tracking method for zebrafish trajectories. The results can be used for further analysis of movement-related behavioral data, contributing to experimental research utilizing zebrafish.

Reusable glassware for routine cell culture—a sterile, sustainable and affordable alternative to single-use plastics

Cell culture is a cornerstone of in vitro biological research. Whilst glassware was once commonplace in tissue culture facilities, in recent decades laboratories have moved towards a heavy reliance on single use plastics for routine procedures. Single use plastics allow for accessible, sterile, and often affordable equipment that comes at a high environmental cost. We developed a glassware preparation and cleaning process that allowed the comparison of “traditional” plastic-heavy, and adapted “sustainable,” cell culture practices, to empirically compare the sterility, viability, and proliferative capacity of cells cultured with differing techniques, by observing IL-6 production, morphology, and proliferation rate of cultured human pulmonary fibroblast cells. During which, we calculated the carbon footprint of traditional versus sustainable methods. We additionally endeavored to provide a realistic overview of the steps required to transition to more sustainable cell culture practices and make suggestions to ease the cost, labor, and time required to uptake similar practices in other laboratories. Cells cultured using reusable glassware did not show signs of contamination or stress compared to cells grown solely with plasticware, and glassware baked at 180°C for 120 min was sufficiently decontaminated and depyrogenated for culturing these cells. An individual researcher adopting the same methodology could reduce their carbon footprint by 105.92 kg of Carbon dioxide equivalent (CO2e) whilst also saving money (£408.78) over a 10-year period. We predict that these benefits would be greater if more researchers were to uptake these adapted practices. We intend for this paper to reassure researchers that viable, sterile, and sustainable routine cell culture can be achieved with little upfront cost to the researcher, with the prospective benefit of greatly reducing the cost to the environment. We additionally hope that increased uptake, and thus demand of more sustainable practices, encourages suppliers, policy makers, and funding bodies to make sustainable practices more accessible to individual researchers and institutions worldwide.

Organizer of biological science: to the 100th anniversary of P. A. Lehr’s birth

2023 marks the 100th anniversary of Pavel Andreyevich Lehr’s birth (09.27.1923–09.15.2005). He was an outstanding Soviet scientist, a leading expert on dipteran insects, a corresponding member of the USSR Academy of Sciences, director of the Institute of Biology and Soil Science of the Far Eastern Scientifi c Center/Far Eastern Branch of the USSR Academy of Sciences during 1981–1991. The article highlights the contribution of P. A. Lehr to the organization and development of biological research in the Far Eastern region between 1988 and 1991, when he was deputy chairman of the Presidium of the Far Eastern Branch of the USSR Academy of Sciences. At the same time, Lehr led a temporary creative team to develop the Environmental Program of Primorsky Krai, which he managed to bring to completion and offi cial approval during the collapse of the USSR. Unique documents from the Archive of the Far Eastern Branch of the Russian Academy of Sciences and the personal archive of the author are presented.

Bridging biosafety and biosecurity gaps: DURC and ePPP policy insights from U.S. institutions.

This study provides empirical data on the knowledge and practices of biosafety and biosecurity professionals and researchers involved in research on enhanced Potential Pandemic Pathogens (ePPPs) and Dual Use Research of Concern (DURC) within various U.S. sectors. The goal is to improve public health interventions and oversight for DURC and ePPP, contributing valuable insights for policy development. A notable finding was the association between larger biosafety/biosecurity teams and a higher likelihood of conducting high-risk biological research. A survey of 541 biosafety and biosecurity professionals was conducted between March 8 and 10 April 2024, with results analyzed using SAS at a significance level of 0.05. The study received approval from the Institutional Review Boards (IRBs) at Arizona State University and the University of Nevada, Reno. Government organizations were more likely to conduct DURC compared to other sectors (e.g., Academic, Commercial, Consulting). Public institutions reviewed more experiments outside the scope of the U.S. DURC Policy than private for-profit institutions. Institutions with larger biosafety/biosecurity teams reported greater research activity and more effective non-compliance reporting mechanisms (e.g., anonymous hotlines, reporting forms). Additionally, financial support and the challenges of policy implementation varied significantly across sectors. The findings emphasize the need for appropriate staffing and resource allocation for high-risk biosafety and biosecurity research. A differentiated regulatory approach and equitable distribution of resources are essential for effective oversight. Moreover, robust non-compliance reporting systems are critical to mitigating the risks associated with DURC and ePPP research.

Impact of Chromatin Organization and Epigenetics on CRISPR-Cas and TALEN Genome Editing.

DNA lies at the heart of the central dogma of life. Altering DNA can modify the flow of information in fundamental cellular processes such as transcription and translation. The ability to precisely manipulate DNA has led to remarkable advances in treating incurable human genetic ailments and has changed the landscape of biological research. Genome editors such as CRISPR-Cas nucleases and TALENs have become ubiquitous tools in basic and applied biological research and have been translated to the clinic to treat patients. The specificity and modularity of these genome editors have made it possible to efficiently engineer genomic DNA; however, underlying principles governing editing outcomes in eukaryotes are still being uncovered. Editing efficiency can vary from cell type to cell type for the same DNA target sequence, necessitating de novo design and validation efforts. Chromatin structure and epigenetic modifications have been shown to affect the activity of genome editors because of the role they play in hierarchical organization of the underlying DNA. Understanding the nuclear search mechanism of genome editors and their molecular interactions with higher order chromatin will lead to improved models for predicting precise genome editing outcomes. Insights from such studies will unlock the entire genome to be engineered for the creation of novel therapies to treat critical illnesses.

Exocyclic and Linker Editing of Lys63-linked Ubiquitin Chains Modulators Specifically Inhibits Non-homologous End-joining Repair.

Despite the great advances in discovering cyclic peptides against protein targets, their reduced aqueous solubility, cell permeability, and activity of the cyclic peptide restrict its utilization in advanced biological research and therapeutic applications. Here we report on a novel approach of structural alternation of the exocyclic and linker parts that led to a new derivative with significantly improved cell activity allowing us to dissect its mode of action in detail. We have identified an effective cyclic peptide (CP7) that induces approximately a 9-fold increase in DNA damage accumulation and a remarkable increase in apoptotic cancer cell death compared to the reported molecule. Notably, treating cells with CP7 leads to a dramatic decrease in the efficiency of non-homologous end joining (NHEJ) repair of DNA double-strand breaks (DSBs), which is accompanied by an increase in homologous recombination (HR) repair. Interestingly, treating BRCA1-deficient cells with CP7 restores HR integrity, which is accompanied by increased resistance to CP7. Additionally, CP7 treatment increases the sensitivity of cancer cells to ionizing radiation. Collectively, our findings demonstrate that CP7 is a selective inhibitor of NHEJ, offering a potential strategy to enhance the effectiveness of radiation therapy.

Exocyclic and Linker Editing of Lys63‐linked Ubiquitin Chains Modulators Specifically Inhibits Non‐homologous End‐joining Repair

AbstractDespite the great advances in discovering cyclic peptides against protein targets, their reduced aqueous solubility, cell permeability, and activity of the cyclic peptide restrict its utilization in advanced biological research and therapeutic applications. Here we report on a novel approach of structural alternation of the exocyclic and linker parts that led to a new derivative with significantly improved cell activity allowing us to dissect its mode of action in detail. We have identified an effective cyclic peptide (CP7) that induces approximately a 9‐fold increase in DNA damage accumulation and a remarkable increase in apoptotic cancer cell death compared to the reported molecule. Notably, treating cells with CP7 leads to a dramatic decrease in the efficiency of non‐homologous end joining (NHEJ) repair of DNA double‐strand breaks (DSBs), which is accompanied by an increase in homologous recombination (HR) repair. Interestingly, treating BRCA1‐deficient cells with CP7 restores HR integrity, which is accompanied by increased resistance to CP7. Additionally, CP7 treatment increases the sensitivity of cancer cells to ionizing radiation. Collectively, our findings demonstrate that CP7 is a selective inhibitor of NHEJ, offering a potential strategy to enhance the effectiveness of radiation therapy.

Progress and opportunities of foundation models in bioinformatics.

Bioinformatics has undergone a paradigm shift in artificial intelligence (AI), particularly through foundation models (FMs), which address longstanding challenges in bioinformatics such as limited annotated data and data noise. These AI techniques have demonstrated remarkable efficacy across various downstream validation tasks, effectively representing diverse biological entities and heralding a new era in computational biology. The primary goal of this survey is to conduct a general investigation and summary of FMs in bioinformatics, tracing their evolutionary trajectory, current research landscape, and methodological frameworks. Our primary focus is on elucidating the application of FMs to specific biological problems, offering insights to guide the research community in choosing appropriate FMs for tasks like sequence analysis, structure prediction, and function annotation. Each section delves into the intricacies of the targeted challenges, contrasting the architectures and advancements of FMs with conventional methods and showcasing their utility across different biological domains. Further, this review scrutinizes the hurdles and constraints encountered by FMs in biology, including issues of data noise, model interpretability, and potential biases. This analysis provides a theoretical groundwork for understanding the circumstances under which certain FMs may exhibit suboptimal performance. Lastly, we outline prospective pathways and methodologies for the future development of FMs in biological research, facilitating ongoing innovation in the field. This comprehensive examination not only serves as an academic reference but also as a roadmap for forthcoming explorations and applications of FMs in biology.

Implementing Optogenetic-Controlled Bacterial Systems in Drosophila melanogaster for Alleviation of Heavy Metal Poisoning.

Drosophila melanogaster (fruit fly) is an animal model chassis in biological and genetic research owing to its short life cycle, ease of cultivation, and acceptability to genetic modification. While the D. melanogaster chassis offers valuable insights into drug efficacy, toxicity, and mechanisms, several obvious challenges such as dosage control and drug resistance still limit its utility in pharmacological studies. Our research combines optogenetic control with engineered gut bacteria to facilitate the precise delivery of therapeutic substances in D. melanogaster for biomedical research. We have shown that the engineered bacteria can be orally administered to D. melanogaster to get a stable density of approximately 28,000 CFUs/per fly, leading to no detectable negative effects on the growth of D. melanogaster. In a model of D. melanogaster exposure to heavy metal, these orally administered bacteria uniformly express target genes under green light control to produce MtnB protein for binding and detoxifying lead, which significantly reduces the level of oxidative stress in the intestinal tract of Pb-treated flies. This pioneering study lays the groundwork for using optogenetic-controlled bacteria in the model chassis D. melanogaster to advance biomedical applications.

Clustering scRNA-seq data with the cross-view collaborative information fusion strategy.

Single-cell RNA sequencing (scRNA-seq) technology has revolutionized biological research by enabling high-throughput, cellular-resolution gene expression profiling. A critical step in scRNA-seq data analysis is cell clustering, which supports downstream analyses. However, the high-dimensional and sparse nature of scRNA-seq data poses significant challenges to existing clustering methods. Furthermore, integrating gene expression information with potential cell structure data remains largely unexplored. Here, we present scCFIB, a novel information bottleneck (IB)-based clustering algorithm that leverages the power of IB for efficient processing of high-dimensional sparse data and incorporates a cross-view fusion strategy to achieve robust cell clustering. scCFIB constructs a multi-feature space by establishing two distinct views from the original features. We then formulate the cell clustering problem as a target loss function within the IB framework, employing a collaborative information fusion strategy. To further optimize scCFIB's performance, we introduce a novel sequential optimization approach through an iterative process. Benchmarking against established methods on diverse scRNA-seq datasets demonstrates that scCFIB achieves superior performance in scRNA-seq data clustering tasks. Availability: the source code is publicly available on GitHub: https://github.com/weixiaojiao/scCFIB.

Bioinformatics in Russia: history and present-day landscape.

Bioinformatics has become an interdisciplinary subject due to its universal role in molecular biology research. The current status of Russia's bioinformatics research in Russia is not known. Here, we review the history of bioinformatics in Russia, present the current landscape, and highlight future directions and challenges. Bioinformatics research in Russia is driven by four major industries: information technology, pharmaceuticals, biotechnology, and agriculture. Over the past three decades, despite a delayed start, the field has gained momentum, especially in protein and nucleic acid research. Dedicated and shared centers for genomics, proteomics, and bioinformatics are active in different regions of Russia. Present-day bioinformatics in Russia is characterized by research issues related to genetics, metagenomics, OMICs, medical informatics, computational biology, environmental informatics, and structural bioinformatics. Notable developments are in the fields of software (tools, algorithms, and pipelines), use of high computation power (e.g. by the Siberian Supercomputer Center), and large-scale sequencing projects (the sequencing of 100 000 human genomes). Government funding is increasing, policies are being changed, and a National Genomic Information Database is being established. An increased focus on eukaryotic genome sequencing, the development of a common place for developers and researchers to share tools and data, and the use of biological modeling, machine learning, and biostatistics are key areas for future focus. Universities and research institutes have started to implement bioinformatics modules. A critical mass of bioinformaticians is essential to catch up with the global pace in the discipline.

Mass Spectrometry Analysis of Nucleic Acid Modifications: From Beginning to Future.

Nucleic acids are fundamental biological molecules that encode and convey genetic information within living organisms. Over 150 modifications have been found in nucleic acids, which are involved in critical biological functions, including regulating gene expression, stabilizing nucleic acid structure, modulating protein translation, and so on. The dysregulation of nucleic acid modifications is correlated with many diseases such as cancers and neurological disorders. However, it is still challenging to simultaneously characterize and quantify diverse modifications using traditional genomic methods. Mass spectrometry (MS) has served as a crucial tool to solve this issue, and can directly identify the modified species through their distinct mass differences compared to the canonical ones and provide accurate quantitative information. This review surveys the history of nucleic acid modification discovery, advancements in MS-based methods, nucleic acid sample preparation, and applications in biological and medical research. We expect the high-throughput and valuable quantitative information from MS analysis will be more broadly applied to studying nucleic acid modification status in different pathological conditions, which is key to filling gaps in traditional genomics and transcriptomics research and enabling researchers to gain insights into epigenetics and epitranscriptomics.