Omics Technologies Research Articles

Omics Technologies: A Strategy to Expedite the Geographical Traceability and Authenticity of Palm Oil

Omics Technologies: A Strategy to Expedite the Geographical Traceability and Authenticity of Palm Oil

Application of metabolomics in quality control of traditional Chinese medicines: a review

Plant metabolites are the components endowing traditional Chinese medicine (TCM) with therapeutic effects, and, simultaneously, they are the primary targets for quality control. From germplasm selection and origin determination to field management, growth duration, harvesting and processing, and, finally, storage and transportation, each step profoundly influences TCM quality. The complexity of these plant or herb metabolites poses numerous quality control challenges. Metabolomics, as a comprehensive and systematic approach, has demonstrated value in this field. This technique not only meets the requirements for studying the complex mechanisms of TCM but also has significant advantages in identifying the TCM components, including active components. Therefore, in this article, several key factors affecting the chemical characteristics and quality traits of TCM, including their origin, harvesting period, medicinal parts, and processing methods, are researched. Additionally, the current challenges of integrating metabolomics with other omics technologies (transcriptomics, spatial metabolomics, etc.) are discussed. Furthermore, a future development trends and prospects are highlighted. With the continuous deepening of research and ongoing updates in technological capabilities, metabolomics will play an increasingly important role in the quality control of TCM, providing more scientific and robust support for quality assurance and safety evaluation.

Integrating Genetic Insights, Technological Advancements, Screening, and Personalized Pharmacological Interventions in Childhood Obesity.

Childhood obesity is a significant global health challenge with rising prevalence over the past 50years, affecting both immediate and long-term health outcomes. The increase in prevalence from 0.7% to 5.6% in girls and 0.9% to 7.8% in boys highlights the urgency of addressing this epidemic. By 2025, it is estimated that 206million children and adolescents aged 5-19years will be living with obesity. This review explores the complex interplay of genomics and genetics in pediatric obesity, transitioning from monogenic and polygenic obesity to epigenetics, and incorporating advancements in omics technologies. The evolutionary purpose of adiposity, systemic evaluation of hyperphagia, and the role of various genetic factors are discussed. Technological advancements in genotyping offer new insights and interventions. The integration of genetic screening into clinical practice for early identification and personalized treatment strategies is emphasized.

Precision Agriculture and Water Conservation Strategies for Sustainable Crop Production in Arid Regions

The intensifying challenges posed by global climate change and water scarcity necessitate enhancements in agricultural productivity and sustainability within arid regions. This review synthesizes recent advancements in genetic engineering, molecular breeding, precision agriculture, and innovative water management techniques aimed at improving crop drought resistance, soil health, and overall agricultural efficiency. By examining cutting-edge methodologies, such as CRISPR/Cas9 gene editing, marker-assisted selection (MAS), and omics technologies, we highlight efforts to manipulate drought-responsive genes and consolidate favorable agronomic traits through interdisciplinary innovations. Furthermore, we explore the potential of precision farming technologies, including the Internet of Things (IoT), remote sensing, and smart irrigation systems, to optimize water utilization and facilitate real-time environmental monitoring. The integration of genetic, biotechnological, and agronomic approaches demonstrates a significant potential to enhance crop resilience against abiotic and biotic stressors while improving resource efficiency. Additionally, advanced irrigation systems, along with soil conservation techniques, show promise for maximizing water efficiency and sustaining soil fertility under saline–alkali conditions. This review concludes with recommendations for a further multidisciplinary exploration of genomics, sustainable water management practices, and precision agriculture to ensure long-term food security and sustainable agricultural development in water-limited environments. By providing a comprehensive framework for addressing agricultural challenges in arid regions, we emphasize the urgent need for continued innovation in response to escalating global environmental pressures.

From Images to Genes: Radiogenomics Based on Artificial Intelligence to Achieve Non-Invasive Precision Medicine in Cancer Patients.

With the increasing demand for precision medicine in cancer patients, radiogenomics emerges as a promising frontier. Radiogenomics is originally defined as a methodology for associating gene expression information from high-throughput technologies with imaging phenotypes. However, with advancements in medical imaging, high-throughput omics technologies, and artificial intelligence, both the concept and application of radiogenomics have significantly broadened. In this review, the history of radiogenomics is enumerated, related omics technologies, the five basic workflows and their applications across tumors, the role of AI in radiogenomics, the opportunities and challenges from tumor heterogeneity, and the applications of radiogenomics in tumor immune microenvironment. The application of radiogenomics in positron emission tomography and the role of radiogenomics in multi-omics studies is also discussed. Finally, the challenges faced by clinical transformation, along with future trends in this field is discussed.

Automated Machine Learning Tools to Build Regression Models for Schizosaccharomyces pombe Omics Data.

Machine learning is a powerful tool for analyzing biological data and making useful predictions. The surge of biological data from high-throughput omics technologies has raised the need for modeling approaches capable of tackling such amounts of data, which is pivotal to understanding the nature of complex molecular systems. Here, we show how to construct a simple model using automated machine learning (AutoML) to predict protein abundance in Schizosaccharomyces pombe, using data obtained from codon usage bias and quantitative proteomics.

Omics Studies in CKD: Diagnostic Opportunities and Therapeutic Potential.

Omics technologies have significantly advanced the prediction and therapeutic approaches for chronic kidney disease (CKD) by providing comprehensive molecular insights. This is a review of the current state and future prospects of integrating biomarkers into the clinical practice for CKD, aiming to improve patient outcomes by targeted therapeutic interventions. In fact, the integration of genomic, transcriptomic, proteomic, and metabolomic data has enhanced our understanding of CKD pathogenesis and identified novel biomarkers for an early diagnosis and targeted treatment. Advanced computational methods and artificial intelligence (AI) have further refined multi-omics data analysis, leading to more accurate prediction models for disease progression and therapeutic responses. These developments highlight the potential to improve CKD patient care with a precise and individualized treatment plan .

Genetics of Wool and Cashmere Fibre: Progress, Challenges, and Future Research

Wool (sheep) and cashmere (goat) fibres have unique biological, physical, and chemical properties and these fibres are becoming more important as the demand for natural products increases. However, these complex protein fibres are at times compromised by natural variability in their properties, and this can impact their use and value. Genetic improvement via selection and breeding can partly overcome this problem, enabling the farming of sheep and goats that produce more desirable fibre. This review explores the challenges in improving wool and cashmere fibre characteristics using genetics, with a focus on improving our understanding of the key protein components of fibres, wool keratins and keratin-associated proteins (KAPs). Despite progress in our knowledge of these proteins, gaining a better understanding of them and how they affect these fibres remains an ongoing challenge. This is not straight-forward, given the large number of similar yet unique genes that produce the proteins and the gaps that remain in their identification and characterisation. More research is required to clarify gene and protein sequence variability and the location and patterns of gene expression, which in turn limits our understanding of fibre growth and variation. Several aspects that currently hinder our progress in this quest include the incomplete identification of all the genes and weaknesses in the approaches used to characterise them, including newer omics technologies. We describe future research directions and challenges, including the need for ongoing gene identification, variation characterisation, and gene expression analysis and association studies to enable further improvement to these valuable natural fibres.

Microbiome science of human excrement composting.

Linear waste management systems are unsustainable and contribute to environmental degradation, economic inequity, and health disparities. Among the array of environmental challenges stemming from anthropogenic impacts, the management of human excrement (human feces and urine) stands as a significant concern. Over two billion people do not have access to adequate sanitation, signifying a global public health crisis. Composting is the microbial biotechnology aimed at cycling organic waste, including human excrement, for improved public health, agricultural productivity and safety, and environmental sustainability. Applications of modern microbiome -omics and related technologies have the capacity to support continued advances in composting science and praxis. In this article, we review literature focused on applications of microbiome technologies to study composting systems and reactions. The studies we survey generally fall into the categories of animal manure composting, biosolids composting, and human excrement composting. We review experiments utilizing microbiome technologies to investigate strategies for enhancing pathogen suppression and accelerating the biodegradation of organic matter. Additionally, we explore studies focused on the bioengineering potential of microbes as inoculants to facilitate degradation of toxins such as pharmaceuticals or per- and polyfluoroalkyl substances. The findings from these studies underscore the importance of advancing our understanding of composting processes through the integration of emerging microbiome -omics technologies. We conclude that work to-date has demonstrated exciting basic and applied science potential from studying compost microbiomes, with promising implications for enhancing global environmental sustainability and public health.

Reproductomics: Exploring the Applications and Advancements of Computational Tools

Over recent decades, advancements in omics technologies, such as proteomics, genomics, epigenomics, metabolomics, transcriptomics, and microbiomics, have significantly enhanced our understanding of the molecular mechanisms underlying various physiological and pathological processes. Nonetheless, the analysis and interpretation of vast omics data concerning reproductive diseases are complicated by the cyclic regulation of hormones and multiple other factors, which, in conjunction with a genetic makeup of an individual, lead to diverse biological responses. Reproductomics investigates the interplay between a hormonal regulation of an individual, environmental factors, genetic predisposition (DNA composition and epigenome), health effects, and resulting biological outcomes. It is a rapidly emerging field that utilizes computational tools to analyze and interpret reproductive data, with the aim of improving reproductive health outcomes. It is time to explore the applications of reproductomics in understanding the molecular mechanisms underlying infertility, identification of potential biomarkers for diagnosis and treatment, and in improving assisted reproductive technologies (ARTs). Reproductomics tools include machine learning algorithms for predicting fertility outcomes, gene editing technologies for correcting genetic abnormalities, and single cell sequencing techniques for analyzing gene expression patterns at the individual cell level. However, there are several challenges, limitations and ethical issues involved with the use of reproductomics, such as the applications of gene editing technologies and their potential impact on future generations are discussed. The review comprehensively covers the applications and advancements of reproductomics, highlighting its potential to improve reproductive health outcomes and deepen our understanding of reproductive molecular mechanisms.

A comparative study on semen quality and cryopreservation ability in Italian native chicken breeds

This study provides a comparative assessment of fresh semen quality and sensitivity to cryopreservation in several Italian chicken breeds. The research involved 145 roosters from 13 breeds. The results showed a wide variability in all the parameters considered among the different breeds, especially in the quantitative variables of fresh semen, such as volume and concentration. For the qualitative characteristics (sperm membrane integrity and motility parameters), the variability across breeds was more pronounced for frozen than fresh semen. Interestingly, apart from total motility in fresh semen, breed had a significant effect on all semen quality parameters in both fresh and thawed ejaculates. Considering the overall qualitative characteristics, the Robusta maculata, Siciliana, and Mericanel della Brianza breeds produced ejaculates with better semen quality compared to other Italian breeds. By evaluating the main parameters of semen quality, our results underline the potential of these traits to influence the reproductive success and genetic conservation. The Bionda piemontese, Bianca di Saluzzo, Livorno bianca, Pepoi, and Siciliana breeds showed better resilience to cryopreservation, suggesting the need for breed-specific protocols to optimise semen quality after thawing. Importantly, the research highlights the central role of semen quality for both immediate fertilisation success and long-term conservation efforts. Future studies integrating OMICS technologies could elucidate molecular markers influencing breed-specific differences, helping to refine cryopreservation techniques and improve conservation strategies for indigenous Italian chicken breeds. This work contributes valuable insights to global efforts aimed at safeguarding poultry genetic diversity and sustainability.

Recent advances in immunotherapy for small cell lung cancer.

This review aims to provide an overview of recent advances in immunotherapy for small cell lung cancer (SCLC), with a focus on the current status of immune checkpoint inhibitors (ICIs), novel combination strategies, and key biomarkers. The integration of ICIs into standard chemotherapy has established them as the first-line treatment for extensive-stage SCLC (ES-SCLC). The ADRIATIC trial further demonstrated the efficacy of ICI maintenance therapy in limited-stage SCLC. Additionally, combining radiotherapy with ICIs has shown promising synergistic effects, including the abscopal and radscopal effects. Ongoing investigations into the combination of ICIs with targeted therapies, such as antiangiogenic agents and DNA damage response inhibitors, have yielded encouraging preliminary results. Notably, the novel therapeutic agent tarlatamab, the first bispecific DLL3-directed CD3 T-cell engager, has recently received FDA approval for second-line treatment of ES-SCLC. Advances in omics technologies have shed light on the intra-tumor and inter-tumor heterogeneity of SCLC, leading to the identification of new molecular subtypes and biomarkers, thereby paving the way for precision medicine. Despite the improved outcomes associated with immunotherapy in SCLC, the overall clinical benefit remains modest. Further preclinical and clinical studies are essential to identify optimal treatment regimens and enhance therapeutic efficacy.

Integration of CRISPR/Cas9 with multi-omics technologies to engineer secondary metabolite productions in medicinal plant: Challenges and Prospects.

Plants acts asliving chemical factories that may create a large variety of secondary metabolites, most of which are used in pharmaceutical products. The production of these secondary metabolites is often much lower. Moreover, the primary constraint after discovering potential metabolites is the capacity to manufacture sufficiently for use in industrial and therapeutic contexts. The development of omics technology has brought revolutionary discoveries in various scientific fields, including transcriptomics, metabolomics, and genome sequencing. The metabolic pathways leading to the utilization of new secondary metabolites in the pharmaceutical industry can be identified with the use of these technologies. Genome editing (GEd) is a versatile technology primarily used for site-directed DNA insertions, deletions, replacements, base editing, and activation/repression at the targeted locus. Utilizing GEd techniques such as clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9), metabolic pathways engineered to synthesize bioactive metabolites optimally. This article will briefly discuss omics and CRISPR/Cas9-based methods to improve secondary metabolite production in medicinal plants.

Application of spatial-omics to the classification of kidney biopsy samples in transplantation.

Improvement of long-term outcomes through targeted treatment is a primary concern in kidney transplant medicine. Currently, the validation of a rejection diagnosis and subsequent treatment depends on the histological assessment of allograft biopsy samples, according to the Banff classification system. However, the lack of (early) disease-specific tissue markers hinders accurate diagnosis and thus timely intervention. This challenge mainly results from an incomplete understanding of the pathophysiological processes underlying late allograft failure. Integration of large-scale multimodal approaches for investigating allograft biopsy samples might offer new insights into this pathophysiology, which are necessary for the identification of novel therapeutic targets and the development of tailored immunotherapeutic interventions. Several omics technologies - including transcriptomic, proteomic, lipidomic and metabolomic tools (and multimodal data analysis strategies) - can be applied to allograft biopsy investigation. However, despite their successful application in research settings and their potential clinical value, several barriers limit the broad implementation of many of these tools into clinical practice. Among spatial-omics technologies, mass spectrometry imaging, which is under-represented in the transplant field, has the potential to enable multi-omics investigations that might expand the insights gained with current clinical analysis technologies.

A review on protein utilization and its interactions with carbohydrate and lipid from a molecular perspective in aquaculture: An implication beyond growth.

The world's increasing need for protein faces challenges in aquaculture production. New applications and tools will need to be added at every stage of the manufacturing line to attain this expansion sustainably, safely, and effectively. Utilizing experimental methods to increase aquatic animal production has become more common as aquatic biotechnology has advanced. High-throughput omics technologies have been introduced to address these issues, including transcriptomic, metabolomic, proteomic, and genomes. But it also faces many difficulties, like other food manufacturing industries. One of the best and most durable approaches to address these issues is probably to understand nutritional requirements and modify diet based on need. Molecular approaches are a subset of multiomics technology. Previously, most of the published work was devoted to the biochemical aspects of protein-lipid interactions in biological systems. In this review, we explore this idea and highlight various works that fall under the umbrella of nutrigenomics, with a particular emphasis on protein utilization and its interactions with carbohydrates and lipids.

Molecular modifications to mitigate oxidative stress and improve red blood cell storability.

The development of red blood cell (RBC) storage lesion during hypothermic storage has long posed challenges for blood transfusion efficacy. These alterations are primarily driven by oxidative stress, concern both structural and biochemical aspects of RBCs, and affect their interactions with the recipient's tissues post-transfusion. Efforts to counteract these effects focus on improving the antioxidant capacity within stored RBCs, reducing oxygen exposure, and scavenging harmful molecules that accumulate during storage. Various supplements, such as ascorbic acid, N-acetylcysteine, polyphenolic compounds, and specific metabolites have shown the potential to improve RBC quality by reducing oxidative lesions and lysis phenomena, and enhancing antioxidant, energy, or proteostasis networks. Accordingly, anaerobic storage has emerged as a promising strategy, demonstrating improved RBC storability and recovery in both animal models and preliminary human studies. Finally, targeted scavenging of harmful storage-related phenotypes and molecules, like removal signals, oxidized proteins, and extracellular hemoglobin, while not so studied, also has the potential to benefit both the unit and the patient in need. Omics technologies have aided a lot in these endeavors by revealing biomarkers of superior storability and, thus, potential novel supplementation strategies. Nonetheless, while the so far examined storage modifications show significant promise, there are not many post-transfusion studies (either in vitro, in animal models, or humans) to evaluate RBC efficacy in the transfusion setting. Looking ahead, the future of blood storage and transfusion will likely depend on the optimization of these interventions to extend the shelf-life and quality of stored RBCs, as well as their therapeutic outcome.

Paediatric systemic inflammatory response syndrome (SIRS) and the development of patient-specific therapy: ethical perspectives through experts' opinions.

Research for personalised therapies concerning the Systemic Inflammatory Response Syndrome (SIRS) in children involves the utilisation of OMICS technologies and Artificial Intelligence (AI). To identify specific ethical challenges through the perspective of healthcare professionals, we conducted 10 semi-structured interviews. The development of interview questions for the interviews was preceded by a systematic review of the scientific literature. To address the complexities of paediatric emergency research, informed consent, and data processing, experts with expertise in paediatric intensive care, computer science, and medical law were sought. After the transcription and anonymisation, the analysis followed established guidelines for qualitative content and thematic analysis. Interviewees highlighted the intricacies of managing consent in personalised SIRS research due to the large amount and complexity of information necessary for autonomous decision-making. Thus, instruments aimed at enhancing the understanding of legal guardians and to empowering the child were appreciated and the need for specific guidelines and establishing standards was expressed. Medical risks were estimated to be low, but the challenges of securing anonymisation and data protection were expected. It was emphasised that risks and benefits cannot be anticipated at this stage. Social justice issues were identified because of possible biases within the research population. Our findings were analysed using current ethical and legal frameworks for research with a focus on the particularities of the patient group and the emergency background. In this particular context, experts advocated for an enabling approach pertaining to AI in combination with OMICS technologies. As with every new technological development, ethical and legal challenges cannot be foreseen for SIRS-personalised treatment. Given this circumstance, experts emphasised the importance of extending the ethics-legal discourse beyond mere restrictions. The organisation of supervision should be reconsidered and not limited only to the precautionary principle, which per se was seen as impeding both the medical progress and clinical flexibility. It was noted that the establishment and monitoring of guidelines were emergent and should evolve through an interdisciplinary discourse. Therefore, it was recommended to enhance the qualifications of physicians in the field of computer science, impart ethics training to AI developers, and involve experts with expertise in medical law and data protection.

Integrated Genomic Approaches to Characterize and Mitigate Heat Stress in Poultry.

With the burgeoning human population, climate change, and expansion of poultry production in hot climates, it is imperative to aid global food security by enhancing the resilience of thermally challenged poultry. As a complement to management approaches used to mitigate heat stress, we give selected examples of recent studies on heat stress in poultry using various omics technologies. An integrated analysis of positional and functional candidate genes is provided, highlighting the most prominent pathways involved in the heat stress response. We finish by discussing efficient strategies to enhance thermal tolerance of poultry by genomics approaches, advocating for preservation of biodiversity that may provide beneficial allelic variation, and identifying current and future challenges in producing climate-resilient poultry.

Omics-Enhanced Nanomedicine for Cancer Therapy.

Cancer nanomedicine has emerged as a promising approach to overcome the limitations of conventional cancer therapies, offering enhanced efficacy and safety in cancer management. However, the inherent heterogeneity of tumors presents increasing challenges for the application of cancer nanomedicine in both diagnosis and treatment. This heterogeneity necessitates the integration of advanced and high-throughput analytical techniques to tailor nanomedicine strategies to individual tumor profiles. Omics technologies, encompassing genomics, epigenomics, transcriptomics, proteomics, metabolomics, and more, provide unparalleled insights into the molecular and cellular mechanisms underlying cancer. By dissecting tumor heterogeneity across multiple levels, these technologies offer robust support for the development of personalized and precise cancer nanomedicine strategies. In this review, the principles, techniques, and applications of key omics technologies are summarized. Especially, the synergistic integration of omics and nanomedicine in cancer therapy is explored, focusing on enhanced diagnostic accuracy, optimized therapeutic strategies and the assessment of nanomedicine-mediated biological responses. Moreover, this review addresses current challenges and outlines future directions in the field of omics-enhanced nanomedicine. By offering valuable insights and guidance, this review aims to advance the integration of omics with nanomedicine, ultimately driving improved diagnostic and therapeutic strategies for cancer.

Diagnosis of sepsis: which clinical and laboratory biomarkers are useful?

The quest for an unequivocal diagnostic tool for sepsis has persisted for decades, but this goal remains elusive. The diagnosis of sepsis is characterized by its complexity, which encompasses dozens of biochemical, hematologic, and immunologic parameters as well as complex microbiological diagnostics. During the last decade, the integration of omics technologies has further complicated this landscape. Despite these advancements, clinical diagnosis remains the gold standard for the diagnosis of sepsis. In the following review, we provide an overview of select diagnostic biomarkers that are deemed readily applicable in routine clinical practice, thus extending beyond the confines of university hospitals. Verification of the reliability and usefulness of a diagnostic parameter generally takes several years, and this process is more difficult in patients with sepsis compared with other patients because of the complexity of this clinical condition. Nevertheless, the introduction of new technologies, the intensive use of bedside diagnostics, and the contribution of omics technologies are moving us toward the realization of personalized medicine and theranostics.