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Interferon (IFN) activity exhibits a gender bias in human skin, skewed toward females. We show that HERC6, an IFN-induced E3 ubiquitin ligase, is induced in human keratinocytes through the epidermal type I IFN; IFN-κ. HERC6 knockdown in human keratinocytes results in enhanced induction of interferon-stimulated genes (ISGs) upon treatment with a double-stranded (ds) DNA STING activator cGAMP but not in response to the RNA-sensing TLR3 agonist. Keratinocytes lacking HERC6 exhibit sustained STING-TBK1 signaling following cGAMP stimulation through modulation of LATS2 and TBK1 activity, unmasking more robust ISG responses in female keratinocytes. This enhanced female-biased immune response with loss of HERC6 depends on VGLL3, a regulator of type I IFN signature. These data identify HERC6 as a previously unrecognized negative regulator of ISG expression specific to dsDNA sensing and establish it as a regulator of female-biased immune responses through modulation of STING signaling.

Multi-omics approaches have been successfully applied to investigate pregnancy and health outcomes at a molecular and genetic level in several studies. As omics technologies advance, research areas are open to study further. Here we discuss overall trends and examples of successfully using omics technologies and techniques (e.g., genomics, proteomics, metabolomics, and metagenomics) to investigate the molecular epidemiology of pregnancy. In addition, we outline omics applications and study characteristics of pregnancy for understanding fundamental biology, causal health, and physiological relationships, risk and prediction modeling, diagnostics, and correlations.

Biomarkers are valuable tools in clinical research where they allow to predict susceptibility to diseases, or response to specific treatments. Likewise, biomarkers can be extremely useful in the biomanufacturing of therapeutic proteins. Indeed, constraints such as short timelines and the need to find hyper-productive cells could benefit from a data-driven approach during cell line and process development. Many companies still rely on large screening capacities to develop productive cell lines, but as they reach a limit of production, there is a need to go from empirical to rationale procedures. Similarly, during bioprocessing runs, substrate consumption and metabolism wastes are commonly monitored. None of them possess the ability to predict the culture behavior in the bioreactor. Big data driven approaches are being adapted to the study of industrial mammalian cell lines, enabled by the publication of Chinese hamster and CHO genome assemblies which allowed the use of next-generation sequencing with these cells, as well as continuous proteome and metabolome annotation. However, if these different -omics technologies contributed to the characterization of CHO cells, there is a significant effort remaining to apply this knowledge to biomanufacturing methods. The correlation of a complex phenotype such as high productivity or rapid growth to the presence or expression level of a specific biomarker could save time and effort in the screening of manufacturing cell lines or culture conditions. In this review we will first discuss the different biological molecules that can be identified and quantified in cells, their detection techniques, and associated challenges. We will then review how these markers are used during the different steps of cell line and bioprocess development, and the inherent limitations of this strategy. • Biomarkers characterize the physiological state of cells and help predict their behavior. • A biomarker can consist of any macromolecule present in the cell that can be detected and quantified. • Discovering and identifying biomarkers requires specific and customized methods. • In an industrial context, biomarkers enable a more rational and efficient approach to bioprocessing. • Biomarkers are often specific to environmental conditions and, as such, have limitations. [ABSTRACT FROM AUTHOR]

Securing a stable food supply and achieving sustainable agricultural production are essential for mitigating future food insecurity. Soil metabolomics is a promising tool for capturing soil status, which is a critical issue for future sustainable food security. This study aims to provide deeper insights into the status of soybean-grown fields under varying soil conditions over three years by employing comprehensive soil volatile organic compound (VOC) profiling, also known as soil volatilomics. Profiling identified approximately 200 peaks in agricultural fields. The soil of soybean-presented plots exhibited markedly higher VOC levels than those of non-soybean plots during the flowering season. Pentanoic acid, 2,2,4-trimethyl-3-carboxyisopropyl, isobutyl ester, a discriminative soil VOC, was identified through multivariate data analysis as a distinctively present VOC in fields with or without soybean plants during the flowering period. Soil VOC profiles exhibited strong correlations with soil-related omics datasets (soil ionome, microbiome, metabolome, and physics) and no significant correlations with root microbiome and rhizosphere chemicals. These findings indicate that soil VOC profiles could serve as a valuable indicator for assessing soil status, thereby supporting efforts to ensure future global food security. [ABSTRACT FROM AUTHOR]

Lentil (Lens culinaris Medik.) is a cool season legume crop that plays vital roles in food and nutritional security, mostly in the least developed countries. Lentil is often cultivated in dry and semi-dry regions, where the primary abiotic factor is drought, which negatively impacts lentil growth and development, resulting in a reduction of yield. To withstand drought-induced multiple negative effects, lentil plants evolved a variety of adaptation strategies that can be classified within three broad categories of drought tolerance mechanisms (i.e., escape, avoidance, and tolerance). Lentil adapts to drought by the modulation of various traits in the root system, leaf architecture, canopy structure, branching, anatomical features, and flowering process. Furthermore, the activation of certain defensive biochemical pathways as well as the regulation of gene functions contributes to lentil drought tolerance. Plant breeders typically employ conventional and mutational breeding approaches to develop lentil varieties that can withstand drought effects; however, little progress has been made in developing drought-tolerant lentil varieties using genomics-assisted technologies. This review highlights the current understanding of morpho-physiological, biochemical, and molecular mechanisms of lentil adaptation to drought stress. We also discuss the potential application of omics-assisted breeding approaches to develop lentil varieties with superior drought tolerance traits. [ABSTRACT FROM AUTHOR]

The endemic, green-lipped mussel (Perna canaliculus), trademarked as Greenshell™ mussel, contributes most to the New Zealand aquaculture industry based on tonnage and export value. Research on mussel immunity is motivated greatly by economical and biosecurity necessities. Indeed, mussel aquaculture is threatened by pathogenic micro-organisms and environmental stressors. As such there is a need to understand the mechanisms that drive mussel immune responses and the associated interactions with the environment. Specifically, this review (1) analyses the existing immunological studies conducted on P. canaliculus, (2) evaluates the literature pertaining to mussel immunity at the cellular and humoral levels, (3) identifies and discusses pathogens that are relevant to P. canaliculus, (4) focuses on the virulent factors employed by mussel pathogens likely to induce diseases, (5) provides a comprehensive analysis of the response mechanisms employed by mussels to various stressors, and (6) explores omics applications and future perspectives in mussel immunology. Finally, this review highlights various strategies from immunological research, such as gene rearrangement, probiotics, immunostimulants, and selective breeding, promising to enhance mussel health and resilience in aquaculture. By exploring these immunological findings and their practical applications, this review contributes to sustainable mussel aquaculture, improving productivity and disease management in the industry. [ABSTRACT FROM AUTHOR]

Genetically engineered cyanobacterial strains that have improved growth rate, biomass productivity, and metabolite productivity could be a better option for sustainable bio-metabolite production. The global demand for biobased metabolites with nutraceuticals and health benefits has increased due to their safety and plausible therapeutic and nutritional utility. Cyanobacteria are solar-powered green cellular factories that can be genetically tuned to produce metabolites with nutraceutical and pharmaceutical benefits. The present review discusses biotechnological endeavors for producing bioprospective compounds from genetically engineered cyanobacteria and discusses the challenges and troubleshooting faced during metabolite production. This review explores the cyanobacterial versatility, the use of engineered strains, and the techno-economic challenges associated with scaling up metabolite production from cyanobacteria. Challenges to produce cyanobacterial bioactive compounds with remarkable nutraceutical values have been discussed. Additionally, this review also summarises the challenges and future prospects of metabolite production from genetically engineered cyanobacteria as a sustainable approach. [ABSTRACT FROM AUTHOR]

Purpose: Radiomics is an emerging field that utilizes quantitative features extracted from medical images to predict clinically meaningful outcomes. Validating findings is crucial to assess radiomics applicability. We aimed to validate previously published magnetic resonance imaging (MRI) radiomics models to predict oncological outcomes in oral tongue squamous cell carcinoma (OTSCC). Materials and methods: Retrospective multicentric study on OTSCC surgically treated from 2010 to 2019. All patients performed preoperative MRI, including contrast-enhanced T1-weighted (CE-T1), diffusion-weighted sequences and apparent diffusion coefficient map. We evaluated overall survival (OS), locoregional recurrence-free survival (LRRFS), cause-specific mortality (CSM). We elaborated different models based on clinical and radiomic data. C-indexes assessed the prediction accuracy of the models. Results: We collected 112 consecutive independent patients from three Italian Institutions to validate the previously published MRI radiomic models based on 79 different patients. The C-indexes for the hybrid clinical-radiomic models in the validation cohort were lower than those in the training cohort but remained > 0.5 in most cases. CE-T1 sequence provided the best fit to the models: the C-indexes obtained were 0.61, 0.59, 0.64 (pretreatment model) and 0.65, 0.69, 0.70 (posttreatment model) for OS, LRRFS and CSM, respectively. Conclusion: Our clinical-radiomic models retain a potential to predict OS, LRRFS and CSM in heterogeneous cohorts across different centers. These findings encourage further research, aimed at overcoming current limitations, due to the variability of imaging acquisition, processing and tumor volume delineation. [ABSTRACT FROM AUTHOR]

The increasing prevalence of omics data sources is pushing the study of regulatory mechanisms underlying complex diseases such as cancer. However, the vast quantities of molecular features produced and the inherent interplay between them lead to a level of complexity that hampers both descriptive and predictive tasks, requiring custom‐built algorithms that can extract relevant information from these sources of data. We propose a transformation that moves data centered on molecules (e.g., transcripts and proteins) to a new data space focused on putative regulatory modules given by statistically relevant co‐expression patterns. To this end, the proposed transformation extracts patterns from the data through biclustering and uses them to create new variables with guarantees of interpretability and discriminative power. The transformation is shown to achieve dimensionality reductions of up to 99% and increase predictive performance of various classifiers across multiple omics layers. Results suggest that omics data transformations from gene‐centric to pattern‐centric data supports both prediction tasks and human interpretation, notably contributing to precision medicine applications. [ABSTRACT FROM AUTHOR]

Microorganisms serve as linchpins in agricultural systems. Classic examples include microbial composting for nutrient recovery, using microorganisms in biogas technology for agricultural waste utilization, and employing biofilters to reduce emissions from stables or improve water quality in aquaculture. This mini-review highlights the importance of microbiome analysis in understanding microbial diversity, dynamics, and functions, fostering innovations for a more sustainable agriculture. In this regard, customized microorganisms for soil improvement, replacements for harmful agrochemicals or antibiotics in animal husbandry, and (probiotic) additives in animal nutrition are already in or even beyond the testing phase for a large-scale conventional agriculture. Additionally, as climate change reduces arable land, new strategies based on closed-loop systems and controlled environment agriculture, emphasizing microbial techniques, are being developed for regional food production. These strategies aim to secure the future food supply and pave the way for a sustainable, resilient, and circular agricultural economy. Key points: • Microbial strategies facilitate the integration of multiple trophic levels, essential for cycling carbon, nitrogen, phosphorus, and micronutrients. • Exploring microorganisms in integrated biological systems is essential for developing practical agricultural solutions. • Technological progress makes sustainable closed-entity re-circulation systems possible, securing resilient future food production. Microorganisms connect plant and animal agriculture through complex cycles involving carbon, nitrogen, phosphate, and additional micronutrients. This mini-review outlines the current and potential future roles of microorganisms in agroindustry. [ABSTRACT FROM AUTHOR]

This editorial discusses the increasing spread of foodborne pathogens and antimicrobial resistance (AMR) due to the global livestock and poultry industry, food processing industry, and international trade. It highlights the challenges posed by pathogens such as Salmonella, Campylobacter, Clostridium, and Escherichia coli, which contaminate various types of foods and contribute to the burden of AMR and foodborne diseases. The editorial emphasizes the need for more research and understanding of these pathogens, their mechanisms of resistance and virulence, and their dissemination, using multi-omics approaches. Several papers included in the editorial focus on AMR and virulence factors in Salmonella, highlighting the prevalence of resistance genes and the importance of whole genome sequencing in understanding complex patterns of AMR and virulence. The document also discusses various studies on antimicrobial resistance in different bacterial populations, the importance of a comprehensive approach combining genomics and transcriptomics, and the need for research on drug resistance mechanisms in fungi. It concludes by emphasizing the importance of technology in ensuring food safety and the need for further research to understand pathogenicity, evolution, and prevention in our food supplies. [Extracted from the article]

Introduction: Blood cultures have low sensitivity for candidemia. Sensitivity can be improved by the culture-independent system T2 Magnetic Resonance (T2). SeptiCyte RAPID is a host response assay quantifying the risk of infection-related inflammation through a scoring system (SeptiScore). We investigate the performance of SeptiScore in detecting persistent candidemia as defined by conventional cultures and T2. Methods: This is a prospective multicentre observational study on patients with candidemia. Blood cultures and blood samples for assessment by T2 and SeptiCyte were collected for 4 consecutive days after the index culture. The performance of SeptiScore was explored to predict persistent candidemia as defined by (1) positive follow-up blood culture (2) either positive follow-up blood culture or T2 sample. Results: 10 patients were enrolled including 34 blood collections assessed with the 3 methods. Overall, 4/34 (12%) follow-up blood cultures and 6/34 (18%) T2 samples were positive. A mixed model showed significantly higher SeptiScores associated with persistent candidemia when this was defined as either a positive follow-up blood culture or T2 sample (0.82, 95%CI 0.06 to 1.58) but not when this was defined as a positive follow-up blood culture only (-0.57, 95%CI -1.28 to 0.14). ROC curve for detection of persistent candidemia by SeptiScore at day 1 follow-up showed an AUC of 0.85 (95%CI 0.52-1.00) when candidemia was defined by positive follow-up blood culture, and an AUC of 1.00 (95%CI 1.00–1.00) when candidemia was defined according to both methods. Conclusion: Integrating transcriptome profiling with culture-independent systems and conventional cultures may increase our ability to diagnose persistent candidemia. [ABSTRACT FROM AUTHOR]

The gut microbiota has been recognized as an important determinant in the initiation and progression of colorectal cancer (CRC), with recent studies shining light on the molecular mechanisms that may contribute to the interactions between microbes and the CRC microenvironment. Despite the increasing wealth of associations being established in the field, proving causality remains challenging. Obstacles include the high variability of the microbiome and its context, both across individuals and across time. Additionally, there is a lack of large and representative cohort studies with long-term follow-up and/or appropriate sampling methods for studying the mucosal microbiome. Finally, most studies focus on CRC, whereas interactions between host and bacteria in early events in carcinogenesis remain elusive, reinforced by the heterogeneity of CRC development. Here, we discuss these current most prominent obstacles, the recent developments, and research needs. The gut microbiota has been recognized as an important determinant in the initiation and progression of colorectal cancer (CRC). Despite recent advances, it remains challenging to establish causal relationships between microbes and CRC carcinogenesis. In this perspective, we discuss current challenges, recent developments, and research needs. [ABSTRACT FROM AUTHOR]

Carotid stenosis is characterized by the progressive narrowing of the carotid arteries due to the formation of atherosclerotic plaque, which can lead to stroke and death as major complications. Numerous biomarkers allow for its study and characterization, particularly those related to "omics" sciences. Through the most common research databases, we report representative studies about carotid stenosis biomarkers based on genomics, transcriptomics, proteomics, and metabolomics in a narrative review. To establish a priority among studies based on their internal validity, we used a quality assessment tool, the Scale for the Assessment of Narrative Review Articles (SANRA). Genes, transcriptomes, proteins, and metabolites can diagnose the disease, define plaque connotations, predict consequences after revascularization interventions, and associate carotid stenosis with other patient comorbidities. It also emerged that many aspects determining the patient's psychological and social sphere are implicated in carotid disease. In conclusion, when taking the multidisciplinary approach that combines human sciences with biological sciences, it is possible to comprehensively define a patient's health and thus improve their clinical management through precision medicine. [ABSTRACT FROM AUTHOR]

Lipids are ubiquitous macromolecules that play essential roles in several metabolic processes in plants, such as primary and secondary metabolism, energy storage, and lipid signaling, also being major constituents of membranes. Considering their importance, lipid contents, proportion, and composition are widely modulated in response to environmental conditions, which is even more important under unfavorable conditions such as abiotic stresses. In recent years, technological advances have allowed for the analysis of the global lipid profile, also known as lipidomics, which has emerged as a powerful tool for the comprehensive analysis of the modulation and roles of lipids under different conditions. This review provides a current overview of plant lipidomics research, covering the different lipid classes found in plants, analytical techniques, and the main lipid-related responses under temperature, water, salt, alkali, heavy metal, nutrient deficiency, light, and oxidative stress. [ABSTRACT FROM AUTHOR]

Grouping/read-across is widely used for predicting the toxicity of data-poor target substance(s) using data-rich source substance(s). While the chemical industry and the regulators recognise its benefits, registration dossiers are often rejected due to weak analogue/category justifications based largely on the structural similarity of source and target substances. Here we demonstrate how multi-omics measurements can improve confidence in grouping via a statistical assessment of the similarity of molecular effects. Six azo dyes provided a pool of potential source substances to predict long-term toxicity to aquatic invertebrates (Daphnia magna) for the dye Disperse Yellow 3 (DY3) as the target substance. First, we assessed the structural similarities of the dyes, generating a grouping hypothesis with DY3 and two Sudan dyes within one group. Daphnia magna were exposed acutely to equi-effective doses of all seven dyes (each at 3 doses and 3 time points), transcriptomics and metabolomics data were generated from 760 samples. Multi-omics bioactivity profile-based grouping uniquely revealed that Sudan 1 (S1) is the most suitable analogue for read-across to DY3. Mapping ToxPrint structural fingerprints of the dyes onto the bioactivity profile-based grouping indicated an aromatic alcohol moiety could be responsible for this bioactivity similarity. The long-term reproductive toxicity to aquatic invertebrates of DY3 was predicted from S1 (21-day NOEC, 40 µg/L). This prediction was confirmed experimentally by measuring the toxicity of DY3 in D. magna. While limitations of this 'omics approach are identified, the study illustrates an effective statistical approach for building chemical groups. [ABSTRACT FROM AUTHOR]

Natural products have played significant roles as medicine and food throughout human history. Here, we first provide a brief historical overview of natural products, their classification and biosynthetic origins, and the microbiological and genetic methods used for their discovery. We also describe and discuss the technologies that revolutionized the field, which transitioned from classic genetics to genome-centric discovery approximately two decades ago. We then highlight the most recent advancements and approaches in the current postgenomic era, in which genome mining is a standard operation and high-throughput analytical methods allow parallel discovery of genes and molecules at an unprecedented pace. Finally, we discuss the new challenges faced by the field of natural products and the future of systematic heterologous expression and strain-independent discovery, which promises to deliver more molecules in vials than ever before. [ABSTRACT FROM AUTHOR]

Artificial intelligence (AI) platforms have emerged as pivotal tools in genetics and molecular medicine, as in many other fields. The growth in patient data, identification of new diseases and phenotypes, discovery of new intracellular pathways, availability of greater sets of omics data, and the need to continuously analyse them have led to the development of new AI platforms. AI continues to weave its way into the fabric of genetics with the potential to unlock new discoveries and enhance patient care. This technology is setting the stage for breakthroughs across various domains, including dysmorphology, rare hereditary diseases, cancers, clinical microbiomics, the investigation of zoonotic diseases, omics studies in all medical disciplines. AI’s role in facilitating a deeper understanding of these areas heralds a new era of personalised medicine, where treatments and diagnoses are tailored to the individual’s molecular features, offering a more precise approach to combating genetic or acquired disorders. The significance of these AI platforms is growing as they assist healthcare professionals in the diagnostic and treatment processes, marking a pivotal shift towards more informed, efficient, and effective medical practice. In this review, we will explore the range of AI tools available and show how they have become vital in various sectors of genomic research supporting clinical decisions. [ABSTRACT FROM AUTHOR]

Background/objective: Omics technology has become a widely applied biological science that can be used to study the etiology, pathogenesis, and treatment of osteosarcoma(OS). Bibliometric analysis is still blank in this field.This study aimed to access the trends and hotspots of omics in OS research through the bibliometric analysis method. Methods: Relevant articles and reviews from 1999 to 2023 were retrieved from the Web of Science Core Collection. The data were processed with CiteSpace, and some graphs were generated with Graphpad, VOSviewer, Scimago Graphica, Bibliometrix and R Studio. Results: A total of 1581 papers were included. China (569, 36.0%) and the United States (523, 33.1%) took the dominant position in the number of published papers, and the links between countries most frequently occurred between North America and East Asia, and between Australia and Europe. Top institutions with the highest number of publications were almost located in the United States, with The University of Texas MD Anderson Cancer Center contributing the most (44, 2.78%). Among the researchers in this field, Cleton-Jansen AM was the author with the highest number of articles in the field (20, 1.27%). According to the keyword cluster analysis, most studies focused on the “comparative genomic hybridization” before 2012. The latest surge words “tumor microenvironment” and “immune infiltration” in the keyword heatmap indicate future research directions. Conclusion: Our study provided the current status of the omics research in OS on a global level and the hottest directions. The field of omics in OS was developing rapidly, and the main focuses of research were revealing the characteristics of tumor microenvironment of OS and how to activate the immune system to fight cancer cells. Research on the immune microenvironment and its relationship with genetic aberrations of OS will be a priority in the future.Highlights: The research of omics in osteosarcoma has been exploding since 1998 due to the development of omics technology and the emphasis of researchers. The research hotspots had shifted from the discovering of new molecular target to revealing the characteristics of tumor microenvironment of osteosarcoma and how to activate the immune system to fight cancer cells. According to the present trend, research on the immune microenvironment and its molecular mechanisms will be a priority in the future. [ABSTRACT FROM AUTHOR]

Buckwheat (Fagopyrum spp.) is an underutilized resilient crop of North Western Himalayas belonging to the family Polygonaceae and is a source of essential nutrients and therapeutics. Common Buckwheat and Tatary Buckwheat are the two main cultivated species used as food. It is the only grain crop possessing rutin, an important metabolite with high nutraceutical potential. Due to its inherent tolerance to various biotic and abiotic stresses and a short life cycle, Buckwheat has been proposed as a model crop plant. Nutritional security is one of the major concerns, breeding for a nutrient-dense crop such as Buckwheat will provide a sustainable solution. Efforts toward improving Buckwheat for nutrition and yield are limited due to the lack of available: genetic resources, genomics, transcriptomics and metabolomics. In order to harness the agricultural importance of Buckwheat, an integrated breeding and OMICS platforms needs to be established that can pave the way for a better understanding of crop biology and developing commercial varieties. This, coupled with the availability of the genome sequences of both Buckwheat species in the public domain, should facilitate the identification of alleles/QTLs and candidate genes. There is a need to further our understanding of the molecular basis of the genetic regulation that controls various economically important traits. The present review focuses on: the food and nutritional importance of Buckwheat, its various omics resources, utilization of omics approaches in understanding Buckwheat biology and, finally, how an integrated platform of breeding and omics will help in developing commercially high yielding nutrient rich cultivars in Buckwheat. [ABSTRACT FROM AUTHOR]

INTRODUCTION: Vervets are non‐human primates that share high genetic homology with humans and develop amyloid beta (Aβ) pathology with aging. We expand current knowledge by examining Aβ pathology, aging, cognition, and biomarker proteomics. METHODS: Amyloid immunoreactivity in the frontal cortex and temporal cortex/hippocampal regions from archived vervet brain samples ranging from young adulthood to old age was quantified. We also obtained cognitive scores, plasma samples, and cerebrospinal fluid (CSF) samples in additional animals. Plasma and CSF proteins were quantified with platforms utilizing human antibodies. RESULTS: We found age‐related increases in Aβ deposition in both brain regions. Bioinformatic analyses assessed associations between biomarkers and age, sex, cognition, and CSF Aβ levels, revealing changes in proteins related to immune‐related inflammation, metabolism, and cellular processes. DISCUSSION: Vervets are an effective model of aging and early‐stage Alzheimer's disease, and we provide translational biomarker data that both align with previous results in humans and provide a basis for future investigations. Highlights: We found changes in immune and metabolic plasma biomarkers associated with age and cognition.Cerebrospinal fluid (CSF) biomarkers revealed changes in cell signaling indicative of adaptative processes.TNFRSF19 (TROY) and Artemin co‐localize with Alzheimer's disease pathology.Vervets are a relevant model for translational studies of early‐stage Alzheimer's disease. [ABSTRACT FROM AUTHOR]

The Poaceae family, commonly known as the grass family, encompasses a diverse group of crops that play an essential role in providing food, fodder, biofuels, environmental conservation, and cultural value for both human and environmental well-being. Crops in Poaceae family are deeply intertwined with human societies, economies, and ecosystems, making it one of the most significant plant families in the world. As the major reservoirs of essential nutrients, seed grain of these crops has garnered substantial attention from researchers. Understanding the molecular and genetic processes that controls seed formation, development and maturation can provide insights for improving crop yield, nutritional quality, and stress tolerance. The diversity in photosynthetic pathways between C3 and C4 plants introduces intriguing variations in their physiological and biochemical processes, potentially affecting seed development. In this review, we explore recent studies performed with omics technologies, such as genomics, transcriptomics, proteomics and metabolomics that shed light on the mechanisms underlying seed development in wheat and maize, as representatives of C3 and C4 plants respectively, providing insights into their unique adaptations and strategies for reproductive success. [ABSTRACT FROM AUTHOR]

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Background: Fold change is a common metric in biomedical research for quantifying group differences in omics variables. However, inconsistent calculation methods and inadequate reporting lead to discrepancies in results. This study evaluated various fold-change calculation methods aiming at a recommendation of a preferred approach. Methods: The primary distinction in fold-change calculations lies in defining group expected values for log ratio computation. To challenge method interchangeability in a "stress test" scenario, we generated diverse artificial data sets with varying distributions (identity, uniform, normal, log-normal, and a mixture of these) and compared calculated fold-changes to known values. Additionally, we analyzed a multi-omics biomedical data set to estimate to what extent the findings apply to real-world data. Results: Using arithmetic means as expected values for treatment and reference groups yielded inaccurate fold-change values more frequently than other methods, particularly when subgroup distributions and/or standard deviations differed significantly. Conclusions: The arithmetic mean method, often perceived as standard or picked without considering alternatives, is inferior to other definitions of the group expected value. Methods using median, geometric mean, or paired fold-change combinations are more robust against violations of equal variances or dissimilar group distributions. Adhering to methods less sensitive to data distribution without trade-offs and accurately reporting calculation methods in scientific reports is a reasonable practice to ensure correct interpretation and reproducibility. [ABSTRACT FROM AUTHOR]

Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as "living fossils" and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts. [ABSTRACT FROM AUTHOR]

Small millets, also known as nutri‐cereals, belong to the grass family Poaceae that have tiny seeds and are drought and heat tolerant, besides being powerhouse of nutrition, hence making them ideal crops that shall combat not just food and nutritional security but also adapt well to the changing climatic conditions. They grow well on marginal soil and require least resources for their cultivation. Nutritional superiority to popularly cultivated major cereals makes them a magnificent alternative food especially in the age of lifestyle related disorders. In this review, we provide insights of the initial commencement of research on small millets and deliberate the breeding progress based on conventional and genomics‐based approaches. The small millets under discussion are finger millet, foxtail millet, proso millet, little millet, barnyard millet, kodo millet and browntop millet. The major focus here is to recapitulate the breeding activities in the above‐mentioned millets rather than providing a way forward for breeding small millets. [ABSTRACT FROM AUTHOR]

The remediation of emerging contaminants presents a pressing environmental challenge, necessitating innovative approaches for effective mitigation. This review article delves into the untapped potential of soil microbial communities in the bioremediation of emerging contaminants. Bioremediation, while a promising method, often proves time-consuming and requires a deep comprehension of microbial intricacies for enhancement. Given the challenges presented by the inability to culture many of these microorganisms, conventional methods are inadequate for achieving this goal. While omics-based methods provide an innovative approach to understanding the fundamental aspects, processes, and connections among microorganisms that are essential for improving bioremediation strategies. By exploring the latest advancements in omics technologies, this review aims to shed light on how these approaches can unlock the hidden capabilities of soil microbial communities, paving the way for more efficient and sustainable remediation solutions. [ABSTRACT FROM AUTHOR]

In light of the post-genomic era, epigenetics brings about an opportunity to better understand how the molecular machinery works and is led by a complex dynamic set of mechanisms, often intricate and complementary in many aspects. In particular, epigenetics links developmental biology and genetics, as well as many other areas of knowledge. The present work highlights substantial scopes and relevant discoveries related to the development of the term from its first notions. To our understanding, the concept of epigenetics needs to be revisited, as it is one of the most relevant and multifaceted terms in human knowledge. To redirect future novel experimental or theoretical efforts, it is crucial to compile all significant issues that could impact human and ecological benefit in the most precise and accurate manner. In this paper, the reader can find one of the widest compilations of the landmarks and epistemic considerations of the knowledge of epigenetics across the history of biology from the earliest epigenetic formulation to genetic determinism until the present. In the present work, we link the current body of knowledge and earlier pre-genomic concepts in order to propose a new definition of epigenetics that is faithful to its regulatory nature. [ABSTRACT FROM AUTHOR]

Oil palm (Elaeis guineensis Jacq.) is a typical tropical oil crop with a temperature of 26–28 °C, providing approximately 35% of the total world's vegetable oil. Growth and productivity are significantly affected by low-temperature stress, resulting in inhibited growth and substantial yield losses. To comprehend the intricate molecular mechanisms underlying the response and acclimation of oil palm under low-temperature stress, multi-omics approaches, including metabolomics, proteomics, and transcriptomics, have emerged as powerful tools. This comprehensive review aims to provide an in-depth analysis of recent advancements in multi-omics studies on oil palm under low-temperature stress, including the key findings from omics-based research, highlighting changes in metabolite profiles, protein expression, and gene transcription, as well as including the potential of integrating multi-omics data to reveal novel insights into the molecular networks and regulatory pathways involved in the response to low-temperature stress. This review also emphasizes the challenges and prospects of multi-omics approaches in oil palm research, providing a roadmap for future investigations. Overall, a better understanding of the molecular basis of the response of oil palm to low-temperature stress will facilitate the development of effective breeding and biotechnological strategies to improve the crop's resilience and productivity in changing climate scenarios. [ABSTRACT FROM AUTHOR]

Background: Both bacterial and viral diseases are a major threat to farmed fish. As the antiviral immune mechanisms in lumpfish (Cyclopterus lumpus L.) are poorly understood, lumpfish leukocytes were stimulated with poly(I:C), a synthetic analog of double stranded RNA, which mimic viral infections, and RNA sequencing was performed. Methods: To address this gap, we stimulated lumpfish leukocytes with poly(I:C) for 6 and 24 hours and did RNA sequencing with three parallels per timepoint. Genome guided mapping was performed to define differentially expressed genes (DEGs). Results: Immune genes were identified, and transcriptome-wide analyses of early immune responses showed that 376 and 2372 transcripts were significantly differentially expressed 6 and 24 hours post exposure (hpe) to poly(I:C), respectively. The most enriched GO terms when time had been accounted for, were immune system processes (GO:0002376) and immune response (GO:0006955). Analysis of DEGs showed that among the most highly upregulated genes were TLRs and genes belonging to the RIG-I signaling pathway, including LGP2, STING and MX, as well as IRF3 and IL12A. RIG-I was not identified, but in silico analyses showed that genes encoding proteins involved in pathogen recognition, cell signaling, and cytokines of the TLR and RIG-I signaling pathway are mostly conserved in lumpfish when compared to mammals and other teleost species. Conclusions: Our analyses unravel the innate immune pathways playing a major role in antiviral defense in lumpfish. The information gathered can be used in comparative studies and lay the groundwork for future functional analyses of immune and pathogenicity mechanisms. Such knowledge is also necessary for the development of immunoprophylactic measures for lumpfish, which is extensively cultivated for use as cleaner fish in the aquaculture for removal of sea lice from Atlantic salmon (Salmo salar L.). [ABSTRACT FROM AUTHOR]

The plants of the genus Physalis L. have been extensively utilized in traditional and indigenous Chinese medicinal practices for treating a variety of ailments, including dermatitis, malaria, asthma, hepatitis, and liver disorders. The present review aims to achieve a comprehensive and up-to-date investigation of the genus Physalis, a new model crop, to understand plant diversity and fruit development. Several chloroplast DNA-, nuclear ribosomal DNA-, and genomic DNA-based markers, such as psbA-trnH, internal-transcribed spacer (ITS), simple sequence repeat (SSR), random amplified microsatellites (RAMS), sequence-characterized amplified region (SCAR), and single nucleotide polymorphism (SNP), were developed for molecular identification, genetic diversity, and phylogenetic studies of Physalis species. A large number of functional genes involved in inflated calyx syndrome development (AP2-L, MPF2, MPF3, and MAGO), organ growth (AG1, AG2, POS1, and CNR1), and active ingredient metabolism (24ISO, DHCRT, P450-CPL, SR, DUF538, TAS14, and 3β-HSB) were identified contributing to the breeding of novel Physalis varieties. Various omic studies revealed and functionally identified a series of reproductive organ development-related factors, environmental stress-responsive genes, and active component biosynthesis-related enzymes. The chromosome-level genomes of Physalis floridana Rydb., Physalis grisea (Waterf.) M. Martínez, and Physalis pruinosa L. have been recently published providing a valuable resource for genome editing in Physalis crops. Our review summarizes the recent progress in genetic diversity, molecular identification, phylogenetics, functional genes, and the application of omics in the genus Physalis and accelerates efficient utilization of this traditional herb. [ABSTRACT FROM AUTHOR]

Trichoderma spp. is known for its ability to enhance plant growth and suppress disease, but the mechanisms for its interaction with host plants and pathogens remain unclear. This study investigated the transcriptomics and metabolomics of peanut plants (Arachis hypogaea L.) inoculated with Trichoderma harzianum QT20045, in the absence and presence of the stem rot pathogen Sclerotium rolfsii JN3011. Under the condition without pathogen stress, the peanut seedlings inoculated with QT20045 showed improved root length and plant weight, increased indole acetic acid (IAA) production, and reduced ethylene level, with more active 1-aminocyclopropane-1-carboxylate acid (ACC) synthase (ACS) and ACC oxidase (ACO), compared with the non-inoculated control. Under the pathogen stress, the biocontrol efficacy of QT20045 against S. rolfsii was 78.51%, with a similar effect on plant growth, and IAA and ethylene metabolisms to the condition with no biotic stress. Transcriptomic analysis of peanut root revealed that Trichoderma inoculation upregulated the expression of certain genes in the IAA family but downregulated the genes in the ACO family (AhACO1 and AhACO) and ACS family (AhACS3 and AhACS1) consistently in the absence and presence of pathogens. During pathogen stress, QT20045 inoculation leads to the downregulation of the genes in the pectinesterase family to keep the host plant's cell wall stable, along with upregulation of the AhSUMM2 gene to activate plant defense responses. In vitro antagonistic test confirmed that QT20045 suppressed S. rolfsii growth through mechanisms of mycelial entanglement, papillary protrusions, and decomposition. Our findings highlight that Trichoderma inoculation is a promising tool for sustainable agriculture, offering multiple benefits from pathogen control to enhanced plant growth and soil health. [ABSTRACT FROM AUTHOR]

AbstractReproduction is a fundamental biological process for producing offspring and ensuring the continuation of the species. With nearly 35,000 fish species worldwide exhibiting a very diverse range of reproductive systems and strategies, the study of fish reproduction is a significant challenge. Research into various fish reproductive models is driven by their use in human biomedical applications, improving the diversification and sustainability of aquaculture species, and developing strategies for biodiversity conservation. These models must be approached from an animal ethics perspective, considering the welfare of the species under study and applying the 3Rs principle (Replacement, Reduction and Refinement). This principle focusses on replacing animals with alternative methods wherever possible, reducing the number of animals used and refining procedures to minimize suffering. While destructive sampling of wild aquatic species should be minimized, the need remains to provide information on reproduction as an important parameter for delineating management and conservation programs. One of the practices that helps reduce and replace the use of animal testing is the scientific study of individuals obtained through bycatch. This is the case for some chondrichthyans, and endangered fish species included in conservation programs. Regarding fish species that are kept under human care (commonly called captivity), studies on reproduction are essential to improve well-being and increase production of farmed species. Research on fish reproduction requires expanding basic knowledge of broodstock management tools, such as gamete quality assessment, reproductive behavior studies, the use of hormone therapies to stimulate reproduction, and the development of non-lethal or less invasive methods using body fluids (e.g., mucus, seminal plasma, blood plasma, or urine) to study reproductive status, as well as novel markers from state-of-the-art omics research. This review describes a multidisciplinary approach that includes the aforementioned reproductive management tools, indicators of welfare, and next-generation sequencing techniques using samples collected by minimally invasive methods. [ABSTRACT FROM AUTHOR]

The persistence of coronavirus disease 2019 (COVID-19)-related hospitalization severely threatens medical systems worldwide and has increased the need for reliable detection of acute status and prediction of mortality. We applied a systems biology approach to discover acute-stage biomarkers that could predict mortality. A total 247 plasma samples were collected from 103 COVID-19 (52 surviving COVID-19 patients and 51 COVID-19 patients with mortality), 51 patients with other infectious diseases (IDCs) and 41 healthy controls (HCs). Paired plasma samples were obtained from survival COVID-19 patients within 1 day after hospital admission and 1–3 days before discharge. There were clear differences between COVID-19 patients and controls, as well as substantial differences between the acute and recovery phases of COVID-19. Samples from patients in the acute phase showed suppressed immunity and decreased steroid hormone biosynthesis, as well as elevated inflammation and proteasome activation. These findings were validated by enzyme-linked immunosorbent assays and metabolomic analyses in a larger cohort. Moreover, excessive proteasome activity was a prominent signature in the acute phase among patients with mortality, indicating that it may be a key cause of poor prognosis. Based on these features, we constructed a machine learning panel, including four proteins [C-reactive protein (CRP), proteasome subunit alpha type (PSMA)1, PSMA7, and proteasome subunit beta type (PSMB)1)] and one metabolite (urocortisone), to predict mortality among COVID-19 patients (area under the receiver operating characteristic curve: 0.976) on the first day of hospitalization. Our systematic analysis provides a novel method for the early prediction of mortality in hospitalized COVID-19 patients. [ABSTRACT FROM AUTHOR]

Background: Despite rapid advances in genomic-resolved metagenomics and remarkable explosion of metagenome-assembled genomes (MAGs), the function of uncultivated anaerobic lineages and their interactions in carbon mineralization remain largely uncertain, which has profound implications in biotechnology and biogeochemistry. Results: In this study, we combined long-read sequencing and metatranscriptomics-guided metabolic reconstruction to provide a genome-wide perspective of carbon mineralization flow from polymers to methane in an anaerobic bioreactor. Our results showed that incorporating long reads resulted in a substantial improvement in the quality of metagenomic assemblies, enabling the effective recovery of 132 high-quality genomes meeting stringent criteria of minimum information about a metagenome-assembled genome (MIMAG). In addition, hybrid assembly obtained 51% more prokaryotic genes in comparison to the short-read-only assembly. Metatranscriptomics-guided metabolic reconstruction unveiled the remarkable metabolic flexibility of several novel Bacteroidales-affiliated bacteria and populations from Mesotoga sp. in scavenging amino acids and sugars. In addition to recovering two circular genomes of previously known but fragmented syntrophic bacteria, two newly identified bacteria within Syntrophales were found to be highly engaged in fatty acid oxidation through syntrophic relationships with dominant methanogens Methanoregulaceae bin.74 and Methanothrix sp. bin.206. The activity of bin.206 preferring acetate as substrate exceeded that of bin.74 with increasing loading, reinforcing the substrate determinantal role. Conclusion: Overall, our study uncovered some key active anaerobic lineages and their metabolic functions in this complex anaerobic ecosystem, offering a framework for understanding carbon transformations in anaerobic digestion. These findings advance the understanding of metabolic activities and trophic interactions between anaerobic guilds, providing foundational insights into carbon flux within both engineered and natural ecosystems. 38JKnB3DNsQtzzVWuKzfx4 Video Abstract [ABSTRACT FROM AUTHOR]

Aquaculture production has been growing consistently over the last few decades to meet the increasing animal protein demand of the human population. However, increased production and rearing intensities raise the challenges of guaranteeing fish health and welfare, which is essential to avoid losses and ensure product quality. Biomarkers can provide insights into the fish's nutritional, physiological, and health status, and aid in the evaluation of early nutritional and physiological imbalances, distress conditions, and pathological diagnosis. The discovery and validation of biomarkers rely mostly on the use of information provided by different parameters, including biochemical, metabolic, or immunologic, as well as several omics, from genomics and transcriptomics to proteomics and metabolomics. In this review, a summary of the main biomarkers used in aquaculture is provided along with an overview of the main omics technologies available for further biomarker research. This review also highlights the need to develop non-lethal biomarkers that can easily and quickly be measured to provide a prompt response to producers. [ABSTRACT FROM AUTHOR]

Summary: Sickle cell anaemia (SCA) patients display elevated levels of circulating pro‐inflammatory cytokines and endothelial activation markers compared to healthy peers. The impact of exercise on the pro‐inflammatory state in SCA remains unclear. This study aimed to characterize the whole‐blood transcriptome profile in response to an acute bout of exercise in paediatric SCA patients. Twenty‐three SCA participants (13 ± 3 years, 52% girls) and 17 healthy controls (14 ± 3 years, 29% girls) performed eight 2‐min bouts of cycle ergometry interspersed with 1‐min rest intervals. Whole‐blood transcriptome profile (RNA‐seq) was performed before and after exercise. At baseline, gene pathways associated with gas transport in erythrocytes were up‐regulated in SCA patients compared to controls. Following exercise, gene pathways associated with innate immunity were altered in both groups. Interaction analyses revealed 160 annotated genes (101 up‐ and 59 down‐regulated) that differentially altered by exercise in SCA patients. Moreover, genes that exhibited a blunted response to exercise in SCA patients were enriched in the IL‐17 signalling pathway, suggesting an impaired innate immune response to exercise. This data will contribute to the development of evidence‐based exercise prescription guidelines for this patient population. [ABSTRACT FROM AUTHOR]

• Genome sequencing enables the study of plant genomes through various approaches, facilitating the examination of gene functions, structures, and genome comparisons. • Genomics is a scientific discipline focused on studying an organism's genome, providing comprehensive insights into its physiological, chemical, and biological processes. • Omics technologies deepen their understanding of molecular responses, aiding in the development of resilient and stress-tolerant crop varieties. • Bioinformatics and computational methodologies accelerate gene discovery and enhance understanding of stress tolerance. • Integrating multi-omics approaches to uncover novel genes or pathways for enhancing desired traits in crops. Understanding the link between crops and environmental stress is critical for creating resilient, high-yielding types. Genomic techniques provide a comprehensive understanding of a plant's genome, including physiological and biological processes, gene architecture, and functional annotations. Genome sequencing has allowed researchers to examine gene functions and architecture, as well as compare genomes using a variety of genomics approaches. Integrating genomics with other omics disciplines like metabolomics, proteomics, and transcriptomics enables a more comprehensive understanding of biological systems. Bioinformatics is crucial for analyzing and understanding large amounts of biological data generated by high-throughput techniques in omics-based research. The combination of genomics and other omics disciplines aids in the identification of regulatory genes and proteins involved in stress responses, as well as the elucidation of critical metabolic pathways for stress adaption. Researchers can unveil the complexity of abiotic stress tolerance in crops by using genomics methods, particularly those based on bioinformatics. These findings help to design stress-tolerant crops with higher yields, thereby tackling the issues faced by environmental stress in agriculture. [ABSTRACT FROM AUTHOR]

Traditional drug screening methods typically focus on a single protein target and exhibit limited efficiency due to the multifactorial nature of most diseases, which result from disturbances within complex networks of protein–protein interactions rather than single gene abnormalities. Addressing this limitation requires a comprehensive drug screening strategy. Network medicine is rooted in systems biology and provides a comprehensive framework for understanding disease mechanisms, prevention, and therapeutic innovations. This approach not only explores the associations between various diseases but also quantifies the relationships between disease genes and drug targets within interactome networks, thus facilitating the prediction of drug–disease relationships and enabling the screening of therapeutic drugs for specific complex diseases. An increasing body of research supports the efficiency and utility of network-based strategies in drug screening. This review highlights the transformative potential of network medicine in virtual therapeutic screening for complex diseases, offering novel insights and a robust foundation for future drug discovery endeavors. [ABSTRACT FROM AUTHOR]

Camouflage is essential for animals to avoid predation or attract prey. Camouflage encompasses a spectrum of strategies aimed at rendering detection and recognition more challenging. Crypsis and masquerade emerge as the predominant manifestations of camouflage in the animal kingdom. Unveiling genetic mechanisms of camouflage requires cross-discipline integration, encompassing comparative genomics, population genetics, developmental biology, and neurobiology. The approaches of ecological evolutionary developmental biology provide a pivotal role in deciphering the genetic bases of camouflage. Camouflage is a classic example of a trait wherein animals respond to natural selection to avoid predation or attract prey. This unique phenomenon has attracted significant recent attention and the rapid development of integrative research methods is facilitating advances in our understanding of the in-depth genetic mechanisms of camouflage. In this review article, we revisit camouflage definitions and strategies and then we examine the underlying mechanisms of the two most common forms of camouflage, crypsis and masquerade, that have recently been elucidated using multiple approaches. We also discuss unresolved questions related to camouflage. Ultimately, we highlight the implications of camouflage for informing various key issues in ecology and evolution. [ABSTRACT FROM AUTHOR]

The aim of this article was to investigate whether Schirmer strips gathered during clinical dry eye examinations can be prepared for omics analyses in a standardized way, to adjust for variations in tear volume and enable two separate omics analyses from the same sample. In addition, the intention was to investigate whether fluorescein dye instillation in the eyes gave bias effects on metabolomic analysis. Twelve samples from six individuals, with normal or reduced tear production, were collected. Half of the samples were harvested after instillation of fluorescein in the eye. Each strip was divided in half along the length and prepared with a new method for extracting tear content from the Schirmer strip. The new method was established to compensate for different dilutions of metabolites in varying Schirmer strip wetting levels when using identical extraction volume for all samples. Metabolomic data were compared in samples with and without fluorescein dye and Schirmer strips ranging from 1 to 35 mm wetting levels using a global LC–MS method. All samples were successfully analyzed with an average of ∼350 relevant features detected per sample after using both positive and negative electrospray ionization mode, despite low tear volumes in some samples and that only one half of the Schirmer strips were used. Principal component analysis plots and heatmaps revealed no bias effects of fluorescein dye presence or different Schirmer strip values when using the proposed method. A high number of relevant metabolomic features can be extracted from longitudinally cut halves of Schirmer strips, which may enable analyses with more than one omics modality from the same sample. With the pre-analytical method described, Schirmer strips can be used for metabolomic analyses even in cases of very low or high tear volume with or without fluorescence. [ABSTRACT FROM AUTHOR]

The current trend of shifting to food naturalness has prompted food industries to switch from synthetic to natural colorants. Concurrently, there is a spike in interest concerning the extraction of pigments from natural sources using non-conventional extraction techniques as the latter are environmental-friendly and sustainable compared to traditional methods. Microwave-assisted extraction (MAE) is one of the emerging technologies that has been reported to be effective in the recovery of bioactive compounds from a plethora of natural sources because of its ability to expeditiously heat the extraction matrix, leading to rapid product recovery. This review focuses on the voluminous demand for natural colorants, their limitations, and potential food applications. Also, this review emphasizes the underlying principle and mechanism of MAE, as well as studies that unveil the efficacy and suitability of the technique for the recovery of pigments. Hence, given that natural pigments are susceptible to natural degradation, MAE is a promising technology for enhanced pigment yield and stability. In addition, recent trends such as technology integration and novel extraction solvents have considerably widened the scope and versatility of MAE as a greener extraction method. Furthermore, when coupled with MAE, waste valorization and further exploration of novel pigment sources (such as algae and other microorganisms) present thrust areas of research concerning the global sustainable development goals (SDGs). [ABSTRACT FROM AUTHOR]

High-throughput omics technologies have become valuable tools for systems science research and clinical management of sepsis. This article analyzes sepsis research using omics technologies in the European Union (EU) and the United Kingdom from 1990 to May 2023 using bibliometric data from the Web of Science database. Using VOSviewer for network analysis, we examined the distribution patterns, funding characteristics, and collaborations among the states, noting trends of convergence and divergence. The analysis included 2078 articles, revealing an increasing rate of publications on sepsis research using omics approaches. The United Kingdom's research output is notably high, contributing 28.3% of the total research from the EU and United Kingdom combined. Germany, France, the Netherlands, and Italy together account for 56.9% of the publications from the EU member states. The United States is the leading international collaborator, particularly with the United Kingdom, followed by Germany and France. The EU-15 countries have significantly more publication outputs in this domain with growing but limited inclusion of the newer members of the EU. We suggest that the role of EU member states and the United Kingdom in sepsis research using omics technologies can be advanced by facilitating high-value, technology-driven health research, fostering collaboration, convergence, and equity in global health and biomedical research. [ABSTRACT FROM AUTHOR]

Chili pepper, widely recognized as a popular spice and an important cash crop worldwide, faces significant threats from climate change-related stress, particularly plant disease outbreaks. Emerging global diseases like Phytophthora blight, anthracnose fruit rot, and Ralstonia bacterial wilt threaten chili-producing countries, causing substantial annual yield losses. These major threatening diseases are difficult to control due to their widespread, extensive, and long-lived survival structures. Disease management practices rely on agrochemicals, leading to resistance to phytopathogens and environmental issues. Current research focuses on developing innovative, effective, chemical-free, and sustainable biosecurity strategies to address these challenges. Endophytes are plant endosymbionts that provide new insights for scientists due to their remarkable genome regulation to host plants. This review highlights the current state of emerging global diseases affecting chili pepper crops based on bibliometric analysis. We also focus on endophytes-mediated plant defense response as a sustainable solution for chemical pesticides. This review discusses the importance of omics-based technologies in deciphering the biochemical and molecular mechanisms of endophytes-mediated chili plant tolerance to various pathogens. A holistic approach of plant endophytes and multi-omics technologies can help develop effective mitigation strategies to prevent disease outbreaks for sustainable crop production and environmental restoration in the modern era of Agriculture 4.0 ‒ a green agricultural revolution. [ABSTRACT FROM AUTHOR]

Herbal standardization is a crucial aspect in the field of herbal medicine and nutraceutical products. It refers to the process of developing and implementing standards to ensure the consistency, quality, and efficacy of herbal products. One important class of bioactive compounds that is widely distributed in plants is bioflavonoids, natural polyphenolic compounds. The significant pharmacological properties of bioflavonoids include antioxidant, anti-inflammatory, anti-diabetic, anti-aging and antimicrobial properties are promising therapeutic nutraceutical agents in the management of several acute and chronic diseases. However, the exploitation of these bioflavonoids demands systematic standardization approaches covering from extraction to enrichment of high-quality standardized multicomponent botanical extract in order to meet the desired efficacy. Hence, this review describes on the plant innovative processing technologies comprising of drying, solvent, extraction technique and adsorbent technologies accompanied with the established quality control methods using high end analytical instrument and omics technology. The importance of bioactive compound standardization and global demand of flavonoid in various applications are also highlighted. [ABSTRACT FROM AUTHOR]

Main conclusion: The review discusses growth and drought-response mechanisms in minor millets under three themes: drought escape, drought avoidance and drought tolerance. Drought is one of the most prominent abiotic stresses impacting plant growth, performance, and productivity. In the context of climate change, the prevalence and severity of drought is expected to increase in many agricultural regions worldwide. Millets (coarse grains) are a group of small-seeded grasses cultivated in arid and semi-arid regions throughout the world and are an important source of food and feed for humans and livestock. Although minor millets, i.e., foxtail millet, finger millet, proso millet, barnyard millet, kodo millet and little millet are generally hardier and more drought-resistant than cereals and major millets (sorghum and pearl millet), understanding their responses, processes and strategies in response to drought is more limited. Here, we review drought resistance strategies in minor millets under three themes: drought escape (e.g., short crop cycle, short vegetative period, developmental plasticity and remobilization of assimilates), drought avoidance (e.g., root traits for better water absorption and leaf traits to control water loss), and drought tolerance (e.g., osmotic adjustment, maintenance of photosynthetic ability and antioxidant potential). Data from ‘omics’ studies are summarized to provide an overview of the molecular mechanisms important in drought tolerance. In addition, the final section highlights knowledge gaps and challenges to improving minor millets. This review is intended to enhance major cereals and millet per se in light of climate-related increases in aridity. [ABSTRACT FROM AUTHOR]

Heat stress presents unique challenges compared to other environmental stressors, as predicting crop responses and understanding the mechanisms for heat tolerance are complex tasks. The escalating impact of devastating climate changes heightens the frequency and intensity of heat stresses, posing a noteworthy threat to global agricultural productivity, especially in rice-dependent regions of the developing world. Humidity has been demonstrated to negatively affect rice yields worldwide. Plants have evolved intricate biochemical adaptations, involving intricate interactions among genes, proteins, and metabolites, to counter diverse external signals and ensure their survival. Modern-omics technologies, encompassing transcriptomics, metabolomics, and proteomics, have revolutionized our comprehension of the intricate biochemical and cellular shifts that occur in stressed agricultural plants. Integrating these multi-omics approaches offers a comprehensive view of cellular responses to heat stress and other challenges, surpassing the insights gained from multi-omics analyses. This integration becomes vital in developing heat-tolerant crop varieties, which is crucial in the face of increasingly unpredictable weather patterns. To expedite the development of heat-resistant rice varieties, aiming at sustainability in terms of food production and food security globally, this review consolidates the latest peer-reviewed research highlighting the application of multi-omics strategies. [ABSTRACT FROM AUTHOR]

Currently, exposome studies include a raft of different monitoring tools, including remote sensors, smartphones, omics analyses, distributed lag models, etc. The similarity in structure between the exposome and the microbiota plus their functions led us to pose three pertinent questions from this viewpoint, looking at the actual relationship between the exposome and the microbiota. In terms of the exposome, a bistable equilibrium between health and disease depends on constantly dealing with an ever-changing totality of exposures that together shape an individual from conception to death. Regarding scientific knowledge, the exposome is still lagging in certain areas, like the importance of microorganisms in the equation. The human microbiome is defined as an aggregate assemblage of gut commensals that are hosted by our surfaces related to the external environment. Commensals' resistance to a variety of environmental exposures, such as antibiotic administration, confirms that a layer of these organisms is protected within the host. The exposome is a conceptual framework defined as the environmental component of the science-inspired systems ideology that shifts from a specificity-based medical approach to reasoning in terms of complexity. A parallel concept in population health research and precision public health is the human flourishing index, which aims to account for the numerous environmental factors that affect individual and population well-being beyond ambient pollution. [ABSTRACT FROM AUTHOR]

The host-microbiome associations occurring on the skin of vertebrates significantly influence hosts health. However, the factors mediating their interactions remain largely unknown. Herein, we used integrated technical and ecological frameworks to investigate the skin metabolites sustaining a beneficial symbiosis between tree frogs and bacteria. We characterize macrocyclic acylcarnitines as the major metabolites secreted by the frogs skin and trace their origin to an enzymatic unbalance of carnitine palmitoyltransferases. We found that these compounds colocalize with bacteria on the skin surface and are mostly represented by members of the Pseudomonas community. We showed that Pseudomonas sp. MPFS isolated from frogs skin can exploit acylcarnitines as its sole carbon and nitrogen source, and this metabolic capability is widespread in Pseudomonas. We summarize frogs multiple mechanisms to filter environmental bacteria and highlight that acylcarnitines likely evolved for another function but were co-opted to provide nutritional benefits to the symbionts.

Intrauterine infection/inflammation (IUI) is a frequent complication of pregnancy leading to preterm labor and fetal inflammation. How inflammation is modulated at the maternal-fetal interface is unresolved. We compared transcriptomics of amnion (a fetal tissue in contact with amniotic fluid) in a preterm Rhesus macaque model of IUI induced by lipopolysaccharide with human cohorts of chorioamnionitis. Bulk RNA sequencing (RNA-seq) amnion transcriptomic profiles were remarkably similar in both Rhesus and human subjects and revealed that induction of key labor-mediating genes such as IL1 and IL6 was dependent on nuclear factor κB (NF-κB) signaling and reversed by the anti-tumor necrosis factor (TNF) antibody Adalimumab. Inhibition of collagen biosynthesis by IUI was partially restored by Adalimumab. Interestingly, single-cell transcriptomics, flow cytometry, and immunohistology demonstrated that a subset of amnion mesenchymal cells (AMCs) increase CD14 and other myeloid cell markers during IUI both in the human and Rhesus macaque. Our data suggest that CD14+ AMCs represent activated AMCs at the maternal-fetal interface.