The challenges for molecular nutrition research 1: linking genotype to healthy nutrition.
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ABSTRACT:
SUBMITTER: Williams CM
PROVIDER: S-EPMC2467452 | biostudies-other | 2008 Jul
REPOSITORIES: biostudies-other
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Project description:Considerable advances have been made in the field of infant feeding research. The last few decades have witnessed the expansion in the number of studies on the composition and benefits of human milk. The practice of breastfeeding and use of human milk represent today's reference standards for infant feeding and nutrition. Additional research regarding the benefits of breastfeeding is needed to determine which factors in human milk and in the act of breastfeeding itself, singly or in combination, are most important for producing the beneficial effects on infant growth, body composition, and neurodevelopmental outcome. We examine evidence that breastfeeding confers health benefits and offer suggestions on how best to interpret the data and present it to the public. We also describe some examples of well-designed infant nutrition studies that provide useful and clinically meaningful data regarding infant feeding, growth, and development. Because not all mothers choose to breastfeed or can breastfeed, other appropriate feeding options should be subjected to critical review to help establish how infant formula and bottle feeding can confer benefits similar to those of human milk and the act of breastfeeding. We conclude with the overarching point that the goal of infant feeding research is to promote optimal infant growth and development. Since parents/families may take different paths to feeding their infants, it is fundamental that health professionals understand how best to interpret research studies and their findings to support optimal infant growth and development.
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Project description:The molecular mechanisms underlying the development of bone metastases in breast cancer remain unclear. Disseminated tumour cells (DTCs) in the bone marrow of breast cancer patients are commonly identified, even in early stage disease, but their potential to initiate metastases is not known. The mechanism whereby DTCs become overt metastatic tumour cells (MTCs) is therefore, an area of considerable interest. This study explored the analysable yield of genetic material from human biopsy samples in order to describe differences in gene expression between DTCs and bone MTCs. Thirteen breast cancer patients with bone metastases underwent a CT-guided bone metastasis biopsy and a bone marrow biopsy. Tumour cells were enriched and gene expression profiling was conducted to identify differentially expressed genes. The analysable yield of sufficient RNA for microarray analysis was 60% from bone metastasis biopsies and 80% from bone marrow biopsies. A signature of 133 candidate genes differentially expressed between DTCs and MTCs was identified. Several genes relevant to breast cancer metastasis to bone (osteopontin, CTGF, parathyroid hormone receptor, EGFR) were significantly overexpressed in MTCs as compared to DTCs. Biopsies of bone metastases and bone marrow rarely yield enough tissue for robust molecular biology studies using clinical samples. The findings obtained however are interesting and seem to overlap with the bone metastasis gene expression signature described in murine xenograft models. Larger biopsy specimens or improved RNA extraction techniques may improve analysable yield and feasibility of these techniques. Gene expression profiling was utilized to compare DTCs obtained from bone marrow aspirates (A) to MTCs isolated from Computed Tomography (C) guided biopsies of bone metastases.
2012-07-05 | E-GEOD-14776 | biostudies-arrayexpress
Project description:The molecular mechanisms underlying the development of bone metastases in breast cancer remain unclear. Disseminated tumour cells (DTCs) in the bone marrow of breast cancer patients are commonly identified, even in early stage disease, but their potential to initiate metastases is not known. The mechanism whereby DTCs become overt metastatic tumour cells (MTCs) is therefore, an area of considerable interest. This study explored the analysable yield of genetic material from human biopsy samples in order to describe differences in gene expression between DTCs and bone MTCs. Thirteen breast cancer patients with bone metastases underwent a CT-guided bone metastasis biopsy and a bone marrow biopsy. Tumour cells were enriched and gene expression profiling was conducted to identify differentially expressed genes. The analysable yield of sufficient RNA for microarray analysis was 60% from bone metastasis biopsies and 80% from bone marrow biopsies. A signature of 133 candidate genes differentially expressed between DTCs and MTCs was identified. Several genes relevant to breast cancer metastasis to bone (osteopontin, CTGF, parathyroid hormone receptor, EGFR) were significantly overexpressed in MTCs as compared to DTCs. Biopsies of bone metastases and bone marrow rarely yield enough tissue for robust molecular biology studies using clinical samples. The findings obtained however are interesting and seem to overlap with the bone metastasis gene expression signature described in murine xenograft models. Larger biopsy specimens or improved RNA extraction techniques may improve analysable yield and feasibility of these techniques.
2012-07-06 | GSE14776 | GEO
Project description:Background:Selenium (Se) is an essential element for mammals and its deficiency in the diet is a global problem. Plants accumulate Se and thus represent a major source of Se to consumers. Agronomic biofortification intends to enrich crops with Se in order to secure its adequate supply by people. Scope:The goal of this review is to report the present knowledge of the distribution and processes of Se in soil and at the plant-soil interface, and of Se behaviour inside the plant in terms of biofortification. It aims to unravel the Se metabolic pathways that affect the nutritional value of edible plant products, various Se biofortification strategies in challenging environments, as well as the impact of Se-enriched food on human health. Conclusions:Agronomic biofortification and breeding are prevalent strategies for battling Se deficiency. Future research addresses nanosized Se biofortification, crop enrichment with multiple micronutrients, microbial-integrated agronomic biofortification, and optimization of Se biofortification in adverse conditions. Biofortified food of superior nutritional quality may be created, enriched with healthy Se-compounds, as well as several other valuable phytochemicals. Whether such a food source might be used as nutritional intervention for recently emerged coronavirus infections is a relevant question that deserves investigation.
| S-EPMC7363690 | biostudies-literature
Project description:Expansion of data-driven research in the 21st century has posed challenges in the evolution of the international agreed framework of research ethics. The World Medical Association (WMA)'s Declaration of Helsinki (DoH) has provided ethical principles for medical research involving humans since 1964, with the last update in 2013. To complement the DoH, WMA issued the Declaration of Taipei (DoT) in 2016 to provide additional principles for health databases and biobanks. However, the ethical principles for secondary use of data or material obtained in research remain unclear. With such a perspective, the Working Group on Ethics (WGE) of the International Federation of Associations of Pharmaceutical Physicians and Pharmaceutical Medicine (IFAPP) suggests a closer scientific linkage in the DoH to the (Declaration of Taipei) DoT focusing specifically on areas that will facilitate data-driven research, and to further strengthen the protection of research participants.
| S-EPMC7723451 | biostudies-literature
Project description:Molecular diagnosis of COVID-19 primarily relies on the detection of RNA of the SARS-CoV-2 virus, the causative infectious agent of the pandemic. Reverse transcription polymerase chain reaction (RT-PCR) enables sensitive detection of specific sequences of genes that encode the RNA dependent RNA polymerase (RdRP), nucleocapsid (N), envelope (E), and spike (S) proteins of the virus. Although RT-PCR tests have been widely used and many alternative assays have been developed, the current testing capacity and availability cannot meet the unprecedented global demands for rapid, reliable, and widely accessible molecular diagnosis. Challenges remain throughout the entire analytical process, from the collection and treatment of specimens to the amplification and detection of viral RNA and the validation of clinical sensitivity and specificity. We highlight the main issues surrounding molecular diagnosis of COVID-19, including false negatives from the detection of viral RNA, temporal variations of viral loads, selection and treatment of specimens, and limiting factors in detecting viral proteins. We discuss critical research needs, such as improvements in RT-PCR, development of alternative nucleic acid amplification techniques, incorporating CRISPR technology for point-of-care (POC) applications, validation of POC tests, and sequencing of viral RNA and its mutations. Improved assays are also needed for environmental surveillance or wastewater-based epidemiology, which gauges infection on the community level through analyses of viral components in the community's wastewater. Public health surveillance benefits from large-scale analyses of antibodies in serum, although the current serological tests do not quantify neutralizing antibodies. Further advances in analytical technology and research through multidisciplinary collaboration will contribute to the development of mitigation strategies, therapeutics, and vaccines. Lessons learned from molecular diagnosis of COVID-19 are valuable for better preparedness in response to other infectious diseases.
| S-EPMC7346719 | biostudies-literature
Project description:Informatics has become an essential component of research in the past few decades, capitalizing on the efficiency and power of computation to improve the knowledge gained from increasing quantities and types of data. While other fields of research such as genomics are well represented in informatics resources, nutrition remains underrepresented. Nutrition is one of the most integral components of human life, and it impacts individuals far beyond just nutrient provisions. For example, nutrition plays a role in cultural practices, interpersonal relationships and body image. Despite this, integrated computational investigations have been limited due to challenges within nutrition informatics (nutri-informatics) and nutrition data. The purpose of this review is to describe the landscape of nutri-informatics resources available for use in computational nutrition research and clinical utilization. In particular, we will focus on the application of biomedical ontologies and their potential to improve the standardization and interoperability of nutrition terminologies and relationships between nutrition and other biomedical disciplines such as disease and phenomics. Additionally, we will highlight challenges currently faced by the nutri-informatics community including experimental design, data aggregation and the roles scientific journals and primary nutrition researchers play in facilitating data reuse and successful computational research. Finally, we will conclude with a call to action to create and follow community standards regarding standardization of language, documentation specifications and requirements for data reuse. With the continued movement toward community standards of this kind, the entire nutrition research community can transition toward greater usage of Findability, Accessibility, Interoperability and Reusability principles and in turn more transparent science.
| S-EPMC7833928 | biostudies-literature
Project description:BackgroundThere is an increasing global trend towards urbanization. In general, there are less food access issues in urban than rural areas, but this "urban advantage" does not benefit the poorest who face disproportionate barriers to accessing healthy food and have an increased risk of malnutrition.ObjectivesThis systematic literature review aimed to assess urban poverty as a determinant of access to a healthy diet, and to examine the contribution of urban poverty to the nutritional status of individuals.MethodsFollowing the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) methodology, our review included quantitative and qualitative studies published in English or in Spanish between 2000 and 2019. The articles were eligible if they focused on nutrition access (i.e. access to a healthy diet) or nutrition outcomes (i.e., anemia, overweight and obesity, micronutrient deficiency, micronutrient malnutrition) among urban poor populations. Articles were excluded if they did not meet pre-established criteria. The quality of the quantitative studies was assessed by applying Khan et al.'s methodology. Similarly, we assessed the quality of qualitative articles through an adapted version of the National Institute for Health and Care Excellence (NICE) methodology checklist. Finally, we systematically analyzed all papers that met the inclusion criteria based on a qualitative content and thematic analysis.ResultsOf the 68 papers included in the systematic review, 55 used quantitative and 13 used qualitative methods. Through the analysis of the literature we found four key themes: (i) elements that affect access to healthy eating in individuals in urban poverty, (ii) food insecurity and urban poverty, (iii) risk factors for the nutritional status of urban poor and (iv) coping strategies to limited access to food. Based on the systematization of the literature on these themes, we then proposed a conceptual framework of urban poverty and nutrition.ConclusionsThis systematic review identified distinct barriers posed by urban poverty in accessing healthy diets and its association with poorer nutrition outcomes, hence, questioning the "urban advantage". A conceptual framework emerging from the existing literature is proposed to guide future studies and policies.Systematic review registrationPROSPERO Registration number: CRD42018089788 .
| S-EPMC7816472 | biostudies-literature
Project description:BackgroundThe need for a better understanding of food consumption behaviour within its behavioural context has sparked the interest of nutrition researchers for user-documented food consumption data collected outside the research context using publicly available nutrition apps. The study aims to characterize the scientific, technical, legal and ethical features of this data in order to identify the opportunities and challenges associated with using this data for nutrition research.MethodA search for apps collecting food consumption data was conducted in October 2016 against UK Google Play and iTunes storefronts. 176 apps were selected based on user ratings and English language support. Publicly available information from the app stores and app-related websites was investigated and relevant data extracted and summarized. Our focus was on characteristics related to scientific relevance, data management and legal and ethical governance of user-documented food consumption data.ResultsFood diaries are the most common form of data collection, allowing for multiple inputs including generic food items, packaged products, or images. Standards and procedures for compiling food databases used for estimating energy and nutrient intakes remain largely undisclosed. Food consumption data is interlinked with various types of contextual data related to behavioural motivation, physical activity, health, and fitness. While exchange of data between apps is common practise, the majority of apps lack technical documentation regarding data export. There is a similar lack of documentation regarding the implemented terms of use and privacy policies. While users are usually the owners of their data, vendors are granted irrevocable and royalty free licenses to commercially exploit the data.ConclusionDue to its magnitude, diversity, and interconnectedness, user-documented food consumption data offers promising opportunities for a better understanding of habitual food consumption behaviour and its determinants. Non-standardized or non-documented food data compilation procedures, data exchange protocols and formats, terms of use and privacy statements, however, limit possibilities to integrate, process and share user-documented food consumption data. An ongoing research effort is required, to keep pace with the technical advancements of food consumption apps, their evolving data networks and the legal and ethical regulations related to protecting app users and their personal data.
| S-EPMC5994240 | biostudies-literature
Project description:Data currently generated in the field of nutrition are becoming increasingly complex and high-dimensional, bringing with them new methods of data analysis. The characteristics of machine learning (ML) make it suitable for such analysis and thus lend itself as an alternative tool to deal with data of this nature. ML has already been applied in important problem areas in nutrition, such as obesity, metabolic health, and malnutrition. Despite this, experts in nutrition are often without an understanding of ML, which limits its application and therefore potential to solve currently open questions. The current article aims to bridge this knowledge gap by supplying nutrition researchers with a resource to facilitate the use of ML in their research. ML is first explained and distinguished from existing solutions, with key examples of applications in the nutrition literature provided. Two case studies of domains in which ML is particularly applicable, precision nutrition and metabolomics, are then presented. Finally, a framework is outlined to guide interested researchers in integrating ML into their work. By acting as a resource to which researchers can refer, we hope to support the integration of ML in the field of nutrition to facilitate modern research.
| S-EPMC9776646 | biostudies-literature