A Case Study Tested Framework for Multivariate Analyses of Microbiomes: Software for Microbial Community Comparisons

The study of microbiomes is important because our understanding of microbial communities is providing insight into human health and many other areas of interest. Researchers often use genomic data to study microbial organisms, demonstrating differences from one organism to the next. Metagenomic data is utilized to study communities of microbial organisms. The research described herein involved the development of a collection of computational methods. This suite of computational methods and tools (written in the R and Perl languages) has become a framework used for metagenomic data analysis and result visualization. Multivariate analyses such as Linear Discriminate Analysis (LDA) are used to determine which microbial organisms are useful in distinguishing between microbial communities. The differences between communities are visualized in two or three dimensions using dimensional reduction techniques. Other analyses provided by the framework include, but are not limited to, feature selection, cross-validation, multi-objective optimization, side-by-side comparisons of communities, and identification of core members in a microbial community. The effectiveness of these methods and techniques was verified in multiple real world case studies such as body fat classification of elk using a fecal microbiome, identification of important changes in community composition when permafrost is thawed, and longitudinal classification of intestinal locations. The fecal microbiome may be used in the future to assist in assessing the health of animal populations using non-invasive samples. Additionally, the analysis of thawing permafrost may yield insight into the release of greenhouse gases into the atmosphere, furthering our understanding of global warming. Our understanding of the intestinal microbiome may someday grant us understanding and control of our intestinal well being, which plays a significant factor in immune system response and overall health

Standardized NEON organismal data for biodiversity research

Understanding patterns and drivers of species distribution and abundance, and thus biodiversity, is a core goal of ecology. Despite advances in recent decades, research into these patterns and processes is currently limited by a lack of standardized, high-quality, empirical data that span large spatial scales and long time periods. The NEON fills this gap by providing freely available observational data that are generated during robust and consistent organismal sampling of several sentinel taxonomic groups within 81 sites distributed across the United States and will be collected for at least 30 years. The breadth and scope of these data provide a unique resource for advancing biodiversity research. To maximize the potential of this opportunity, however, it is critical that NEON data be maximally accessible and easily integrated into investigators\u27 workflows and analyses. To facilitate its use for biodiversity research and synthesis, we created a workflow to process and format NEON organismal data into the ecocomDP (ecological community data design pattern) format that were available through the ecocomDP R package; we then provided the standardized data as an R data package (neonDivData). We briefly summarize sampling designs and data wrangling decisions for the major taxonomic groups included in this effort. Our workflows are open-source so the biodiversity community may: add additional taxonomic groups; modify the workflow to produce datasets appropriate for their own analytical needs; and regularly update the data packages as more observations become available. Finally, we provide two simple examples of how the standardized data may be used for biodiversity research. By providing a standardized data package, we hope to enhance the utility of NEON organismal data in advancing biodiversity research and encourage the use of the harmonized ecocomDP data design pattern for community ecology data from other ecological observatory networks

Mitochondria-localized AMPK responds to local energetics and contributes to exercise and energetic stress-induced mitophagy

Mitochondria form a complex, interconnected reticulum that is maintained through coordination among biogenesis, dynamic fission, and fusion and mitophagy, which are initiated in response to various cues to maintain energetic homeostasis. These cellular events, which make up mitochondrial quality control, act with remarkable spatial precision, but what governs such spatial specificity is poorly understood. Herein, we demonstrate that specific isoforms of the cellular bioenergetic sensor, 5′ AMP-activated protein kinase (AMPKα1/α2/β2/γ1), are localized on the outer mitochondrial membrane, referred to as mitoAMPK, in various tissues in mice and humans. Activation of mitoAMPK varies across the reticulum in response to energetic stress, and inhibition of mitoAMPK activity attenuates exercise-induced mitophagy in skeletal muscle in vivo. Discovery of a mitochondrial pool of AMPK and its local importance for mitochondrial quality control underscores the complexity of sensing cellular energetics in vivo that has implications for targeting mitochondrial energetics for disease treatment

A Future for the Dead Sea Basin: Water Culture among Israelis, Palestinians and Jordanians

The Dead Sea basin plays a major role for regional economic development (industry, tourism and agriculture) in the Middle East. This potential is threatened by the steady disappearance of the Dead Sea. Since around 1930 the water level of the Dead Sea has fallen by about 25 m, about half of this alone in the last 20 years. The Dead Sea is a transboundary resource shared by Israel, the Palestinian Authority and Jordan. The Dead Sea is the terminal point of the Jordan River watershed and as such, it serves as a barometer for the health of the overall system. Its rapid decline reflects the present water management strategies of the riparian and upstream countries. This includes the different water cultures of the three countries. Throughout history, the Dead Sea basin has served as a source of refuge and inspiration for followers of Judaism, Christianity and Islam. Today, the religious significance of the Dead Sea is being overshadowed by its rapid disappearance. This may be explained in part by the water cultures of the three countries that influence water policy in the region. Ideology, together with culture and tradition, such as that of Zionism in Israel, has played a central role in water development in the region. In many cases, this has been at the expense of the environment. Elements pertaining to environmental security and water culture and tradition, whereby a sustainably managed environment provides for social, economic as well as environmental benefits are evident with regards the Dead Sea. The decline for example, undermines its potential as a tourist destination, despite the enormous investment in hotel and resort infrastructures in Israel and in Jordan. The decline also raises ethical issues about the exploitation of water resources by present generations at the expense of this natural heritage to future generations. This paper provides an analysis of a European Union funded project whose aims are to synthesize and assess existing physical and socio-economic data and to assess options for a better future for the Dead Sea. It will identify the patterns of water supply and use in the region, and the factors that control these patterns, including those of water culture. The underlying assumption is that solutions for a more sustainable development than todays scenario will not come from simply providing more water for more development, but from a new land and water management system, indeed ethic, that is sensitive to social, cultural and ecological resources thereby providing security and stability across cultures, economic sectors and nations

Association of the PHACTR1/EDN1 genetic locus with spontaneous coronary artery dissection

Background: Spontaneous coronary artery dissection (SCAD) is an increasingly recognized cause of acute coronary syndromes (ACS) afflicting predominantly younger to middle-aged women. Observational studies have reported a high prevalence of extracoronary vascular anomalies, especially fibromuscular dysplasia (FMD) and a low prevalence of coincidental cases of atherosclerosis. PHACTR1/EDN1 is a genetic risk locus for several vascular diseases, including FMD and coronary artery disease, with the putative causal noncoding variant at the rs9349379 locus acting as a potential enhancer for the endothelin-1 (EDN1) gene. Objectives: This study sought to test the association between the rs9349379 genotype and SCAD. Methods: Results from case control studies from France, United Kingdom, United States, and Australia were analyzed to test the association with SCAD risk, including age at first event, pregnancy-associated SCAD (P-SCAD), and recurrent SCAD. Results: The previously reported risk allele for FMD (rs9349379-A) was associated with a higher risk of SCAD in all studies. In a meta-analysis of 1,055 SCAD patients and 7,190 controls, the odds ratio (OR) was 1.67 (95% confidence interval [CI]: 1.50 to 1.86) per copy of rs9349379-A. In a subset of 491 SCAD patients, the OR estimate was found to be higher for the association with SCAD in patients without FMD (OR: 1.89; 95% CI: 1.53 to 2.33) than in SCAD cases with FMD (OR: 1.60; 95% CI: 1.28 to 1.99). There was no effect of genotype on age at first event, P-SCAD, or recurrence. Conclusions: The first genetic risk factor for SCAD was identified in the largest study conducted to date for this condition. This genetic link may contribute to the clinical overlap between SCAD and FMD

Harnessing the NEON data revolution to advance open environmental science with a diverse and data-capable community

It is a critical time to reflect on the National Ecological Observatory Network (NEON) science to date as well as envision what research can be done right now with NEON (and other) data and what training is needed to enable a diverse user community. NEON became fully operational in May 2019 and has pivoted from planning and construction to operation and maintenance. In this overview, the history of and foundational thinking around NEON are discussed. A framework of open science is described with a discussion of how NEON can be situated as part of a larger data constellation—across existing networks and different suites of ecological measurements and sensors. Next, a synthesis of early NEON science, based on >100 existing publications, funded proposal efforts, and emergent science at the very first NEON Science Summit (hosted by Earth Lab at the University of Colorado Boulder in October 2019) is provided. Key questions that the ecology community will address with NEON data in the next 10 yr are outlined, from understanding drivers of biodiversity across spatial and temporal scales to defining complex feedback mechanisms in human–environmental systems. Last, the essential elements needed to engage and support a diverse and inclusive NEON user community are highlighted: training resources and tools that are openly available, funding for broad community engagement initiatives, and a mechanism to share and advertise those opportunities. NEON users require both the skills to work with NEON data and the ecological or environmental science domain knowledge to understand and interpret them. This paper synthesizes early directions in the community’s use of NEON data, and opportunities for the next 10 yr of NEON operations in emergent science themes, open science best practices, education and training, and community building