Ecological Impacts of the 2015/16 El Niño in the Central Equatorial Pacific

The authors thank Cisco Werner (NOAA/NMFS) for proposing this special issue and encouraging our submission. We thank each of the editors, Stephanie Herring, Peter Stott, and Nikos Christidis, for helpful guidance and support throughout the submittal process. We also thank each of the anonymous external reviewers for thoughtful guidance and suggestions to improve the manuscript. REB, TO, RV, AH, and BVA are grateful for support from the NOAA Coral Reef Conservation Program. AC acknowledges support from the National Science Foundation for the following awards: OCE 1537338, OCE 1605365, and OCE 1031971. This is PMEL contribution no. 4698. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. government. The views expressed in the article are not necessarily those of the U.S. government. (NOAA Coral Reef Conservation Program; OCE 1537338 - National Science Foundation; OCE 1605365 - National Science Foundation; OCE 1031971 - National Science Foundation

Integration of Genome and Chromatin Structure with Gene Expression Profiles To Predict c-MYC Recognition Site Binding and Function

The MYC genes encode nuclear sequence specific–binding DNA-binding proteins that are pleiotropic regulators of cellular function, and the c-MYC proto-oncogene is deregulated and/or mutated in most human cancers. Experimental studies of MYC binding to the genome are not fully consistent. While many c-MYC recognition sites can be identified in c-MYC responsive genes, other motif matches—even experimentally confirmed sites—are associated with genes showing no c-MYC response. We have developed a computational model that integrates multiple sources of evidence to predict which genes will bind and be regulated by MYC in vivo. First, a Bayesian network classifier is used to predict those c-MYC recognition sites that are most likely to exhibit high-occupancy binding in chromatin immunoprecipitation studies. This classifier incorporates genomic sequence, experimentally determined genomic chromatin acetylation islands, and predicted methylation status from a computational model estimating the likelihood of genomic DNA methylation. We find that the predictions from this classifier are also applicable to other transcription factors, such as cAMP-response element-binding protein, whose binding sites are sensitive to DNA methylation. Second, the MYC binding probability is combined with the gene expression profile data from nine independent microarray datasets in multiple tissues. Finally, we may consider gene function annotations in Gene Ontology to predict the c-MYC targets. We assess the performance of our prediction results by comparing them with the c-myc targets identified in the biomedical literature. In total, we predict 460 likely c-MYC target genes in the human genome, of which 67 have been reported to be both bound and regulated by MYC, 68 are bound by MYC, and another 80 are MYC-regulated. The approach thus successfully identifies many known c-MYC targets and suggests many novel sites. Our findings suggest that to identify c-MYC genomic targets, integration of different data sources helps to improve the accuracy

Identifying nonalcoholic fatty liver disease patients with active fibrosis by measuring extracellular matrix remodeling rates in tissue and blood.

Excess collagen synthesis (fibrogenesis) in the liver plays a causal role in the progression of nonalcoholic fatty liver disease (NAFLD). Methods are needed to identify patients with more rapidly progressing disease and to demonstrate early response to treatment. We describe here a novel method to quantify hepatic fibrogenesis flux rates both directly in liver tissue and noninvasively in blood. Twenty-one patients with suspected NAFLD ingested heavy water (2 H2 O, 50-mL aliquots) two to three times daily for 3-5 weeks prior to a clinically indicated liver biopsy. Liver collagen fractional synthesis rate (FSR) and plasma lumican FSR were measured based on 2 H labeling using tandem mass spectrometry. Patients were classified by histology for fibrosis stage (F0-F4) and as having nonalcoholic fatty liver or nonalcoholic steatohepatitis (NASH). Magnetic resonance elastography measurements of liver stiffness were also performed. Hepatic collagen FSR in NAFLD increased with advancing disease stage (e.g., higher in NASH than nonalcoholic fatty liver, positive correlation with fibrosis score and liver stiffness) and correlated with hemoglobin A1C. In addition, plasma lumican FSR demonstrated a significant correlation with hepatic collagen FSR.ConclusionUsing a well-characterized cohort of patients with biopsy-proven NAFLD, this study demonstrates that hepatic scar in NASH is actively remodeled even in advanced fibrosis, a disease that is generally regarded as static and slowly progressive. Moreover, hepatic collagen FSR correlates with established risks for fibrotic disease progression in NASH, and plasma lumican FSR correlates with hepatic collagen FSR, suggesting applications as direct or surrogate markers, respectively, of hepatic fibrogenesis in humans. (Hepatology 2017;65:78-88)

Human interaction with the divine, the sacred, and the deceased: topics that warrant increased attention by psychologists

Humans have likely been attempting to communicate with entities believed to exist, such as the divine, sacred beings, and deceased people, since the dawn of time. Across cultures and countries, many believe that interaction with the immaterial world is not only possible but a frequent experience. Most religious traditions across the globe focus many rituals and activities around prayer to an entity deemed divine or sacred. Additionally, many people–religious, agnostic, and atheists alike–report communication with their departed loved ones. During highly stressful times associated with natural disasters, war, pandemics, and other threats to human life, the frequency and intensity of these activities and associated experiences substantially increase. Although this very human phenomenon seems to be universal, the empirical literature on the topic within psychology is thin. This paper discussed the topic and reviews what we know from the professional literature about how people perceive communication with these unseen entities. It highlights the perceptual and social cognition evidence and discussed the role of attribution theory, which might help us understand the beliefs, motivations, and practices of those engaged with communication with the unseen. Empirical laboratory research with mediums is discussed as well, examining the evidence for communication with the deceased. Final reflections and suggestions for future research are also offered

The MUSICA IASI CH4 and N2O products and their comparison to HIPPO, GAW and NDACC FTIR references

This work presents the methane (CH4) and nitrous oxide (N2O) products as generated by the IASI (Infrared Atmospheric Sounding Interferometer) processor developed during the project MUSICA (MUlti-platform remote Sensing of Isotopologues for investigating the Cycle of Atmospheric water). The processor retrieves CH4 and N2O with different water vapour and water vapour isotopologues (as well as HNO3) and uses a single a priori data set for all the retrievals (no variation in space and time). Firstly, the characteristics and errors of the products are analytically described. Secondly, the products are comprehensively evaluated by comparisons to the following reference data measured by different techniques and from different platforms as follows: (1) aircraft CH4 and N2O profiles from the five HIAPER Pole-to-Pole Observation (HIPPO) missions; (2) continuous in situ CH4 and N2O observations performed between 2007 and 2017 at subtropical and mid-latitude highmountain observatories (Izaña Atmospheric Observatory and Jungfraujoch, respectively) in the framework of the WMO–GAW (World Meteorological Organization–Global Atmosphere Watch) programme; (3) ground-based FTIR (Fouriertransform infrared spectrometer) measurements made between 2007 and 2017 in the framework of the NDACC (Network for the Detection of Atmospheric Composition Change) at the subtropical Izaña Atmospheric Observatory, the mid-latitude station of Karlsruhe and the Kiruna polar site. The theoretical estimations and the comparison studies suggest a precision for the N2O and CH4 retrieval products of about 1.5–3% and systematic errors due to spectroscopic parameters of about 2 %. The MUSICA IASI CH4 data offer a better sensitivity than N2O data. While for the latter the sensitivity is mainly limited to the UTLS (upper troposphere–lower stratosphere) region, for CH4 we are able to prove that at low latitudes the MUSICA IASI processor can detect variations that take place in the free troposphere independently from the variations in the UTLS region.We demonstrate that the MUSICA IASI data qualitatively capture the CH4 gradients between low and high latitudes and between the Southern Hemisphere and Northern Hemisphere; however, we also find an inconsistency between low- and high-latitude CH4 data of up to 5 %. The N2O latitudinal gradients are very weak and cannot be detected. We make comparisons over a 10-year time period and analyse the agreement with the reference data on different timescales. The MUSICA IASI data can detect day-to-day signals (only in the UTLS), seasonal cycles and long-term evolution (in the UTLS and for CH4 also in the free troposphere) similar to the reference data; however, there are also inconsistencies in the long-term evolution connected to inconsistencies in the used atmospheric temperature a priori data. Moreover, we present a method for analytically describing the a posteriori-calculated logarithmic-scale difference of the CH4 and N2O retrieval estimates. By correcting errors that are common in the CH4 and N2O retrieval products, the a posteriori-calculated difference can be used for generating an a posteriori-corrected CH4 product with a theoretically better precision than the original CH4 retrieval products. We discuss and evaluate two different approaches for such a posteriori corrections. It is shown that the correction removes the inconsistencies between low and high latitudes and enables the detection of day-to-day signals also in the free troposphere. Furthermore, they reduce the impact of short-term atmospheric dynamics, which is an advantage, because respective signals are presumably hardly comparable to model data. The approach that affects the correction solely on the scales on which the errors dominate is identified as the most efficient, because it reduces the inconsistencies and errors without removing measurable real atmospheric signals. We give a brief outlook on a possible usage of this a posterioricorrected MUSICA IASI CH4 product in combination with inverse modelling

Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades.

BackgroundCurrently, much is unknown about the taxonomic diversity and the mechanisms of methane metabolism in the Florida Everglades ecosystem. The Loxahatchee National Wildlife Refuge is a section of the Florida Everglades that is almost entirely unstudied in regard to taxonomic profiling. This short report analyzes the metagenome of soil samples from this Refuge to investigate the predominant taxa, as well as the abundance of genes involved in environmentally significant metabolic pathways related to methane production (nitrogen fixation and dissimilatory sulfite reduction).MethodsShotgun metagenomic sequencing using the Illumina platform was performed on 17 soil samples from four different sites within the Loxahatchee National Wildlife Refuge, and underwent quality control, assembly, and annotation. The soil from each sample was tested for water content and concentrations of organic carbon and nitrogen.ResultsThe three most common phyla of bacteria for every site were Actinobacteria, Acidobacteria, and Proteobacteria; however, there was variation in relative phylum composition. The most common phylum of Archaea was Euryarchaeota for all sites. Alpha and beta diversity analyses indicated significant congruity in taxonomic diversity in most samples from Sites 1, 3, and 4 and negligible congruity between Site 2 and the other sites. Shotgun metagenomic sequencing revealed the presence of biogeochemical biomarkers of particular interest (e.g., mrcA, nifH, and dsrB) within the samples. The normalized abundances of mcrA, nifH, and dsrB exhibited a positive correlation with nitrogen concentration and water content, and a negative correlation with organic carbon concentration.ConclusionThis Everglades soil metagenomic study allowed examination of wetlands biological processes and showed expected correlations between measured organic constituents and prokaryotic gene frequency. Additionally, the taxonomic profile generated gives a basis for the diversity of prokaryotic microbial life throughout the Everglades

Proteome Analyses of Strains Cyanothece ATCC 51142 and PCC 7822 of the Diazotrophic Cyanobacterium Cyanothece sp. Under Culture Conditions Resulting in Enhanced H2 Production.

Cultures of the cyanobacterial genus Cyanothece have been shown to produce high levels of biohydrogen. These strains are diazotrophic and undergo pronounced diurnal cycles when grown under N2-fixing conditions in light-dark cycles. We seek to better understand the way in which proteins respond to these diurnal changes, and we performed quantitative proteome analysis of Cyanothecesp. strains ATCC 51142 and PCC 7822 grown under 8 different nutritional conditions. Nitrogenase expression was limited to N2-fixing conditions, and in the absence of glycerol, nitrogenase gene expression was linked to the dark period. However, glycerol induced expression of nitrogenase during part of the light period, together with cytochrome c oxidase (Cox), glycogen phosphorylase (Glp), and glycolytic and pentose phosphate pathway (PPP) enzymes. This indicated that nitrogenase expression in the light was facilitated via higher levels of respiration and glycogen breakdown. Key enzymes of the Calvin cycle were inhibited in Cyanothece ATCC 51142 in the presence of glycerol under H2-producing conditions, suggesting a competition between these sources of carbon. However, in Cyanothece PCC 7822, the Calvin cycle still played a role in cofactor recycling during H2 production. Our data comprise the first comprehensive profiling of proteome changes in Cyanothece PCC 7822 and allow an in-depth comparative analysis of major physiological and biochemical processes that influence H2 production in both strains. Our results revealed many previously uncharacterized proteins that may play a role in nitrogenase activity and in other metabolic pathways and may provide suitable targets for genetic manipulation that would lead to improvement of large-scale H2 production

Astro2020 Science White Paper: Triggered High-Priority Observations of Dynamic Solar System Phenomena

Unexpected dynamic phenomena have surprised solar system observers in the past and have led to important discoveries about solar system workings. Observations at the initial stages of these events provide crucial information on the physical processes at work. We advocate for long-term/permanent programs on ground-based and space-based telescopes of all sizes - including Extremely Large Telescopes (ELTs) - to conduct observations of high-priority dynamic phenomena, based on a predefined set of triggering conditions. These programs will ensure that the best initial dataset of the triggering event are taken; separate additional observing programs will be required to study the temporal evolution of these phenomena. While not a comprehensive list, the following are notional examples of phenomena that are rare, that cannot be anticipated, and that provide high-impact advances to our understandings of planetary processes. Examples include: new cryovolcanic eruptions or plumes on ocean worlds; impacts on Jupiter, Saturn, Uranus, or Neptune; extreme eruptions on Io; convective superstorms on Saturn, Uranus, or Neptune; collisions within the asteroid belt or other small-body populations; discovery of an interstellar object passing through our solar system (e.g. 'Oumuamua); and responses of planetary atmospheres to major solar flares or coronal mass ejections.Comment: Astro2020 white pape

Cytokinin Determines Thiol-Mediated Arsenic Tolerance and Accumulation

The presence of arsenic in soil and water is a constant threat to plant growth in many regions of the world. Phytohormones act in the integration of growth control and stress response, but their role in plant responses to arsenic remains to be elucidated. Here, we show that arsenate [As(V)], the most prevalent arsenic chemical species in nature, causes severe depletion of endogenous cytokinins (CKs) in the model plant Arabidopsis (Arabidopsis thaliana). We found that CK signaling mutants and transgenic plants with reduced endogenous CK levels showed an As(V)-tolerant phenotype. Our data indicate that in CK-depleted plants exposed to As(V), transcript levels of As(V)/phosphate-transporters were similar or even higher than in wild-type plants. In contrast, CK depletion provoked the coordinated activation of As(V) tolerance mechanisms, leading to the accumulation of thiol compounds such as phytochelatins and glutathione, which are essential for arsenic sequestration. Transgenic CK-deficient Arabidopsis and tobacco lines show a marked increase in arsenic accumulation. Our findings indicate that CK is an important regulatory factor in plant adaptation to arsenic stress