Towards using NMR to screen for spoiled tomatoes stored in 1,000 L, aseptically sealed, metal-lined totes.

Nuclear magnetic resonance (NMR) spectroscopy is used to track factory relevant tomato paste spoilage. It was found that spoilage in tomato paste test samples leads to longer spin lattice relaxation times T1 using a conventional low magnetic field NMR system. The increase in T1 value for contaminated samples over a five day room temperature exposure period prompted the work to be extended to the study of industry standard, 1,000 L, non-ferrous, metal-lined totes. NMR signals and T1 values were recovered from a large format container with a single-sided NMR sensor. The results of this work suggest that a handheld NMR device can be used to study tomato paste spoilage in factory process environments

Major shifts in nutrient and phytoplankton dynamics in the North Pacific Subtropical Gyre over the last 5000 years revealed by high-resolution proteinaceous deep-sea coral δ\u3csup\u3e15\u3c/sup\u3eN and δ\u3csup\u3e13\u3c/sup\u3eC records

The North Pacific Subtropical Gyre (NPSG) is the largest continuous ecosystem on Earth and is a critical component of global oceanic biogeochemical cycling and carbon sequestration. We report here multi-millennial-scale, sub-decadal-resolution records of bulk stable nitrogen (δ15N) and carbon (δ13C) isotope records from proteinaceous deep-sea corals. Data from three Kulamanamana haumeaae specimens from the main Hawaiian Islands extend the coral-based time-series back ∼5000 yrs for the NPSG and bypass constraints of low resolution sediment cores in this oligotrophic ocean region. We interpret these records in terms of shifting biogeochemical cycles and plankton community structure, with a main goal of placing the extraordinarily rapid ecosystem biogeochemical changes documented by recent coral records during the Anthropocene in a context of broader Late-Holocene variability. During intervals where new data overlaps with previous records, there is strong correspondence in isotope values, indicating that this older data represents a direct extension of Anthropocene records. These results reveal multiple large isotopic shifts in both δ15N and δ13C values similar to or larger in magnitude to those reported in the last 150 yrs. This shows that large fluctuations in the isotopic composition of export production in this region are not unique to the recent past, but have occurred multiple times through the Mid- to Late-Holocene. However, these earlier isotopic shifts occurred over much longer time intervals (∼millennial vs. decadal timescales). Further, the δ15N data confirm that the extremely low present day δ15N values recorded by deep sea corals (∼8‰) are unprecedented for the NPSG, at least within the past five millennia. Together these records reveal centennial to millennial-scale oscillations in NPSG biogeochemical cycles. Further, these data also suggest a number of independent biogeochemical regimes during which δ15N and δ13C trends were synchronous (similar to recent coral records) or distinctly decoupled. We propose that phytoplankton species composition and nutrient source changes are the dominant mechanisms controlling the coupling and de-coupling of δ15N and δ13C values, likely primarily influenced by changing oceanographic conditions (e.g., stratification vs. entrainment). The decoupling observed in the past further suggests that oceanographic forcing and ecosystem responses controlling δ15N and δ13C values of export production have been substantially different earlier in the Holocene compared to mechanisms controlling the present day system

Carbon and nitrogen isotope fractionation of amino acids in an avian marine predator, the gentoo penguin (Pygoscelis papua)

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 5 (2015): 1278–1290, doi:10.1002/ece3.1437.Compound-specific stable isotope analysis (CSIA) of amino acids (AA) has rapidly become a powerful tool in studies of food web architecture, resource use, and biogeochemical cycling. However, applications to avian ecology have been limited because no controlled studies have examined the patterns in AA isotope fractionation in birds. We conducted a controlled CSIA feeding experiment on an avian species, the gentoo penguin (Pygoscelis papua), to examine patterns in individual AA carbon and nitrogen stable isotope fractionation between diet (D) and consumer (C) (Δ13CC-D and Δ15NC-D, respectively). We found that essential AA δ13C values and source AA δ15N values in feathers showed minimal trophic fractionation between diet and consumer, providing independent but complimentary archival proxies for primary producers and nitrogen sources respectively, at the base of food webs supporting penguins. Variations in nonessential AA Δ13CC-D values reflected differences in macromolecule sources used for biosynthesis (e.g., protein vs. lipids) and provided a metric to assess resource utilization. The avian-specific nitrogen trophic discrimination factor (TDFGlu-Phe = 3.5 ± 0.4‰) that we calculated from the difference in trophic fractionation (Δ15NC-D) of glutamic acid and phenylalanine was significantly lower than the conventional literature value of 7.6‰. Trophic positions of five species of wild penguins calculated using a multi-TDFGlu-Phe equation with the avian-specific TDFGlu-Phe value from our experiment provided estimates that were more ecologically realistic than estimates using a single TDFGlu-Phe of 7.6‰ from the previous literature. Our results provide a quantitative, mechanistic framework for the use of CSIA in nonlethal, archival feathers to study the movement and foraging ecology of avian consumers.This research was funded by National Science Foundation Office of Polar Programs [grants ANT-0125098, ANT-0739575] and the 2013 Antarctic Science Bursaries

Calibrating amino acid δ\u3csup\u3e13\u3c/sup\u3eC and δ\u3csup\u3e15\u3c/sup\u3eN offsets between polyp and protein skeleton to develop proteinaceous deep-sea corals as paleoceanographic archives.

Compound-specific stable isotopes of amino acids (CSI-AA) from proteinaceous deep-sea coral skeletons have the potential to improve paleoreconstructions of plankton community composition, and our understanding of the trophic dynamics and biogeochemical cycling of sinking organic matter in the Ocean. However, the assumption that the molecular isotopic values preserved in protein skeletal material reflect those of the living coral polyps has never been directly investigated in proteinaceous deep-sea corals. We examined CSI-AA from three genera of proteinaceous deep-sea corals from three oceanographically distinct regions of the North Pacific: Primnoa from the Gulf of Alaska, Isidella from the Central California Margin, and Kulamanamana from the North Pacific Subtropical Gyre. We found minimal offsets in the δ13C values of both essential and non-essential AAs, and in the δ15N values of source AAs, between paired samples of polyp tissue and protein skeleton. Using an essential AA δ13C fingerprinting approach, we show that estimates of the relative contribution of eukaryotic microalgae and prokaryotic cyanobacteria to the sinking organic matter supporting deep-sea corals are the same when calculated from polyp tissue or recently deposited skeletal tissue. The δ15N values of trophic AAs in skeletal tissue, on the other hand, were consistently 3–4‰ lower than polyp tissue for all three genera. We hypothesize that this offset reflects a partitioning of nitrogen flux through isotopic branch points in the synthesis of polyp (fast turnover tissue) and skeleton (slow, unidirectional incorporation). This offset indicates an underestimation, albeit correctable, of approximately half a trophic position from gorgonin protein-based deep-sea coral skeleton. Together, our observations open the door for applying many of the rapidly evolving CSI-AA based tools developed for metabolically active tissues in modern systems to archival coral tissues in a paleoceanographic context

Divergent trophic responses of sympatric penguin species to historic anthropogenic exploitation and recent climate change

The Southern Ocean is in an era of significant change. Historic overharvesting of marine mammals and recent climatic warming have cascading impacts on resource availability and, in turn, ecosystem structure and function. We examined trophic responses of sympatric chinstrap (Pygoscelis antarctica) and gentoo (Pygoscelis papua) penguins to nearly 100 y of shared environmental change in the Antarctic Peninsula region using compound-specific stable isotope analyses of museum specimens. A century ago, gentoo penguins fed almost exclusively on low-trophic level prey, such as krill, during the peak of historic overexploitation of marine mammals, which was hypothesized to have resulted in a krill surplus. In the last 40 y, gentoo penguin trophic position has increased a full level as krill declined in response to recent climate change, increased competition from recovering marine mammal populations, and the development of a commercial krill fishery. A shifting isotopic baseline supporting gentoo penguins suggests a concurrent increase in coastal productivity over this time. In contrast, chinstrap penguins exhibited no change in trophic position, despite variation in krill availability over the past century. The specialized foraging niche of chinstrap penguins likely renders them more sensitive to changes in krill availability, relative to gentoo penguins, as evinced by their declining population trends in the Antarctic Peninsula over the past 40 y. Over the next century, similarly divergent trophic and population responses are likely to occur among Antarctic krill predators if climate change and other anthropogenic impacts continue to favor generalist over specialist species

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes.

We are rapidly approaching the point where we have sequenced millions of human genomes. There is a pressing need for new data structures to store raw sequencing data and efficient algorithms for population scale analysis. Current reference-based data formats do not fully exploit the redundancy in population sequencing nor take advantage of shared genetic variation. In recent years, the Burrows-Wheeler transform (BWT) and FM-index have been widely employed as a full-text searchable index for read alignment and de novo assembly. We introduce the concept of a population BWT and use it to store and index the sequencing reads of 2705 samples from the 1000 Genomes Project. A key feature is that, as more genomes are added, identical read sequences are increasingly observed, and compression becomes more efficient. We assess the support in the 1000 Genomes read data for every base position of two human reference assembly versions, identifying that 3.2 Mbp with population support was lost in the transition from GRCh37 with 13.7 Mbp added to GRCh38. We show that the vast majority of variant alleles can be uniquely described by overlapping 31-mers and show how rapid and accurate SNP and indel genotyping can be carried out across the genomes in the population BWT. We use the population BWT to carry out nonreference queries to search for the presence of all known viral genomes and discover human T-lymphotropic virus 1 integrations in six samples in a recognized epidemiological distribution

Transparency of Regulatory Data across the European Medicines Agency, Health Canada, and US Food and Drug Administration

Based on an analysis of relevant laws and policies, regulator data portals, and information requests, we find that clinical data, including clinical study reports, submitted to the European Medicines Agency and Health Canada to support approval of medicines are routinely made publicly available

Physiological Differences Between Low Versus High Skeletal Muscle Hypertrophic Responders to Resistance Exercise Training: Current Perspectives and Future Research Directions

Numerous reports suggest there are low and high skeletal muscle hypertrophic responders following weeks to months of structured resistance exercise training (referred to as low and high responders herein). Specifically, divergent alterations in muscle fiber cross sectional area (fCSA), vastus lateralis thickness, and whole body lean tissue mass have been shown to occur in high versus low responders. Differential responses in ribosome biogenesis and subsequent protein synthetic rates during training seemingly explain some of this individual variation in humans, and mechanistic in vitro and rodent studies provide further evidence that ribosome biogenesis is critical for muscle hypertrophy. High responders may experience a greater increase in satellite cell proliferation during training versus low responders. This phenomenon could serve to maintain an adequate myonuclear domain size or assist in extracellular remodeling to support myofiber growth. High responders may also express a muscle microRNA profile during training that enhances insulin-like growth factor-1 (IGF-1) mRNA expression, although more studies are needed to better validate this mechanism. Higher intramuscular androgen receptor protein content has been reported in high versus low responders following training, and this mechanism may enhance the hypertrophic effects of testosterone during training. While high responders likely possess “good genetics,” such evidence has been confined to single gene candidates which typically share marginal variance with hypertrophic outcomes following training (e.g., different myostatin and IGF-1 alleles). Limited evidence also suggests pre-training muscle fiber type composition and self-reported dietary habits (e.g., calorie and protein intake) do not differ between high versus low responders. Only a handful of studies have examined muscle biomarkers that are differentially expressed between low versus high responders. Thus, other molecular and physiological variables which could potentially affect the skeletal muscle hypertrophic response to resistance exercise training are also discussed including rDNA copy number, extracellular matrix and connective tissue properties, the inflammatory response to training, and mitochondrial as well as vascular characteristics