Contemporary visions of progress in ecology and thoughts for the future

Although ecological research is progressing rapidly, the answers to certain key questions continue to elude us. This paper considers several of the contemporary challenges facing ecology. (1) Terminology is voluminous and often poorly defined, resulting in inefficient communication. (2) The concept of scale affects our inferences about system structure and function, requiring us to continue an almost heuristic investigation of breaks, domains, and integration. New tools that more explicitly incorporate scalar issues will need to be developed for progress to take place in the field of ecology. (3) Increasingly, it is expected that applied questions will be solved in less than a year. This demand for solutions from ecologists often produces short-term and inadequate responses. (4) How can ecologists improve communication between subdisciplines, with undergraduate students, and with the public? How will ecology be done in the future, and by whom? We provide some background to these observations and questions, and offer some potential solutions from the viewpoint of young practicing ecologists

Allele-specific Characterization of Alanine: Glyoxylate Aminotransferase Variants Associated with Primary Hyperoxaluria

Primary Hyperoxaluria Type 1 (PH1) is a rare autosomal recessive kidney stone disease caused by deficiency of the peroxisomal enzyme alanine: glyoxylate aminotransferase (AGT), which is involved in glyoxylate detoxification. Over 75 different missense mutations in AGT have been found associated with PH1. While some of the mutations have been found to affect enzyme activity, stability, and/or localization, approximately half of these mutations are completely uncharacterized. In this study, we sought to systematically characterize AGT missense mutations associated with PH1. To facilitate analysis, we used two high-throughput yeast-based assays: one that assesses AGT specific activity, and one that assesses protein stability. Approximately 30% of PH1-associated missense mutations are found in conjunction with a minor allele polymorphic variant, which can interact to elicit complex effects on protein stability and trafficking. To better understand this allele interaction, we functionally characterized each of 34 mutants on both the major (wild-type) and minor allele backgrounds, identifying mutations that synergize with the minor allele. We classify these mutants into four distinct categories depending on activity/stability results in the different alleles. Twelve mutants were found to display reduced activity in combination with the minor allele, compared with the major allele background. When mapped on the AGT dimer structure, these mutants reveal localized regions of the protein that appear particularly sensitive to interactions with the minor allele variant. While the majority of the deleterious effects on activity in the minor allele can be attributed to synergistic interaction affecting protein stability, we identify one mutation, E274D, that appears to specifically affect activity when in combination with the minor allele

Alkenone producers inferred from well-preserved 18S rDNA in Greenland lake sediments

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 111 (2006): G03013, doi:10.1029/2005JG000121.The 18S ribosomal DNA (rDNA) sequences of haptophyte algae were successfully amplified using the polymerase chain reaction (PCR) from water filtrate, surface sediments, and a late-Holocene sediment sample (∼1000 years old) from a group of lakes in the Søndre Strømfjord region of west Greenland. The DNA of the algal primary producer is extremely well preserved in the laminated lake sediments which have been deposited in cold (1°–2°C), anoxic, and sulphidic bottom water. Phylogenetic analyses of the Greenland haptophyte rDNA sequences suggest that alkenones in the Greenland lake sediments are produced by haptophyte algae of the class Prymnesiophyceae. The 18S rDNA sequences from the Greenland samples cluster within a distinct phylotype, differing from both marine haptophytes and from those reported previously from Ace Lake, Antarctica. The similarity of haptophyte rDNA sequences among all samples in this study suggests a single alkenone-based temperature calibration may be applied to these lakes for at least the past 1000 years. These sedimentary archives hold great promise for high-resolution, alkenone-based paleotemperature reconstruction of southern west Greenland, a region sensitive to atmospheric-oceanic climate phenomena such as the North Atlantic Oscillation (NAO).This work was supported by grants from the National Science Foundation (NSF0081478, 0318050, 0318123, 0402383, 0520718), NASA (NAG5-10665, NNG04GJ34G) and the American Chemical Society, Petroleum Research Fund (ACS-PRF38878-AC2) to Y. Huang

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Group IV: mutants defective in activity only.

<p>(A) Indicated mutations in AGTma were tested for effects on activity (left) or stability (right). Growth of mutants was normalized to % growth of wild-type AGTma. Average and standard error of at least three independent assays is presented. (B). Comparison of growth in activity (left) or stability (right) assay of each mutant in AGTma or AGTmi. The growth difference was obtained by normalizing growth of each mutant to either AGTma or AGTmi, as appropriate, and subtracting the difference. Mutants indicated with an asterik (**) indicate samples in which normalized growth in AGTma vs AGTmi was significantly different (p<.05).</p

Group II: mutants defective in activity/stability, greater effects in AGTmi allele.

<p>Indicated mutations in AGTma (top) or AGTmi (bottom) were tested for effects on activity (<b>A</b>) or stability (<b>B</b>). Growth of mutants was normalized to % growth of wild-type AGTma (top) or AGTmi (bottom). Average and standard error of at least three independent assays is presented.</p

Biochemical characterization of AGTmi E274D.

<p>(<b>A</b>) Enzymatic activity of bacterially-purified AGTmi-his compared with AGTmi E274D-his. (<b>B</b>) Absorbance spectra of 10 μM AGTmi E274D or AGTmi in the presence of 100 μM PLP in 100 mM potassium phosphate buffer (pH 7.4). (<b>C</b>) Fluorescence emission spectra (excitation at 280 nm) of AGTmi and AGTmi E274D at 1 μM enzyme concentration in the presence of 100 μM PLP in 100 mM potassium phosphate buffer (pH 7.4).</p

List of PH1-associated mutations tested.

<p>List of PH1-associated mutations tested.</p