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- 2019
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Journal article (peer-reviewed)
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| 2. |
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| 3. |
- Falster, Daniel, et al.
(author)
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AusTraits, a curated plant trait database for the Australian flora
- 2021
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In: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Journal article (peer-reviewed)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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| 4. |
- Hindell, Mark A., et al.
(author)
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Circumpolar habitat use in the southern elephant seal : implications for foraging success and population trajectories
- 2016
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In: Ecosphere. - : Wiley. - 2150-8925 .- 2150-8925. ; 7:5
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Journal article (peer-reviewed)abstract
- In the Southern Ocean, wide-ranging predators offer the opportunity to quantify how animals respond to differences in the environment because their behavior and population trends are an integrated signal of prevailing conditions within multiple marine habitats. Southern elephant seals in particular, can provide useful insights due to their circumpolar distribution, their long and distant migrations and their performance of extended bouts of deep diving. Furthermore, across their range, elephant seal populations have very different population trends. In this study, we present a data set from the International Polar Year project; Marine Mammals Exploring the Oceans Pole to Pole for southern elephant seals, in which a large number of instruments (N = 287) deployed on animals, encompassing a broad circum-Antarctic geographic extent, collected in situ ocean data and at-sea foraging metrics that explicitly link foraging behavior and habitat structure in time and space. Broadly speaking, the seals foraged in two habitats, the relatively shallow waters of the Antarctic continental shelf and the Kerguelen Plateau and deep open water regions. Animals of both sexes were more likely to exhibit area-restricted search (ARS) behavior rather than transit in shelf habitats. While Antarctic shelf waters can be regarded as prime habitat for both sexes, female seals tend to move northwards with the advance of sea ice in the late autumn or early winter. The water masses used by the seals also influenced their behavioral mode, with female ARS behavior being most likely in modified Circumpolar Deepwater or northerly Modified Shelf Water, both of which tend to be associated with the outer reaches of the Antarctic Continental Shelf. The combined effects of (1) the differing habitat quality, (2) differing responses to encroaching ice as the winter progresses among colonies, (3) differing distances between breeding and haul-out sites and high quality habitats, and (4) differing long-term -regional trends in sea ice extent can explain the differing population trends observed among elephant seal colonies.
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| 5. |
- Huang, Yi Shu, et al.
(author)
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Pharmacological modulation of T cell immunity results in long-term remission of autoimmune arthritis
- 2021
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 1091-6490. ; 118:19
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Journal article (peer-reviewed)abstract
- Chronic inflammatory diseases like rheumatoid arthritis are characterized by a deficit in fully functional regulatory T cells. DNA-methylation inhibitors have previously been shown to promote regulatory T cell responses and, in the present study, we evaluated their potential to ameliorate chronic and acute animal models of rheumatoid arthritis. Of the drugs tested, decitabine was the most effective, producing a sustained therapeutic effect that was dependent on indoleamine 2,3-dioxygenase (IDO) and was associated with expansion of induced regulatory T cells, particularly at the site of disease activity. Treatment with decitabine also caused apoptosis of Th1 and Th17 cells in active arthritis in a highly selective manner. The molecular basis for this selectivity was shown to be ENT1, a nucleoside transporter, which facilitates intracellular entry of the drug and is up-regulated on effector T cells during active arthritis. It was further shown that short-term treatment with decitabine resulted in the generation of a population of regulatory T cells that were able to suppress arthritis upon adoptive transfer. In summary, a therapeutic approach using an approved drug is described that treats active inflammatory disease effectively and generates robust regulatory T cells with the IDO-dependent capacity to maintain remission.
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| 6. |
- Kern, Jan, et al.
(author)
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Room temperature femtosecond X-ray diffraction of photosystem II microcrystals
- 2012
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:25, s. 9721-9726
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Journal article (peer-reviewed)abstract
- Most of the dioxygen on earth is generated by the oxidation of water by photosystem II (PS II) using light from the sun. This lightdriven, four-photon reaction is catalyzed by the Mn4CaO5 cluster located at the lumenal side of PS II. Various X-ray studies have been carried out at cryogenic temperatures to understand the intermediate steps involved in the water oxidation mechanism. However, the necessity for collecting data at room temperature, especially for studying the transient steps during the O-O bond formation, requires the development of new methodologies. In this paper we report room temperature X-ray diffraction data of PS II microcrystals obtained using ultrashort (<50 fs) 9 keV X-ray pulses from a hard X-ray free electron laser, namely the Linac Coherent Light Source. The results presented here demonstrate that the probe before destroy approach using an X-ray free electron laser works even for the highly-sensitive Mn4CaO5 cluster in PS II at room temperature. We show that these data are comparable to those obtained in synchrotron radiation studies as seen by the similarities in the overall structure of the helices, the protein subunits and the location of the various cofactors. This work is, therefore, an important step toward future studies for resolving the structure of the Mn4CaO5 cluster without any damage at room temperature, and of the reaction intermediates of PS II during O-O bond formation.
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| 7. |
- Laksmono, Hartawan, et al.
(author)
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Anomalous Behavior of the Homogeneous Ice Nucleation Rate in No-Man's Land
- 2015
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In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 6:14, s. 2826-2832
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Journal article (peer-reviewed)abstract
- We present an analysis of ice nucleation kinetics from near-ambient pressure water as temperature decreases below the homogeneous limit T-H by cooling micrometer-sized droplets (microdroplets) evaporatively at 10(3)-10(4) K/s and probing the structure ultrafast using femtosecond pulses from the Linac Coherent Light Source (LCLS) free-electron X-ray laser. Below 232 K, we observed a slower nucleation rate increase with decreasing temperature than anticipated from previous measurements, which we suggest is due to the rapid decrease in water's diffusivity. This is consistent with earlier findings that microdroplets do not crystallize at <227 K, but vitrify at cooling rates of 10(6)-10(7) K/s. We also hypothesize that the slower increase in the nucleation rate is connected with the proposed fragile-to-strong transition anomaly in water.
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| 8. |
- Popp, David, et al.
(author)
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Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser
- 2017
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In: CYTOSKELETON. - : WILEY. - 1949-3584 .- 1949-3592. ; 74:12, s. 472-481
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Journal article (peer-reviewed)abstract
- A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked -strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual -synuclein amyloids.
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| 9. |
- Pälike, Heiko, et al.
(author)
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A Cenozoic record of the equatorial Pacific carbonate compensation depth
- 2012
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 488:7413, s. 609-614
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Journal article (peer-reviewed)abstract
- Atmospheric carbon dioxide concentrations and climate are regulated on geological timescales by the balance between carbon input from volcanic and metamorphic outgassing and its removal by weathering feedbacks; these feedbacks involve the erosion of silicate rocks and organic-carbon-bearing rocks. The integrated effect of these processes is reflected in the calcium carbonate compensation depth, which is the oceanic depth at which calcium carbonate is dissolved. Here we present a carbonate accumulation record that covers the past 53 million years from a depth transect in the equatorial Pacific Ocean. The carbonate compensation depth tracks long-term ocean cooling, deepening from 3.0-3.5 kilometres during the early Cenozoic (approximately 55 million years ago) to 4.6 kilometres at present, consistent with an overall Cenozoic increase in weathering. We find large superimposed fluctuations in carbonate compensation depth during the middle and late Eocene. Using Earth system models, we identify changes in weathering and the mode of organic-carbon delivery as two key processes to explain these large-scale Eocene fluctuations of the carbonate compensation depth.
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| 10. |
- Roquet, Fabien, et al.
(author)
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Estimates of the Southern Ocean general circulation improved by animal-borne instruments
- 2013
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In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 40:23, s. 6176-6180
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Journal article (peer-reviewed)abstract
- Over the last decade, several hundred seals have been equipped with conductivity-temperature-depth sensors in the Southern Ocean for both biological and physical oceanographic studies. A calibrated collection of seal-derived hydrographic data is now available, consisting of more than 165,000 profiles. The value of these hydrographic data within the existing Southern Ocean observing system is demonstrated herein by conducting two state estimation experiments, differing only in the use or not of seal data to constrain the system. Including seal-derived data substantially modifies the estimated surface mixed-layer properties and circulation patterns within and south of the Antarctic Circumpolar Current. Agreement with independent satellite observations of sea ice concentration is improved, especially along the East Antarctic shelf. Instrumented animals efficiently reduce a critical observational gap, and their contribution to monitoring polar climate variability will continue to grow as data accuracy and spatial coverage increase.
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| 11. |
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| 12. |
- Sellberg, Jonas A., et al.
(author)
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How Cubic Can Ice Be?
- 2017
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In: The Journal of Physical Chemistry Letters. - : American Chemical Society (ACS). - 1948-7185. ; 8:14, s. 3216-3222
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Journal article (peer-reviewed)abstract
- Using an X-ray laser, we investigated the crystal structure of ice formed by homogeneous ice nucleation in deeply supercooled water nanodrops (r approximate to 10 nm) at similar to 225 K The nanodrops were formed by condensation of vapor in a supersonic nozzle, and the ice was probed within 100 mu s of freezing using femtosecond wide-angle X-ray scattering at the Linac Coherent Light Source free-electron X-ray laser. The X-ray diffraction spectra indicate that this ice has a metastable, predominantly cubic structure; the shape of the first ice diffraction peak suggests stacking-disordered ice with a cubicity value, chi, in the range of 0.78 +/- 0.05. The cubicity value determined here is higher than those determined in experiments with micron-sized drops but comparable to those found in molecular dynamics simulations. The high cubicity is most likely caused by the extremely low freezing temperatures and by the rapid freezing, which occurs on a similar to 1 mu s time scale in single nanodroplets.
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| 13. |
- Sierra, Raymond G., et al.
(author)
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Nanoflow electrospinning serial femtosecond crystallography
- 2012
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In: Acta Crystallographica Section D. - : Wiley-Blackwell. - 0907-4449 .- 1399-0047. ; 68, s. 1584-1587
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Journal article (peer-reviewed)abstract
- An electrospun liquid microjet has been developed that delivers protein microcrystal suspensions at flow rates of 0.14-3.1 mu l min(-1) to perform serial femtosecond crystallography (SFX) studies with X-ray lasers. Thermolysin microcrystals flowed at 0.17 mu l min(-1) and diffracted to beyond 4 angstrom resolution, producing 14 000 indexable diffraction patterns, or four per second, from 140 mu g of protein. Nanoflow electrospinning extends SFX to biological samples that necessitate minimal sample consumption.
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| 14. |
- Sumaila, U. Rashid, et al.
(author)
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WTO must ban harmful fisheries subsidies
- 2021
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 374:6567, s. 544-544
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Journal article (other academic/artistic)
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| 15. |
- Treasure, Anne M., et al.
(author)
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Marine Mammals Exploring the Oceans Pole to Pole A Review of the MEOP Consortium
- 2017
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In: Oceanography. - : The Oceanography Society. - 1042-8275. ; 30:2, s. 132-138
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Journal article (peer-reviewed)abstract
- Polar oceans are poorly monitored despite the important role they play in regulating Earth's climate system. Marine mammals equipped with biologging devices are now being used to fill the data gaps in these logistically difficult to sample regions. Since 2002, instrumented animals have been generating exceptionally large data sets of oceanographic CTD casts (>500,000 profiles), which are now freely available to the scientific community through the MEOP data portal (http://meop.net). MEOP (Marine Mammals Exploring the Oceans Pole to Pole) is a consortium of international researchers dedicated to sharing animal-derived data and knowledge about the polar oceans. Collectively, MEOP demonstrates the power and cost-effectiveness of using marine mammals as data-collection platforms that can dramatically improve the ocean observing system for biological and physical oceanographers. Here, we review the MEOP program and database to bring it to the attention of the international community.
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| 16. |
- Williams, Amanda M, et al.
(author)
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Intestinal alpha beta T cells differentiate and rearrange antigen receptor genes in situ in the human infant.
- 2004
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In: Journal of immunology (Baltimore, Md. : 1950). - 0022-1767. ; 173:12, s. 7190-9
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Journal article (peer-reviewed)abstract
- Intestinal Ag exposure during neonatal life influences appropriate adult immune responses. To define the mechanisms shaping the T cell repertoire during this period, we examined T cell differentiation and receptor diversity in the intestine of human infants. Developmental phenotypes of intraepithelial and lamina propria intestinal T cells from infants aged 1 day to 2 years were assessed ex vivo by flow cytometry and in situ by triple-fluorescent immunohistochemistry. Gene recombination-specific enzymes were assessed by PCR. TCR beta-chain V region gene diversity was determined by sequencing. Several different early lineage T cell populations were present neonatally: CD3(+)4(-)8(-) T cells were present at birth and numbers decreased during the neonatal period; CD3(+)4(+)8(+) T cells were present in low numbers throughout infancy; and CD3(+)4(+)8(-) or CD3(+)4(-)8(+) T cells increased with age. Very early lineage T cells, CD3(-)2(-)7(+) and CD3(-)2(+)7(+), were present neonatally, but were essentially absent at 1 year. Most lamina propria T cells differentiated rapidly after birth, but maturation of intraepithelial T cells took place over 1 year. Intestinal samples from infants less than 6 mo old contained transcripts of T early alpha and TdT, and 15 of 19 infant samples contained mRNA for RAG-1, some coexpressing RAG-2. TCR beta-chain repertoires were polyclonal in infants. Immature T cells, pre-T cells, and genes involved in T cell recombination were found in the intestine during infancy. T cell differentiation occurs within the neonatal human intestine, and the TCR repertoire of these developing immature T cells is likely to be influenced by luminal Ags. Thus, mucosal T cell responsiveness to environmental Ag is shaped in situ during early life.
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