Publications by authors named "Gordon D Love"

44 Publications

A new constraint on the antiquity of ancient haloalkaliphilic green algae that flourished in a ca. 300 Ma Paleozoic lake.

Geobiology 2021 03 16;19(2):147-161. Epub 2020 Dec 16.

Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.

It is established that green algae and land plants progressively colonized freshwater and terrestrial habitats throughout the Paleozoic Era, but little is known about the ecology of Paleozoic saline lakes. Here, we report lipid biomarker and petrographic evidence for the occurrence of a green alga as a major primary producer in a late Paleozoic alkaline lake (Fengcheng Formation; 309-292 Ma). A persistently saline and alkaline lacustrine setting is supported by mineralogical and lipid biomarker evidence alongside extremely enriched δ N values (+16 to +24‰) for the lake depocenter. The prominence of C and C steroids, co-occurring with abundant carotene-derived accessory pigment markers in these ancient rocks, is suggestive of prolific primary production and elevated source inputs from haloalkaliphilic green algae. The high C /C -sterane ratios (0.78-1.29) are significantly higher than the typical marine value reported for late Paleozoic rocks (<0.5) and thus are associated with certain groups of chlorophytes. Adaptation to such extreme lacustrine environments, aided by enhanced biosynthesis of certain cell membrane lipids, likely played an important role in the evolution and physiological development of ancient green algae.
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http://dx.doi.org/10.1111/gbi.12423DOI Listing
March 2021

Understanding the geobiology of the terminal Ediacaran Khatyspyt Lagerstätte (Arctic Siberia, Russia).

Geobiology 2020 11 3;18(6):643-662. Epub 2020 Sep 3.

Trofimuk Institute of Petroleum Geology and Geophysics, Siberian Branch Russian Academy of Sciences, Novosibirsk, Russia.

The Khatyspyt Lagerstätte (~544 Ma, Russia) provides a valuable window into late Ediacaran Avalon-type ecosystems with rangeomorphs, arboreomorphs, and mega-algae. Here, we tackle the geobiology of this Lagerstätte by the combined analysis of paleontological features, sedimentary facies, and lipid biomarkers. The Khatyspyt Formation was deposited in carbonate ramp environments. Organic matter (0.12-2.22 wt.% TOC) displays characteristic Ediacaran biomarker features (e.g., eukaryotic steranes dominated by the C stigmastane). Some samples contain a putative 2-methylgammacerane that was likely sourced by ciliates and/or bacteria. 24-isopropylcholestane and 26-methylstigmastane are consistently scarce (≤0.4% and ≤0.2% of ∑C regular steranes, respectively). Thus, Avalon-type organisms occupied different niches than organisms capable of directly synthesizing C sterane precursors among their major lipids. Relative abundances of eukaryotic steranes and bacterial hopanes (sterane/hopane ratios = 0.07-0.30) demonstrate oligotrophic and bacterially dominated marine environments, similar to findings from other successions with Ediacara-type fossils. Ediacara-type fossils occur in facies characterized by microbial mats and biomarkers indicative for a stratified marine environment with normal-moderate salinities (moderate-high gammacerane index of 2.3-5.7; low C homohopane index of 0.1-0.2). Mega-algae, in contrast, are abundant in facies that almost entirely consist of allochthonous event layers. Biomarkers in these samples indicate a non-stratified marine environment and normal salinities (low gammacerane index of 0.6-0.8; low C homohopane index of 0.1). Vertical burrowers occur in similar facies but with biomarker evidence for stratification in the water column or around the seafloor (high gammacerane index of 5.6). Thus, the distribution of macro-organisms and burrowers was controlled by various, dynamically changing environmental factors. It appears likely that dynamic settings like the Khatyspyt Lagerstätte provided metabolic challenges for sustenance and growth which primed eukaryotic organisms to cope with changing environmental habitats, allowing for a later diversification and expansion of complex macroscopic life in the marine realm.
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http://dx.doi.org/10.1111/gbi.12412DOI Listing
November 2020

The impact of marine nutrient abundance on early eukaryotic ecosystems.

Geobiology 2020 03 17;18(2):139-151. Epub 2020 Feb 17.

NASA Astrobiology Institute, Alternative Earths Team, Riverside, California.

The rise of eukaryotes to ecological prominence represents one of the most dramatic shifts in the history of Earth's biosphere. However, there is an enigmatic temporal lag between the emergence of eukaryotic organisms in the fossil record and their much later ecological expansion. In parallel, there is evidence for a secular increase in the availability of the key macronutrient phosphorus (P) in Earth's oceans. Here, we use an Earth system model equipped with a size-structured marine ecosystem to explore relationships between plankton size, trophic complexity, and the availability of marine nutrients. We find a strong dependence of planktonic ecosystem structure on ocean nutrient abundance, with a larger ocean nutrient inventory leading to greater overall biomass, broader size spectra, and increasing abundance of large Zooplankton. If existing estimates of Proterozoic marine nutrient levels are correct, our results suggest that increases in the ecological impact of eukaryotic algae and trophic complexity in eukaryotic ecosystems were directly linked to restructuring of the global P cycle associated with the protracted rise of surface oxygen levels. Our results thus suggest an indirect but potentially important mechanism by which ocean oxygenation may have acted to shape marine ecological function during late Proterozoic time.
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http://dx.doi.org/10.1111/gbi.12384DOI Listing
March 2020

Free and kerogen-bound biomarkers from late Tonian sedimentary rocks record abundant eukaryotes in mid-Neoproterozoic marine communities.

Geobiology 2020 05 21;18(3):326-347. Epub 2019 Dec 21.

Department of Earth and Planetary Sciences, University of California, Riverside, CA, USA.

Lipid biomarker assemblages preserved within the bitumen and kerogen phases of sedimentary rocks from the ca. 780-729 Ma Chuar and Visingsö Groups facilitate paleoenvironmental reconstructions and reveal fundamental aspects of emerging mid-Neoproterozoic marine communities. The Chuar and Visingsö Groups were deposited offshore of two distinct paleocontinents (Laurentia and Baltica, respectively) during the Tonian Period, and the rock samples used had not undergone excessive metamorphism. The major polycyclic alkane biomarkers detected in the rock bitumens and kerogen hydropyrolysates consist of tricyclic terpanes, hopanes, methylhopanes, and steranes. Major features of the biomarker assemblages include detectable and significant contribution from eukaryotes, encompassing the first robust occurrences of kerogen-bound regular steranes from Tonian rocks, including 21-norcholestane, 27-norcholestane, cholestane, ergostane, and cryostane, along with a novel unidentified C sterane series from our least thermally mature Chuar Group samples. Appreciable values for the sterane/hopane (S/H) ratio are found for both the free and kerogen-bound biomarker pools for both the Chuar Group rocks (S/H between 0.09 and 1.26) and the Visingsö Group samples (S/H between 0.03 and 0.37). The more organic-rich rock samples generally yield higher S/H ratios than for organic-lean substrates, which suggests a marine nutrient control on eukaryotic abundance relative to bacteria. A C sterane (cholestane) predominance among total C -C steranes is a common feature found for all samples investigated, with lower amounts of C steranes (ergostane and crysotane) also present. No traces of known ancient C sterane compounds; including 24-isopropylcholestanes, 24-n-propylcholestanes, or 26-methylstigmastanes, are detectable in any of these pre-Sturtian rocks. These biomarker characteristics support the view that the Tonian Period was a key interval in the history of life on our planet since it marked the transition from a bacterially dominated marine biosphere to an ocean system which became progressively enriched with eukaryotes. The eukaryotic source organisms likely encompassed photosynthetic primary producers, marking a rise in red algae, and consumers in a revamped trophic structure predating the Sturtian glaciation.
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http://dx.doi.org/10.1111/gbi.12378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7233469PMC
May 2020

Sources of C steroid biomarkers in Neoproterozoic-Cambrian rocks and oils.

Nat Ecol Evol 2020 01 25;4(1):34-36. Epub 2019 Nov 25.

Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41559-019-1048-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7236378PMC
January 2020

Absence of biomarker evidence for early eukaryotic life from the Mesoproterozoic Roper Group: Searching across a marine redox gradient in mid-Proterozoic habitability.

Geobiology 2019 05 10;17(3):247-260. Epub 2019 Jan 10.

Department of Earth Sciences, University of California, Riverside, California.

By about 2.0 billion years ago (Ga), there is evidence for a period best known for its extended, apparent geochemical stability expressed famously in the carbonate-carbon isotope data. Despite the first appearance and early innovation among eukaryotic organisms, this period is also known for a rarity of eukaryotic fossils and an absence of organic biomarker fingerprints for those organisms, suggesting low diversity and relatively small populations compared to the Neoproterozoic era. Nevertheless, the search for diagnostic biomarkers has not been performed with guidance from paleoenvironmental redox constrains from inorganic geochemistry that should reveal the facies that were most likely hospitable to these organisms. Siltstones and shales obtained from drill core of the ca. 1.3-1.4 Ga Roper Group from the McArthur Basin of northern Australia provide one of our best windows into the mid-Proterozoic redox landscape. The group is well dated and minimally metamorphosed (of oil window maturity), and previous geochemical data suggest a relatively strong connection to the open ocean compared to other mid-Proterozoic records. Here, we present one of the first integrated investigations of Mesoproterozoic biomarker records performed in parallel with established inorganic redox proxy indicators. Results reveal a temporally variable paleoredox structure through the Velkerri Formation as gauged from iron mineral speciation and trace-metal geochemistry, vacillating between oxic and anoxic. Our combined lipid biomarker and inorganic geochemical records indicate at least episodic euxinic conditions sustained predominantly below the photic zone during the deposition of organic-rich shales found in the middle Velkerri Formation. The most striking result is an absence of eukaryotic steranes (4-desmethylsteranes) and only traces of gammacerane in some samples-despite our search across oxic, as well as anoxic, facies that should favor eukaryotic habitability and in low maturity rocks that allow the preservation of biomarker alkanes. The dearth of Mesoproterozoic eukaryotic sterane biomarkers, even within the more oxic facies, is somewhat surprising but suggests that controls such as the long-term nutrient balance and other environmental factors may have throttled the abundances and diversity of early eukaryotic life relative to bacteria within marine microbial communities. Given that molecular clocks predict that sterol synthesis evolved early in eukaryotic history, and (bacterial) fossil steroids have been found previously in 1.64 Ga rocks, then a very low environmental abundance of eukaryotes relative to bacteria is our preferred explanation for the lack of regular steranes and only traces of gammacerane in a few samples. It is also possible that early eukaryotes adapted to Mesoproterozoic marine environments did not make abundant steroid lipids or tetrahymanol in their cell membranes.
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http://dx.doi.org/10.1111/gbi.12329DOI Listing
May 2019

Demosponge steroid biomarker 26-methylstigmastane provides evidence for Neoproterozoic animals.

Nat Ecol Evol 2018 11 15;2(11):1709-1714. Epub 2018 Oct 15.

Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.

Sterane biomarkers preserved in ancient sedimentary rocks hold promise for tracking the diversification and ecological expansion of eukaryotes. The earliest proposed animal biomarkers from demosponges (Demospongiae) are recorded in a sequence around 100 Myr long of Neoproterozoic-Cambrian marine sedimentary strata from the Huqf Supergroup, South Oman Salt Basin. This C sterane biomarker, informally known as 24-isopropylcholestane (24-ipc), possesses the same carbon skeleton as sterols found in some modern-day demosponges. However, this evidence is controversial because 24-ipc is not exclusive to demosponges since 24-ipc sterols are found in trace amounts in some pelagophyte algae. Here, we report a new fossil sterane biomarker that co-occurs with 24-ipc in a suite of late Neoproterozoic-Cambrian sedimentary rocks and oils, which possesses a rare hydrocarbon skeleton that is uniquely found within extant demosponge taxa. This sterane is informally designated as 26-methylstigmastane (26-mes), reflecting the very unusual methylation at the terminus of the steroid side chain. It is the first animal-specific sterane marker detected in the geological record that can be unambiguously linked to precursor sterols only reported from extant demosponges. These new findings strongly suggest that demosponges, and hence multicellular animals, were prominent in some late Neoproterozoic marine environments at least extending back to the Cryogenian period.
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http://dx.doi.org/10.1038/s41559-018-0676-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589438PMC
November 2018

A stable and productive marine microbial community was sustained through the end-Devonian Hangenberg Crisis within the Cleveland Shale of the Appalachian Basin, United States.

Geobiology 2019 01 24;17(1):27-42. Epub 2018 Sep 24.

Department of Earth Sciences, University of California, Riverside, Riverside, California.

The end-Devonian Hangenberg Crisis constituted one of the greatest ecological and environmental perturbations of the Paleozoic Era. To date, however, it has been difficult to precisely constrain the occurrence of the Hangenberg Crisis in the Appalachian Basin of the United States and thus to directly assess the effects of this crisis on marine microbial communities and paleoenvironmental conditions. Here, we integrate organic and inorganic chemostratigraphic records compiled from two discrete outcrop locations to characterize the onset and paleoenvironmental transitions associated with the Hangenberg Crisis within the Cleveland Shale member of the Ohio Shale. The upper Cleveland Shale records both positive carbon (δ C ) and nitrogen (δ N ) isotopic excursions, and replenished trace metal inventories with links to eustatic rise. These dual but apparently temporally offset isotope excursions may be useful for stratigraphic correlation with other productive end-Devonian epeiric marine locations. Deposition of the black shale succession occurred locally beneath a redox-stratified water column with euxinic zones, with signs of strengthening denitrification during the Hangenberg Crisis interval, but with an otherwise stable and algal-rich marine microbial community structure sustained in the surface mixed layer as ascertained by lipid biomarker assemblages. Discernible trace fossil signals in some horizons suggest, however, that bioturbation and seafloor oxygenation occurred episodically throughout this succession and highlight that geochemical proxies often fail to capture these rapid and sporadic redox fluctuations in ancient black shales. The paleoenvironmental conditions, source biota, and accumulations of black shale are consistent with expressions of the Hangenberg Crisis globally, suggesting this event is likely captured within the uppermost strata of the Cleveland Shale in North America.
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http://dx.doi.org/10.1111/gbi.12314DOI Listing
January 2019

Creating correct blur and its effect on accommodation.

J Vis 2018 09;18(9)

Optometry & Vision Science, University of California, Berkeley, Berkeley, CA, USA.

Blur occurs naturally when the eye is focused at one distance and an object is presented at another distance. Computer-graphics engineers and vision scientists often wish to create display images that reproduce such depth-dependent blur, but their methods are incorrect for that purpose. They take into account the scene geometry, pupil size, and focal distances, but do not properly take into account the optical aberrations of the human eye. We developed a method that, by incorporating the viewer's optics, yields displayed images that produce retinal images close to the ones that occur in natural viewing. We concentrated on the effects of defocus, chromatic aberration, astigmatism, and spherical aberration and evaluated their effectiveness by conducting experiments in which we attempted to drive the eye's focusing response (accommodation) through the rendering of these aberrations. We found that accommodation is not driven at all by conventional rendering methods, but that it is driven surprisingly quickly and accurately by our method with defocus and chromatic aberration incorporated. We found some effect of astigmatism but none of spherical aberration. We discuss how the rendering approach can be used in vision science experiments and in the development of ophthalmic/optometric devices and augmented- and virtual-reality displays.
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http://dx.doi.org/10.1167/18.9.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6126933PMC
September 2018

Tracking the rise of eukaryotes to ecological dominance with zinc isotopes.

Geobiology 2018 07 5;16(4):341-352. Epub 2018 Jun 5.

Geology and Geophysics, Yale University, New Haven, Connecticut.

The biogeochemical cycling of zinc (Zn) is intimately coupled with organic carbon in the ocean. Based on an extensive new sedimentary Zn isotope record across Earth's history, we provide evidence for a fundamental shift in the marine Zn cycle ~800 million years ago. We discuss a wide range of potential drivers for this transition and propose that, within available constraints, a restructuring of marine ecosystems is the most parsimonious explanation for this shift. Using a global isotope mass balance approach, we show that a change in the organic Zn/C ratio is required to account for observed Zn isotope trends through time. Given the higher affinity of eukaryotes for Zn relative to prokaryotes, we suggest that a shift toward a more eukaryote-rich ecosystem could have provided a means of more efficiently sequestering organic-derived Zn. Despite the much earlier appearance of eukaryotes in the microfossil record (~1700 to 1600 million years ago), our data suggest a delayed rise to ecological prominence during the Neoproterozoic, consistent with the currently accepted organic biomarker records.
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http://dx.doi.org/10.1111/gbi.12289DOI Listing
July 2018

Ediacara biota flourished in oligotrophic and bacterially dominated marine environments across Baltica.

Nat Commun 2018 05 4;9(1):1807. Epub 2018 May 4.

Department of Earth Sciences, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.

Middle-to-late Ediacaran (575-541 Ma) marine sedimentary rocks record the first appearance of macroscopic, multicellular body fossils, yet little is known about the environments and food sources that sustained this enigmatic fauna. Here, we perform a lipid biomarker and stable isotope (δN and δC) investigation of exceptionally immature late Ediacaran strata (<560 Ma) from multiple locations across Baltica. Our results show that the biomarker assemblages encompass an exceptionally wide range of hopane/sterane ratios (1.6-119), which is a broad measure of bacterial/eukaryotic source organism inputs. These include some unusually high hopane/sterane ratios (22-119), particularly during the peak in diversity and abundance of the Ediacara biota. A high contribution of bacteria to the overall low productivity may have bolstered a microbial loop, locally sustaining dissolved organic matter as an important organic nutrient. These oligotrophic, shallow-marine conditions extended over hundreds of kilometers across Baltica and persisted for more than 10 million years.
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http://dx.doi.org/10.1038/s41467-018-04195-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935690PMC
May 2018

Snowball Earth climate dynamics and Cryogenian geology-geobiology.

Sci Adv 2017 11 8;3(11):e1600983. Epub 2017 Nov 8.

Department of Atmospheric Sciences, University of Washington, Seattle, WA 98195-1640, USA.

Geological evidence indicates that grounded ice sheets reached sea level at all latitudes during two long-lived Cryogenian (58 and ≥5 My) glaciations. Combined uranium-lead and rhenium-osmium dating suggests that the older (Sturtian) glacial onset and both terminations were globally synchronous. Geochemical data imply that CO was 10 PAL (present atmospheric level) at the younger termination, consistent with a global ice cover. Sturtian glaciation followed breakup of a tropical supercontinent, and its onset coincided with the equatorial emplacement of a large igneous province. Modeling shows that the small thermal inertia of a globally frozen surface reverses the annual mean tropical atmospheric circulation, producing an equatorial desert and net snow and frost accumulation elsewhere. Oceanic ice thickens, forming a sea glacier that flows gravitationally toward the equator, sustained by the hydrologic cycle and by basal freezing and melting. Tropical ice sheets flow faster as CO rises but lose mass and become sensitive to orbital changes. Equatorial dust accumulation engenders supraglacial oligotrophic meltwater ecosystems, favorable for cyanobacteria and certain eukaryotes. Meltwater flushing through cracks enables organic burial and submarine deposition of airborne volcanic ash. The subglacial ocean is turbulent and well mixed, in response to geothermal heating and heat loss through the ice cover, increasing with latitude. Terminal carbonate deposits, unique to Cryogenian glaciations, are products of intense weathering and ocean stratification. Whole-ocean warming and collapsing peripheral bulges allow marine coastal flooding to continue long after ice-sheet disappearance. The evolutionary legacy of Snowball Earth is perceptible in fossils and living organisms.
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http://dx.doi.org/10.1126/sciadv.1600983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5677351PMC
November 2017

Dynamic lens and monovision 3D displays to improve viewer comfort.

Opt Express 2016 May;24(11):11808-27

Stereoscopic 3D (S3D) displays provide an additional sense of depth compared to non-stereoscopic displays by sending slightly different images to the two eyes. But conventional S3D displays do not reproduce all natural depth cues. In particular, focus cues are incorrect causing mismatches between accommodation and vergence: The eyes must accommodate to the display screen to create sharp retinal images even when binocular disparity drives the eyes to converge to other distances. This mismatch causes visual discomfort and reduces visual performance. We propose and assess two new techniques that are designed to reduce the vergence-accommodation conflict and thereby decrease discomfort and increase visual performance. These techniques are much simpler to implement than previous conflict-reducing techniques. The first proposed technique uses variable-focus lenses between the display and the viewer's eyes. The power of the lenses is yoked to the expected vergence distance thereby reducing the mismatch between vergence and accommodation. The second proposed technique uses a fixed lens in front of one eye and relies on the binocularly fused percept being determined by one eye and then the other, depending on simulated distance. We conducted performance tests and discomfort assessments with both techniques and compared the results to those of a conventional S3D display. The first proposed technique, but not the second, yielded clear improvements in performance and reductions in discomfort. This dynamic-lens technique therefore offers an easily implemented technique for reducing the vergence-accommodation conflict and thereby improving viewer experience.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025225PMC
http://dx.doi.org/10.1364/OE.24.011808DOI Listing
May 2016

Blur and the perception of depth at occlusions.

J Vis 2016 ;16(6):17

The depth ordering of two surfaces, one occluding the other, can in principle be determined from the correlation between the occlusion border's blur and the blur of the two surfaces. If the border is blurred, the blurrier surface is nearer; if the border is sharp, the sharper surface is nearer. Previous research has found that observers do not use this informative cue. We reexamined this finding. Using a multiplane display, we confirmed the previous finding: Our observers did not accurately judge depth order when the blur was rendered and the stimulus presented on one plane. We then presented the same simulated scenes on multiple planes, each at a different focal distance, so the blur was created by the optics of the eye. Performance was now much better, which shows that depth order can be reliably determined from blur information but only when the optical effects are similar to those in natural viewing. We asked what the critical differences were in the single- and multiplane cases. We found that chromatic aberration provides useful information but accommodative microfluctuations do not. In addition, we examined how image formation is affected by occlusions and observed some interesting phenomena that allow the eye to see around and through occluding objects and may allow observers to estimate depth in da Vinci stereopsis, where one eye's view is blocked. Finally, we evaluated how accurately different rendering and displaying techniques reproduce the retinal images that occur in real occlusions. We discuss implications for computer graphics.
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http://dx.doi.org/10.1167/16.6.17DOI Listing
September 2016

No evidence for high atmospheric oxygen levels 1,400 million years ago.

Proc Natl Acad Sci U S A 2016 May 20;113(19):E2550-1. Epub 2016 Apr 20.

Department of Earth Science, University of California, Riverside, CA 92521;

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http://dx.doi.org/10.1073/pnas.1601925113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4868423PMC
May 2016

Why do animal eyes have pupils of different shapes?

Sci Adv 2015 Aug 7;1(7):e1500391. Epub 2015 Aug 7.

Department of Physics and Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK.

There is a striking correlation between terrestrial species' pupil shape and ecological niche (that is, foraging mode and time of day they are active). Species with vertically elongated pupils are very likely to be ambush predators and active day and night. Species with horizontally elongated pupils are very likely to be prey and to have laterally placed eyes. Vertically elongated pupils create astigmatic depth of field such that images of vertical contours nearer or farther than the distance to which the eye is focused are sharp, whereas images of horizontal contours at different distances are blurred. This is advantageous for ambush predators to use stereopsis to estimate distances of vertical contours and defocus blur to estimate distances of horizontal contours. Horizontally elongated pupils create sharp images of horizontal contours ahead and behind, creating a horizontally panoramic view that facilitates detection of predators from various directions and forward locomotion across uneven terrain.
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http://dx.doi.org/10.1126/sciadv.1500391DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4643806PMC
August 2015

Multiple Cosmic Sources for Meteorite Macromolecules?

Astrobiology 2015 Oct 29;15(10):779-86. Epub 2015 Sep 29.

2 School of Chemical, Environmental and Mining Engineering, University of Nottingham, University Park , Nottingham, UK .

The major organic component in carbonaceous meteorites is an organic macromolecular material. The Murchison macromolecular material comprises aromatic units connected by aliphatic and heteroatom-containing linkages or occluded within the wider structure. The macromolecular material source environment remains elusive. Traditionally, attempts to determine source have strived to identify a single environment. Here, we apply a highly efficient hydrogenolysis method to liberate units from the macromolecular material and use mass spectrometric techniques to determine their chemical structures and individual stable carbon isotope ratios. We confirm that the macromolecular material comprises a labile fraction with small aromatic units enriched in (13)C and a refractory fraction made up of large aromatic units depleted in (13)C. Our findings suggest that the macromolecular material may be derived from at least two separate environments. Compound-specific carbon isotope trends for aromatic compounds with carbon number may reflect mixing of the two sources. The story of the quantitatively dominant macromolecular material in meteorites appears to be made up of more than one chapter.
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http://dx.doi.org/10.1089/ast.2015.1331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623988PMC
October 2015

Reappraisal of hydrocarbon biomarkers in Archean rocks.

Proc Natl Acad Sci U S A 2015 May 27;112(19):5915-20. Epub 2015 Apr 27.

Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139.

Hopanes and steranes found in Archean rocks have been presented as key evidence supporting the early rise of oxygenic photosynthesis and eukaryotes, but the syngeneity of these hydrocarbon biomarkers is controversial. To resolve this debate, we performed a multilaboratory study of new cores from the Pilbara Craton, Australia, that were drilled and sampled using unprecedented hydrocarbon-clean protocols. Hopanes and steranes in rock extracts and hydropyrolysates from these new cores were typically at or below our femtogram detection limit, but when they were detectable, they had total hopane (<37.9 pg per gram of rock) and total sterane (<32.9 pg per gram of rock) concentrations comparable to those measured in blanks and negative control samples. In contrast, hopanes and steranes measured in the exteriors of conventionally drilled and curated rocks of stratigraphic equivalence reach concentrations of 389.5 pg per gram of rock and 1,039 pg per gram of rock, respectively. Polycyclic aromatic hydrocarbons and diamondoids, which exceed blank concentrations, exhibit individual concentrations up to 80 ng per gram of rock in rock extracts and up to 1,000 ng per gram of rock in hydropyrolysates from the ultraclean cores. These results demonstrate that previously studied Archean samples host mixtures of biomarker contaminants and indigenous overmature hydrocarbons. Therefore, existing lipid biomarker evidence cannot be invoked to support the emergence of oxygenic photosynthesis and eukaryotes by ∼ 2.7 billion years ago. Although suitable Proterozoic rocks exist, no currently known Archean strata lie within the appropriate thermal maturity window for syngenetic hydrocarbon biomarker preservation, so future exploration for Archean biomarkers should screen for rocks with milder thermal histories.
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http://dx.doi.org/10.1073/pnas.1419563112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434754PMC
May 2015

Accounting for the phase, spatial frequency and orientation demands of the task improves metrics based on the visual Strehl ratio.

Vision Res 2013 Sep 20;90:57-67. Epub 2013 Jul 20.

Department of Experimental Psychology, University of Oxford, 9 South Parks Road, Oxford OX1 3UD, UK.

Advances in ophthalmic instrumentation have allowed high order aberrations to be measured in vivo. These measurements describe the distortions to a plane wavefront entering the eye, but not the effect they have on visual performance. One metric for predicting visual performance from a wavefront measurement uses the visual Strehl ratio, calculated in the optical transfer function (OTF) domain (VSOTF) (Thibos et al., 2004). We considered how well such a metric captures empirical measurements of the effects of defocus, coma and secondary astigmatism on letter identification and on reading. We show that predictions using the visual Strehl ratio can be significantly improved by weighting the OTF by the spatial frequency band that mediates letter identification and further improved by considering the orientation of phase and contrast changes imposed by the aberration. We additionally showed that these altered metrics compare well to a cross-correlation-based metric. We suggest a version of the visual Strehl ratio, VScombined, that incorporates primarily those phase disruptions and contrast changes that have been shown independently to affect object recognition processes. This metric compared well to VSOTF for letter identification and was the best predictor of reading performance, having a higher correlation with the data than either the VSOTF or cross-correlation-based metric.
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http://dx.doi.org/10.1016/j.visres.2013.06.007DOI Listing
September 2013

Laser-targeted ablation of the zebrafish embryonic ventricle: a novel model of cardiac injury and repair.

Int J Cardiol 2013 Oct 18;168(4):3913-9. Epub 2013 Jul 18.

University/BHF Centre for Cardiovascular Science, The Queen's Medical Research Institute, The University of Edinburgh, Edinburgh, EH16 4TJ, United Kingdom.

Background: While the adult zebrafish (Danio rerio) heart demonstrates a remarkable capacity for self-renewal following apical resection little is known about the response to injury in the embryonic heart.

Methods: Injury to the beating zebrafish embryo heart was induced by laser using a transgenic zebrafish expressing cardiomyocyte specific green fluorescent protein. Changes in ejection fraction (EF), heart rate (HR), and caudal vein blood flow (CVBF) assessed by video capture techniques were assessed at 2, 24 and 48 h post-laser. Change in total and mitotic ventricular cardiomyocyte number following laser injury was also assessed by counting respectively DAPI (VCt) and Phospho-histone H3 (VCm) positive nuclei in isolated hearts using confocal microscopy.

Results: Laser injury to the ventricle resulted in bradycardia and mild bleeding into the pericardium. At 2 h post-laser injury, there was a significant reduction in cardiac performance in lasered-hearts compared with controls (HR 117 ± 11 vs 167 ± 9 bpm, p ≤ 0.001; EF 14.1 ± 1.8 vs 20.1 ± 1.3%, p ≤ 0.001; CVBF 103 ± 15 vs 316 ± 13 μms(-1), p ≤ 0.001, respectively). Isolated hearts showed a significant reduction in VCt at 2 h post-laser compared to controls (195 ± 15 vs 238 ± 15, p ≤ 0.05). Histology showed necrosis and apoptosis (TUNEL assay) at the site of laser injury. At 24 h post-laser cardiac performance and VCt had recovered fully to control levels. Pretreatment with the cell-cycle inhibitor, aphidicolin, significantly inhibited functional recovery of the ventricle accompanied by a significant inhibition of cardiomyocyte proliferation.

Conclusions: Laser-targeted injury of the zebrafish embryonic heart is a novel and reproducible model of cardiac injury and repair suitable for pharmacological and molecular studies.
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http://dx.doi.org/10.1016/j.ijcard.2013.06.063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819623PMC
October 2013

Different aberrations raise contrast thresholds for single-letter identification in line with their effect on cross-correlation-based confusability.

J Vis 2013 Jun 20;13(7):12. Epub 2013 Jun 20.

Department of Physics, Durham University, Durham, UK.

We previously showed that different types of aberration defocus, coma, and secondary astigmatism affect reading performance via different mechanisms. In this paper, we show the contrary result that, for identification of isolated letters, the effects of rendering different types of aberration can be described by a single cross-correlation-based metric. Aberrations reduce the effective resolution of an optical system, quantified by the high-frequency fall-off of the modulation transfer function. They additionally cause spatial-frequency-dependent phase and contrast changes, which have a size-dependent effect on letter forms. We used contrast threshold as our performance measure, instead of distance acuity, to separate the effects of form alterations from those of resolution limits. This measure is additionally appropriate in comparing single-letter-based performance to reading at a fixed distance. The relationship between a cross-correlation-based measure of letter confusability and performance was the same for all three types of aberration. For reading, we had found a different relationship for coma than for defocus and secondary astigmatism. We conclude that even when two tasks--letter identification and reading--use the same component stimulus set, the combination of multiple letters in a reading task produces functional differences between the effects of these aberrations that are not present for isolated letters.
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http://dx.doi.org/10.1167/13.7.12DOI Listing
June 2013

Speeding up liquid crystal SLMs using overdrive with phase change reduction.

Opt Express 2013 Jan;21(2):1779-97

Division for Biomedical Physics, Innsbruck Medical University, Mullerstraße 44, A-6020 Innsbruck, Austria.

Nematic liquid crystal spatial light modulators (SLMs) with fast switching times and high diffraction efficiency are important to various applications ranging from optical beam steering and adaptive optics to optical tweezers. Here we demonstrate the great benefits that can be derived in terms of speed enhancement without loss of diffraction efficiency from two mutually compatible approaches. The first technique involves the idea of overdrive, that is the calculation of intermediate patterns to speed up the transition to the target phase pattern. The second concerns optimization of the target pattern to reduce the required phase change applied to each pixel, which in addition leads to a substantial reduction of variations in the intensity of the diffracted light during the transition. When these methods are applied together, we observe transition times for the diffracted light fields of about 1 ms, which represents up to a tenfold improvement over current approaches. We experimentally demonstrate the improvements of the approach for applications such as holographic image projection, beam steering and switching, and real-time control loops.
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http://dx.doi.org/10.1364/OE.21.001779DOI Listing
January 2013

High-resolution 3D optical microscopy inside the beating zebrafish heart using prospective optical gating.

Biomed Opt Express 2012 Dec 31;3(12):3043-53. Epub 2012 Oct 31.

Centre for Advanced Instrumentation, Department of Physics, Durham University, UK ; Biophysical Sciences Institute, Durham University, UK.

3D fluorescence imaging is a fundamental tool in the study of functional and developmental biology, but effective imaging is particularly difficult in moving structures such as the beating heart. We have developed a non-invasive real-time optical gating system that is able to exploit the periodic nature of the motion to acquire high resolution 3D images of the normally-beating zebrafish heart without any unnecessary exposure of the sample to harmful excitation light. In order for the image stack to be artefact-free, it is essential to use a synchronization source that is invariant as the sample is scanned in 3D. We therefore describe a scheme whereby fluorescence image slices are scanned through the sample while a brightfield camera sharing the same objective lens is maintained at a fixed focus, with correction of sample drift also included. This enables us to maintain, throughout an extended 3D volume, the same standard of synchronization we have previously demonstrated in and near a single 2D plane. Thus we are able image the complete beating zebrafish heart exactly as if the heart had been artificially stopped, but sidestepping this undesirable interference with the heart and instead allowing the heart to beat as normal.
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http://dx.doi.org/10.1364/BOE.3.003043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521314PMC
December 2012

Image jitter enhances visual performance when spatial resolution is impaired.

Invest Ophthalmol Vis Sci 2012 Sep 6;53(10):6004-10. Epub 2012 Sep 6.

Department of Life Sciences, Glasgow Caledonian University, Glasgow, UK.

Purpose: Visibility of low-spatial frequency stimuli improves when their contrast is modulated at 5 to 10 Hz compared with stationary stimuli. Therefore, temporal modulations of visual objects could enhance the performance of low vision patients who primarily perceive images of low-spatial frequency content. We investigated the effect of retinal-image jitter on word recognition speed and facial emotion recognition in subjects with central visual impairment.

Methods: Word recognition speed and accuracy of facial emotion discrimination were measured in volunteers with AMD under stationary and jittering conditions. Computer-driven and optoelectronic approaches were used to induce retinal-image jitter with duration of 100 or 166 ms and amplitude within the range of 0.5 to 2.6° visual angle. Word recognition speed was also measured for participants with simulated (Bangerter filters) visual impairment.

Results: Text jittering markedly enhanced word recognition speed for people with severe visual loss (101 ± 25%), while for those with moderate visual impairment, this effect was weaker (19 ± 9%). The ability of low vision patients to discriminate the facial emotions of jittering images improved by a factor of 2. A prototype of optoelectronic jitter goggles produced similar improvement in facial emotion discrimination. Word recognition speed in participants with simulated visual impairment was enhanced for interjitter intervals over 100 ms and reduced for shorter intervals.

Conclusions: Results suggest that retinal-image jitter with optimal frequency and amplitude is an effective strategy for enhancing visual information processing in the absence of spatial detail. These findings will enable the development of novel tools to improve the quality of life of low vision patients.
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http://dx.doi.org/10.1167/iovs.11-9157DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3440939PMC
September 2012

3D adaptive optics in a light sheet microscope.

Opt Express 2012 Jun;20(12):13252-61

Department of Physics & Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK.

We report on a single plane illumination microscope (SPIM) incorporating adaptive optics in the imaging arm. We show how aberrations can occur from the sample mounting tube and quantify the aberrations both experimentally and computationally. A wavefront sensorless approach was taken to imaging a green fluorescent protein (GFP) labelled transgenic zebrafish. We show improvements in image quality whilst recording a 3D "z-stack" and show how the aberrations come from varying depths in the fish.
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http://dx.doi.org/10.1364/OE.20.013252DOI Listing
June 2012

Refractive elements for the measurement of the orbital angular momentum of a single photon.

Opt Express 2012 Jan;20(3):2110-5

School of Physics and Astronomy, University of Glasgow, Glasgow, G12 8QQ, UK.

We have developed a mode transformer comprising two custom refractive optical elements which convert orbital angular momentum states into transverse momentum states. This transformation allows for an efficient measurement of the orbital angular momentum content of an input light beam. We characterise the channel capacity of the system for 50 input modes, giving a maximum value of 3.46 bits per photon. Using an electron multiplying CCD (EMCCD) camera with a laser source attenuated such that on average there is less than one photon present within the system per measurement period, we demonstrate that the elements are efficient for the use in single photon experiments.
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http://dx.doi.org/10.1364/OE.20.002110DOI Listing
January 2012

Real-time optical gating for three-dimensional beating heart imaging.

J Biomed Opt 2011 Nov;16(11):116021

Durham University, Centre for Advanced Instrumentation, Department of Physics, Durham, United Kingdom.

We demonstrate real-time microscope image gating to an arbitrary position in the cycle of the beating heart of a zebrafish embryo. We show how this can be used for high-precision prospective gating of fluorescence image slices of the moving heart. We also present initial results demonstrating the application of this technique to 3-D structural imaging of the beating embryonic heart.
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http://dx.doi.org/10.1117/1.3652892DOI Listing
November 2011

Not all aberrations are equal: reading impairment depends on aberration type and magnitude.

J Vis 2011 Nov 22;11(13):20. Epub 2011 Nov 22.

Department of Physics, Durham University, Science Laboratories, UK.

The eye's optical components are imperfect and cause distortions in the retinal image that cannot be corrected completely by conventional spectacles. It is important to understand how these uncorrected aberrations (those excluding defocus and primary astigmatism) affect visual performance. We assessed reading performance using text with a simulated monochromatic aberration (defocus, coma, or secondary astigmatism), all of which typically occur in the normal population. We found that the rate of decline in reading performance with increasing aberration amplitude was smaller for coma than for secondary astigmatism or defocus. Defocus and secondary astigmatism clearly had an impact on word identification, as revealed by an analysis of a lexical frequency effect. The spatial form changes caused by these aberrations are particularly disruptive to letter identification, which in turn impacts word recognition and has consequences for further linguistic processing. Coma did not have a significant effect on word identification. We attribute reading impairment caused by coma to effects on saccade targeting, possibly due to changes in the spacings between letters. Effects on performance were not accompanied by a loss of comprehension confirming that even if an aberration is not severe enough to make text illegible it may still have a significant impact on reading.
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http://dx.doi.org/10.1167/11.13.20DOI Listing
November 2011

Widespread iron-rich conditions in the mid-Proterozoic ocean.

Nature 2011 Sep 7;477(7365):448-51. Epub 2011 Sep 7.

Department of Earth Sciences, University of California, Riverside, California 92521, USA.

The chemical composition of the ocean changed markedly with the oxidation of the Earth's surface, and this process has profoundly influenced the evolutionary and ecological history of life. The early Earth was characterized by a reducing ocean-atmosphere system, whereas the Phanerozoic eon (less than 542 million years ago) is known for a stable and oxygenated biosphere conducive to the radiation of animals. The redox characteristics of surface environments during Earth's middle age (1.8-1 billion years ago) are less well known, but it is generally assumed that the mid-Proterozoic was home to a globally sulphidic (euxinic) deep ocean. Here we present iron data from a suite of mid-Proterozoic marine mudstones. Contrary to the popular model, our results indicate that ferruginous (anoxic and Fe(2+)-rich) conditions were both spatially and temporally extensive across diverse palaeogeographic settings in the mid-Proterozoic ocean, inviting new models for the temporal distribution of iron formations and the availability of bioessential trace elements during a critical window for eukaryotic evolution.
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http://dx.doi.org/10.1038/nature10327DOI Listing
September 2011

Interferometry using binary holograms without high order diffraction effects.

Opt Lett 2011 Jun;36(12):2357-9

Department of Physics, Indian Institute of Technology Guwahati, Guwahati-39, Assam, India.

We describe a technique for a phase-stepping interferometer based on programmable binary phase holograms, particularly useful for optical testing of aspheric or free-form surfaces. It is well-known that binary holograms can be used to generate reference surfaces for interferometry, but a major problem is that cross talk from higher diffraction orders and aliasing can reduce the fidelity of the system. Here, we propose a new encoding technique which improves the accuracy of the technique and demonstrate its implementation using a binary liquid crystal spatial light modulator.
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http://dx.doi.org/10.1364/OL.36.002357DOI Listing
June 2011