scholarly journals Calcium [Ca] tracers using X-Ray fluorescence (XRF) as a potential high throughput measurement technique in ringless highly diverse tropical ecosystems.

2021 ◽  
Author(s):  
Koen Hufkens ◽  
Solenn Regeur ◽  
Camille Rivard ◽  
Jan Van den Bulcke ◽  
Hans Beeckman ◽  
...  
Keyword(s):  
Stable Isotope ◽  
High Throughput ◽  
Large Scale ◽  
Isotope Composition ◽  
Tropical Tree ◽  
Congo Basin ◽  
Plant Responses ◽  
Ancillary Data ◽  
Local Climate ◽  
X Ray

<p>Our understanding of plant responses to climate change, and their feedbacks to the climate system, rely heavily on consistent long-term observations. Yet, measuring tropical plant species is particularly demanding and results in a lack of spatial and temporal coverage to build relationships between forest dynamics and climatology in the central Congo Basin. Here dendrochronology and wood chemical analyses might provide important ecophysiological information addressing this knowledge gap, especially in tropical forests where the lack of a pronounced seasonality often makes it difficult to discern variability in xylem cell size and density. Conventional optical dendrochronology measurements therefore have strong limitations within these ecosystems, however chemical and elemental analysis can provide additional information. For example, seasonal fluctuations in the carbon (δ13C) and oxygen (δ18O) stable isotope composition of cellulose is linked to variations in local climate and changes in physiological function. A fewstudies have shown that intra-annual and inter-annual variations in the content of calcium [Ca] in tropical tree rings can be used to age tropical trees without rings, constraining estimates of biomass accumulation. Other studies have linked calcium accumulation in different plant organs to the rate of transpiration in trees making it a powerful predictor of inter-annual variability in rainfall for monsoon regions and a strong novel proxy for drought stress.</p><p>Here we present the first results of X-ray Fluorescence (XRF) measurements conducted at the SOLEIL synchrotron and analysis of [Ca] and [Sr], combined with ancillary data such as anatomical, stable isotope and climatological measurements for three tropical tree species. Most species show variability in calcium corresponding to previous proxy measurements, corroborating previous results and showing the potential of non-destructive XRF measurements of wood samples in support of ecophysiological research. The potential of high throughput scanning, in contrast to stable isotope measurements, opens possibilities to gather data on the large scale required to understand diverse tropical forest ecosystems and their responses to (drought) disturbances.</p>

scholarly journals High-Throughput Phenotyping Methods for Breeding Drought-Tolerant Crops

2021 ◽  
Vol 22 (15) ◽  
pp. 8266
Author(s):  
Minsu Kim ◽  
Chaewon Lee ◽  
Subin Hong ◽  
Song Lim Kim ◽  
Jeong-Ho Baek ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Large Scale ◽  
Crop Yields ◽  
Plant Traits ◽  
Rapid Development ◽  
Plant Responses ◽  
Phenotypic Data ◽  
Agricultural Technologies ◽  
High Throughput Phenotyping

Drought is a main factor limiting crop yields. Modern agricultural technologies such as irrigation systems, ground mulching, and rainwater storage can prevent drought, but these are only temporary solutions. Understanding the physiological, biochemical, and molecular reactions of plants to drought stress is therefore urgent. The recent rapid development of genomics tools has led to an increasing interest in phenomics, i.e., the study of phenotypic plant traits. Among phenomic strategies, high-throughput phenotyping (HTP) is attracting increasing attention as a way to address the bottlenecks of genomic and phenomic studies. HTP provides researchers a non-destructive and non-invasive method yet accurate in analyzing large-scale phenotypic data. This review describes plant responses to drought stress and introduces HTP methods that can detect changes in plant phenotypes in response to drought.

scholarly journals Saurichthys (Pisces, Actinopterygii) teeth from the Lower Triassic of Spitsbergen, with comments on their stable isotope composition (δ13C and δ18O) and X−ray microtomography

2013 ◽  
Vol 34 (1) ◽  
pp. 23-38 ◽  
Author(s):  
Błażej Błażejowski ◽  
Christopher J. Duffin ◽  
Piotr Gieszcz ◽  
Krzysztof Małkowski ◽  
Marcin Binkowski ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Isotope Composition ◽  
Isotope Analysis ◽  
Lower Triassic ◽  
X Ray ◽  
Tooth Histology ◽  
Fish Remains ◽  
First Time ◽  
Fish Teeth ◽  
Non Destructive

Abstract A rich collection of exceptionally preserved Lower Triassic fossil fish remains obtained during the Polish Spitsbergen Expedition of 2005 includes many isolated teeth be− lieved to belong to a saurichthyid actinopterygian. Stable isotope analysis (δ13C and δ18O) of putative Saurichthys teeth from the Hornsund area (South Spitsbergen) acting as a paleoenvironmental proxy has permitted trophic−level reconstruction and comparison with other Lower Triassic fish teeth from the same location. The broader range of δ13C values ob− tained for durophagous teeth of the hybodont selachian, Lissodus, probably reflects its mi− gratory behaviour and perhaps a greater feeding diversity. X−ray microcomputed tomogra− phy (XMT), a non−destructive technique, is used for the first time in order to elucidate de− tails of tooth histology, the results of which suggest that the method has considerable poten− tial as a future analytical tool.

scholarly journals High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Christy A. Hipsley ◽  
Rocio Aguilar ◽  
Jay R. Black ◽  
Scott A. Hocknull
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Three Dimensions ◽  
Museum Collections ◽  
Evolutionary Time ◽  
Phenotypic Data ◽  
Queensland Museum ◽  
X Ray ◽  
Degrade Image Quality ◽  
Spatio Temporal

Abstract High-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

scholarly journals Stable isotopes in cave ice suggest summer temperatures in east-central Europe are linked to Atlantic Multidecadal Oscillation variability

2020 ◽  
Vol 16 (6) ◽  
pp. 2445-2458
Author(s):  
Carmen-Andreea Bădăluţă ◽  
Aurel Perșoiu ◽  
Monica Ionita ◽  
Natalia Piotrowska
Keyword(s):  
Stable Isotope ◽  
Central Europe ◽  
North Atlantic ◽  
Large Scale ◽  
Isotope Composition ◽  
Atlantic Multidecadal Oscillation ◽  
Summer Temperature ◽  
Ice Age ◽  
East Central Europe ◽  
East Central

Abstract. The climate of east-central Europe (ECE) is the result of a combination of influences originating in the wider North Atlantic realm, the Mediterranean Sea, and the western Asian and Siberian regions. Previous studies have shown that the complex interplay between the large-scale atmospheric patterns across the region results in strongly dissimilar summer and winter conditions on timescales ranging from decades to millennia. To put these into a wider context, long-term climate reconstructions are required, but, largely due to historical reasons, these are lacking in ECE. We address these issues by presenting a high-resolution, radiocarbon-dated record of summer temperature variations during the last millennium in ECE, based on stable isotope analysis of a 4.84 m long ice core extracted from Focul Viu Ice Cave (Western Carpathians, Romania). Comparisons with both instrumental and proxy-based data indicate that the stable isotope composition of cave ice records the changes in summer air temperature and has a similar temporal evolution to that of the Atlantic Multidecadal Oscillation on decadal to multidecadal timescales, suggesting that changes in the North Atlantic are transferred, likely via atmospheric processes towards the wider Northern Hemisphere. On centennial timescales, the data show little summer temperature differences between the Medieval Warm Period (MWP) and the Little Ice Age (LIA) in eastern Europe. These findings are contrary to those that show a marked contrast between the two periods in terms of both winter and annual air temperatures, suggesting that cooling during the LIA was primarily the result of wintertime climatic changes.

scholarly journals High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

2019 ◽  
Author(s):  
Shota Teramoto ◽  
Satoko Takayasu ◽  
Yuka Kitomi ◽  
Yumiko Arai-Sanoh ◽  
Takanari Tanabata ◽  
...  
Keyword(s):  
Image Processing ◽  
High Throughput ◽  
Large Scale ◽  
Three Dimensional ◽  
Ct Scanning ◽  
Root System Architecture ◽  
Ct Images ◽  
X Ray ◽  
X Ray Computed ◽  
Crown Roots

Abstract Background: Plants adjust their root system architecture (RSA) against changing environments to optimize their growth. Nondestructive phenotyping of roots beneath the soil not only reveal the response of RSA against environmental stimuli but also allow for designing an ideal RSA for crop cultivation. Generally, roots beneath the soil surface are three-dimensionally visualized using X-ray computed tomography (CT). However, root isolation from X-ray CT images involves a longer time; in addition, CT scanning and reconstruction processes require longer periods. For large-scale root phenotyping, a shorter image acquisition time is required. Thus, the objective of this study is to develop a high-throughput pipeline to visualize rice RSA consisting of radicle and crown roots in the soil, from X-ray CT images.Results: We performed the following three processes to develop the pipeline. First, we used calcined clay with uniform soil particle size as the soil substrate. The size of voids between the soil particles was less than the scanning resolution, resulting in a clear root shape in the CT images. Second, we optimized the parameters for rapid X-ray CT scanning. Higher tube voltage and current produced the highest root-to-soil contrast images. Third, we used a 3-D median filter to reduce noise, and an edge detection alogism to isolate the root segments. The detection limits of the root diameters of the pots of diameters 16 cm and 20 cm were 0.2 mm and 0.3 mm, respectively. Because the crown root diameter of rice is generally higher than 0.2 mm, almost all crown roots could be visualized. Our condition allows for simultaneously performing CT scanning and reconstruction by a high-performance computing technology. Consequently, our pipeline visualizes rice RSA in the soil, requiring less than 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing to visualize rice RSA. We scanned the roots of the upland rice (considered in this study) daily, and our pipeline successfully visualized the root development dynamics over three weeks. Conclusions: We developed a rapid three-dimensional visualization method to visualize rice RSA in the soil using X-ray CT and a fully automated-image processing method known as RSAvis3D. Our methodology allows for high-throughput measuring and requires no manual operators in image processing, thereby providing a potentially efficient large-scale root phenotyping.

scholarly journals Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures

2018 ◽  
Author(s):  
Mari Kamitani ◽  
Makoto Kashima ◽  
Ayumi Tezuka ◽  
Atsushi J. Nagano
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Preparation Method ◽  
Low Cost ◽  
Cost Effective ◽  
Plant Responses ◽  
Library Preparation ◽  
Rna Seq ◽  
Temperature Responses ◽  
Library Preparation Method

AbstractRNA-Seq is a whole-transcriptome analysis method used to research biological mechanisms and functions; its use in large-scale experiments is limited by costs and labour. In this study, we established a high-throughput and cost effective RNA-Seq library preparation method that did not require mRNA enrichment. The method adds unique index sequences to samples during reverse transcription (RT) that is conducted at a higher temperature (≥62°C) to suppress RT of A-rich sequences in rRNA, and then pools all samples into a single tube. Both single-read and paired end sequencing of libraries is enabled. We found that the pooled RT products contained large amounts of RNA, mainly rRNA, and caused over-estimations of the quantity of DNA, resulting in unstable tagmentation results. Degradation of RNA before tagmentation was necessary for the stable preparation of libraries. We named this protocol low-cost and easy RNA-Seq (Lasy-Seq), and used it to investigate temperature responses in Arabidopsis thaliana. We analysed how sub-ambient temperatures (10–30°C) affected the plant transcriptomes, using time-courses of RNA-Seq from plants grown in randomly fluctuating temperature conditions. Our results suggest that there are diverse mechanisms behind plant temperature responses at different time scales.

scholarly journals High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

2020 ◽  
Author(s):  
Christy A. Hipsley ◽  
Rocio Aguilar ◽  
Jay R. Black ◽  
Scott A. Hocknull
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Three Dimensions ◽  
Museum Collections ◽  
Evolutionary Time ◽  
Phenotypic Data ◽  
Queensland Museum ◽  
X Ray ◽  
Degrade Image Quality ◽  
Spatio Temporal

AbstractHigh-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualise internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite its potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitising numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

scholarly journals Lake water based isoscape in central-south Chile reflects meteoric water

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wesley P. Scott ◽  
Sergio Contreras ◽  
Gabriel J. Bowen ◽  
T. Elliott Arnold ◽  
Ramón Bustamante-Ortega ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Isotopic Composition ◽  
Meteoric Water ◽  
Isotope Composition ◽  
Global Network ◽  
Ancillary Data ◽  
Energy Agency ◽  
Significant Information ◽  
Field Equipment ◽  
Central South

AbstractWarming across the globe is expected to alter the strength and amount of regional precipitation, but there is uncertainty associated with the magnitude of these expected changes, and also how these changes in temperature and the hydrologic cycle will affect humans. For example, the climate in central-south Chile is projected to become significantly warmer and drier over the next several decades in response to anthropogenically driven warming, but these anthropogenic changes are superimposed on natural climate variability. The stable isotope composition of meteoric water provides significant information regarding the moisture source, pathways, and rain-out history of an air mass, but precipitation samples suitable for stable isotope measurements require long-term placement of field equipment making them difficult to obtain. The International Atomic Energy Agency (IAEA) Global Network of Isotopes in Precipitation (GNIP) stations generate isotopic and ancillary data of precipitation from many locations around the world, but remote areas of developing countries like Chile typically have sparse networks of meteorological stations, which inhibit our ability to accurately model regional precipitation. Central-south Chile, in particular, has a sparse network of GNIP stations and, as a result, the isotopic composition of meteoric water is underrepresented in the global database complicating efforts to constrain modern day hydroclimate variability as well as paleohydrologic reconstruction for southern South America. In this study, we measured the stable isotope compositions of hydrogen (δ2H) and oxygen (δ18O) in surface lacustrine waters of central-south Chile to determine what physical and/or climatic features are the dominant controls on lacustrine δ18O and δ2H composition, assess whether or not the isotopic composition of the lakes record time-averaged isotope composition of meteoric water, and determine whether an isoscape map based on lake surface waters could predict the H and O isotope compositions of precipitation at the few GNIP stations in the region.

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