Natural variation in abiotic stress responsive gene expression and local adaptation to climate in Arabidopsis thaliana.

Gene expression varies widely in natural populations, yet the proximate and ultimate causes of this variation are poorly known. Understanding how variation in gene expression affects abiotic stress tolerance, fitness, and adaptation is central to the field of evolutionary genetics. We tested the hypothesis that genes with natural genetic variation in their expression responses to abiotic stress are likely to be involved in local adaptation to climate in Arabidopsis thaliana. Specifically, we compared genes with consistent expression responses to environmental stress (expression stress responsive, "eSR") to genes with genetically variable responses to abiotic stress (expression genotype-by-environment interaction, "eGEI"). We found that on average genes that exhibited eGEI in response to drought or cold had greater polymorphism in promoter regions and stronger associations with climate than those of eSR genes or genomic controls. We also found that transcription factor binding sites known to respond to environmental stressors, especially abscisic acid responsive elements, showed significantly higher polymorphism in drought eGEI genes in comparison to eSR genes. By contrast, eSR genes tended to exhibit relatively greater pairwise haplotype sharing, lower promoter diversity, and fewer nonsynonymous polymorphisms, suggesting purifying selection or selective sweeps. Our results indicate that cis-regulatory evolution and genetic variation in stress responsive gene expression may be important mechanisms of local adaptation to climatic selective gradients

Deglacial grounding-line retreat in the Ross Embayment, Antarctica, controlled by ocean and atmosphere forcing

Modern observations appear to link warming oceanic conditions with Antarctic ice sheet grounding-line retreat. Yet, interpretations of past ice sheet retreat over the last deglaciation in the Ross Embayment, Antarctica’s largest catchment, differ considerably and imply either extremely high or very low sensitivity to environmental forcing. To investigate this, we perform regional ice sheet simulations using a wide range of atmosphere and ocean forcings. Constrained by marine and terrestrial geological data, these models predict earliest retreat in the central embayment and rapid terrestrial ice sheet thinning during the Early Holocene. We find that atmospheric conditions early in the deglacial period can enhance or diminish ice sheet sensitivity to rising ocean temperatures, thereby controlling the initial timing and spatial pattern of grounding-line retreat. Through the Holocene, however, grounding-line position is much more sensitive to subshelf melt rates, implicating ocean thermal forcing as the key driver of past ice sheet retreat

Mid-Holocene Antarctic sea-ice increase driven by marine ice sheet retreat

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ashley, K. E., McKay, R., Etourneau, J., Jimenez-Espejo, F. J., Condron, A., Albot, A., Crosta, X., Riesselman, C., Seki, O., Mass, G., Golledge, N. R., Gasson, E., Lowry, D. P., Barrand, N. E., Johnson, K., Bertler, N., Escutia, C., Dunbar, R., & Bendle, J. A. Mid-Holocene Antarctic sea-ice increase driven by marine ice sheet retreat. Climate of the Past, 17(1), (2021): 1-19, https://doi.org/10.5194/cp-17-1-2021.Over recent decades Antarctic sea-ice extent has increased, alongside widespread ice shelf thinning and freshening of waters along the Antarctic margin. In contrast, Earth system models generally simulate a decrease in sea ice. Circulation of water masses beneath large-cavity ice shelves is not included in current Earth System models and may be a driver of this phenomena. We examine a Holocene sediment core off East Antarctica that records the Neoglacial transition, the last major baseline shift of Antarctic sea ice, and part of a late-Holocene global cooling trend. We provide a multi-proxy record of Holocene glacial meltwater input, sediment transport, and sea-ice variability. Our record, supported by high-resolution ocean modelling, shows that a rapid Antarctic sea-ice increase during the mid-Holocene (∼ 4.5 ka) occurred against a backdrop of increasing glacial meltwater input and gradual climate warming. We suggest that mid-Holocene ice shelf cavity expansion led to cooling of surface waters and sea-ice growth that slowed basal ice shelf melting. Incorporating this feedback mechanism into global climate models will be important for future projections of Antarctic changes.This research has been supported by the Natural Environment Research Council (CENTA PhD; NE/L002493/1 and Standard Grant Ne/I00646X/1), Japanese Society for the Promotion of Science (JSPS/FF2/60 no. L-11523), NZ Marsden Fund (grant nos. 18-VUW-089 and 15-VUW-131), NSF (grant nos. PLR-1443347 and ACI-1548562), the U.S. Dept. of Energy (grant no. DE-SC0016105), ERC (StG ICEPROXY, 203441; ANR CLIMICE, FP7 Past4Future, 243908), L'Oréal-UNESCO New Zealand For Women in Science Fellowship, University of Otago Research Grant, the IODP U.S. Science Support Program, Spanish Ministry of Science and Innovation (grant no. CTM2017-89711-C2-1-P), and the European Union (FEDER)

Pre- and post-initiation modulating effects of green tea ingestion on rat hepatocarcinogenesis

The purpose of this study was to investigate the effects of green tea ingestion on hepatocarcinogenesis before and after its initiation. Male Sprague-Dawley rats were fed an AIN76A diet with or without green tea. Initiation was induced by a single dose (200 mg/kg) of diethylnitrosamine at week 4 and 0.02% (w/w) 2-acetylaminofluorene was supplied in the diets. The control group had free access to water for 13 weeks (CTR13). Tea infusion was provided from the beginning of the experiment for 13 weeks (PRE13) or from the post-initiation stage until week 13 (POST13). Three other groups (CTR24, PRE24 and POST24) were added to examine the longer-term effects (24 weeks) with the same experimental design. The percentage area of liver sections that were positive for hepatic placental glutathione S-transferase (GST-P), which was used as a marker of preneoplastic lesions, was smaller in PRE13 (20.2 ± 5.0%, mean ± SD) and POST13 (26.0 ± 4.8%) than in CTR13 (33.2 ± 5.8%, p<0.05). Over the longer period, the GST-P lesions were significantly smaller for both PRE24 and POST24 (21.6 ± 8.5% and 22.2 ± 4.0%, respectively) than for CTR24 (28.6 ± 5.1%, p<0.05), but there was no significant difference between PRE24 and POST24. The liver content of thiobarbituric acid reactive substances was significantly lower in the tea groups than in the controls (p<0.05). However, no significant differences were observed among groups of GST activity. The results show that tea consumption exhibits a stronger short-term initiation-inhibiting ability in liver carcinogenesis, but over a longer period, the preventive effects of green tea ingestion do not differ in post- and pre-initiation

A Widespread Chromosomal Inversion Polymorphism Contributes to a Major Life-History Transition, Local Adaptation, and Reproductive Isolation

A set of experiments demonstrates the involvement of a chromosomal inversion in the adaptive transition between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatu

The taxonomic name resolution service : an online tool for automated standardization of plant names

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in BMC Bioinformatics 14 (2013): 16, doi:10.1186/1471-2105-14-16.The digitization of biodiversity data is leading to the widespread application of taxon names that are superfluous, ambiguous or incorrect, resulting in mismatched records and inflated species numbers. The ultimate consequences of misspelled names and bad taxonomy are erroneous scientific conclusions and faulty policy decisions. The lack of tools for correcting this ‘names problem’ has become a fundamental obstacle to integrating disparate data sources and advancing the progress of biodiversity science. The TNRS, or Taxonomic Name Resolution Service, is an online application for automated and user-supervised standardization of plant scientific names. The TNRS builds upon and extends existing open-source applications for name parsing and fuzzy matching. Names are standardized against multiple reference taxonomies, including the Missouri Botanical Garden's Tropicos database. Capable of processing thousands of names in a single operation, the TNRS parses and corrects misspelled names and authorities, standardizes variant spellings, and converts nomenclatural synonyms to accepted names. Family names can be included to increase match accuracy and resolve many types of homonyms. Partial matching of higher taxa combined with extraction of annotations, accession numbers and morphospecies allows the TNRS to standardize taxonomy across a broad range of active and legacy datasets. We show how the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, the TNRS can aid the integration of disparate biological datasets. Although the TNRS was developed to aid in standardizing plant names, its underlying algorithms and design can be extended to all organisms and nomenclatural codes. The TNRS is accessible via a web interface at http://tnrs.iplantcollaborative.org/ webcite and as a RESTful web service and application programming interface. Source code is available at https://github.com/iPlantCollaborativeOpenSource/TNRS/ webcite.BJE was supported by NSF grant DBI 0850373 and TR by CSIRO Marine and Atmospheric Research, Australia,. BB and BJE acknowledge early financial support from Conservation International and TEAM who funded the development of early prototypes of taxonomic name resolution. The iPlant Collaborative (http://www.iplantcollaborative.org) is funded by a grant from the National Science Foundation (#DBI-0735191)

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

The iPlant Collaborative (iPlant) is a United States National Science Foundation (NSF) funded project that aims to create an innovative, comprehensive, and foundational cyberinfrastructure in support of plant biology research (PSCIC, 2006). iPlant is developing cyberinfrastructure that uniquely enables scientists throughout the diverse fields that comprise plant biology to address Grand Challenges in new ways, to stimulate and facilitate cross-disciplinary research, to promote biology and computer science research interactions, and to train the next generation of scientists on the use of cyberinfrastructure in research and education. Meeting humanity's projected demands for agricultural and forest products and the expectation that natural ecosystems be managed sustainably will require synergies from the application of information technologies. The iPlant cyberinfrastructure design is based on an unprecedented period of research community input, and leverages developments in high-performance computing, data storage, and cyberinfrastructure for the physical sciences. iPlant is an open-source project with application programming interfaces that allow the community to extend the infrastructure to meet its needs. iPlant is sponsoring community-driven workshops addressing specific scientific questions via analysis tool integration and hypothesis testing. These workshops teach researchers how to add bioinformatics tools and/or datasets into the iPlant cyberinfrastructure enabling plant scientists to perform complex analyses on large datasets without the need to master the command-line or high-performance computational services

Overexpression of Dyrk1A Is Implicated in Several Cognitive, Electrophysiological and Neuromorphological Alterations Found in a Mouse Model of Down Syndrome

Down syndrome (DS) phenotypes result from the overexpression of several dosage-sensitive genes. The DYRK1A (dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A) gene, which has been implicated in the behavioral and neuronal alterations that are characteristic of DS, plays a role in neuronal progenitor proliferation, neuronal differentiation and long-term potentiation (LTP) mechanisms that contribute to the cognitive deficits found in DS. The purpose of this study was to evaluate the effect of Dyrk1A overexpression on the behavioral and cognitive alterations in the Ts65Dn (TS) mouse model, which is the most commonly utilized mouse model of DS, as well as on several neuromorphological and electrophysiological properties proposed to underlie these deficits. In this study, we analyzed the phenotypic differences in the progeny obtained from crosses of TS females and heterozygous Dyrk1A (+/-) male mice. Our results revealed that normalization of the Dyrk1A copy number in TS mice improved working and reference memory based on the Morris water maze and contextual conditioning based on the fear conditioning test and rescued hippocampal LTP. Concomitant with these functional improvements, normalization of the Dyrk1A expression level in TS mice restored the proliferation and differentiation of hippocampal cells in the adult dentate gyrus (DG) and the density of GABAergic and glutamatergic synapse markers in the molecular layer of the hippocampus. However, normalization of the Dyrk1A gene dosage did not affect other structural (e.g., the density of mature hippocampal granule cells, the DG volume and the subgranular zone area) or behavioral (i.e., hyperactivity/attention) alterations found in the TS mouse. These results suggest that Dyrk1A overexpression is involved in some of the cognitive, electrophysiological and neuromorphological alterations, but not in the structural alterations found in DS, and suggest that pharmacological strategies targeting this gene may improve the treatment of DS-associated learning disabilities