bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can gene editing reduce postharvest waste and loss of fruit, vegetables, and ornamentals?
Authors: Shipman Emma N. , Yu Jingwei , Zhou Jiaqi , Albornoz Karin , Beckles Diane M. 
Published: January 2021

AbstractPostharvest waste and loss of horticultural crops exacerbates the agricultural problems facing humankind and will continue to do so in the next decade. Fruits and vegetables provide us with a vast spectrum of healthful nutrients, and along with ornamentals, enrich our lives with a wide array of pleasant sensory experiences. These commodities are, however, highly perishable. Approximately 33% of the produce that is harvested is never consumed since these products naturally have a short shelf-life, which leads to postharvest loss and waste. This loss, however, could be reduced by breeding new crops that retain desirable traits and accrue less damage over the course of long supply chains. New gene-editing tools promise the rapid and inexpensive production of new varieties of crops with enhanced traits more easily than was previously possible. Our aim in this review is to critically evaluate gene editing as a tool to modify the biological pathways that determine fruit, vegetable, and ornamental quality, especially after storage. We provide brief and accessible overviews of both the CRISPR–Cas9 method and the produce supply chain. Next, we survey the literature of the last 30 years, to catalog genes that control or regulate quality or senescence traits that are “ripe” for gene editing. Finally, we discuss barriers to implementing gene editing for postharvest, from the limitations of experimental methods to international policy. We conclude that in spite of the hurdles that remain, gene editing of produce and ornamentals will likely have a measurable impact on reducing postharvest loss and waste in the next 5–10 years.
SlGRAS4 accelerates fruit ripening by regulating ethylene biosynthesis genes and SlMADS1 in tomato
Authors: Liu Yudong , Shi Yuan , Su Deding , Lu Wang , Li Zhengguo 
Published: January 2021

AbstractGRAS proteins are plant-specific transcription factors that play crucial roles in plant development and stress responses. However, their involvement in the ripening of economically important fruits and their transcriptional regulatory mechanisms remain largely unclear. Here, we demonstrated that SlGRAS4, encoding a transcription factor of the GRAS family, was induced by the tomato ripening process and regulated by ethylene. Overexpression of SlGRAS4 accelerated fruit ripening, increased the total carotenoid content and increased PSY1 expression in SlGRAS4-OE fruit compared to wild-type fruit. The expression levels of key ethylene biosynthesis genes (SlACS2, SlACS4, SlACO1, and SlACO3) and crucial ripening regulators (RIN and NOR) were increased in SlGRAS4-OE fruit. The negative regulator of tomato fruit ripening, SlMADS1, was repressed in OE fruit. Exogenous ethylene and 1-MCP treatment revealed that more endogenous ethylene was derived in SlGRAS4-OE fruit. More obvious phenotypes were observed in OE seedlings after ACC treatment. Yeast one-hybrid and dual-luciferase assays confirmed that SlGRAS4 can directly bind SlACO1 and SlACO3 promoters to activate their transcription, and SlGRAS4 can also directly repress SlMADS1 expression. Our study identified that SlGRAS4 acts as a new regulator of fruit ripening by regulating ethylene biosynthesis genes in a direct manner. This provides new knowledge of GRAS transcription factors involved in regulating fruit ripening.
Genome and transcriptome of Papaver somniferum Chinese landrace CHM indicates that massive genome expansion contributes to high benzylisoquinoline alkaloid biosynthesis
Authors: Pei Li , Wang Baishi , Ye Jian , Hu Xiaodi , Fu Lihong , Li Kui , Ni Zhiyu , Wang Zhenlong , Wei Yujie , Shi Luye , Zhang Ying , Bai Xue , Jiang Mengwan , Wang Shuhui , Ma Chunling , Li Shujin , Liu Kaihui , Li Wanshui , Cong Bin 
Published: January 2021

AbstractOpium poppy (Papaver somniferum) is a source of morphine, codeine, and semisynthetic derivatives, including oxycodone and naltrexone. Here, we report the de novo assembly and genomic analysis of P. somniferum traditional landrace ‘Chinese Herbal Medicine’. Variations between the 2.62 Gb CHM genome and that of the previously sequenced high noscapine 1 (HN1) variety were also explored. Among 79,668 protein-coding genes, we functionally annotated 88.9%, compared to 68.8% reported in the HN1 genome. Gene family and 4DTv comparative analyses with three other Papaveraceae species revealed that opium poppy underwent two whole-genome duplication (WGD) events. The first of these, in ancestral Ranunculales, expanded gene families related to characteristic secondary metabolite production and disease resistance. The more recent species-specific WGD mediated by transposable elements resulted in massive genome expansion. Genes carrying structural variations and large-effect variants associated with agronomically different phenotypes between CHM and HN1 that were identified through our transcriptomic comparison of multiple organs and developmental stages can enable the development of new varieties. These genomic and transcriptomic analyses will provide a valuable resource that informs future basic and agricultural studies of the opium poppy.
The transcription factor OpWRKY2 positively regulates the biosynthesis of the anticancer drug camptothecin in Ophiorrhiza pumila
Authors: Hao Xiaolong , Xie Chenhong , Ruan Qingyan , Zhang Xichen , Wu Chao , Han Bing , Qian Jun , Zhou Wei , Nützmann Hans-Wilhelm , Kai Guoyin 
Published: January 2021

AbstractThe limited bioavailability of plant-derived natural products with anticancer activity poses major challenges to the pharmaceutical industry. An example of this is camptothecin, a monoterpene indole alkaloid with potent anticancer activity that is extracted at very low concentrations from woody plants. Recently, camptothecin biosynthesis has been shown to become biotechnologically amenable in hairy-root systems of the natural producer Ophiorrhiza pumila. Here, time-course expression and metabolite analyses were performed to identify novel transcriptional regulators of camptothecin biosynthesis in O. pumila. It is shown here that camptothecin production increased over cultivation time and that the expression pattern of the WRKY transcription factor encoding gene OpWRKY2 is closely correlated with camptothecin accumulation. Overexpression of OpWRKY2 led to a more than three-fold increase in camptothecin levels. Accordingly, silencing of OpWRKY2 correlated with decreased camptothecin levels in the plant. Further detailed molecular characterization by electrophoretic mobility shift, yeast one-hybrid and dual-luciferase assays showed that OpWRKY2 directly binds and activates the central camptothecin pathway gene OpTDC. Taken together, the results of this study demonstrate that OpWRKY2 acts as a direct positive regulator of camptothecin biosynthesis. As such, a feasible strategy for the over-accumulation of camptothecin in a biotechnologically amenable system is presented.
Genomic consequences of apple improvement
Authors: Migicovsky Zoë , Gardner Kyle M. , Richards Christopher , Thomas Chao C. , Schwaninger Heidi R. , Fazio Gennaro , Zhong Gan-Yuan , Myles Sean 
Published: January 2021

AbstractThe apple (Malus domestica) is one of the world’s most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species,Malus sieversiifrom Central Asia, and find that cider apples derive more of their ancestry from the European crabapple,Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of ‘Honeycrisp’, the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars ‘Golden Delicious’ and ‘Red Delicious’ were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple’s future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.
Ecological adaptations influence the susceptibility of plants in the genus Zantedeschia to soft rot Pectobacterium spp.
Authors: Guttman Yelena , Joshi Janak Raj , Chriker Nofar , Khadka Nirmal , Kleiman Maya , Reznik Noam , Wei Zunzheng , Kerem Zohar , Yedidia Iris 
Published: January 2021

AbstractSoft rot disease caused by Pectobacterium spp. is responsible for severe agricultural losses in potato, vegetables, and ornamentals. The genus Zantedeschia includes two botanical groups of tuberous ornamental flowers that are highly susceptible to the disease. Previous studies revealed that Z. aethiopica, a member of the section Zantedeschia, is significantly more resistant to Pectobacterium spp. than members of the same genus that belong to the section Aestivae. During early infection, we found different patterns of bacterial colonization on leaves of hosts belonging to the different sections. Similar patterns of bacterial colonization were observed on polydimethylsiloxane (PDMS) artificial inert replicas of leaf surfaces. The replicas confirmed the physical effect of leaf texture, in addition to a biochemical plant–bacterium interaction. The differential patterns may be associated with the greater roughness of the abaxial leaf surfaces of Aestivae group that have evolutionarily adapted to mountainous environments, as compared to Zantedeschia group species that have adapted to warm, marshy environments. Transverse leaf sections also revealed compact aerenchyma and reduced the total volume of leaf tissue air spaces in Aestivae members. Finally, an analysis of defense marker genes revealed differential expression patterns in response to infection, with significantly higher levels of lipoxygenase 2 (lox2) and phenylalanine ammonia lyase (pal) observed in the more resistant Z. aethiopica, suggesting greater activation of induced systemic resistance (ISR) mechanisms in this group. The use of Zantedeschia as a model plant sheds light on how natural ecological adaptations may underlay resistance to bacterial soft rot in cultivated agricultural environments.
Divided attention does not affect the acquisition and consolidation of transitional probabilities
Authors: Horváth Kata , Török Csenge , Pesthy Orsolya , Nemeth Dezso , Janacsek Karolina 
Published: December 2020

AbstractStatistical learning facilitates the efficient processing and prediction of environmental events and contributes to the acquisition of automatic behaviors. Whereas a minimal level of attention seems to be required for learning to occur, it is still unclear how acquisition and consolidation of statistical knowledge are affected when attention is divided during learning. To test the effect of divided attention on statistical learning and consolidation, ninety-six healthy young adults performed the Alternating Serial Reaction Time task in which they incidentally acquired second-order transitional probabilities. Half of the participants completed the task with a concurrent secondary intentional sequence learning task that was applied to the same stimulus stream. The other half of the participants performed the task without any attention manipulation. Performance was retested after a 12-h post-learning offline period. Half of each group slept during the delay, while the other half had normal daily activity, enabling us to test the effect of delay activity (sleep vs. wake) on the consolidation of statistical knowledge. Divided attention had no effect on statistical learning: The acquisition of second-order transitional probabilities was comparable with and without the secondary task. Consolidation was neither affected by divided attention: Statistical knowledge was similarly retained over the 12-h delay, irrespective of the delay activity. Our findings can contribute to a better understanding of the role of attentional processes in and the robustness of visuomotor statistical learning and consolidation.
Reanalysis datasets outperform other gridded climate products in vegetation change analysis in peripheral conservation areas of Central Asia
Authors: Zandler Harald , Senftl Thomas , Vanselow Kim André 
Published: December 2020

AbstractGlobal environmental research requires long-term climate data. Yet, meteorological infrastructure is missing in the vast majority of the world’s protected areas. Therefore, gridded products are frequently used as the only available climate data source in peripheral regions. However, associated evaluations are commonly biased towards well observed areas and consequently, station-based datasets. As evaluations on vegetation monitoring abilities are lacking for regions with poor data availability, we analyzed the potential of several state-of-the-art climate datasets (CHIRPS, CRU, ERA5-Land, GPCC-Monitoring-Product, IMERG-GPM, MERRA-2, MODIS-MOD10A1) for assessing NDVI anomalies (MODIS-MOD13Q1) in two particularly suitable remote conservation areas. We calculated anomalies of 156 climate variables and seasonal periods during 2001–2018, correlated these with vegetation anomalies while taking the multiple comparison problem into consideration, and computed their spatial performance to derive suitable parameters. Our results showed that four datasets (MERRA-2, ERA5-Land, MOD10A1, CRU) were suitable for vegetation analysis in both regions, by showing significant correlations controlled at a false discovery rate < 5% and in more than half of the analyzed areas. Cross-validated variable selection and importance assessment based on the Boruta algorithm indicated high importance of the reanalysis datasets ERA5-Land and MERRA-2 in both areas but higher differences and variability between the regions with all other products. CHIRPS, GPCC and the bias-corrected version of MERRA-2 were unsuitable and not important in both regions. We provide evidence that reanalysis datasets are most suitable for spatiotemporally consistent environmental analysis whereas gauge- or satellite-based products and their combinations are highly variable and may not be applicable in peripheral areas.
Genetic information from discordant sibling pairs points to ESRP2 as a candidate trans-acting regulator of the CF modifier gene SCNN1B
Authors: Becker Tim , Pich Andreas , Tamm Stephanie , Hedtfeld Silke , Ibrahim Mohammed , Altmüller Janine , Dalibor Nina , Toliat Mohammad Reza , Janciauskiene Sabina , Tümmler Burkhard , Stanke Frauke 
Published: December 2020

AbstractSCNN1B encodes the beta subunit of the epithelial sodium channel ENaC. Previously, we reported an association between SNP markers of SCNN1B gene and disease severity in cystic fibrosis-affected sibling pairs. We hypothesized that factors interacting with the SCNN1B genomic sequence are responsible for intrapair discordance. Concordant and discordant pairs differed at six SCNN1B markers (Praw = 0.0075, Pcorr = 0.0397 corrected for multiple testing). To identify the factors binding to these six SCNN1B SNPs, we performed an electrophoretic mobility shift assay and captured the DNA–protein complexes. Based on protein mass spectrometry data, the epithelial splicing regulatory protein ESRP2 was identified when using SCNN1B-derived probes and the ESRP2-SCNN1B interaction was independently confirmed by coimmunoprecipitation assays. We observed an alternative SCNN1B transcript and demonstrated in 16HBE14o− cells that levels of this transcript are decreased upon ESRP2 silencing by siRNA. Furthermore, we confirmed that mildly and severely affected siblings have different ESPR2 genetic backgrounds and that ESRP2 markers are linked to the response of CF patients’ nasal epithelium to amiloride, indicating ENaC involvement (Pbest = 0.0131, Pcorr = 0.068 for multiple testing). Our findings demonstrate that sibling pairs clinically discordant for CF can be used to identify meaningful DNA regulatory elements and interacting factors.
Sensory capability and information integration independently explain the cognitive status of healthy older adults
Authors: Misselhorn Jonas , Göschl Florian , Higgen Focko L. , Hummel Friedhelm C. , Gerloff Christian , Engel Andreas K. 
Published: December 2020

AbstractWhile there is evidence that sensory processing and multisensory integration change with age, links between these alterations and their relation to cognitive status remain unclear. In this study, we assessed sensory thresholds and performance of healthy younger and older adults in a visuotactile delayed match-to-sample task. Using Bayesian structural equation modelling (BSEM), we explored the factors explaining cognitive status in the group of older adults. Additionally, we applied transcranial alternating current stimulation (tACS) to a parieto-central network found to underlie visuotactile interactions and working memory matching in our previous work. Response times and signal detection measures indicated enhanced multisensory integration and enhanced benefit from successful working memory matching in older adults. Further, tACS caused a frequency-specific speeding (20 Hz) and delaying (70 Hz) of responses. Data exploration suggested distinct underlying factors for sensory acuity and sensitivity d’ on the one side, and multisensory and working memory enhancement on the other side. Finally, BSEM showed that these two factors labelled ‘sensory capability’ and ‘information integration’ independently explained cognitive status. We conclude that sensory decline and enhanced information integration might relate to distinct processes of ageing and discuss a potential role of the parietal cortex in mediating augmented integration in older adults.
Averaging sleep spindle occurrence in dogs predicts learning performance better than single measures
Authors: Iotchev Ivaylo Borislavov , Reicher Vivien , Kovács Enikő , Kovács Tímea , Kis Anna , Gácsi Márta , Kubinyi Enikő 
Published: December 2020

AbstractAlthough a positive link between sleep spindle occurrence and measures of post-sleep recall (learning success) is often reported for humans and replicated across species, the test–retest reliability of the effect is sometimes questioned. The largest to date study could not confirm the association, however methods for automatic spindle detection diverge in their estimates and vary between studies. Here we report that in dogs using the same detection method across different learning tasks is associated with observing a positive association between sleep spindle density (spindles/minute) and learning success. Our results suggest that reducing measurement error by averaging across measurements of density and learning can increase the visibility of this effect, implying that trait density (estimated through averaged occurrence) is a more reliable predictor of cognitive performance than estimates based on single measures.
The implication of the air quality pattern in South Korea after the COVID-19 outbreak
Authors: Koo Ja-Ho , Kim Jhoon , Lee Yun Gon , Park Sang Seo , Lee Seoyoung , Chong Heesung , Cho Yeseul , Kim Jaemin , Choi Kyungbae , Lee Taegyung 
Published: December 2020

AbstractBy using multiple satellite measurements, the changes of the aerosol optical depth (AOD) and nitrogen dioxide (NO2) over South Korea were investigated from January to March 2020 to evaluate the COVID-19 effect on the regional air quality. The NO2 decrease in South Korea was found but not significant, which indicates the effects of spontaneous social distancing under the maintenance of ordinary life. The AODs in 2020 were normally high in January, but they became lower starting from February. Since the atmosphere over Eastern Asia was unusually stagnant in January and February 2020, the AOD decrease in February 2020 clearly reveals the positive effect of the COVID-19. Considering the insignificant NO2 decrease in South Korea and the relatively long lifetime of aerosols, the AOD decrease in South Korea may be more attributed to the improvement of the air quality in neighboring countries. In March, regional atmosphere became well mixed and ventilated over South Korea, contributing to large enhancement of air quality. While the social activity was reduced after the COVID-19 outbreak, the regional meteorology should be also examined significantly to avoid the biased evaluation of the social impact on the change of the regional air quality.
Thin silicon solid-state detectors for energetic particle measurements
Authors: Wiedenbeck M. E. , Burnham J. A. , Cohen C. M. S. , Cook W. R. , Crabill R. M. , Cummings A. C. , Davis A. J. , Kecman B. , Labrador A. W. , Leske R. A. , Mewaldt R. A. , Rankin J. S. , Rusert M. D. , Stone E. C. , Christian E. R. , Goodwin P. A. , Link J. T. , Nahory B. W. , Shuman S. A. , von Rosenvinge T. T. , Tindall C. S. , Black H. , Bullough M. , Clarke N. , Glasson V. , Greenwood N. , Hawkins C. , Johnson T. L. , Newton A. , Richardson K. , Walsh S. , Wilburn C. , Birdwell B. , Everett D. T. , McComas D. J. , Weidner S. E. , Angold N. G. , Schwadron N. A. 
Published: January 2021

Context. Silicon solid-state detectors are commonly used for measuring the specific ionization, dE∕dx, in instruments designed for identifying energetic nuclei using the dE∕dx versus total energy technique in space and in the laboratory. The energy threshold and species resolution of the technique strongly depend on the thickness and thickness uniformity of these detectors.
Aims. Research has been carried out to develop processes for fabricating detectors that are thinner than 15 μm, that have a thickness uniformity better than 0.2 μm over cm2 areas, and that are rugged enough to survive the acoustic and vibration environments of a spacecraft launch.
Methods. Silicon-on-insulator wafers that have a device layer of the desired detector thickness supported by a thick handle layer were used as starting material. Standard processing techniques were used to fabricate detectors on the device layer, and the underlying handle-layer material was etched away leaving a thin, uniform detector surrounded by a thick, supporting frame.
Results. Detectors as thin as 12 μm were fabricated in two laboratories and successfully subjected to environmental and performance tests. Two detector designs were used in the High-energy Energetic Particles Instrument, which is part of the Integrated Science Investigation of the Sun instrument suite on NASA’s Parker Solar Probe spacecraft. These detectors have been performing well for more than two years in space.
Conclusions. Thin silicon detectors in d E∕dx versus total energy instruments enable the identification of nuclei with energies down to ~1 MeV nuc−1. This research suggests that detectors at least a factor of two thinner should be achievable using this fabrication technique.