bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modification of tomato breeding traits and plant hormone signaling by Target-AID, the genome-editing system inducing efficient nucleotide substitution
Authors: Kashojiya Sachiko , Lu Yu , Takayama Mariko , Komatsu Hiroki , Minh Luyen Hieu Thi , Nishida Keiji , Shirasawa Kenta , Miura Kenji , Nonaka Satoko , Masuda Jun-ichiro , Kondo Akihiko , Ezura Hiroshi , Ariizumi Tohru 
Published: January 2022

Abstract
Target activation-induced cytidine deaminase (Target-AID), a novel CRISPR/Cas9-based genome-editing tool, confers the base-editing capability on the Cas9 genome-editing system. It involves the fusion of cytidine deaminase (CDA), which catalyzes cytidine (C) to uridine (U) substitutions, to the mutated nickase-type nCas9 or deactivated-type dCas9. To confirm and extend the applicability of the Target-AID genome-editing system in tomatoes (Solanum lycopersicum L.), we transformed the model tomato cultivar “Micro-Tom” and commercial tomato cultivars using this system by targeting SlDELLA, which encodes a negative regulator of the plant phytohormone gibberellic acid (GA) signaling pathway. We confirmed that the nucleotide substitutions were induced by the Target-AID system, and we isolated mutants showing high GA sensitivity in both “Micro-Tom” and the commercial cultivars. Moreover, by successfully applying this system to ETHYLENE RECEPTOR 1 (SlETR1) with single sgRNA targeting, double sgRNA targeting, as well as dual-targeting of both SlETR1 and SlETR2 with a single sgRNA, we demonstrated that the Target-AID genome-editing system is a promising tool for molecular breeding in tomato crops. This study highlights an important aspect of the scientific and agricultural potential of the combinatorial use of the Target-AID and other base-editing systems.
Horticultural innovation by viral-induced gene regulation of carotenogenesis
Authors: Paudel Lucky , Kerr Stephanie , Prentis Peter , Tanurdžić Miloš , Papanicolaou Alexie , Plett Jonathan M , Cazzonelli Christopher I 
Published: January 2022

AbstractMultipartite viral vectors provide a simple, inexpensive and effective biotechnological tool to transiently manipulate (i.e. reduce or increase) gene expression in planta and characterise the function of genetic traits. The development of virus-induced gene regulation (VIGR) systems usually involve the targeted silencing or overexpression of genes involved in pigment biosynthesis or degradation in plastids, thereby providing rapid visual assessment of success in establishing RNA- or DNA-based VIGR systems in planta. Carotenoids pigments provide plant tissues with an array of yellow, orange, and pinkish-red colours. VIGR-induced transient manipulation of carotenoid-related gene expression has advanced our understanding of carotenoid biosynthesis, regulation, accumulation and degradation, as well as plastid signalling processes. In this review, we describe mechanisms of VIGR, the importance of carotenoids as visual markers of technology development, and knowledge gained through manipulating carotenogenesis in model plants as well as horticultural crops not always amenable to transgenic approaches. We outline how VIGR can be utilised in plants to fast-track the characterisation of gene function(s), accelerate fruit tree breeding programs, edit genomes, and biofortify plant products enriched in carotenoid micronutrients for horticultural innovation.
PbrROP1/2-elicited imbalance of cellulose deposition is mediated by a CrRLK1L-ROPGEF module in the pollen tube of Pyrus
Authors: Kou Xiaobing , Cao Peng , He Qianke , Wang Peng , Zhang Shaoling , Wu Juyou 
Published: January 2022

Abstract
Pollen tube growth is critical for the sexual reproduction of flowering plants. Catharanthus roseus receptor-like kinases (CrRLK1L) play an important role in plant sexual reproduction, pollen tube growth, and male and female gametophyte recognition. Here, we identified a CrRLK1L protein in pear (Pyrus bretschneideri), PbrCrRLK1L13, which is necessary for normal tip growth of the pollen tube. When PbrCrRLK1L13 was knocked down, the pollen tube grew faster. Interaction analysis showed that the kinase domain of PbrCrRLK1L13 interacted with the C-terminal region of PbrGEF8, and PbrCrRLK1L13 activated the phosphorylation of PbrGEF8 in vitro. Furthermore, PbrROP1 and PbrROP2 were the downstream targets of PbrCrRLK1L13-PbrGEF8. When we knocked down the expression of PbrCrRLK1L13, PbrGEF8, or PbrROP1/2, the balance of cellulose deposition in the pollen tube wall was disrupted. Considering these factors, we proposed a model for a signaling event regulating pear pollen tube growth. During pear pollen tube elongation, PbrCrRLK1L13 acted as a surface regulator of the PbrROP1 and PbrROP2 signaling pathway via PbrGEF8 to affect the balance of cellulose deposition and regulate pear pollen tube growth.
A novel inhibitor of the jasmonic acid signaling pathway represses herbivore resistance in tea plants
Authors: Lin Songbo , Ye Meng , Li Xiwang , Xing Yuxian , Liu Miaomiao , Zhang Jin , Sun Xiaoling 
Published: January 2022

Abstract
The jasmonic acid (JA) signaling pathway plays a vital role in mediating plant resistance to herbivores. The tea plant (Camellia sinensis) is one of the most important woody cash crops in the world. Due to the lack of genetic transformation systems for tea plants, how the JA signaling pathway works in tea plants has not yet been determined. Now, with the development of cross-disciplines, chemical biology provides new means for analyzing the JA signaling pathway. In the present study, the structure of the small-molecule isoquinoline compound ZINC71820901 (lyn3) was obtained from the ZINC molecular library through virtual screening based on the structure of the crystal COI1-JAZ1 co-receptor and was found to act as an inhibitor of the JA signaling pathway in both Arabidopsis and tea plants. Our results revealed that lyn3 repressed tea plant resistance to Ectropis grisescens mainly by decreasing the accumulation of (−)-epicatechin and (−)-epigallocatechin via repression of the JA signaling pathway, which functioned in a modulation manner different from that of the already known inhibitor salicylhydroxamic acid (SHAM). As a novel inhibitor of the JA signaling pathway, lyn3 provides a specific option for further research on the JA pathway.
Cucurbitaceae genome evolution, gene function, and molecular breeding
Authors: Ma Lili , Wang Qing , Zheng Yanyan , Guo Jing , Yuan Shuzhi , Fu Anzhen , Bai Chunmei , Zhao Xiaoyan , Zheng Shufang , Wen Changlong , Guo Shaogui , Gao Lipu , Grierson Donald , Zuo Jinhua , Xu Yong 
Published: January 2022

Abstract
Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation, and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae, and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationships, and functional genes associated with important agronomic traits (e.g. fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.
Snakin-2 interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenase 1 to inhibit sprout growth in potato tubers
Authors: Li Liqin , Lyu Chengcheng , Chen Jing , Lu Yifei , Yang Shiming , Ni Su , Zheng Shunlin , Yu Liping , Wang Xiyao , Wang Qiang , Lu Liming 
Published: January 2022

Abstract
The potato tuber is the main nutrient supply and reproductive organ; however, tuber sprouting can reduce its commercial value. Snakin-2 (StSN2) was first reported as an antimicrobial peptide that positively regulates potato disease resistance. Our recent study suggested StSN2 overexpression inhibited sprout growth, while the sprouting process was accelerated in StSN2 RNAi lines. Cytoplasmic glyceraldehyde-3-phosphate dehydrogenase 1 (StGAPC1) was identified as a candidate protein that interacts with StSN2 in co-immunoprecipitation/mass spectrometry experiments. Here, we report that the expression levels of StSN2 and StGAPC1 decreased during sprouting compared with dormancy. Coexpression of StSN2 and StGAPC1 in bud eyes and apical buds was verified by immunofluorescence analysis of paraffin sections. In addition, interaction of StSN2 and StGAPC1 was confirmed by yeast two-hybrid, co-immunoprecipitation, and split luciferase complementation assays. Overexpression of StGAPC1 depressed sprout growth, which is similar to the function of StSN2, and StSN2- and StGAPC1-overexpressing lines showed decreased glucose, fructose, and galactose contents. The interaction of StSN2 and StGAPC1 enhanced StGAPC1 activity and decreased its oxidative modification to inhibit sprout growth. Our results suggest that StSN2 plays a regulatory role in tuber sprout growth through interaction with StGAPC1.
An ARF1-binding factor triggering programmed cell death and periderm development in pear russet fruit skin
Authors: Wang Yuezhi , Dai Meisong , Wu Xinyi , Zhang Shujun , Shi Zebin , Cai Danying , Miao Lixiang 
Published: January 2022

AbstractPlants have a cuticular membrane (CM) and periderm membrane (PM), which act as barriers to terrestrial stresses. The CM covers primary organs with a continuous hydrophobic layer of waxes embedded in cutin, while the PM includes suberized cells stacked externally to the secondary tissues. The formation of native periderm is regulated by a postembryonic meristem phellogen that produces suberized phellem (cork) outwardly. However, the mechanism controlling phellogen differentiation to phellem remains to be clarified. Here, map-based cloning in a pear F1 population with segregation for periderm development in fruit skin facilitated the identification of an aspartic acid repeat deletion in Pyrus Periderm Programmed Cell Death 1.1 (PyPPCD1.1) that triggers phellogen activity for cork formation in russet fruit skin of pear. PyPPCD1.1 showed preferential expression in pear fruit skin, and the encoded protein shares a structural similarity to that of the viral capsid proteins. Aspartic acid deletion in PyPPCD1.1 weakened its nuclear localization but increased its accumulation in the chloroplast. The products of both PyPPCD1.1 and its recessive allele directly interact with ADP-ribosylation factor 1 (ARF1). PyPPCD1.1 triggered programmed cell death in an ARF1-dependent manner. Thus, this study identified the switch gene for programmed cell death and periderm development and provided a new molecular regulatory mechanism underlying the development of this trait.
Merging genotyping-by-sequencing data from two ex situ collections provides insights on the pea evolutionary history
Authors: Pavan Stefano , Delvento Chiara , Nazzicari Nelson , Ferrari Barbara , D’Agostino Nunzio , Taranto Francesca , Lotti Concetta , Ricciardi Luigi , Annicchiarico Paolo 
Published: January 2022

Abstract
Pea (Pisum sativum L. subsp. sativum) is one of the oldest domesticated species and a widely cultivated legume. In this study, we combined next generation sequencing (NGS) data referring to two genotyping-by-sequencing (GBS) libraries, each one prepared from a different Pisum germplasm collection. The selection of single nucleotide polymorphism (SNP) loci called in both germplasm collections caused some loss of information; however, this did not prevent the obtainment of one of the largest datasets ever used to explore pea biodiversity, consisting of 652 accessions and 22 127 markers. The analysis of population structure reflected genetic variation based on geographic patterns and allowed the definition of a model for the expansion of pea cultivation from the domestication centre to other regions of the world. In genetically distinct populations, the average decay of linkage disequilibrium (LD) ranged from a few bases to hundreds of kilobases, thus indicating different evolutionary histories leading to their diversification. Genome-wide scans resulted in the identification of putative selective sweeps associated with domestication and breeding, including genes known to regulate shoot branching, cotyledon colour and resistance to lodging, and the correct mapping of two Mendelian genes. In addition to providing information of major interest for fundamental and applied research on pea, our work describes the first successful example of integration of different GBS datasets generated from ex situ collections – a process of potential interest for a variety of purposes, including conservation genetics, genome-wide association studies, and breeding.
Starch content changes and metabolism-related gene regulation of Chinese cabbage synergistically induced by Plasmodiophora brassicae infection
Authors: Ma Yinbo , Choi Su Ryun , Wang Yu , Chhapekar Sushil Satish , Zhang Xue , Wang Yingjun , Zhang Xueying , Zhu Meiyu , Liu Di , Zuo Zhennan , Yan Xinyu , Gan Caixia , Zhao Di , Liang Yue , Pang Wenxing , Lim Yong Pyo 
Published: January 2022

Abstract
Clubroot is one of the major diseases adversely affecting Chinese cabbage (Brassica rapa) yield and quality. To precisely characterize the Plasmodiophora brassicae infection of Chinese cabbage, we developed a dual fluorescent staining method for simultaneously examining the pathogen, cell structures, and starch grains. The number of starch (amylopectin) grains increased in B. rapa roots infected by P. brassicae, especially from 14 to 21 days after inoculation. Therefore, the expression levels of 38 core starch metabolism genes were investigated by quantitative real-time PCR. Most genes related to starch synthesis were up-regulated at 7 days after P. brassicae inoculation, whereas the expression levels of starch degradation-related genes were increased at 14 days after inoculation. Then, genes encoding the core enzymes involved in starch metabolism were investigated by assessing their chromosomal distributions, structures, duplication events, and synteny among Brassica species. Genome comparisons indicated that 38 non-redundant genes belonging to six core gene families related to starch metabolism are highly conserved among Arabidopsis thaliana, B. rapa, Brassica nigra, and Brassica oleracea. Previous genome sequencing projects have revealed that P. brassicae obtained host nutrients by manipulating plant metabolism. Starch may serve as a carbon source for P. brassicae colonization, as indicated by histological observations and transcriptomic analysis. Results of this study may elucidate the evolution and expression of core starch metabolism genes and provide researchers with novel insights into the pathogenesis of clubroot in B. rapa.
Comparative transcriptomic analysis on compatible/incompatible grafts in Citrus
Authors: He Wen , Xie Rui , Wang Yan , Chen Qing , Wang Hao , Yang Shaofeng , Luo Ya , Zhang Yong , Tang Haoru , Gmitter Frederick G , Wang Xiaorong 
Published: January 2022

Abstract
Grafting is a useful cultivation technology to resist abiotic and biotic stresses and is an integral part of citrus production. However, some widely utilized rootstocks may still exhibit graft incompatibility in the orchard. ‘Hongmian miyou’ (Citrus maxima (Burm.) Merrill) is mutated from ‘Guanxi miyou’, but these two scions showed different compatibility with available Poncirus trifoliata rootstock. Foliage etiolation is an observed symptom of graft incompatibility, but its mechanism remains poorly understood. This study is the first to investigate the morphological, physiological, and anatomical differences between compatible and incompatible grafts, and perform transcriptome profiling at crucial stages of the foliage etiolation process. Based on comprehensive analyses, hormonal balance was disordered, and two rate-limiting genes, NCED3 (9-cis-epoxycarotenoid dioxygenase 3) and NCED5, being responsible for ABA (abscisic acid) accumulation, were highlighted. Further correlation analysis indicated that IAA (indole-3-acetic acid) and ABA were the most likely inducers of the expression of stress-related genes. In addition, excessive starch accumulation was observed in the lamina and midribs of leaves of incompatible grafts. These results provide a new insight into the role of hormonal balance and ABA biosynthesis genes in regulating and contributing to graft incompatibility, and will further define and deploy candidate genes to explore the mechanisms underlying citrus rootstock–scion interactions.
The activation of gene expression and alternative splicing in the formation and evolution of allopolyploid Brassica napus
Authors: Li Mengdi , Hu Meimei , Xiao Yafang , Wu Xiaoming , Wang Jianbo 
Published: January 2022

Abstract
Allopolyploids contain two or more sets of subgenomes. To establish a compatible relationship between subgenomes, a series of gene expression changes has occurred in allopolyploids. What evolutionary changes have taken place in transcripts of Brassica napus during its early establishment and subsequent evolution is a fascinating scientific question. Here, we study this issue using a set of materials (natural and resynthesized B. napus and their progenitors/parents) and long-read RNA sequencing technology. The results showed that more genes were upregulated in resynthesized B. napus compared with its two parents, and more upregulated expressed genes were observed in natural B. napus than in resynthesized B. napus. The presence of upregulated genes in an organism may help it to adapt to the influence of “genomic shock” and cope with the natural environment. Isoforms are produced from precursor mRNAs by alternative splicing (AS) events, and more than 60% of the isoforms identified in all materials were novel, potentially improving the reference genome information for B. napus. We found that the isoform numbers and the numbers of genes potentially involved in AS and alternative polyadenylation increased in B. napus after evolution, and they may have been involved in the adaptation of plants to the natural environment. In addition, all identified isoforms were functionally annotated by searching seven databases. In general, this study can improve our overall understanding of the full-length transcriptome of B. napus and help us to recognize the significant changes in gene expression and isoform abundance that have occurred in allopolyploid B. napus during evolution.
Deaths Among U.S. Air Force Basic Military Trainees, 2008-2020
Authors: Butler Cody R , Kasper Korey B , Huggins Robert A , Cropper Thomas Leo , Frankel Dianne N , Pawlak Mary T , Casey Theresa , Casa Douglas J 
Published: January 2022

ABSTRACT

Introduction
The U.S. Air Force (USAF) Basic Military Training (BMT), a rigorous training program for all enlisted members of the USAF, trains roughly 36,000 recruits annually. Transforming civilians into ready warrior airmen has inherent risks to trainee health, which has infrequently included death. While the average death rate at USAF BMT has decreased between 1956 and 2007 due to process improvement and preventive medicine efforts, further review is warranted to examine the deaths that have occurred since the last published period (1997-2007) and to determine the impact policy changes and updates have had on death rates since that time. Therefore, the purpose of this paper is to identify death rates and types from 2008 to 2020, explore policy implementation, and identify areas needing further improvement or modifications to the overall safety, fitness, and health of USAF BMT trainees.

Materials and Methods
All deaths were examined and reviewed from 2008 through 2020 for trainees attending the USAF BMT using medical records and autopsy reports. Death rates were calculated using the total population of trainees in a given year as well as over the entire 13-year study period.

Results
From 2008 to 2020, five deaths occurred among USAF BMT trainees (one cardiac, two exertional sickling due to sickle cell trait, one infection, and one suicide). This resulted in an overall average death rate of 1.08 per 100,000 trainees, as compared to 1.46 per 100,000 from 1997 to 2007. The last death in the study period occurred in 2016.

Conclusion
A modest downward trend of average death rate has continued since 2007, and no deaths from 2016 through 2020 represents the longest time frame without any deaths at USAF BMT over all times reported (dating back to 1956) which suggest that emergency best practice policies are/have improved. However, cardiac death rate and suicide rate have not changed since the last report. Policies and practices should be continuously reviewed and refined to reduce the risk of death at USAF BMT.
Using Contact-Based Education to Reduce Diabetes-Related Stigma Among Medical Residents in a Military Health System
Authors: Wan WingYee , Kravchenko Maria , Wardian Jana 
Published: January 2022

ABSTRACT

Introduction
Healthcare provider-related stigma against patients with diabetes is associated with worse doctor–patient relationships and patient self-care. A previous feasibility study showed benefit in using a contact-based education approach to improve attitudes of medical students toward patients with diabetes. We hosted a panel of people who had personal experience with diabetes. The panel was attended by internal medicine residents in a military health system. We compared diabetes-related stigma among the residents before and after the panel.

Materials and Methods
Panel participants included a Black male active duty service member diagnosed with type 2 diabetes, a Black veteran with type 2 diabetes, and a White woman with two sons who have type 1 diabetes. During a 1 hour panel for medicine residents, these panelists were asked to discuss their personal experiences with diabetes, common misconceptions regarding diabetes, and what they wish healthcare providers understood about diabetes. The validated Diabetes Attitude Scale-3 (DAS-3) questionnaire, which assesses diabetes-related attitudes based on a five-point Likert scale (strongly agree = 5, strongly disagree = 1), was given to the trainees before and after the panel. The survey also collected demographic information and contained short-answer questions about personal experiences with diabetes and diabetes-related stigma. Survey responses were linked with identifier questions to preserve anonymity.

Results
Twelve participants completed both the pre- and post-panel survey. Seven were female (58%), 10 were White (83%), and eight were from suburban communities (67%). Mean scores improved for all five DAS-3 subscales scores, with the largest improvement in the Patient Autonomy subscale (4.12 to 4.4), followed by Psychosocial Impact of Diabetes Mellitus (4.34 to 4.56), Seriousness of Non-Insulin Dependent Diabetes Mellitus (4.27 to 4.44), Need for Special Training (4.52 to 4.68), and Value of Tight Control (4.07 to 4.10).

Conclusions
Contact-based education can be considered as a tool for reducing diabetes-related stigma among medical trainees.