bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Amino Acid Transporter OsAAP4 Contributes to Rice Tillering and Grain Yield by Regulating Neutral Amino Acid Allocation through Two Splicing Variants
Authors: Fang Zhongming , Wu Bowen , Ji Yuanyuan 
Published: January 2021

Abstract
Background
Amino acids, which are transported by amino acid transporters, are the major forms of organic nitrogen utilized by higher plants. Among the 19 Amino Acid Permease transporters (AAPs) in rice, only a small number of these genes have been reported to influence rice growth and development. However, whether other OsAAPs are responsible for rice growth and development is unclear.

Results
In this study, we demonstrate that OsAAP4 promoter sequences are divergent between Indica and Japonica, with higher expression in the former, which produces more tillers and higher grain yield than does Japonica. Overexpression of two different splicing variants of OsAAP4 in Japonica ZH11 significantly increased rice tillering and grain yield as result of enhancing the neutral amino acid concentrations of Val, Pro, Thr and Leu. OsAAP4 RNA interference (RNAi) and mutant lines displayed opposite trends compared with overexpresing (OE) lines. In addition, exogenous Val or Pro at 0.5 mM significantly promoted the bud outgrowth of lines overexpressing an OsAAP4a splicing variant compared with ZH11, and exogenous Val or Pro at 2.0 mM significantly enhanced the bud outgrowth of lines overexpressing splicing variant OsAAP4b compared with ZH11. Of note, the results of a protoplast amino acid-uptake assay showed that Val or Pro at different concentrations was specifically transported and accumulated in these overexpressing lines. Transcriptome analysis further demonstrated that OsAAP4 may affect nitrogen transport and metabolism, and auxin, cytokinin signaling in regulating rice tillering.

Conclusion
Our results suggested that OsAAP4 contributes to rice tiller and grain yield by regulating neutral amino acid allocation through two different splicing variants and that OsAAP4 might have potential applications in rice breeding.
PCirc: random forest-based plant circRNA identification software
Authors: Yin Shuwei , Tian Xiao , Zhang Jingjing , Sun Peisen , Li Guanglin 
Published: January 2021

Abstract
Background
Circular RNA (circRNA) is a novel type of RNA with a closed-loop structure. Increasing numbers of circRNAs are being identified in plants and animals, and recent studies have shown that circRNAs play an important role in gene regulation. Therefore, identifying circRNAs from increasing amounts of RNA-seq data is very important. However, traditional circRNA recognition methods have limitations. In recent years, emerging machine learning techniques have provided a good approach for the identification of circRNAs in animals. However, using these features to identify plant circRNAs is infeasible because the characteristics of plant circRNA sequences are different from those of animal circRNAs. For example, plants are extremely rich in splicing signals and transposable elements, and their sequence conservation in rice, for example is far less than that in mammals. To solve these problems and better identify circRNAs in plants, it is urgent to develop circRNA recognition software using machine learning based on the characteristics of plant circRNAs.

Results
In this study, we built a software program named PCirc using a machine learning method to predict plant circRNAs from RNA-seq data. First, we extracted different features, including open reading frames, numbers of k-mers, and splicing junction sequence coding, from rice circRNA and lncRNA data. Second, we trained a machine learning model by the random forest algorithm with tenfold cross-validation in the training set. Third, we evaluated our classification according to accuracy, precision, and F1 score, and all scores on the model test data were above 0.99. Fourth, we tested our model by other plant tests, and obtained good results, with accuracy scores above 0.8. Finally, we packaged the machine learning model built and the programming script used into a locally run circular RNA prediction software, Pcirc (https://github.com/Lilab-SNNU/Pcirc).

Conclusion
Based on rice circRNA and lncRNA data, a machine learning model for plant circRNA recognition was constructed in this study using random forest algorithm, and the model can also be applied to plant circRNA recognition such as Arabidopsis thaliana and maize. At the same time, after the completion of model construction, the machine learning model constructed and the programming scripts used in this study are packaged into a localized circRNA prediction software Pcirc, which is convenient for plant circRNA researchers to use.
Transcriptional response of Asarum heterotropoides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. leaves grown under full and partial daylight conditions
Authors: Wang Zhiqing , Ma Haiqin , Zhang Min , Wang Ziqing , Tian Yixin , Li Wei , Wang Yingping 
Published: January 2021

Abstract
Background
Asarum heterotropides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. is an important medicinal and industrial plant, which is used in the treatment of various diseases. The main bioactive ingredient is the volatile oil having more than 82 identified components of which methyleugenol, safrole, myristicin, and toluene account for about 70% of the total volume. As a sciophyte plant, the amount of light it absorbs through leaves is an important factor for growth and metabolism.

Results
We grew Asarum plants under full, 50, 28, and 12% sunlight conditions to investigate the effect of different light irradiances on the four major volatile oil components. We employed de novo transcriptome sequencing to understand the transcriptional behavior of Asarum leaves regarding the biosynthetic pathways of the four volatile oil components, photosynthesis and biomass accumulation, and hormone signaling. Our results demonstrated that the increasing light conditions promoted higher percent of the four components. Under full sunlight conditions, cinnamyl alcohol dehydrogenase and cytochrome p450719As were upregulated and led the increased methyleugenol, safrole, and myristicin. The transcriptomic data also showed that Asarum leaves, under full sunlight conditions, adjust their photosynthesis-antenna proteins as a photoprotective response with the help of carotenoids. Plant hormone-signaling related genes were also differentially expressed between full sunlight and low light conditions.

Conclusions
High light induces accumulation of major bioactive ingredients A. heterotropides volatile oil and this is ascribed to upregulation of key genes such as cinnamyl alcohol dehydrogenase and cytochrome p450719As. The transcriptome data presented here lays the foundation of further understanding of light responses in sciophytes and provides guidance for increasing bioactive molecules in Asarum.
Three metabolic pathways are responsible for the accumulation and maintenance of high AsA content in kiwifruit (Actinidia eriantha)
Authors: Liao Guanglian , Chen Lu , He Yanqun , Li Xishi , Lv Zhengxin , Yi Shuyao , Zhong Min , Huang Chunhui , Jia Dongfeng , Qu Xueyan , Xu Xiaobiao 
Published: January 2021

Abstract
Background
Actinidia eriantha is a precious material to study the metabolism and regulation of ascorbic acid (AsA) because of its high AsA content. Although the pathway of AsA biosynthesis in kiwifruit has been identified, the mechanism of AsA metabolism and regulation is still unclear. The purpose of this experiment is to reveal the AsA metabolic characteristics of A. eriantha ‘Ganmi 6’ from the molecular level, and lay a theoretical foundation for the research on the genetic improvement of kiwifruit quality.

Results
We found that AsA reached the accumulation peak at S7 (110 DAF) during the process of fruit growth and development. The activity of GalDH, GalLDH, MDHAR and DHAR in fruit was similar to AsA accumulation trend, and both of them were significantly positively correlated with AsA content. It was speculated that GalDH and GalLDH were key enzymes in AsA biosynthesis, while MDHAR and DHAR were key enzymes in AsA regeneration cycle, which together regulated AsA accumulation in fruit. Also, we identified 98,656 unigenes with an average length of 932 bp from the transcriptome libraries using RNA-seq technology after data assembly. There were 50,184 (50.87%) unigenes annotations in four databases. Two thousand nine hundred forty-nine unigenes were enriched into the biosynthesis pathway of secondary metabolites, among which 133 unigenes involved in the AsA and aldehyde metabolism pathways, and 23 candidate genes related to AsA biosynthesis, cycling and degradation were screened out.

Conclusions
Considering gene expression levels and changes of physiological traits and related enzyme activity, we concluded that the accumulation of AsA depends mainly on the L-galactose pathway, and the D-galacturonic acid pathway and AsA recycling pathway as the secondary pathways, which co-maintain the high AsA content in fruit of A. eriantha.
Epidemic and molecular characterization of fluoroquinolone-resistant Shigella dysenteriae 1 isolates from calves with diarrhea
Authors: Cao Mingze , Wang Weiwei , Zhang Liwei , Liu Guanhui , Zhou Xuzheng , Li Bing , Shi Yuxiang , Zhu Zhen , Zhang Jiyu 
Published: January 2021

Abstract
Background
The widespread distribution of antimicrobial-resistant Shigella has become a recurrent challenge in many parts of the developing world. Previous studies indicate that the host of Shigella has expanded from humans to animals. This study aimed to investigate the prevalence of fluoroquinolone resistance and associated molecular characterization of S. dysenteriae 1 isolated from calves.

Results
All 38 unduplicated S. dysenteriae 1 isolates were collected from calves in Gansu Province from October 2014 to December 2016. According to MLST and PFGE analysis, these isolates were separated into 4 and 28 genotypes, respectively. The most common STs identified were ST228 (34.21%, 13/38) and ST229 (39.47%, 15/38), which were first found in the present study. All isolates harbored virulence genes, and the incidence of the seven virulence genes were ipaH (100%), ipaBCD (92.11%), stx (73.68%), ial (57.89%), sen (28.95%), set1A and set1B (0%). According to the results of antimicrobial susceptibilities, 76.32% (29/38) were resistant to fluoroquinolone and showed multidrug resistance. In a study on the polymorphism of quinolone resistance–determining region (QRDR) of gyrA/B and parC/E genes, we identified two mutations in gyrA (Ser83 → Leu and Asp87 → Asn) and parC (Ser80 → Ile and Ser83 → Leu), respectively. Among them, 55.17% (16/29) of resistant strains had the gyrA point mutations (Ser83 → Leu) and parC point mutation (Ser83 → Leu). Moreover, 41.38% (12/29) of isolates had all five point mutations of gyrA and parC. In addition, the prevalence of the plasmid-mediated quinolone resistance (PMQR) determinant genes was also investigated. All 29 fluoroquinolone-resistant isolates were positive for the aac (6′)-Ib-cr gene but negative for qepA, except for SD001. In addition, only 6 (20.69%, 6/29) isolates harbored the qnr gene, including two with qnrB (6.90%, 2/29) and four with qnrS (13.79%, 4/29).

Conclusion
Given the increased common emergence of multidrug resistant isolates, uninterrupted surveillance will be necessary to understand the actual epidemic burden and control this infection.
Proteome changes in pepper (Capsicum annuum L.) leaves induced by the green peach aphid (Myzus persicae Sulzer)
Authors: Florencio-Ortiz Victoria , Sellés-Marchart Susana , Casas José L. 
Published: January 2021

Abstract
Background
Aphid attack induces defense responses in plants activating several signaling cascades that led to the production of toxic, repellent or antinutritive compounds and the consequent reorganization of the plant primary metabolism. Pepper (Capsicum annuum L.) leaf proteomic response against Myzus persicae (Sulzer) has been investigated and analyzed by LC-MS/MS coupled with bioinformatics tools.

Results
Infestation with an initially low density (20 aphids/plant) of aphids restricted to a single leaf taking advantage of clip cages resulted in 6 differentially expressed proteins relative to control leaves (3 proteins at 2 days post-infestation and 3 proteins at 4 days post-infestation). Conversely, when plants were infested with a high density of infestation (200 aphids/plant) 140 proteins resulted differentially expressed relative to control leaves (97 proteins at 2 days post-infestation, 112 proteins at 4 days post-infestation and 105 proteins at 7 days post-infestation). The majority of proteins altered by aphid attack were involved in photosynthesis and photorespiration, oxidative stress, translation, protein folding and degradation and amino acid metabolism. Other proteins identified were involved in lipid, carbohydrate and hormone metabolism, transcription, transport, energy production and cell organization. However proteins directly involved in defense were scarce and were mostly downregulated in response to aphids.

Conclusions
The unexpectedly very low number of regulated proteins found in the experiment with a low aphid density suggests an active mitigation of plant defensive response by aphids or alternatively an aphid strategy to remain undetected by the plant.
Under a high density of aphids, pepper leaf proteome however changed significantly revealing nearly all routes of plant primary metabolism being altered. Photosynthesis was so far the process with the highest number of proteins being regulated by the presence of aphids.
In general, at short times of infestation (2 days) most of the altered proteins were upregulated. However, at longer times of infestation (7 days) the protein downregulation prevailed.
Proteins involved in plant defense and in hormone signaling were scarce and mostly downregulated.
Genome-wide identification and characterization of COMT gene family during the development of blueberry fruit
Authors: Liu Yushan , Wang Yizhou , Pei Jiabo , Li Yadong , Sun Haiyue 
Published: January 2021

Abstract
Background
Caffeic acid O-methyltransferases (COMTs) play an important role in the diversification of natural products, especially in the phenylalanine metabolic pathway of plant. The content of COMT genes in blueberry and relationship between their expression patterns and the lignin content during fruit development have not clearly investigated by now.

Results
Ninety-two VcCOMTs were identified in Vaccinium corymbosum. According to phylogenetic analyses, the 92 VcCOMTs were divided into 2 groups. The gene structure and conserved motifs within groups were similar which supported the reliability of the phylogenetic structure groupings. Dispersed duplication (DSD) and whole-genome duplication (WGD) were determined to be the major forces in VcCOMTs evolution. The results showed that the results of qRT-PCR and lignin content for 22 VcCOMTs, VcCOMT40 and VcCOMT92 were related to lignin content at different stages of fruit development of blueberry.

Conclusion
We identified COMT gene family in blueberry, and performed comparative analyses of the phylogenetic relationships in the 15 species of land plant, and gene duplication patterns of COMT genes in 5 of the 15 species. We found 2 VcCOMTs were highly expressed and their relative contents were similar to the variation trend of lignin content during the development of blueberry fruit. These results provide a clue for further study on the roles of VcCOMTs in the development of blueberry fruit and could promisingly be foundations for breeding blueberry clutivals with higher fruit firmness and longer shelf life.
The apple MdCOP1-interacting protein 1 negatively regulates hypocotyl elongation and anthocyanin biosynthesis
Authors: Kang Hui , Zhang Ting-Ting , Fu Lu-Lu , Yao Yu-Xin , You Chun-Xiang , Wang Xiao-Fei , Hao Yu-Jin 
Published: January 2021

AbstractBackgroundIn plants, CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is a key negative regulator in photoperiod response. However, the biological function of COP1-interacting protein 1 (CIP1) and the regulatory mechanism of the CIP1-COP1 interaction are not fully understood.ResultsHere, we identified the appleMdCIP1gene based on the ArabidopsisAtCIP1gene. Expression pattern analysis showed thatMdCIP1was constitutively expressed in various tissues of apple, and responded to stress and hormone signals at the transcriptional level. Ectopic expression ofMdCIP1complemented the phenotypes of the Arabidopsiscip1mutant, and MdCIP1 inhibited anthocyanin biosynthesis in apple calli. In addition, the biochemical assay demonstrated that MdCIP1 could interact with MdCOP1 protein by their coiled-coil domain, andMdCIP1-OX/cop1–4had a similar phenotype in photomorphogenesis with thecop1–4mutant, suggesting thatCOP1is epistatic toCIP1. Furthermore, the transient transformation assay indicated that MdCIP1 repressed anthocyanin biosynthesis in an MdCOP1-mediated pathway.ConclusionTake together, this study finds that MdCIP1 acts as a repressor in regulating hypocotyl elongation and anthocyanin biosynthesis through MdCOP1 in apple.
CRISPR-Cas9 multiplex genome editing of the hydroxyproline-O-galactosyltransferase gene family alters arabinogalactan-protein glycosylation and function in Arabidopsis
Authors: Zhang Yuan , Held Michael A. , Kaur Dasmeet , Showalter Allan M. 
Published: January 2021

Abstract
Background
Arabinogalactan-proteins (AGPs) are a class of hydroxyproline-rich proteins (HRGPs) that are heavily glycosylated (> 90%) with type II arabinogalactans (AGs). AGPs are implicated in various plant growth and development processes including cell expansion, somatic embryogenesis, root and stem growth, salt tolerance, hormone signaling, male and female gametophyte development, and defense. To date, eight Hyp-O-galactosyltransferases (GALT2–6, HPGT1–3) have been identified; these enzymes are responsible for adding the first sugar, galactose, onto AGPs. Due to gene redundancy among the GALTs, single or double galt genetic knockout mutants are often not sufficient to fully reveal their biological functions.

Results
Here, we report the successful application of CRISPR-Cas9 gene editing/multiplexing technology to generate higher-order knockout mutants of five members of the GALT gene family (GALT2–6). AGPs analysis of higher-order galt mutants (galt2 galt5, galt3 galt4 galt6, and galt2 galt3 galt4 galt5 gal6) demonstrated significantly less glycosylated AGPs in rosette leaves, stems, and siliques compared to the corresponding wild-type organs. Monosaccharide composition analysis of AGPs isolated from rosette leaves revealed significant decreases in arabinose and galactose in all the higher-order galt mutants. Phenotypic analyses revealed that mutation of two or more GALT genes was able to overcome the growth inhibitory effect of β-D-Gal-Yariv reagent, which specifically binds to β-1,3-galactan backbones on AGPs. In addition, the galt2 galt3 galt4 galt5 gal6 mutant exhibited reduced overall growth, impaired root growth, abnormal pollen, shorter siliques, and reduced seed set. Reciprocal crossing experiments demonstrated that galt2 galt3 galt4 galt5 gal6 mutants had defects in the female gametophyte which were responsible for reduced seed set.

Conclusions
Our CRISPR/Cas9 gene editing/multiplexing approach provides a simpler and faster way to generate higher-order mutants for functional characterization compared to conventional genetic crossing of T-DNA mutant lines. Higher-order galt mutants produced and characterized in this study provide insight into the relationship between sugar decorations and the various biological functions attributed to AGPs in plants.
Participation in disease management programs and major adverse cardiac events in patients after acute myocardial infarction: a longitudinal study based on registry data
Authors: Fischer Christian , Höpner Jens , Hartwig Saskia , Noutsias Michel , Mikolajczyk Rafael 
Published: January 2021

Abstract
Background
Cardiovascular diseases are still the main cause of death in the western world. However, diminishing mortality rates of acute myocardial infarction (AMI) are motivating the need to investigate the process of secondary prevention after AMI. Besides cardiac rehabilitation, disease management programs (DMPs) are an important component of outpatient care after AMI in Germany. This study aims to analyze outcomes after AMI among those who participated in DMPs and cardiac rehabilitation (CR) in a region with overall increased cardiovascular morbidity and mortality.

Methods
Based on data from a regional myocardial infarction registry and a 2-year follow-up period, we assessed the occurrence of major adverse cardiac events (MACE) in relation to participation in CR and DMP, risk factors for complications and individual healths well as lifestyle characteristics. Multivariable Cox regression was performed to compare survival time between participants and non-participants until an adverse event occurred.

Results
Of 1094 observed patients post-AMI, 272 were enrolled in a DMP. An association between DMP participation and lower hazard rates for MACE compared to non-enrollees could not be proven in the crude model (hazard ratio = 0.93; 95% confidence interval = 0.65–1.33). When adjusted for possible confounding variables, these results remained virtually unchanged (1.03; 0.72–1.48). Furthermore, smokers and obese patients showed a distinctly lower chance of DMP enrollment. In contrast, those who participated in CR showed a lower risk for MACE in crude (0.52; 0.41–0.65) and adjusted analysis (0.56; 0.44–0.71).

Conclusions
Participation in DMP was not associated with a lower risk of MACE, but participation in CR showed beneficial effects. Adjustment only slightly changed effect estimates in both cases, but it is still important to consider potential effects of additional confounding variables.
Ordinal outcome analysis improves the detection of between-hospital differences in outcome
Authors: Ceyisakar I. E. , van Leeuwen N. , Dippel Diederik W. J. , Steyerberg Ewout W. , Lingsma H. F. 
Published: January 2021

Abstract
Background
There is a growing interest in assessment of the quality of hospital care, based on outcome measures. Many quality of care comparisons rely on binary outcomes, for example mortality rates. Due to low numbers, the observed differences in outcome are partly subject to chance. We aimed to quantify the gain in efficiency by ordinal instead of binary outcome analyses for hospital comparisons. We analyzed patients with traumatic brain injury (TBI) and stroke as examples.

Methods
We sampled patients from two trials. We simulated ordinal and dichotomous outcomes based on the modified Rankin Scale (stroke) and Glasgow Outcome Scale (TBI) in scenarios with and without true differences between hospitals in outcome. The potential efficiency gain of ordinal outcomes, analyzed with ordinal logistic regression, compared to dichotomous outcomes, analyzed with binary logistic regression was expressed as the possible reduction in sample size while keeping the same statistical power to detect outliers.

Results
In the IMPACT study (9578 patients in 265 hospitals, mean number of patients per hospital = 36), the analysis of the ordinal scale rather than the dichotomized scale (‘unfavorable outcome’), allowed for up to 32% less patients in the analysis without a loss of power. In the PRACTISE trial (1657 patients in 12 hospitals, mean number of patients per hospital = 138), ordinal analysis allowed for 13% less patients. Compared to mortality, ordinal outcome analyses allowed for up to 37 to 63% less patients.

Conclusions
Ordinal analyses provide the statistical power of substantially larger studies which have been analyzed with dichotomization of endpoints. We advise to exploit ordinal outcome measures for hospital comparisons, in order to increase efficiency in quality of care measurements.

Trial registration
We do not report the results of a health care intervention.