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Haploids can be induced in knockout mutants of OsPLA1,but not OsDMP3 or OsDMP6,in rice

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The Crop Journal 2024年第1期12卷 213-221页

作者： Zongkai Liu Yu Zhong Xiaolong Qi Tai An Shuwei Guo Dong Wang Yuwen Wang Bin Feng Zuofeng Zhu Shaojiang Chen Chenxu Liu National Maize Improvement Center Engineering Research Center of Ministry of EducationChina Agricultural UniversityBeijing 100193China National Center for Evaluation of agricultural Wild Plants(Rice) Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China

Doubled haploid(DH)technology is an important tool in crop breeding because it can significantly accelerate the breeding process.ZmPLA1/MATL/NLD and ZmDMP are two key genes controlling haploid induction(HI)in maize,exhibiting a synergistic effect.However,it is unknown whether knock out of ZmDMP orthologs can stimulate HI in rice.In this study,a ZmPLA1 ortholog(OsPLA1)and two ZmDMP orthologs(OsDMP3 and OsDMP6)were identified in rice.All three genes encode plasma membrane-localized proteins and were highly expressed in mature anthers.Knockout of OsPLA1 in both Minghui 63 and Nipponbare resulted in reduced seed setting rate(SSR)and caused HI.The osdmp3,osdmp6 and the double mutant failed to trigger HI independently,nor increased the haploid induction rate(HIR)when combined with ospla1.Repeated pollinations operations of QX654A with the ospla1 mutant significantly improve SSR,while reducing HIR.RNA-seq profiling of mature ospla1 mutant anthers indicated that a large number of differentially expressed genes(DEGs)were enriched in redox homeostasis and lipid metabolic GO terms,plant hormone signal transduction,and MAPK signaling pathways.These findings provide important insights towards construction of an efficient DH breeding technology and study of the molecular mechanism of HI in rice.

关键词： Doubled haploid breeding Haploid induction Mutation anlaysis Rice

Synergistic effects of planting density and nitrogen fertilization on chlorophyll degradation and leaf senescence after silking in maize

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The Crop Journal 2024年第2期12卷 605-613页

作者： Tianqiong Lan Lunjing Du Xinglong Wang Xiaoxu Zhan Qinlin Liu Gui Wei Chengcheng Lyu Fan Liu Jiaxu Gao Dongju Feng Fanlei Kong Jichao Yuan Key Laboratory of Crop Physiology Ecologyand Cultivation SouthwestMinistry of AgricultureSichuan Agricultural UniversityChengdu 611130SichuanChina Chongqing Academy of agricultural Sciences Chongqing 401329China College of Agronomy Sichuan Agricultural UniversityChengdu 611130SichuanChina

Regulating planting density and nitrogen(N)fertilization could delay chlorophyll(Chl)degradation and leaf senescence in maize cultivars.This study measured changes in ear leaf green area(GLA_(ear)),Chl content,the activities of Chl a-degrading enzymes after silking,and the post-silking dry matter accumulation and grain yield under multiple planting densities and N fertilization rates.The dynamic change of GLA_(ear)after silking fitted to the logistic model,and the GLA_(ear) duration and the GLAearat 42 d after silking were affected mainly by the duration of the initial senescence period(T_(1))which was a key factor of the leaf senescence.The average chlorophyllase(CLH)activity was 8.3 times higher than pheophytinase activity and contributed most to the Chl content,indicating that CLH is a key enzyme for degrading Chl a in maize.Increasing density increased the CLH activity and decreased the Chl content,T1,GLAear,and GLA_(ear) duration.Under high density,appropriate N application reduced CLH activity,increased Chl content,prolonged T1,alleviated high-density-induced leaf senescence,and increased post-silking dry matter accumulation and grain yield.

关键词： Density Nitrogen fertilization Leaf senescence Chlorophyll-degrading enzyme Logistic model

Deep learning for drug-drug interaction prediction:A comprehensive review

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Quantitative Biology 2024年第1期12卷 30-52页

作者： Xinyue Li Zhankun Xiong Wen Zhang Shichao Liu College of Informatics Huazhong Agricultural UniversityWuhanChina

The prediction of drug-drug interactions(DDIs)is a crucial task for drug safety research,and identifying potential DDIs helps us to explore the mechanism behind combinatorial therapy.Traditional wet chemical experiments for DDI are cumbersome and time-consuming,and are too small in scale,limiting the efficiency of DDI predictions.Therefore,it is particularly crucial to develop improved computational methods for detecting drug interactions.With the development of deep learning,several computational models based on deep learning have been proposed for DDI prediction.In this review,we summarized the high-quality DDI prediction methods based on deep learning in recent years,and divided them into four categories:neural network-based methods,graph neural network-based methods,knowledge graph-based methods,and multimodal-based methods.Furthermore,we discuss the challenges of existing methods and future potential perspectives.This review reveals that deep learning can significantly improve DDI prediction performance compared to traditional machine learning.Deep learning models can scale to large-scale datasets and accept multiple data types as input,thus making DDI predictions more efficient and accurate.

关键词： deep learning drug-drug interactions graph neural network knowledge graph multimodal deep learning neural network

Preface:Special issue on soil ecology and sustainability for celebrating the 70th anniversary of ISSCAS

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Pedosphere 2024年第1期34卷 1-2页

作者： Fusuo ZHANG China agricultural university Beijing 100193China

The Institute of Soil Science, Chinese Academy of Sciences (ISSAS) was founded in 1953. The institute aims to solve the problems of agricultural development, ecological conservation, and environmental protection and to promote the development of soil science.China’s arable land is facing dual pressure of construction occupation and ecological degradation. This is because the rapid urbanization and industrialization continue to occupy high-quality arable land and the quality of complementary arable land is relatively low (Cumming et al., 2014;Wang S T et al., 2021). To ensure national food security, agricultural product quality, and agricultural ecology security,it is particularly important to ensure soil health to maintain sustainable agricultural production.

关键词： soil occupation maintain

DeepCRBP:improved predicting function of circRNA-RBP binding sites with deep feature learning

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Frontiers of Computer Science 2024年第2期18卷 235-237页

作者： Zishan XU Linlin SONG Shichao LIU Wen ZHANG College of Informatics Huazhong Agricultural UniversityWuhan 430070China

1 Introduction Recently,there is growing evidence that it is essential to predict the interactions between circRNAs and RBP binding sites for diagnosing diseases and providing a potential target to treat diseases[1].Many studies have predicted the binding sites of circRNA-RBPs by using deep learning methods based on the sequence information of circRNAs for each RBP.Furthermore,many methods focus on diversified view of sequence encoding for improving the performance of the predictive models.

关键词： learning Deep function

Preventive effect of kiwi berry(Actinidia arguta)on loperamide-induced constipation

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Food Science and Human Wellness 2024年第3期13卷 1410-1421页

作者： Jiyue Zhang Bin Li Ningxuan Gao Haikun Li Xingyue Cui Hanqian Jiang Siyi Tang Chenyu Jin Jinlong Tian College of Food Science Shenyang Agricultural UniversityShenyang 110866China

Constipation is a common intestinal disease.Kiwi berries can effectively prevent constipation.However,studies have yet to be done to determine how kiwi berries prevent constipation.For two weeks,mice in this study were continually orally gavaged with kiwi berry,loperamide,or a combination of the 2.This study found that the kiwi group's feces had more water than the constipated mice.In addition,kiwi berries can speed up gastrointestinal transit(GI),shorten the time it takes to pass the first dark stool,and dramatically enhance body weight gain.In the interstitial cells of Caj al(ICC)cells and colon tissues,alterations in the protein expression of vasoactive intestinal peptide(VIP),cyclic adenosine monophosphate(cAMP),protein kinase A(PKA),and aquapcrin-3(AQP3)were found.At 3,6,and 12 h of ICC cells and mouse colon,the kiwi group's VIP,cAMP,PKA,and AQP3 protein expression levels were lower than those of the constipated mice.The kiwi berry can decrease the Firmicutes to Bacteroidetes ratio and boost the diversity and quantity of gut microbiota.By influencing the gut microbiota and VIP-cAMP-PKA-AQP3 signaling pathway,kiwi berries prevent constipation.

关键词： Kiwi berry Constipation VIP-cAMP-PKA-AQP3 Gut microbiota

Probiotic cocktails accelerate baicalin metabolism in the ileum to modulate intestinal health in broiler chickens

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Journal of Animal Science and Biotechnology 2024年第2期15卷 779-794页

作者： Mingkun Gao Chaoyong Liao Jianyang Fu Zhonghua Ning Zengpeng Lv Yuming Guo State Key Laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China National Engineering Laboratory for Animal Breeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Background Baicalin and probiotic cocktails are promising feed additives with broad application prospects.While probiotic cocktails are known to enhance intestinal health,the potential synergistic impact of combining baicalin with probiotic cocktails on the gut health of broiler chickens remains largely unexplored.Therefore,this study aims to investigate the influence of the combined administration of baicalin and probiotic cocktails on the composition of ileal and cecal microbiota in broiler chickens to elucidate the underlying mechanisms responsible for the healthpromoting effects.Results A total of 3201-day-old male Arbor Acres broilers were divided into 4 groups,each with 8 replicates of 10 chicks per replicate.Over a period of 42 d,the birds were fed a basal diet or the same diet supplemented with 37.5 g/t baicalin(BC),1,000 g/t probiotic cocktails(PC),or a combination of both BC(37.5 g/t)and PC(1,000 g/t).The results demonstrated that BC+PC exhibited positive synergistic effects,enhancing intestinal morphology,immune function,and barrier function.This was evidenced by increased VH/CD ratio,sIgA levels,and upregulated expression of occludin and claudin-1(P<0.05).16S rRNA analysis indicated that PC potentiated the effects of BC,particularly in the ileum,where BC+PC significantly increased theα-diversity of the ileal microbiota,altered itsβ-diversity,and increased the relative abundance of Flavonifractor(P<0.05),a flavonoid-metabolizing bacterium.Furthermore,Flavonifractor positively correlated with chicken ileum crypt depth(P<0.05).While BC+PC had a limited effect on cecal microbiota structure,the PC group had a very similar microbial composition to BC+PC,suggesting that the effect of PC at the distal end of the gut overshadowed those of BC.Conclusions We demonstrated the synergistic enhancement of gut health regulation in broiler chickens by combining baicalin and probiotic cocktails.Probiotic cocktails enhanced the effects of baicalin and accelerated its metabolism in the ileum,thereby influencing the ileal

关键词： Baicalin Gut health Ileal microbiota Probiotic cocktails Synergistic effects

How neonatal diet affects the long-term development of rumination behavior, rumen fermentation and feed digestion in dairy calves fed a high milk level?

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Animal Nutrition 2024年第1期16卷 326-337页

作者： Jianxin Xiao Tianyu Chen Rong Peng Gibson M. Alugongo Hui Yang Shuai Liu Yulin Ma Jingjun Wang Shengli Li Zhijun Cao State Key Laboratory of Animal Nutrition and Feeding International Calf and Heifer Organization College of Animal Science and Technology China Agricultural University Key Laboratory of Low Carbon Culture and Safety Production in Cattle in Sichuan Animal Nutrition Institute Sichuan Agricultural University

This study was to investigate growth performance, rumination development, rumen fermentation and feed digestion in young calves provided high volumes(about 20% of calf birth weight) of milk with or without forage inclusion and how these parameters correlate with each other. Immediately after birth,160 newborn Holstein female calves(41.6 ± 4.2 kg of initial BW) were randomly divided into 2 treatments: 1) starter(CON, only starter) and 2) starter and hay(HAY, both starter and hay). The calves were fed their respective experimental diets from d 4 to 84, after which they were all introduced to similar diets until the end of the experiment on d 196. Treatment had no effect on growth and structural measurements throughout the experimental period. However, treatment had an effect on the other parameters, mainly during the post-weaning period. Forage supplementation tended to reduce starter dry matter intake(P = 0.05), while increasing the forage intake(P < 0.01) and the feed-to-gain ratio(P < 0.01). HAY calves had increased neutral detergent fiber(NDF) and physically effective NDF(peNDF)intakes(P < 0.05) and tended to lower(P < 0.01) starch intake compared to CON calves. The HAY calves had a higher rumination time(P < 0.01), ruminal pH(P < 0.01), and acetate-to-propionate ratio(P = 0.05)compared to the CON calves. Spearman correlation analysis showed that rumination time was positively related to the ruminal p H at d 84(P = 0.01) and 196(P = 0.02). The HAY calves had similar apparent total-tract digestibility of dry matter(DM), NDF and ether extract(EE), but lower digestibility of organic matter(OM, P = 0.03), crude protein(CP, P < 0.01) and starch(P < 0.01) compared to those of the CON calves at week 12. Furthermore, there were no positive relationships between rumination time and nutrient digestibility or between rumination time per kilogram DM and nutrient digestibility. In conclusion, feeding hay to calves fed a high milk level improved rumination during the post-weaning period only, without a concomitant effect on

关键词： Neonatal calf Early forage feeding Rumination Rumen fermentation Nutrient digestibility

Effects of long-term partial substitution of inorganic fertilizer with pig manure and/or straw on nitrogen fractions and microbiological properties in greenhouse vegetable soils

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Journal of Integrative Agriculture 2024年第6期23卷 2083-2098页

作者： Shuo Yuan Ruonan Li Yinjie Zhang Hao'an Luan Jiwei Tang Liying Wang Hongjie Ji Shaowen Huang State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of agricultural Resources and Regional Planning Chinese Academy of Agricultural SciencesBeijing 100081China Institute of agricultural Resources and Environment Hebei Academy of Agriculture and Forestry SciencesShijiazhuang 050051China College of Resources and Environment Henan Agricultural UniversityZhengzhou 450002China College of Forestry Hebei Agricultural UniversityBaoding 071000China

Partial substitution of inorganic fertilizers with organic amendments is an important agricultural management practice.An 11-year field experiment(22 cropping periods)was carried out to analyze the impacts of different partial substitution treatments on crop yields and the transformation of nitrogen fractions in greenhouse vegetable soil.Four treatments with equal N,P_(2)O_(5),and K_(2)O inputs were selected,including complete inorganic fertilizer N(CN),50%inorganic fertilizer N plus 50%pig manure N(CPN),50%inorganic fertilizer N plus 25%pig manure N and 25%corn straw N(CPSN),and 50%inorganic fertilizer N plus 50%corn straw N(CSN).Organic substitution treatments tended to increase crop yields since the 6th cropping period compared to the CN treatment.From the 8th to the 22nd cropping periods,the highest yields were observed in the CPSN treatment where yields were 7.5-11.1%greater than in CN treatment.After 11-year fertilization,compared to CN,organic substitution treatments significantly increased the concentrations of NO_(3)^(-)-N,NH_(4)^(+)-N,acid hydrolysis ammonium-N(AHAN),amino acid-N(AAN),amino sugar-N(ASN),and acid hydrolysis unknown-N(AHUN)in soil by 45.0-69.4,32.8-58.1,49.3-66.6,62.0-69.5,34.5-100.3,and 109.2-172.9%,respectively.Redundancy analysis indicated that soil C/N and OC concentration significantly affected the distribution of N fractions.The highest concentrations of NO_(3)^(-)-N,AHAN,AAN,AHUN were found in the CPSN treatment.Organic substitution treatments increased the activities ofβ-glucosidase,β-cellobiosidase,N-acetyl-glucosamidase,L-aminopeptidase,and phosphatase in the soil.Organic substitution treatments reduced vector length and increased vector angle,indicating alleviation of constraints of C and N on soil microorganisms.Organic substitution treatments increased the total concentrations of phospholipid fatty acids(PLFAs)in the soil by 109.9-205.3%,and increased the relative abundance of G^(+)bacteria and fungi taxa,but decreased the relative abundance of G-bacteria,total bacteria,and a

关键词： organic substitution management greenhouse vegetable production N fractions microbial community composition extracellular enzyme activity enzyme stoichiometry coefficients