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  1. Article ; Online: Time-Course Transcriptome Landscape of Bursa of Fabricius Development and Degeneration in Chickens

    Lan Huang / Yaodong Hu / Qixin Guo / Guobin Chang / Hao Bai

    Agriculture, Vol 12, Iss 8, p

    2022  Volume 1194

    Abstract: The bursa of Fabricius (BF) is a target organ for various pathogenic microorganisms; however, the genes that regulate BF development and decline have not been fully characterized. Therefore, in this study, histological sections of the BF were obtained ... ...

    Abstract The bursa of Fabricius (BF) is a target organ for various pathogenic microorganisms; however, the genes that regulate BF development and decline have not been fully characterized. Therefore, in this study, histological sections of the BF were obtained from black-boned chickens at 7 (N7), 42 (N42), 90 (N90) and 120 days (N120) of age, and the differential expression and expression trends of the BF at different stages were analyzed by transcriptome analysis. The results showed that the growth of the BF progressively matured with age, followed by gradual shrinkage and disappearance. Transcriptome differential analysis revealed 5914, 5513, 4575, 577, 530 and 66 differentially expressed genes (DEG) in six different comparison groups: N7 vs. N42, N7 vs. N90, N7 vs. N120, N42 vs. N90, N42 vs. N120 and N90 vs. N120, respectively. Moreover, we performed transcriptomic analysis of the time series of BF development and identified the corresponding stages of biological process enrichment. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the expression of the 16 DEGs during bursal growth and development. These results were consistent with the transcriptome results, indicating that they reflect the expression of the BF during growth and development and that these genes reflect the characteristics of the BF at different times of development and decline. These findings reflect the characteristics of the BF at different time intervals.
    Keywords bursa of Fabricius ; development ; degradation ; chicken ; transcriptomic analysis ; Agriculture (General) ; S1-972
    Subject code 380
    Language English
    Publishing date 2022-08-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Effects of Dried Blueberry Pomace and Pineapple Pomace on Growth Performance and Meat Quality of Broiler Chickens

    Yaodong Hu / Shi Tang / Wei Zhao / Silu Wang / Caiyun Sun / Binlong Chen / Yuxing Zhu

    Animals, Vol 13, Iss 2198, p

    2023  Volume 2198

    Abstract: The purpose of this study was to investigate the effects of dried blueberry pomace (BP) and pineapple pomace (PP) on the growth performance and meat quality of broiler chickens. A total of 240 1-day-old Ross 308 broiler chickens were randomly divided ... ...

    Abstract The purpose of this study was to investigate the effects of dried blueberry pomace (BP) and pineapple pomace (PP) on the growth performance and meat quality of broiler chickens. A total of 240 1-day-old Ross 308 broiler chickens were randomly divided into 3 groups, with 10 replicates per treatment group and 8 birds per replicate (4 males and 4 females). The three groups were the control (CON) group, the 3% BP group, and 3% PP group. The entire trial period lasted 42 days. The results show that the average daily feed intake, average daily gain, and feed-to-gain ratio of the BP group and the PP group were not significantly different from those in the CON group ( p > 0.05). Adding BP to the diet significantly reduced the proportion of liver and giblets ( p < 0.05). Adding PP to the diet significantly reduced the proportion of liver, while the proportion of gizzard significantly increased ( p < 0.05). The pH 24h and L* of breast muscles were significantly lower in the PP group than in the CON group ( p < 0.05). The water-holding capacity of the leg muscles in the BP group and the PP group was significantly lower than that in the CON group ( p < 0.05). The crude protein content of breast muscle and the ether extract content of leg muscle in the BP group were significantly lower than those in the CON group ( p < 0.05). In conclusion, the addition of 3% BP and PP to broiler chickens’ diets had no adverse effects on growth performance or meat quality.
    Keywords blueberry pomace ; pineapple pomace ; growth performance ; meat quality ; broiler chicken ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
    Subject code 796
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana

    Hainan Zhao / Wenli Zhang / Tao Zhang / Yuan Lin / Yaodong Hu / Chao Fang / Jiming Jiang

    Genome Biology, Vol 21, Iss 1, Pp 1-

    2020  Volume 17

    Abstract: Abstract Background Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, ... ...

    Abstract Abstract Background Regulation of transcription depends on interactions between cis-regulatory elements (CREs) and regulatory proteins. Active CREs are imbedded in open chromatin that are accessible to nucleases. Several techniques, including DNase-seq, which is based on nuclease DNase I, and ATAC-seq, which is based on transposase Tn5, have been widely used to identify genomic regions associated with open chromatin. These techniques have played a key role in dissecting the regulatory networks in gene expression in both animal and plant species. Results We develop a technique, named MNase hypersensitivity sequencing (MH-seq), to identify genomic regions associated with open chromatin in Arabidopsis thaliana. Genomic regions enriched with MH-seq reads are referred as MNase hypersensitive sites (MHSs). MHSs overlap with the majority (~ 90%) of the open chromatin identified previously by DNase-seq and ATAC-seq. Surprisingly, 22% MHSs are not covered by DNase-seq or ATAC-seq reads, which are referred to “specific MHSs” (sMHSs). sMHSs tend to be located away from promoters, and a substantial portion of sMHSs are derived from transposable elements. Most interestingly, genomic regions containing sMHSs are enriched with epigenetic marks, including H3K27me3 and DNA methylation. In addition, sMHSs show a number of distinct characteristics including association with transcriptional repressors. Thus, sMHSs span distinct classes of open chromatin that may not be accessible to DNase I or Tn5. We hypothesize that the small size of the MNase enzyme relative to DNase I or Tn5 allows its access to relatively more condensed chromatin domains. Conclusion MNase can be used to identify open chromatin regions that are not accessible to DNase I or Tn5. Thus, MH-seq provides an important tool to identify and catalog all classes of open chromatin in plants.
    Keywords Open chromatin ; cis-regulatory elements ; Histone modification ; DNA methylation ; DNase-seq ; ATAC-seq ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Subject code 570
    Language English
    Publishing date 2020-02-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
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  4. Article ; Online: Contribution of both positive selection and relaxation of selective constraints to degeneration of flyability during geese domestication.

    Ye Wang / Yaodong Hu / Daqian He / Shiyi Chen / Siming Li / Dan Lan / Peng Ren / Zhenping Lin / Yiping Liu

    PLoS ONE, Vol 12, Iss 9, p e

    2017  Volume 0185328

    Abstract: Flyability is the most discrepant trait between modern-day geese and their wild ancestors, and the degeneration of flyability is a key marker of the successful domestication of wild geese. In light of the relatively short history of domestic geese, ... ...

    Abstract Flyability is the most discrepant trait between modern-day geese and their wild ancestors, and the degeneration of flyability is a key marker of the successful domestication of wild geese. In light of the relatively short history of domestic geese, intense artificial selection is thought to play an important role in the degeneration of flyability. However, the underlying mechanism behind this phenomenon has seldom been investigated. In this study, we applied a molecular evolutionary approach to the evaluation of partial breeds of domestic geese in order to look for genes involved in the selection pressure toward degeneration of flyability. The haplotype networks, pairwise fixation index (FST) values, and analysis of molecular variance results all clearly illustrated a population variance between Landes geese and partial Chinese domestic geese. We also detected signatures of positive artificial selection in the COX2 and COX3 genes, and related selection in the HBB gene. Our results support the independent origins of partial European domestic geese and Chinese domestic geese. In addition, both positive artificial selection and the relaxation of functional constraints appeared to play important roles in the degeneration of flyability in domestic geese.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
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  5. Article ; Online: Fast and Large-Scale Anodizing Synthesis of Pine-Cone TiO2 for Solar-Driven Photocatalysis

    Yan Liu / Yanzong Zhang / Lilin Wang / Gang Yang / Fei Shen / Shihuai Deng / Xiaohong Zhang / Yan He / Yaodong Hu / Xiaobo Chen

    Catalysts, Vol 7, Iss 8, p

    2017  Volume 229

    Abstract: Anodization has been widely used to synthesize nanostructured TiO2 films with promising photocatalytic performance for solar hydrogen production and pollution removal. However, it usually takes a few hours to obtain the right nanostructures even on a ... ...

    Abstract Anodization has been widely used to synthesize nanostructured TiO2 films with promising photocatalytic performance for solar hydrogen production and pollution removal. However, it usually takes a few hours to obtain the right nanostructures even on a small scale (e.g., 10 mm × 20 mm). In order to attract interest for industrial applications, fast and large-scale fabrication is highly desirable. Herein, we demonstrate a fast and large-scale (e.g., 300 mm × 360 mm) synthesis of pine-cone TiO2 nanostructures within two min. The formation mechanism of pine-cone TiO2 is proposed. The pine-cone TiO2 possesses a strong solar absorption, and exhibits high photocatalytic activities in photo-oxidizing organic pollutants in wastewater and producing hydrogen from water under natural sunlight. Thus, this study demonstrates a promising method for fabricating TiO2 films towards practical photocatalytic applications.
    Keywords pine-cone TiO2 nanoclusters ; formation mechanism ; lattice defects ; optical absorption ; large-sized films ; printing and dyeing wastewater ; Chemical technology ; TP1-1185 ; Chemistry ; QD1-999
    Subject code 620
    Language English
    Publishing date 2017-08-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article: Mitigating biochar phytotoxicity via lanthanum (La) participation in pyrolysis

    Li, Yang / Fei Shen / Gang Yang / Jing Zhang / Shihuai Deng / Yanqi Yang / Yanzong Zhang / Yaodong Hu / Yongmei Zeng

    Environmental science and pollution research international. 2017 Apr., v. 24, no. 11

    2017  

    Abstract: Biochar (BC) produced from oak sawdust by slow pyrolysis was investigated to check the potential inhibition to early growth of tomato for phytotoxicity assessment. An inverted-U-shaped dose-response relationship between BC dosage and seed germination/ ... ...

    Abstract Biochar (BC) produced from oak sawdust by slow pyrolysis was investigated to check the potential inhibition to early growth of tomato for phytotoxicity assessment. An inverted-U-shaped dose-response relationship between BC dosage and seed germination/seedling growth can be observed. Half maximal effective concentration (EC₅₀), based on the inhibition rate of root and stem length, was 65.7 and 74.0 g kg⁻¹, respectively. At the highest BC dosage of 80.0 g kg⁻¹, germination rate, root, and shoot length were notably inhibited by 34.9, 62.3, and 62.2% compared with their corresponding controls (without BC). Fluorescence intensity, indicating reactive oxygen species (ROS) generation in leaf and root, was 177.7 and 344.5% higher than the control. Similar results on H₂O₂ content in leaf and root were observed as well. Besides, membrane leakage from the leaf and root cells was 2.1- and 1.3-fold higher than the corresponding controls. These results proved that BC exhibited significant phytotoxicity in the early growth stage of tomato. Unlike BC, the inhibitions on seed germination and seedling growth, the ROS accumulation, and the plasma membrane damage were not obvious with increasing La-BC dosage. These results indicated that BC phytotoxicity can be greatly mitigated by La involvement in pyrolysis, which was potentially associated with the reduced organic compounds and free radicals in La-BC. Besides, bio-available La in La-BC was partially involved in mitigating the phytotoxicity.
    Keywords biochar ; developmental stages ; dose response ; fluorescence ; free radicals ; hydrogen peroxide ; lanthanum ; leaves ; median effective concentration ; organic compounds ; phytotoxicity ; plasma membrane ; pyrolysis ; roots ; sawdust ; seed germination ; seedling growth ; shoots ; tomatoes
    Language English
    Dates of publication 2017-04
    Size p. 10267-10278.
    Publishing place Springer Berlin Heidelberg
    Document type Article
    ZDB-ID 1178791-0
    ISSN 1614-7499 ; 0944-1344
    ISSN (online) 1614-7499
    ISSN 0944-1344
    DOI 10.1007/s11356-017-8653-x
    Database NAL-Catalogue (AGRICOLA)

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  7. Article: Pretreating wheat straw by phosphoric acid plus hydrogen peroxide for enzymatic saccharification and ethanol production at high solid loading

    Qiu, Jingwen / Fei Shen / Gang Yang / Jing Zhang / Lunjie Ma / Shihuai Deng / Yanzong Zhang / Yaodong Hu / Yongmei Zeng

    Bioresource technology. 2017 Aug., v. 238

    2017  

    Abstract: Wheat straw was pretreated by phosphoric acid plus hydrogen peroxide (PHP) for enzymatic hydrolysis and ethanol fermentation at high solid loadings. Results indicated solid loading could reach 20% with 77.4% cellulose-glucose conversion and glucose ... ...

    Abstract Wheat straw was pretreated by phosphoric acid plus hydrogen peroxide (PHP) for enzymatic hydrolysis and ethanol fermentation at high solid loadings. Results indicated solid loading could reach 20% with 77.4% cellulose-glucose conversion and glucose concentration of 164.9g/L in hydrolysate, it even was promoted to 25% with only 3.4% decrease on cellulose-glucose conversion as the pretreated-wheat straw was dewatered by air-drying. 72.9% cellulose-glucose conversion still was achieved as the minimized enzyme input of 20mg protein/g cellulose was employed for hydrolysis at 20% solid loading. In the corresponding conditions, 100g wheat straw can yield 11.2g ethanol with concentration of 71.2g/L by simultaneous saccharification and fermentation. Thus, PHP-pretreatment benefitted the glucose or ethanol yield at high solid loadings with lower enzyme input. Additionally, decreases on the maximal cellulase adsorption and the direct-orange/direct-blue indicated drying the PHP-pretreated substrates negatively affected the hydrolysis due to the shrinkage of cellulase-size-accommodable pores.
    Keywords adsorption ; air drying ; cellulose ; endo-1,4-beta-glucanase ; enzymatic hydrolysis ; ethanol ; ethanol fermentation ; ethanol production ; glucose ; hydrogen peroxide ; hydrolysates ; hydrolysis ; phosphoric acid ; saccharification ; shrinkage ; wheat straw
    Language English
    Dates of publication 2017-08
    Size p. 174-181.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1065195-0
    ISSN 1873-2976 ; 0960-8524
    ISSN (online) 1873-2976
    ISSN 0960-8524
    DOI 10.1016/j.biortech.2017.04.040
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  8. Article ; Online: Effects of Slaughter Age on Muscle Characteristics and Meat Quality Traits of Da-Heng Meat Type Birds

    Jingjing Li / Chaowu Yang / Han Peng / Huadong Yin / Yan Wang / Yaodong Hu / Chunlin Yu / Xiaosong Jiang / Huarui Du / Qingyun Li / Yiping Liu

    Animals, Vol 10, Iss 1, p

    2019  Volume 69

    Abstract: Due to the increasing demand for producing chickens with high meat quality, there is a need to determine its mode of action on chicken meat quality traits across a wider age spectrum. In this study, five groups of 200 male Da-Heng meat type birds were ... ...

    Abstract Due to the increasing demand for producing chickens with high meat quality, there is a need to determine its mode of action on chicken meat quality traits across a wider age spectrum. In this study, five groups of 200 male Da-Heng meat type birds were reared until slaughter age of 60, 90, 120, 150, 180 days old and breast muscle performance, meat quality traits, and myofiber characteristics were evaluated. The larger body weight and breast weight of chicken are based on larger myofiber diameter and area, less myofiber density for the older birds than younger birds. There was an age effect on all meat quality traits of chicken breast muscle ( p < 0.05). Older chickens often presented a higher pH, lower drip loss, higher shear force, darker, and redder breast meat. The correlation coefficients showed that myofiber characteristics played an important role in breast pH values, drip loss, and meat color ( p < 0.05). Besides, significant correlations were also found between meat quality traits ( p < 0.05). Further studies are needed to explore the biochemical character and potential molecular mechanism of chicken breast muscle to determine the factors that causes these age-related differences in meat quality in the current study.
    Keywords chicken ; slaughter age ; myofiber ; meat quality ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
    Language English
    Publishing date 2019-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
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  9. Article: Evolution of DUF1313 family members across plant species and their association with maize photoperiod sensitivity

    Li, Jia / Chuan Li / Erliang Hu / Hai Lan / Jie Xu / Xueying Chen / Yanli Lu / Yaodong Hu

    Genomics. 2016 May, v. 107, no. 5

    2016  

    Abstract: Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into ...

    Abstract Proteins of the DUF1313 family contain a highly conserved domain and are only found in plants; they play important roles in most plant functions. In this study, 269 DUF1313 genes from 81 photoautotrophic species were identified; they were classified into three major types based on the amino acid substitutions in the conserved region: IARV, I(S/T/F)(K/R)V, and IRRV. Phylogenic tree constructed from 51 DUF1313 genes from graminoids revealed three clades: A, B1, and B2. Clade B1 was found to have undergone episodic positive selection after a gene duplication event and included four amino acid sites under positive selection. The association between DUF1313 family members and traits investigated in maize indicated that three of four genes (GRMZM2G025646, GRMZM5G877647, GRMZM2G359322, and GRMZM2G382774) were associated with the target traits such as days to silking, days to tasselling, and plant height. The nucleotide diversity of the most primitive and highly conserved DUF1313 gene, ELF4-like4, was the highest in Tripsacum and the lowest in maize. Tajima's D and Fu and Li's D tests revealed that significant purifying selection had occurred in the coding sequence region of this DUF1313 gene in teosinte and maize. No significant signal was detected in the 5′-untranslated region of this gene in each of the three species (maize, teosinte, and Tripsacum) or in any gene regions of Tripsacum. Phylogenetic analyses revealed that the 103 accessions of maize, teosinte, and Tripsacum can be grouped into four clades based on the ELF4-like4 gene sequence similarity. Thus, this gene can be used to determine the relationships between maize and its relatives, and the DUF1313 family members and alleles identified in this study might be valuable genetic resources for molecular marker-assisted breeding in maize.
    Keywords alleles ; amino acid substitution ; amino acids ; corn ; gene duplication ; genetic variation ; graminoids ; marker-assisted selection ; nucleotide sequences ; photoperiod ; phylogeny ; proteins ; sequence homology ; Tripsacum ; Zea
    Language English
    Dates of publication 2016-05
    Size p. 199-207.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 356334-0
    ISSN 1089-8646 ; 0888-7543
    ISSN (online) 1089-8646
    ISSN 0888-7543
    DOI 10.1016/j.ygeno.2016.01.003
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  10. Article: Pretreating wheat straw by the concentrated phosphoric acid plus hydrogen peroxide (PHP): Investigations on pretreatment conditions and structure changes

    Wang, Qing / Fei Shen / Gang Yang / Jing Zhang / Jinguang Hu / Shihuai Deng / Yanzong Zhang / Yaodong Hu / Zili Mei

    Bioresource technology. 2016 Jan., v. 199

    2016  

    Abstract: Wheat straw was pretreated by PHP (the concentrated H3PO4 plus H2O2) to clarify effects of temperature, time and H3PO4 proportion on hemicellulose removal, delignification, cellulose recovery and enzymatic digestibility. Overall, hemicellulose removal ... ...

    Abstract Wheat straw was pretreated by PHP (the concentrated H3PO4 plus H2O2) to clarify effects of temperature, time and H3PO4 proportion on hemicellulose removal, delignification, cellulose recovery and enzymatic digestibility. Overall, hemicellulose removal was intensified by PHP comparing to the concentrated H3PO4. Moreover, efficient delignification specially happened in PHP pretreatment. Hemicellulose removal and delignification by PHP positively responded to temperature and time. Increasing H3PO4 proportion in PHP can promote hemicellulose removal, however, decrease the delignification. Maximum hemicellulose removal and delignification were achieved at 100% and 83.7% by PHP. Enzymatic digestibility of PHP-pretreated wheat straw was greatly improved by increasing temperature, time and H3PO4 proportion, and complete hydrolysis can be achieved consequently. As temperature of 30–40°C, time of 2.0h and H3PO4 proportion of 60% were employed, more than 92% cellulose was retained in the pretreated wheat straw, and 29.1–32.6g glucose can be harvested from 100g wheat straw.
    Keywords cellulose ; delignification ; enzymatic hydrolysis ; glucose ; hemicellulose ; hydrogen peroxide ; hydrolysis ; phosphoric acid ; temperature ; wheat straw
    Language English
    Dates of publication 2016-01
    Size p. 245-257.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1065195-0
    ISSN 1873-2976 ; 0960-8524
    ISSN (online) 1873-2976
    ISSN 0960-8524
    DOI 10.1016/j.biortech.2015.07.112
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