bluuebunny/crossref_metadata_2025 huggingface dataset:
Aspirin eugenol ester affects ileal barrier function, inflammatory response and microbiota in broilers under lipopolysaccharide-induced immune stress conditions
Authors: Zhang Ruilin , Bai Dongying , Zhen Wenrui , Hu Xiaodi , Zhang Haojie , Zhong Jiale , Zhang Yi , Ito Koichi , Zhang Bingkun , Yang Yajun , Li Jianyong , Ma Yanbo
Published: May 2024

Aims

The aim of this study was to investigate the effects of aspirin eugenol ester (AEE) on ileal immune function in broilers under lipopolysaccharide (LPS)-induced immune stress.

Methods

Two hundred and forty one-day-old male Arbor Acres chicks were randomly divided into four groups (saline, LPS, saline + AEE and LPS + AEE) with six replicates of ten broilers each. The saline group and LPS group were fed the normal diet, while the other two groups received normal diet plus 0.1 g/kg AEE. Broilers in the LPS and LPS + AEE groups were injected intraperitoneally with 0.5 mg/kg B.W LPS in saline for seven consecutive days beginning at 14 days of age, while broilers in the saline and saline + AEE groups were injected with saline only.

Results

The results showed that AEE improved the ileal morphology and increased the ratio of villus height to crypt depth of immune-stressed broilers. LPS-induced immune stress significantly reduced the expression of the genes for the tight junction proteins occludin, zonula occludens-1 (ZO-1), claudin-1 and claudin-2, in the ileum, while AEE significantly up-regulated the expression of these genes. Compared with the saline group, the LPS-treated chickens showed significantly increased mRNA expression of the inflammatory factors tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-10 (IL-10), cyclooxygenase-2 (COX-2), and microsomal Prostaglandin E Synthesase-1 (mPGES-1) in the ileum, while they were significantly decreased by AEE supplementation. In addition, analysis of the ileal bacterial composition showed that compared with saline and LPS + AEE groups, the proportion of Firmicutes and Lactobacillus in the LPS group was lower, while the proportion of Proteobacteria and Escherichia-Shigella was higher. Similarly, Line Discriminant Analysis Effect Size (LEfSe) analysis showed that compared with the LPS group, Brevibacillus was dominant in the saline group, while the LPS + AEE group was rich in Rhizobium, Lachnoclostridium, Ruminococcaceae, Faecalibacterium, Negativibacillus, Oscillospiraceae, and Flavonifractor.

Conclusion

These results indicate that dietary supplementation with 0.1 g/kg AEE could protect the intestinal health by improving the intestinal villus morphology, enhancing the expression of tight junction genes and alleviating inflammation to resist the immune stress caused by LPS stimulation in broilers, and the mechanism may involve COX-2-related signal transduction and improved intestinal microbiota composition.
The N-glycosylation at positions 652 and 661 of viral spike protein negatively modulates porcine deltacoronavirus entry
Authors: Wang Hai-Ming , Qiao Yang-Yang , Liu Yong-Gang , Cai Bing-Yan , Yang Yue-Lin , Lu Hui , Tang Yan-Dong
Published: May 2024

N-glycosylation is a highly conserved glycan modification that plays crucial roles in various physiological processes, including protein folding, trafficking, and signal transduction. Porcine deltacoronavirus (PDCoV) poses a newly emerging threat to the global porcine industry. The spike protein of PDCoV exhibits a high level of N-glycosylation; however, its role in viral infection remains poorly understood. In this study, we applied a lentivirus-based entry reporter system to investigate the role of N-glycosylation on the viral spike protein during PDCoV entry stage. Our findings demonstrate that N-glycosylation at positions 652 and 661 of the viral spike protein significantly reduces the infectivity of PDCoV pseudotyped virus. Overall, our results unveil a novel function of N-glycosylation in PDCoV infection, highlighting its potential for facilitating the development of antiviral strategies.
A Sparse Neural Network-Based Control Method for Saturated Nonlinear Affine Systems
Authors: Zhang Jing , Yin Baoqun , Huo Jianwen , Guo Hongliang , Li Zhan
Published: May 2024

Saturated nonlinear affine systems are widely encountered in many engineering fields. Currently, most control methods on saturated nonlinear affine systems are not specifically designed based on sparsity-based control methodologies, and they might require sparse identification at the beginning stage and applying tracking control afterwards. In this paper, a sparse neural network (SNN)-based control method from an lp-norm (1≤p<2) optimization perspective is proposed for saturated nonlinear affine systems by taking advantage of the nice properties of primal dual neural networks for optimization. In particular, when p=1, a new alternative controller based on SNN is derived, encountering computational difficulties distinct from those of another solution set in the basic dual neural network. The convergence properties of such SNN-based controllers are investigated and analyzed to find a control solution. Five illustrative examples further are shown to demonstrate the efficiency of the proposed SNN-based control method for tracking the desired references of saturated nonlinear affine systems. In the practical application scenario involving the UR5 robot control, the trajectory’s average errors are consistently confined to a minimal magnitude of 10−4 m. These findings substantiate the efficacy of the SNN-based control approach proposed for precise tracking control in saturated nonlinear affine systems.
Robust Geometric Control for a Quadrotor UAV with Extended Kalman Filter Estimation
Authors: Lei Bo , Liu Bo , Wang Changhong
Published: May 2024

This study proposes a robust geometric controller tailored for quadrotor unmanned aerial vehicles (UAVs). The original geometric controller exhibits excellent performance in quadrotor UAV maneuvers. However, as a model-based nonlinear control method, it is sensitive to system model parameters. By integrating a novel extended Kalman filter (EKF)-based estimator for real-time, online estimation of the quadrotor’s inertia parameters, the controller adeptly handles internal uncertainties and external perturbations during flight maneuvers. This approach significantly improves the robustness of the control system against model inaccuracies. Empirical evidence is provided through both simulation and extensive real-world flight tests, demonstrating the controller’s effectiveness and its practical applicability in dynamic environments. The results confirm that this integration substantially enhances system reliability and performance under varied operational conditions.
The Dysfunction of Mission-Oriented Innovation Policy: Impeding the Accumulation of Scientific Knowledge in the Japanese Academic Sector
Authors: Hirao Takashi , Hoshino Yusuke
Published: May 2024

Since the Organisation for Economic Cooperation and Development presented its comprehensive Innovation Strategy in 2010, numerous countries have been updating their innovation policies. Subsequent to the promulgation, the innovation policies of Japan shifted the focus from discipline-specific to social issue-oriented approaches. This study investigates the response of the Japanese academic sector to this policy shift and the characteristics of the research projects associated with innovation policy by utilizing descriptive statistics from policy documents and the database of Grants-in-Aid for Scientific Research. The findings reveal that Japanese researchers have increasingly aligned their efforts with government-proposed research themes in recent years, with a notable shift toward short-term research projects. Moreover, Japanese universities are undergoing reforms that are transforming them into entrepreneurial institutions by altering incentive structures. Although these reforms may yield short-term research outcomes, they may not always address long-term societal needs. The narrowing focus on research themes could restrict the potential impact of research and impede the development of innovative solutions to societal challenges. From this viewpoint, assessing the relationship between government-proposed research themes and the research productivity of Japan is critical. Universities and public research institutions play a vital social role in broadening the foundational knowledge base through basic research, while private enterprises may lack the motivation to invest in research and development with low appropriability. These results may be beneficial for policymakers in reconsidering the division of labor in industry-academic collaboration in a knowledge-intensive economy.
Prediction Model of Nitrogen, Phosphorus, and Potassium Fertilizer Application Rate for Greenhouse Tomatoes under Different Soil Fertility Conditions
Authors: Yu Xiaoyu , Luo Yuzhu , Bai Bing , Chen Xin , Lu Caiyan , Peng Xiuyuan
Published: May 2024

To reach the target yield of crops, nutrient management is essential. Selecting the appropriate prediction model and adjusting the nutrient supply based on the actual situation can effectively improve the nutrient utilization efficiency, crop yield, and product quality. Therefore, a prediction model of the NPK fertilizer application rate for greenhouse tomatoes under the target yield was studied in this study. Under low, medium, and high soil fertility conditions, a neural network prediction model based on the sparrow search algorithm (SSA-NN), a neural network prediction model based on the improved sparrow search algorithm (ISSA-NN), and a neural network prediction model based on the hybrid algorithm (HA-NN) were used to predict the NPK fertilizer application rate for greenhouse tomatoes. The experimental results indicated that the evaluation indexes (i.e., the mean square error (MSE), explained variance score (EVS), and coefficient of determination (R2)) of the HA-NN prediction model proposed in this study were superior than the SSA-NN and ISSA-NN prediction models under three different soil fertility conditions. Under high soil fertility, compared with the SSA-NN prediction model, the MSE of the ISSA-NN and HA-NN prediction models decreased to 0.007 and 0.005, respectively; the EVS increased to 0.871 and 0.908, respectively; and the R2 increased to 0.862 and 0.899, respectively. This study showed that the HA–NN prediction model was superior in predicting the NPK fertilizer application rate for greenhouse tomatoes under three different soil fertility conditions. Due to the significance of NPK fertilizer application rate prediction for greenhouse tomatoes, this technique is expected to bring benefits to agricultural production management and decision support.
Effects of Exogenous Brassinosteroid and Reduced Leaf Source on Source–Sink Relationships and Boll Setting in Xinjiang Cotton
Authors: Lou Shanwei , Jiang Hui , Li Jie , Tian Liwen , Du Mingwei , Ma Tengfei , Zhang Lizhen , Zhang Pengzhong
Published: May 2024

Xinjiang cotton is characterized by high-density planting, which easily leads to competition between the source and sink, the shading of leaves and reproductive organs, and yield reduction. Balancing the relationship between source and sink can promote high and stable cotton yield. In this study, field experiments were conducted by combining the exogenous application of brassinosteroid with a reduction in leaf source to study their effects on the physiological and yield attributes of cotton. The results indicate that brassinosteroid application increased the yield, with a maximum yield increase of 6.3%. The number of bolls per plant increased by 1.3 nos. The photosynthetic rate and dry matter accumulation were enhanced, and the proportion of reproductive organs in the dry matter increased by >4%. Under the reduced leaf source, brassinosteroid application increased the number of new leaves by 20%, delayed the shedding of reproductive organs by 5–10 days, and reduced the average shedding rate by 8.9%. Additionally, the number of bolls increased in the middle and upper parts and at the edge of the plant. The number of bolls increased by 19.4% on the 4th–8th fruiting branches and 60.7% at the edge. Under leaf reduction treatment, brassinosteroid application could generally increase yield. After brassinosteroid application and removing half the leaves of fruiting branches and all leaves of the vegetive branches, the yield was higher than that of the control. Thus, brassinosteroid application could improve the efficiency of the leaf source and promote dry matter accumulation in sinks. Moreover, it could optimize boll distribution and increase yield by reducing reproductive organ shedding. Under the high-density planting of cotton in Xinjiang, leaf source is a slight surplus, and a moderate reduction in plant density is conducive to increasing yield.
Intercropping as a Strategy for Weed Management in Faba Bean (Vicia faba L.)
Authors: Villegas-Fernández Ángel M. , Amarna Ahmed A. , Moral Juan , Rubiales Diego
Published: May 2024

Faba bean is an important legume crop worldwide, which is grown both for food and feed. As for many legume crops, postemergence weed control is difficult. The aim of this work was to assess the potential of intercropping in weed management by assessing the effect of mixing faba bean with different crops (wheat, barley, and pea) on weeds in the South of Spain. Four field trials were conducted over four consecutive seasons, and the results found that the addition of alternate intercropping of faba bean and barley achieved high levels of weed control, both for coverage and biomass (92.7% and 76.6%, respectively). Intercropping with wheat did not reduce weed coverage but did decrease weed biomass by 46.1% as compared with the faba bean monocrop. Intercropping with pea did not provide significant reductions in weed coverage or weed biomass. The diversity of the weed community was not altered by the different crop combinations tested. Additional experiments under controlled conditions were carried out to determine the possible role of barley allelopathy in weed suppression. A strong allelopathic effect entailing a reduction in the number of plants and biomass was detected for four weeds including Sinapis arvensis, Polypogon monspeliensis, Matricaria camomilla, and Medicago truncatula. It can be concluded that intercropping faba bean with barley is an excellent strategy for weed control in Southern Spain.
Effects of Decreasing Hill Number per Unit Area Combined with Increasing Seedling Number per Hill on Grain Quality in Hybrid Rice
Authors: Xiao Zhengwu , Zhang Ruichun , Cao Fangbo , Liu Longsheng , Chen Jiana , Huang Min
Published: May 2024

Hill number per unit area and seedling number per hill are foundational agrotechnical factors shaping the growth and development of rice plants. This study aimed to determine the effects of decreasing the hill number per unit area combined with increasing the seedling number per hill on grain quality in hybrid rice. Field experiments were performed in Hengyang, Hunan Province, China, in 2022 and 2023 using the hybrid rice variety Huazheyou 261, as well as in Liuyang, Hunan Province, China, in 2023 using the hybrid rice varieties Yueyou 2646 and Zhenliangyouyuzhan. Treatments (combining hill number per unit area and seedling number per hill) encompassed a combination of 24 hills per m2 and one seedling per hill (H24S1) and a combination of 14 hills per m2 and three seedlings per hill (H14S3) in Hengyang, as well as a combination of 28 hills per m2 and two seedlings per hill (H28S2) and a combination of 14 hills per m2 and four seedlings per hill (H14S4) in Liuyang. There were no significant differences in the leaf area index at the heading stage, as well as no significant differences in canopy light transmittance during the grain-filling period between H24S1 and H14S3 in Hengyang, or between H28S2 and H14S4 in Liuyang. The differences in grain quality traits, including milling traits (brown, milled, and head rice rate), appearance traits (rice length, rice length-width ratio, chalky grain rate, and chalkiness degree), amylose and protein content, and pasting characteristics were also not significant between H24S1 and H14S3 in Hengyang, nor between H28S2 and H14S4 in Liuyang. This study indicates that the grain quality in hybrid rice is unaffected by decreasing the hill number per unit area integrated with increasing the seedling number per hill.
Replacing Chemical Fertilizer with Separated Biogas Slurry to Reduce Soil Nitrogen Loss and Increase Crop Yield—A Two-Year Field Study
Authors: Zhao Zichao , Fu Longyun , Yao Li , Wang Yanqin , Li Yan
Published: May 2024

The application of biogas slurry in agriculture production is regarded as a sustainable method for mitigating the environmental impacts of fertilization. To investigate the effects of biogas slurry application on soil nitrogen loss and crop yield, a field plot experiment was conducted within a wheat–maize rotation system. This study assessed the effects of three levels of biogas slurry nitrogen substitution, 50% (BSF), 100% (BS), and 150% (EBS), on the yield of silage maize and wheat, nitrogen use efficiency, and soil nitrogen loss. The findings revealed that in the first year (characterized by high rainfall), the application of the biogas slurry led to increased NH3 emissions and nitrogen leaching, resulting in a notable rise in the annual nitrogen loss. Additionally, it was observed that as the amount of applied biogas slurry increased, the nitrogen loss also rose correspondingly. However, in the second year (a period of drought conditions), despite the elevated NH3 emissions from the biogas slurry, there was a significant reduction in nitrogen leaching, which resulted in reductions of 14.2% and 20.0% in annual nitrogen loss for the BSF and BS treatments, respectively, with comparable nitrogen input to the fertilizer treatment. Throughout both years, the application of biogas slurry did not decrease the yield of silage maize and wheat, and notably, the BS treatment even enhanced the crop nitrogen utilization efficiency. Compared with other nitrogen fertilizer treatments, the EBS treatment did not increase crop yield even with an increased nitrogen application rate; it also reduced the nitrogen utilization efficiency and N loss. In conclusion, employing biogas slurry to replace chemical fertilizer (equivalent nitrogen substitution) during drought years can enhance nitrogen utilization efficiency, reduce nitrogen loss, and sustain crop yield. When applying biogas slurry in years with substantial rainfall, effective measures should be implemented to mitigate nitrogen loss.
Does the Biennial Straw Return Have an Identical Characteristic of Soil Organic Carbon Sequestration as the Annual? A Case Study of Cornfield in Northeast China
Authors: Liu Jinhua , Zhao Xingmin , Zhang Zhongqing , Zhao Chenyu , Huang Ning , Wang Hongbin
Published: May 2024

Straw return is a common cultivation to improve soil fertility and realize sustainable agricultural development. However, the effect of returning interval on the corn straw humification process in northeast China is little known. In this study, a four-year field trial was conducted to investigate the characteristics of soil carbon sequestration under the annual deep straw return (T1), the biennial deep straw return (T2), and the non-straw return (T3) in Jilin Province, China. In order to precisely evaluate the soil organic carbon density (SOCD), each soil horizon was divided differently according to the actual situation, rather than a fixed thickness. The results show that both the annual and the biennial deep straw return had a significantly positive influence on the content of soil organic carbon (SOC), humic acid, fulvic acid, and humin in the plough pan (straw-applied horizon), compared to the no-straw return. SOC of the cambic horizon and the C horizon in annual straw return was 28.78%, 47.44% higher than the biennial straw return, but it was 27.58% lower in the plough pan. The SOCD in the plough pan in the biennial straw return was higher than the annual straw return, but their difference in the entire soil profile was not significant. However, the conversion rate of straw carbon to SOC was 18.42% in the annual straw return and 21.05% in the biennial straw return. The straw return amount was not a key factor affecting the SOC sequestration in the cold area; it was restricted by the comprehensive effects of the cold weather, the intensity of soil disturbance, C/V and the initial SOC content. In conclusion, the biennial deep straw return was a better management tool, as it generally had an identical quality and quantity of soil organic carbon and a higher straw conversion rate relative to the annual deep straw return.
A Novel Approach for Asparagus Comprehensive Classification Based on TOPSIS Evaluation and SVM Prediction
Authors: Chen Qiang , Xia Chuang , Shi Yinyan , Wang Xiaochan , Zhang Xiaolei , He Ye
Published: May 2024

As a common vegetable variety, asparagus is rich in B vitamins, vitamin A, and trace elements such as folate, selenium, iron, manganese, and zinc. With the increasing market demand, China has become the world’s largest cultivated area for asparagus production and product exportation. However, traditional asparagus grading mostly relies on manual visual judgment and needs a lot of manpower input to carry out the classification operation, which cannot meet the needs of large-scale production. To address the high labor cost and labor-intensive production process resulting from the large amount of manpower input and low accuracy of existing asparagus grading devices, this study proposed an improved asparagus grading system and method based on TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution) objective evaluation and SVM (support vector machine) prediction. The key structure of classification device was analyzed first, the key components were designed, and the structural parameters were determined by theoretical calculation. Through analysis of the factors affecting asparagus quality, three key attributes were determined: length, diameter, and bruises, which were used as reference attributes to conduct experimental analysis. Then, the graded control groups were set up, combining the TOPSIS principle with weighting, and a score for each asparagus sample was determined. These scores were compared with those of a graded control group to derive the grade of each asparagus, and these subsets of the dataset were used as the training set and the test set, excluding the error caused by the subjectivity of the manual judgment. Based on a comparison of the accuracies of different machine learning models, the support vector machine (SVM) was determined to be the most accurate, and four SVM methods were used to evaluate the test set: linear SVM, quadratic SVM, cubic SVM, and medium Gaussian SVM. The test results showed that the grading device was feasible for asparagus. The bruises had a large influence on asparagus quality. The training accuracy of the medium Gaussian SVM method was high (96%), whereas its test accuracy was low (86.67%). The training accuracies and test accuracy of the quadratic and cubic SVM methods were 93.34%. The quadratic SVM and cubic SVM were demonstrated to have better generalization ability than the medium Gaussian SVM method for predicting unknown grades of asparagus and meeting the operational requirements of the asparagus grading.
HPPEM: A High-Precision Blueberry Cluster Phenotype Extraction Model Based on Hybrid Task Cascade
Authors: Gai Rongli , Gao Jin , Xu Guohui
Published: May 2024

Blueberry fruit phenotypes are crucial agronomic trait indicators in blueberry breeding, and the number of fruits within the cluster, maturity, and compactness are important for evaluating blueberry harvesting methods and yield. However, the existing instance segmentation model cannot extract all these features. And due to the complex field environment and aggregated growth of blueberry fruits, the model is difficult to meet the demand for accurate segmentation and automatic phenotype extraction in the field environment. To solve the above problems, a high-precision phenotype extraction model based on hybrid task cascade (HTC) is proposed in this paper. ConvNeXt is used as the backbone network, and three Mask RCNN networks are cascaded to construct the model, rich feature learning through multi-scale training, and customized algorithms for phenotype extraction combined with contour detection techniques. Accurate segmentation of blueberry fruits and automatic extraction of fruit number, ripeness, and compactness under severe occlusion were successfully realized. Following experimental validation, the average precision for both bounding boxes (bbox) and masks stood at 0.974 and 0.975, respectively, with an intersection over union (IOU) threshold of 0.5. The linear regression of the extracted value of the fruit number against the true value showed that the coefficient of determination (R2) was 0.902, and the root mean squared error (RMSE) was 1.556. This confirms the effectiveness of the proposed model. It provides a new option for more efficient and accurate phenotypic extraction of blueberry clusters.
Effect of Agroforestry Systems on Soil NPK and C Improvements in Karst Graben Basin of Southwest China
Authors: Wan Long , Yang Jiaqi , Zheng Chenghao , Guo Jianbin , Zhou Jinxing , Han Yuguo , Rebi Ansa
Published: May 2024

Agroforestry systems can fully exploit the ecological benefits of an ecosystem’s component plants, and improve the ecological environment, soil quality, and land use efficiency, all of which have recently attracted the attention of many scholars. Southwest China’s karst graben basins have barren soil that needs immediate improvement. The karst graben basin in southwest China was used for this study to examine the impacts of several forest–grass composite systems of Bingtang orange–alfalfa–ryegrass on soil improvement, which is located in Jianshui County, Honghe Prefecture, Yunnan Province. The experiment had four treatments, Bingtang orange–alfalfa sowing (B2), Bingtang orange–ryegrass × alfalfa mixed sowing (A), Bingtang orange–ryegrass × alfalfa intercropping (R), and Bingtang orange monocropping (CK). The results showed that different forest–grass composite patterns had noticeable effects on improving the soil’s organic carbon (SOC), total nutrients, and available nutrients, especially in the rainy season when plants grew vigorously. Forage grass intercropping under forest exerted the best effect on soil improvement in the surface layer, and the effect decreased with the increase in soil depth. Alfalfa intercropping under Bingtang orange forest had the strongest effect on improving SOC, total N, ammonia nitrogen, and nitrate nitrogen, whose content increased by 30.7%, 27.3%, 35%, and 36.3%, respectively, in the dry season and 38%, 46.7%, 48.7%, and 55.3%, in the rainy season. However, the effect of alfalfa–ryegrass intercropping under the Bingtang orange forest on soil total P, total K, and available P was better than that of the Bingtang orange–alfalfa intercropping system. The C:N ratio is more suitable in the Bingtang orange–ryegrass-alfalfa composite system. Forage grass intercropping under the Bingtang orange forest effectively improved the soil NPK and C status, and the results of this study provided a basis for the selection of forest–grass composite patterns for soil improvement.
Genome-Wide Association Study and Candidate Gene Mining of Seed Size Traits in Soybean
Authors: Zhang Pu , Yang Zhiya , Jia Shihao , Chen Guoliang , Li Nannan , Karikari Benjamin , Cao Yongce
Published: May 2024

Seed size traits, including seed length (SL), seed width (SW), and seed thickness (ST), are crucial appearance parameters that determine soybean seed weight, yield, and ultimate utilization. However, there is still a large gap in the understanding of the genetic mechanism of these traits. Here, 281 soybeans were utilized to analyze the genetic architecture of seed size traits in different years through multiple (single-locus and multi-locus) genome-wide association study (GWAS) models, and candidate genes were predicted by integrating information on gene function and transcriptome sequencing data. As a result, two, seven, and three stable quantitative trait nucleotides (QTNs) controlling SL, SW, and ST were detected in multiple environments using the single-locus GWAS model, and concurrently detected by the results of the multi-locus GWAS models. These stable QTNs are located on 10 linkage disequilibrium blocks, with single genome regions ranging in size from 20 to 440 kb, and can serve as the major loci controlling soybean seed size. Furthermore, by combining gene functional annotation and transcriptome sequencing data of seeds at different developmental stages from two extreme soybean accessions, nine candidate genes, including Glyma.05G038000, Glyma.05G244100, Glyma.05G246900, Glyma.07G070200, Glyma.11G010000, Glyma.11G012400, Glyma.17G165500, Glyma.17G166500, and Glyma.20G012600 within the major loci that may regulate soybean seed size, were mined. Overall, these findings offer valuable insights for molecular improvement breeding as well as gene functional studies to unravel the mechanism of soybean seed size.
Genome Sequence Comparisons between Small and Large Colony Phenotypes of Equine Clinical Isolates of Arcanobacterium hippocoleae
Authors: Ayalew Lisanework E. , Mekuria Zelalem H. , Despres Beatrice , Saab Matthew E. , Ojha Shivani
Published: May 2024

Arcanobacterium hippocoleae is a Gram-positive fastidious bacterium and is occasionally isolated from the reproductive tract of apparently healthy mares (Equus caballus) or from mares with reproductive tract abnormalities. Apart from a few 16S rRNA gene-based GenBank sequences and one recent report on complete genome assembly, detailed genomic sequence and clinical experimental data are not available on the bacterium. Recently, we observed an unusual increase in the detection of the organism from samples associated with mare reproductive failures in Atlantic Canada. Two colony morphotypes (i.e., small, and large) were detected in culture media, which were identified as A. hippocoleae by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Here, we report the whole genome sequencing and characterization of the morphotype variants. The genome length of the large phenotypes was between 2.42 and 2.43, and the small phenotype was 1.99 Mbs. The orthologous nucleotide identity between the large colony phenotypes was ~99%, and the large and small colony phenotypes was between 77.86 and 78.52%, which may warrant the classification of the two morphotypes into different species. Phylogenetic analysis based on 16S rRNA genes or concatenated housekeeping genes grouped the small and large colony variants into two different genotypic clusters. The UvrA protein, which is part of the nucleotide excision repair (NER) system, and 3-isopropoylmalate dehydratase small subunit protein expressed by the leuD gene were identified as potential virulence factors in the large and small colony morphotypes, respectively. However, detailed functional studies will be required to determine the exact roles of these and other identified hypothetical proteins in the cellular metabolism and potential pathogenicity of A. hippocoleae in mares.
The In Vitro Antibacterial Activity of Phytogenic and Acid-Based Eubiotics against Major Foodborne Zoonotic Poultry Pathogens
Authors: Kiskinis Konstantinos , Mantzios Tilemachos , Economou Vangelis , Petridou Evanthia , Tsitsos Anestis , Patsias Apostolos , Apostolou Ioanna , Papadopoulos Georgios A. , Giannenas Ilias , Fortomaris Paschalis , Tsiouris Vasilios
Published: May 2024

The aim of the study was to investigate in vitro the antibacterial activity of 8 commercial drinking water additives against major zoonotic poultry pathogens (Campylobacter spp., Escherichia coli, Salmonella Typhimurium, Staphylococcus aureus and Listeria spp.). We tested two essential oil-based phytogenics (Phyto CSC Liquide B, AEN 350 B Liquid), two acid-based eubiotics (Salgard® liquid, Intesti-Flora), and four blends of essential oils and organic acids (ProPhorceTM SA Exclusive, Herbal acid, Rigosol-N and Eubisan 3000). The antibacterial activity was determined by estimating the minimum inhibitory concentration (MIC) using a microdilution method. The MICs of the products against Campylobacter spp. ranged from 0.071% to 0.568% v/v, in which Herbal acid, a blend rich in lactic and phosphoric acids, also containing thyme and oregano oils, exhibited the highest efficacy (MIC: 0.071% v/v) against all the tested strains. The MICs of the tested products against Escherichia coli ranged between 0.071% and 1.894% v/v. Specifically, the MIC of Rigosol-N, a blend of high concentrations of lactic and acetic acid, was 0.142% v/v for both tested strains, whereas the MICs of Intesti-Flora, a mixture rich in lactic and propionic acid, ranged from 0.284% to 0.568% v/v. The MICs of the products against Salmonella Typhimurium were between 0.095% and 1.894% v/v. Specifically, the MIC of Eubisan 3000, a blend rich in oregano oil, was 0.284% v/v. The MICs against Staphylococcus aureus were between 0.142% and 9.090% v/v. The MICs of Phyto CSC Liquide B, which is rich in trans-cinnamaldehyde, were between 3.030% and 9.090% v/v, showing the highest MIC values of all tested products. Finally, the MIC values of the tested commercial products against Listeria spp. were 0.095% to 3.030% v/v. The MICs of ProPhorceTM SA Exclusive, a highly concentrated blend of formic acid and its salts, were 0.095–0.142% v/v against Listeria spp., while the MICs of AEN 350 B Liquid were between 0.284% and 1.894% exhibiting high Listeria spp. strain variability. In conclusion, all the selected commercial products exhibited more or less antibacterial activity against pathogenic bacteria and, thus, can be promising alternatives to antibiotics for the control of zoonotic poultry pathogens and the restriction of antimicrobial-resistant bacteria.
Global Overview of Environmental Enrichment Studies: What Has Been Done and Future Directions
Authors: Bachetti Érica da Silva , Viol Layane Yamile , Viana-Junior Arleu Barbosa , Young Robert John , de Azevedo Cristiano Schetini
Published: May 2024

(1) Background: Environmental enrichment (EE) is a management principle aimed at meeting the needs of animals under human care by identifying and providing essential environmental stimuli to contribute to the integrity of their psychological and physiological well-being. Studies on EE have been carried out worldwide, but consolidated information on how it has been used, who it has been used for, how it has been evaluated, and what gaps still exist in the subject is scarce in the scientific literature. This study assessed, employing a systematic review, the global scenario of research into EE in animals kept under human care over the last 17 years, answering the above-mentioned questions. (2) Methods: A search for EE papers was carried out in the Web of Science and Scopus databases from January 2005 to December 2021, resulting in 2002 articles from which information was extracted. (3) Results: Results showed an increase in the number of articles published on EE, especially in farms, but studies in laboratory environments continue to be more frequent. Mammals and birds are the most studied animal groups. Cognitive enrichment is the least utilised by researchers. The number of publications by researchers from countries in the southern hemisphere is low. (4) Conclusions: Although the technique of EE is being widely used, it is still focused on certain groups of animals in certain captive environments and carried out mainly in the northern hemisphere of the planet. Therefore, the gaps pointed out here need to be filled by future studies.
The Detection of a Functional 168 bp Deletion of the HOXB13 Gene Determining Short Tail and Its Association with Senior Growth Traits in Sheep Breeds Worldwide
Authors: Zhu Qihui , Liu Peiyao , Zhang Mingshi , Kang Yuxin , Lv Linmi , Xu Hongwei , Zhang Qingfeng , Li Ran , Pan Chuanying , Lan Xianyong
Published: May 2024

In recent years, genome-wide association studies (GWAS) have uncovered that the HOXB13 gene is a key regulatory factor for the tail length trait of sheep. Further research has found that there is a functional 168 bp SINE element insertion upstream of the HOXB13 gene, which leads to the occurrence of long tails in sheep. However, the frequency of mutations in the 168 bp SINE element of the HOXB13 gene among different sheep breeds around the world and its relationship with growth traits are still unclear. This study used whole-genome sequencing (WGS) data, including 588 samples from 33 different sheep breeds around the world, to evaluate the frequency of HOXB13 gene mutations in different sheep breeds globally. At the same time, this study also selected 3392 sheep samples from six breeds. The genetic variation in the 168 bp InDel locus in the HOXB13 gene was determined through genotyping, and its association with the growth traits of Luxi black-headed sheep was analyzed. The research results indicate that the polymorphism of the 168 bp InDel locus is significantly correlated with the hip width of adult ewes in the Luxi black-headed sheep breed (p < 0.05) and that the hip width of adult ewes with the DD genotype is significantly larger than that of adult ewes with the ID genotype (p < 0.05). This study indicates that there is consistency between the research results on the sheep tail length trait and growth traits, which may contribute to the promotion of sheep breed improvement.
Exploring Variability: Inflammation Mediator Levels across Tissues and Time in Poultry Experimentally Infected by the G1a and G6 Genogroups of Infectious Bursal Disease Virus (IBDV)
Authors: Franzo Giovanni , Dotto Giorgia , Lupini Caterina , Legnardi Matteo , Tucciarone Claudia Maria , Poletto Francesca , Catelli Elena , Graziosi Giulia , Cecchinato Mattia , Pasotto Daniela
Published: May 2024

Infectious bursal disease virus (IBDV) is a significant burden for poultry production and market due to both direct disease and induced immunosuppression. In the present study, the expression of different cytokines in the bursa of Fabricius and thymus was evaluated during a 28-day-long experimental infection with two strains classified in the G1a (Classical) and G6 (ITA) genogroups. Although both strains significantly affected and modulated the expression of different molecules, the G6 strain seemed to induce a delayed immune response or suppress it more promptly. A recovery in the expression of several mediators was observed in the G1a-infected group at the end of the study, but not in the G6 one, further supporting a more persistent immunosuppression. This evidence fits with the higher replication level previously reported for the G6 and with the clinical outcome, as this genotype, although subclinical, has often been considered more immunosuppressive. However, unlike other studies focused on shorter time periods after infection, the patterns observed in this paper were highly variable and complex, depending on the strain, tissue, and time point, and characterized by a non-negligible within-group variability. Besides confirming the strain/genogroup effect on immune system modulation, the present study suggests the usefulness of longer monitoring activities after experimental infection to better understand the complex patterns and interactions with the host response.
Gastrointestinal Helminths in Wild Felids in the Cerrado and Pantanal: Zoonotic Bioindicators in Important Brazilian Biomes
Authors: Moraes Iago de Sá , Silva Victória Luiza de Barros , Andrade-Silva Beatriz Elise de , Gomes Ana Paula Nascimento , Urzedo Nicoly Ferreira de , Abolis Vitória Breda , Gonçalves Renata de Souza , Arpon Karina Varella , Assis-Silva Zara Mariana de , Silva Lizandra Fernandes da , Zago Ellen Amanda , Gonçalves Michelle Benevides , Braga Ísis Assis , Saturnino Klaus Casaro , Colodel Edson Moleta , Júnior Arnaldo Maldonado , Pacheco Richard de Campos , Ramos Dirceu Guilherme de Souza
Published: May 2024

Environmental changes in the Brazilian Pantanal and Cerrado facilitate the spread of parasitic diseases in wildlife, with significant implications for public health owing to their zoonotic potential. This study aimed to examine the occurrence and diversity of gastrointestinal parasites in wild felids within these regions to assess their ecological and health impacts. We collected and analyzed helminth-positive samples from 27 wild felids using specific taxonomic keys. Diverse parasitic taxa were detected, including zoonotic helminths, such as Ancylostoma braziliense, Ancylostoma caninum, Ancylostoma pluridentatum, Toxocara cati, Toxocara canis, Dipylidium caninum, Taenia spp., Echinococcus spp., and Spirometra spp. Other nematodes, such as Physaloptera praeputialis and Physaloptera anomala, were identified, along with acanthocephalans from the genus Oncicola and a trematode, Neodiplostomum spp. (potentially the first record of this parasite in wild felids in the Americas). Human encroachment into natural habitats has profound effects on wild populations, influencing parasitic infection rates and patterns. This study underscores the importance of continuous monitoring and research on parasitic infections as a means of safeguarding both wildlife and human populations and highlights the role of wild felids as bioindicators of environmental health.
Genetic Variation in Natural and Induced Antibody Responses in Layer Chickens
Authors: Arango Jesus , Wolc Anna , Owen Jeb , Weston Kendra , Fulton Janet E.
Published: May 2024

Selection of livestock for disease resistance is challenging due to the difficulty in obtaining reliable phenotypes. Antibodies are immunological molecules that provide direct and indirect defenses against infection and link the activities of both the innate and adaptive compartments of the immune system. As a result, antibodies have been used as a trait in selection for immune defense. The goal of this study was to identify genomic regions associated with natural and induced antibodies in chickens using low-pass sequencing. Enzyme-linked immunosorbent assays were used to quantify innate (natural) antibodies binding KLH, OVA, and PHA and induced (adaptive) antibodies binding IBD, IBV, NDV, and REO. We collected plasma from four White Leghorn (WL), two White Plymouth Rock (WPR), and two Rhode Island Red (RIR) lines. Samples numbers ranged between 198 and 785 per breed. GWAS was performed within breed on data pre-adjusted for Line-Hatch-Sex effects using GCTA. A threshold of p = 10−6 was used to select genes for downstream annotation and enrichment analysis with SNPEff and Panther. Significant enrichment was found for the defense/immunity protein, immunoglobulin receptor superfamily, and the antimicrobial response protein in RIR; and the immunoglobulin receptor superfamily, defense/immunity protein, and protein modifying enzyme in WL. However, none were present in WPR, but some of the selected SNP were annotated in immune pathways. This study provides new insights regarding the genetics of the antibody response in layer chickens.
Fermented Astragalus Powder, a New Potential Feed Additive for Broilers to Improve the Growth Performance and Health
Authors: Han Songwei , Xu Guowei , Zhang Kang , Ahmad Saad , Wang Lei , Chen Fubin , Liu Jiahui , Gu Xueyan , Li Jianxi , Zhang Jingyan
Published: May 2024

A total of 320 1-day-old broilers were randomly divided into five groups. The control group (CON) received a basal diet, while the FAP4, FAP2, and FAP1 groups were provided with the basal diet supplemented with 4%, 2%, and 1% fermented Astragalus powder, respectively. The unfermented Astragalus powder (UAP2) group was fed the basal diet supplemented with 2% UAP. Each group contained eight replicates of eight chicks each. The results revealed that the final BW and ADG in the FAP 1 and FAP2 were higher than those in the UAP2 and CON groups, while reducing F/G from day 14 to day 42. On day 42, the thymus index in the UAP and FAP groups as well as the bursa index in the FAP4 group showed significant increases compared to those in the CON group. Supplementation with 2% FAP elevated serum IgA levels in broilers on day 28 and day 42, and it also increased serum IgG levels on day 42. Furthermore, supplementation with 2% FAP elevated serum albumin (ALB) levels in broilers, while supplementation with 4% FAP increased serum (glucose) GLU levels in broilers on day 28. The serum biochemical parameters and pathological observation of the liver and kidney in the groups did not show any adverse effects on broilers’ health. In addition, the serum total antioxidant capacity (T-AOC) level significantly increased in the FAP4 and FAP2 groups on day 28, and the malondialdehyde (MDA) level in both serum and liver tissue decreased in the FAP2 group on day 28 and day 42. Compared to the CON group, 2% FAP and 2% UAP supplementation reduced the relative abundance of Bacteroides and supplementation with 2% FAP increased the relative abundance of Alistipes on day 42. In conclusion, the dietary supplementation of FAP can enhance the growth performance, immune function, and antioxidant capacity and regulate microflora in broilers, of which 2% FAP is more effective. It indicates FAP exhibits significant application potential as a promising feed additive for broilers.
Tracing the Dynamical Genetic Diversity Changes of Russian Livni Pigs during the Last 50 Years with the Museum, Old, and Modern Samples
Authors: Abdelmanova Alexandra A. , Deniskova Tatiana E. , Kharzinova Veronika R. , Chinarov Roman Yu , Boronetskaya Oksana I. , Sölkner Johann , Brem Gottfried , Ai Huashui , Huang Lusheng , Trukhachev Vladimir I. , Zinovieva Natalia A.
Published: May 2024

The pig industry is usually considered an intensive livestock industry, mainly supported by hybrid breeding between commercial pig breeds. However, people’s pursuit of a more natural environment and higher meat quality has led to an increasing demand for eco-friendly and diverse pig feeding systems. Therefore, the importance of rearing and conserving local pig breeds is increasing. The Livni pig is a local breed with good adaptability to the environmental and fodder conditions in central Russia. In this study, we aimed to analyze the genetic diversity and population structure of Livni pigs using whole-genome single nucleotide polymorphism (SNP) data. We utilized the Porcine GGP HD BeadChip on genotype samples from old (n = 32, 2004) and modern (n = 32, 2019) populations of Livni pigs. For the museum samples of Livni pigs (n = 3), we extracted DNA from their teeth, performed genomic sequencing, and obtained SNP genotypes from the whole-genome sequences. SNP genotypes of Landrace (n = 32) and Large White (n = 32) pigs were included for comparative analysis. We observed that the allelic richness of Livni pigs was higher than those of Landrace and Large White pigs (AR = 1.775–1.798 vs. 1.703 and 1.668, respectively). The effective population size estimates (NE5 = 108 for Livni pigs, NE5 = 59 for Landrace and Large White pigs) confirmed their genetic diversity tendency. This was further supported by the length and number of runs of homozygosity, as well as the genomic inbreeding coefficient (almost twofold lower in Livni pigs compared to Landrace and Large White pigs). These findings suggest that the Livni pig population exhibits higher genetic diversity and experiences lower selection pressure compared to commercial pig populations. Furthermore, both principal component and network tree analyses demonstrated a clear differentiation between Livni pigs and transboundary commercial pigs. The TreeMix results indicated gene flow from Landrace ancestors to Livni pigs (2019) and from Large White ancestors to Livni pigs (2004), which was consistent with their respective historical breeding backgrounds. The comparative analysis of museum, old, and modern Livni pigs indicated that the modern Livni pig populations have preserved their historical genomic components, suggesting their potential suitability for future design selection programs.