Sichuan Agricultural University

// Linlin Chen 1, * , Huidan Deng 1, * , Hengmin Cui 1, 2 , Jing Fang 1, 2 , Zhicai Zuo 1, 2 , Junliang Deng 1, 2 , Yinglun Li 1, 2 , Xun Wang 1, 2 and Ling Zhao 1, 2 1 College of Veterinary Medicine, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China 2 Key Laboratory of Animal Diseases and Environmental Hazards of Sichuan Province, Sichuan Agriculture University, Wenjiang, Chengdu 611130, China * These authors contributed equally to this work Correspondence to: Hengmin Cui, email: cui580420@sicau.edu.cn Keywords: inflammation; inflammatory signaling pathways; chemokines; cytokines; organ diseases Received: April 19, 2017      Accepted: November 03, 2017      Published: December 14, 2017 ABSTRACT Inflammation is a biological response of the immune system that can be triggered by a variety of factors, including pathogens, damaged cells and toxic compounds. These factors may induce acute and/or chronic inflammatory responses in the heart, pancreas, liver, kidney, lung, brain, intestinal tract and reproductive system, potentially leading to tissue damage or disease. Both infectious and non-infectious agents and cell damage activate inflammatory cells and trigger inflammatory signaling pathways, most commonly the NF-κB, MAPK, and JAK-STAT pathways. Here, we review inflammatory responses within organs, focusing on the etiology of inflammation, inflammatory response mechanisms, resolution of inflammation, and organ-specific inflammatory responses.

In this paper, the biosynthesis process of phenolic compounds in plants is summarized, which include the shikimate, pentose phosphate and phenylpropanoid pathways. Plant phenolic compounds can act as antioxidants, structural polymers (lignin), attractants (flavonoids and carotenoids), UV screens (flavonoids), signal compounds (salicylic acid, flavonoids) and defense response chemicals (tannins, phytoalexins). From a human physiological standpoint, phenolic compounds are vital in defense responses, such as anti-aging, anti-inflammatory, antioxidant and anti-proliferative activities. Therefore, it is beneficial to eat such plant foods that have a high antioxidant compound content, which will cut down the incidence of certain chronic diseases, for instance diabetes, cancers and cardiovascular diseases, through the management of oxidative stress. Furthermore, berries and other fruits with low-amylase and high-glucosidase inhibitory activities could be thought of as candidate food items in the control of the early stages of hyperglycemia associated with type 2 diabetes.

Short-chain fatty acids (SCFAs), particularly acetate, propionate and butyrate, are mainly produced by anaerobic fermentation of gut microbes. SCFAs play an important role in regulating energy metabolism and energy supply, as well as maintaining the homeostasis of the intestinal environment. In recent years, many studies have shown that SCFAs demonstrate physiologically beneficial effects, and the signalling pathways related to SCFA production, absorption, metabolism, and intestinal effects have been discovered. Two major signalling pathways concerning SCFAs, G-protein-coupled receptors (GPRCs) and histone deacetylases (HDACs), are well recognized. In this review, we summarize the recent advances concerning the biological properties of SCFAs and the signalling pathways in inflammation and glucose and lipid metabolism.

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.

In experimental research a scientific conclusion is always drawn from the statistical testing of hypothesis, in which an acceptable cutoff of probability, such as 0.05 or 0.01, is used for decision-making. However, the probability of committing false statistical inferences would considerably increase when more than one hypothesis is simultaneously tested (namely the multiple comparisons), which therefore requires proper adjustment. Although the adjustment for multiple comparisons is proposed to be mandatory in some journals, it still remains difficult to select a proper method suitable for the various experimental properties and study purposes, especially for researchers without good background in statistics. In the present paper, we provide a brief review on mathematical framework, general concepts and common methods of adjustment for multiple comparisons, which is expected to facilitate the understanding and selection of adjustment methods.

Spotting off-targets from gene editing Unintended genomic modifications limit the potential therapeutic use of gene-editing tools. Available methods to find off-targets generally do not work in vivo or detect single-nucleotide changes. Three papers in this issue report new methods for monitoring gene-editing tools in vivo (see the Perspective by Kempton and Qi). Wienert et al. followed the recruitment of a DNA repair protein to DNA breaks induced by CRISPR-Cas9, enabling unbiased detection of off-target editing in cellular and animal models. Zuo et al. identified off-targets without the interference of natural genetic heterogeneity by injecting base editors into one blastomere of a two-cell mouse embryo and leaving the other genetically identical blastomere unedited. Jin et al. performed whole-genome sequencing on individual, genome-edited rice plants to identify unintended mutations. Cytosine, but not adenine, base editors induced numerous single-nucleotide variants in both mouse and rice. Science , this issue p. 286 , p. 289 , p. 292 ; see also p. 234

It is widely known that branched chain amino acids (BCAA) are not only elementary components for building muscle tissue but also participate in increasing protein synthesis in animals and humans. BCAA (isoleucine, leucine and valine) regulate many key signaling pathways, the most classic of which is the activation of the mTOR signaling pathway. This signaling pathway connects many diverse physiological and metabolic roles. Recent years have witnessed many striking developments in determining the novel functions of BCAA including: (1) Insufficient or excessive levels of BCAA in the diet enhances lipolysis. (2) BCAA, especially isoleucine, play a major role in enhancing glucose consumption and utilization by up-regulating intestinal and muscular glucose transporters. (3) Supplementation of leucine in the diet enhances meat quality in finishing pigs. (4) BCAA are beneficial for mammary health, milk quality and embryo growth. (5) BCAA enhance intestinal development, intestinal amino acid transportation and mucin production. (6) BCAA participate in up-regulating innate and adaptive immune responses. In addition, abnormally elevated BCAA levels in the blood (decreased BCAA catabolism) are a good biomarker for the early detection of obesity, diabetes and other metabolic diseases. This review will provide some insights into these novel metabolic and physiological functions of BCAA.

Abstract A facile and controllable in situ reduction strategy is used to create surface oxygen vacancies (OVs) on Aurivillius‐phase Sr 2 Bi 2 Nb 2 TiO 12 nanosheets, which were prepared by a mineralizer‐assisted soft‐chemical method. Introduction of OVs on the surface of Sr 2 Bi 2 Nb 2 TiO 12 extends photoresponse to cover the whole visible region and also tremendously promotes separation of photoinduced charge carriers. Adsorption and activation of CO 2 molecules on the surface of the catalyst are greatly enhanced. In the gas‐solid reaction system without co‐catalysts or sacrificial agents, OVs‐abundant Sr 2 Bi 2 Nb 2 TiO 12 nanosheets show outstanding CO 2 photoreduction activity, producing CO with a rate of 17.11 μmol g −1 h −1 , about 58 times higher than that of the bulk counterpart, surpassing most previously reported state‐of‐the‐art photocatalysts. Our study provides a three‐in‐one integrated solution to advance the performance of photocatalysts for solar‐energy conversion and generation of renewable energy.

Breast milk is a complex liquid rich in immunological components that affect the development of the infant's immune system. Exosomes are membranous vesicles of endocytic origin that are found in various body fluids and that can mediate intercellular communication. MicroRNAs (miRNAs), a well-defined group of non-coding small RNAs, are packaged inside exosomes in human breast milk. Here, we identified 602 unique miRNAs originating from 452 miRNA precursors (pre-miRNAs) in human breast milk exosomes using deep sequencing technology. We found that, out of 87 well-characterized immune-related pre-miRNAs, 59 (67.82%) are presented and enriched in breast milk exosomes (P < 10(-16), χ(2) test). In addition, compared with exogenous synthetic miRNAs, these endogenous immune-related miRNAs are more resistant to relatively harsh conditions. It is, therefore, tempting to speculate that these exosomal miRNAs are transferred from the mother's milk to the infant via the digestive tract, and that they play a critical role in the development of the infant immune system.

Rice blast, caused by the fungal pathogen Magnaporthe grisea, is one of the most devastating diseases in rice worldwide. The dominant resistance gene, Pi-d2 [previously named Pi-d(t)2], present in the rice variety Digu, confers gene-for-gene resistance to the Chinese blast strain, ZB15. Pi-d2 was previously mapped close to the centromere of chromosome 6. In this study, the Pi-d2 gene was isolated by a map-based cloning strategy. Pi-d2 encodes a receptor-like kinase protein with a predicted extracellular domain of a bulb-type mannose specific binding lectin (B-lectin) and an intracellular serine-threonine kinase domain. Pi-d2 is a single-copy gene that is constitutively expressed in the rice variety Digu. Transgenic plants carrying the Pi-d2 transgene confer race-specific resistance to the M. grisea strain, ZB15. The Pi-d2 protein is plasma membrane localized. A single amino acid difference at position 441 of Pi-d2 distinguishes resistant and susceptible alleles of rice blast resistance gene Pi-d2. Because of its novel extracellular domain, Pi-d2 represents a new class of plant resistance genes.

BACKGROUND: Despite recent advances in the understanding of the swine gut microbiome at different growth stages, a comprehensive longitudinal study of the lifetime (birth to market) dynamics of the swine gut microbiome is lacking. RESULTS: To fill in this gap of knowledge, we repeatedly collected a total of 273 rectal swabs from 18 pigs during lactation (day (d) 0, 11, 20), nursery (d 27, 33, 41, 50, 61), growing (d 76, 90, 104, 116), and finishing (d 130, 146, 159, 174) stages. DNA was extracted and subjected to sequencing with an Illumina Miseq sequencer targeting the V4 region of the 16S rRNA gene. Sequences were analyzed with the Deblur algorithm in the QIIME2 package. A total of 19 phyla were detected in the lifetime pig gut microbiome with Firmicutes and Bacteroidetes being the most abundant. Alpha diversity including community richness (e.g., number of observed features) and diversity (e.g., Shannon index) showed an overall increasing trend. Distinct shifts in microbiome structure along different growth stages were observed. LEfSe analysis revealed 91 bacterial features that are stage-specific. To validate these discoveries, we performed fecal microbiota transplantation (FMT) by inoculating weanling pigs with mature fecal microbiota from a growing stage pig. Similar stage-specific patterns in microbiome diversity and structures were also observed in both the FMT pigs and their littermates. Although FMT remarkably increased growth performance, it did not change the overall swine gut microbiome. Only a few taxa including those associated with Streptococcus and Clostridiaceae were enriched in the FMT pigs. These data, together with several other lines of evidence, indicate potential roles these taxa play in promoting animal growth performance. Diet, especially crude fiber from corn, was a major factor shaping the swine gut microbiome. The priority effect, i.e., the order and timing of species arrival, was more evident in the solid feed stages. CONCLUSIONS: The distinct stage-associated swine gut microbiome may be determined by the differences in diet and/or gut physiology at different growth stages. Our study provides insight into mechanisms governing gut microbiome succession and also underscores the importance of optimizing stage-specific probiotics aimed at improving animal health and production.

Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.

AIMS: To investigate whether the relative abundance of the Bacteroidetes and Firmicutes divisions in pigs is different between obese and lean animals. METHODS AND RESULTS: Group-specific primers were designed to target the 16S rRNA genes of Bacteroidetes and Firmicutes present in the gut. After the validation of their specificity, these primers were used in the real-time PCR quantification of all Bacteria, Firmicutes division, Bacteroidetes division and Bacteroides spp. in the faecal samples of obese and lean pigs from Banna mini-pig inbred line. The obese pigs had a approximately 61% fewer percentage (based on all Bacteria) of Bacteroidetes division (P = 0.033) and a approximately 56% fewer proportion of Bacteroides spp. (P = 0.047) than the lean pigs. The proportions of both Bacteroidetes and Bacteroides had a negative correlation (P < 0.01) with the body weight. CONCLUSION: The results suggested that the fat storage might affect the proportion of Bacteroidetes division in the gut. SIGNIFICANCE AND IMPACT OF THE STUDY: The real-time PCR assays developed for Firmicutes and Bacteroidetes will be useful for investigating the composition of gut microbiota.

Flexible growth and immune responses in rice Plants that are fighting microbial pathogens often divert resources that could be used for growth into the immune response. For crops, this translates into lower yield when plant immunity is activated. Wang et al. show that, in rice, reversible phosphorylation of a key transcription factor allows the plant to defend against fungal attack when needed but then, within days, reallocate resources back to growth (see the Perspective by Greene and Dong). Thus, both pathogen defense and crop yield can be sustained. Science , this issue p. 1026 ; see also p. 976

BACKGROUND: The MYB superfamily constitutes one of the most abundant groups of transcription factors described in plants. Nevertheless, their functions appear to be highly diverse and remain rather unclear. To date, no genome-wide characterization of this gene family has been conducted in a legume species. Here we report the first genome-wide analysis of the whole MYB superfamily in a legume species, soybean (Glycine max), including the gene structures, phylogeny, chromosome locations, conserved motifs, and expression patterns, as well as a comparative genomic analysis with Arabidopsis. RESULTS: A total of 244 R2R3-MYB genes were identified and further classified into 48 subfamilies based on a phylogenetic comparative analysis with their putative orthologs, showed both gene loss and duplication events. The phylogenetic analysis showed that most characterized MYB genes with similar functions are clustered in the same subfamily, together with the identification of orthologs by synteny analysis, functional conservation among subgroups of MYB genes was strongly indicated. The phylogenetic relationships of each subgroup of MYB genes were well supported by the highly conserved intron/exon structures and motifs outside the MYB domain. Synonymous nucleotide substitution (dN/dS) analysis showed that the soybean MYB DNA-binding domain is under strong negative selection. The chromosome distribution pattern strongly indicated that genome-wide segmental and tandem duplication contribute to the expansion of soybean MYB genes. In addition, we found that ~ 4% of soybean R2R3-MYB genes had undergone alternative splicing events, producing a variety of transcripts from a single gene, which illustrated the extremely high complexity of transcriptome regulation. Comparative expression profile analysis of R2R3-MYB genes in soybean and Arabidopsis revealed that MYB genes play conserved and various roles in plants, which is indicative of a divergence in function. CONCLUSIONS: In this study we identified the largest MYB gene family in plants known to date. Our findings indicate that members of this large gene family may be involved in different plant biological processes, some of which may be potentially involved in legume-specific nodulation. Our comparative genomics analysis provides a solid foundation for future functional dissection of this family gene.

The agricultural industry is getting more data-centric and requires precise, more advanced data and technologies than before, despite being familiar with agricultural processes. The agriculture industry is being advanced by various information and advanced communication technologies, such as the Internet of Things (IoT). The rapid emergence of these advanced technologies has restructured almost all other industries, as well as advanced agriculture, which has shifted the industry from a statistical approach to a quantitative one. This radical change has shaken existing farming techniques and produced the latest prospects in a series of challenges. This comprehensive review article enlightens the potential of the IoT in the advancement of agriculture and the challenges faced when combining these advanced technologies with conventional agricultural systems. A brief analysis of these advanced technologies with sensors is presented in advanced agricultural applications. Numerous sensors that can be implemented for specific agricultural practices require best management practices (e.g., land preparation, irrigation systems, insect, and disease management). This review includes the integration of all suitable techniques, from sowing to harvesting, packaging, transportation, and advanced technologies available for farmers throughout the cropping system. Besides, this review article highlights the utilization of other tools such as unmanned aerial vehicles (UAVs) for crop monitoring and other beneficiary measures, such as optimizing crop yields. In addition, advanced programs based on the IoT are also discussed. Finally, based on our comprehensive review, we identified advanced prospects regarding the IoT, which are essential tools for sustainable agriculture.

Developing a facile, cost-saving, and environment-friendly method for fabricating a multifunctional humidity sensor is of great significance to expand its practical applications. However, most humidity sensors involve a complex fabrication process, resulting in their high cost and narrow application fields. Herein, a multifunctional paper-based humidity sensor with many advantages is proposed. This humidity sensor is fabricated using conventional printing paper and flexible conductive adhesive tape by a facile pasting method, in which the paper is used as both the humidity-sensing material and the substrate of the sensor. Owing to the moderate hydrophilicity of the paper and the rational structure design of the paper-based humidity sensor, the sensor exhibits an excellent humidity-sensing response of more than 103 as well as good linearity (R2 = 0.9549) within the humidity range from 41.1 to 91.5% relative humidity. Furthermore, the paper-based humidity sensor has good flexibility and compatibility, endowing it with multifunctional applications for breath rate, baby diaper wetting, noncontact switch, skin humidity, and spatial localization monitoring. Although the resistance of the paper-based humidity sensor is relatively large, the humidity-sensing response signals of the sensor can be conveniently processed by the designed signal processing system. The readily available starting materials and facile fabrication technique provide useful strategies for the development of multifunctional humidity sensors.

Qiang Xu and colleagues sequence four citrus species de novo, along with 100 accessions, including primitive, wild and cultivated citrus. Their genomic analyses associate the CitRWP gene with polyembryony and suggest that regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. The emergence of apomixis—the transition from sexual to asexual reproduction—is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.

Abstract Several clay-organic complexes were synthesized by placing quaternary ammonium cations on smectite by cation exchange. They were then examined for their ability to adsorb phenol and several of its chlorinated congeners. The organic cations used were: hexadecylpyridinium (HDPY + ), hexadecyltri-methyl ammonium (HDTMA + ), trimethylphenyl ammonium (TMPA), and tetramethylammonium (TMA + ). The complexes containing long-chain alkyl (hexadecyl) groups were the most hydrophobic and adsorbed the phenols from water in proportion to their hydrophobicities, which increase with chlorine addition (phenol &lt; chlorophenol &lt; dichloropohenol &lt; trichlorophenol). With n-hexane as the solvent, different adsorption was found which depended on the type and degree of solvent interactions with the compound and the clay-organic complex. Thus, the amount of adsorption of these phenols on clay-organic complexes was dependent on the relative energies of adsorbent-adsorbate and adsorbate-solvent interactions.

Exposure to a variety of environmental factors such as salinity, drought, metal toxicity, extreme temperature, air pollutants, ultraviolet-B (UV-B) radiation, pesticides, and pathogen infection leads to subject oxidative stress in plants, which in turn affects multiple biological processes via reactive oxygen species (ROS) generation. ROS include hydroxyl radicals, singlet oxygen, and hydrogen peroxide in the plant cells and activates signaling pathways leading to some changes of physiological, biochemical, and molecular mechanisms in cellular metabolism. Excessive ROS, however, cause oxidative stress, a state of imbalance between the production of ROS and the neutralization of free radicals by antioxidants, resulting in damage of cellular components including lipids, nucleic acids, metabolites, and proteins, which finally leads to the death of cells in plants. Thus, maintaining a physiological level of ROS is crucial for aerobic organisms, which relies on the combined operation of enzymatic and nonenzymatic antioxidants. In order to improve plants' tolerance towards the harsh environment, it is vital to reinforce the comprehension of oxidative stress and antioxidant systems. In this review, recent findings on the metabolism of ROS as well as the antioxidative defense machinery are briefly updated. The latest findings on differential regulation of antioxidants at multiple levels under adverse environment are also discussed here.