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1.
Sci Rep ; 14(1): 12950, 2024 06 05.
Artículo en Inglés | MEDLINE | ID: mdl-38839805

RESUMEN

Endophytes have been shown to promote plant growth and health. In the present study, a Bacillus velezensis CH1 (CH1) strain was isolated and identified from high-quality oats, which was capable of producing indole-3-acetic acid (IAA) and strong biofilms, and capabilities in the nitrogen-fixing and iron carriers. CH1 has a 3920 kb chromosome with 47.3% GC content and 3776 code genes. Compared genome analysis showed that the largest proportion of the COG database was metabolism-related (44.79%), and 1135 out of 1508 genes were associated with the function "biosynthesis, transport, and catabolism of secondary metabolites." Furthermore, thirteen gene clusters had been identified in CH1, which were responsible for the synthesis of fifteen secondary metabolites that exhibit antifungal and antibacterial properties. Additionally, the strain harbors genes involved in plant growth promotion, such as seven putative genes for IAA production, spermidine and polyamine synthase genes, along with multiple membrane-associated genes. The enrichment of these functions was strong evidence of the antimicrobial properties of strain CH1, which has the potential to be a biofertilizer for promoting oat growth and disease resistance.


Asunto(s)
Avena , Bacillus , Ácidos Indolacéticos , Bacillus/genética , Bacillus/metabolismo , Bacillus/aislamiento & purificación , Avena/microbiología , Avena/crecimiento & desarrollo , Ácidos Indolacéticos/metabolismo , Biopelículas/crecimiento & desarrollo , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/prevención & control , Fijación del Nitrógeno , Filogenia , Endófitos/aislamiento & purificación , Endófitos/metabolismo , Endófitos/genética , Genoma Bacteriano
2.
Heliyon ; 10(9): e30276, 2024 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-38711667

RESUMEN

Investigating oat tissue microflora during its different developmental stages is necessary for understanding its growth and anti-disease mechanism. In this study, 16S rDNA and ITS (Internally Transcribed Spacer) high-throughput sequencing technology were used to explore the microflora diversity of oat tissue. Twenty-seven samples of leaves, stems, and roots from three developmental stages, namely the seedling stage (SS), jointing stage (JS), and maturity stage (MS), underwent sequencing analysis. The analysis showed that 6480 operational taxonomic units (OTUs) were identified in the examined samples, of which 1698 were fungal and 4782 were bacterial. Furthermore, 126 OTUs were shared by fungi, mainly Ascomycota, Basidiomycota, and Mucoromycota at the phylum level, and 39 OTUs were shared by bacteria, mainly Actinobacteriota and Proteobacteria at the phylum level. The microbial diversity of oat tissue in the three developmental stages showed differences, and the α-diversity of the bacteria and ß-diversity of the bacteria and fungi in the roots were higher than those of the stems and leaves. Among the bacteria species, Thiiopseudomonas, Rikenellaceae RC9 gut group, and Brevibacterium were predominant in the leaves, MND1 was predominant in the roots, and Lactobacillus was predominant in the stems. Moreover, Brevibacterium maintained a stable state at all growth stages. In the fungal species, Phomatospora was dominant in the leaves, Kondoa was dominant in the roots, and Pyrenophora was dominant in the stems. All species with a high abundance were related to the growth process of oats and antagonistic bacteria. Furthermore, connection modules were denser in bacterial than in fungal populations. The samples were treated with superoxide dismutase and peroxidase. There were 42 strains associated with SOD (Superoxide dismutase), 60 strains associated with POD (Peroxidase), and 38 strains in total, which much higher than fungi. The network analysis showed that bacteria might have more dense connection modules than fungi, The number of bacterial connections to enzymes were much higher than that of fungi. Furthermore, these results provide a basis for further mechanistic research.

3.
Plants (Basel) ; 13(5)2024 Mar 02.
Artículo en Inglés | MEDLINE | ID: mdl-38475556

RESUMEN

The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.

4.
BMC Microbiol ; 23(1): 253, 2023 09 09.
Artículo en Inglés | MEDLINE | ID: mdl-37689675

RESUMEN

BACKGROUND: Anaerobic fungi are effective fibre-degrading microorganisms in the digestive tract of horses. However, our understanding of their diversity and community structure is limited, especially in different parts of the gastrointestinal tract. RESULTS: For the first time, high-throughput sequencing technology was used to analyse and predict fungal microbial diversity in different parts of the gastrointestinal tract of Mongolian horses. The results revealed that the richness and diversity of fungi in the hindgut of Mongolian horses were much higher than those in the foregut. The foregut was dominated by Basidiomycota and Ascomycota, whereas the hindgut was dominated by Neocallimastigomycota and Basidiomycota. At the genus level, the relative abundance of many pathogenic fungi (Cryptococcus, Cladosporium, Alternaria, and Sarocladium) in the foregut was significantly higher than that in the posterior gut, indicating that Mongolian horses have strong disease resistance. The prediction of fungal function also showed significant differences in the fungal flora between the foregut and the hindgut. The fungi in Mongolian horses' foreguts were mainly pathologically nutritive and contained many animal and plant pathogens, particularly in the small intestine (jejunum and ileum). This indicates that the foregut may be the most important immune site in the digestive system of Mongolian horses, which explains the high disease resistance of Mongolian horses. The number of unassigned functional groups in the posterior gut was significantly higher than that in the anterior gut, indicating that the functions of fungal groups in the posterior gut have not been fully explored, and further studies are required in the future. CONCLUSIONS: Analysis of high-throughput sequencing results revealed that the fungal composition varied greatly among different gastrointestinal tract segments in Mongolian horses, whose hindgut contains many anaerobic fungi involved in plant cellulose degradation. This provides important basic data for studying fungal diversity in the digestive system of healthy horses, which can be used for the health assessment of horses and provides clues for further research on the disease resistance and digestive capacity of horses, as well as a reference for the early diagnosis of intestinal diseases and innovative treatment methods.


Asunto(s)
Micobioma , Caballos , Animales , Resistencia a la Enfermedad , Íleon , Yeyuno , Digestión
5.
Front Microbiol ; 14: 1167293, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37637133

RESUMEN

Crop straw contains huge amounts of exploitable energy, and efficient biomass degradation measures have attracted worldwide attention. Mining strains with high yields of cellulose-degrading enzymes is of great significance for developing clean energy and industrial production of related enzymes. In this study, we reported a high-quality genome sequence of Bacillus velezensis SSF6 strain using high-throughput sequencing technology (Illumina PE150 and PacBio) and assessed its lignocellulose degradation potential. The results demonstrated that the genome of B. velezensis SSF6 was 3.89 Mb and contained 4,015 genes, of which 2,972, 3,831 and 158 genes were annotated in the COGs (Clusters of Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes) and CAZyme (Carbohydrate-Active enZymes) databases, respectively, and contained a large number of genes related to carbohydrate metabolism. Furthermore, B. velezensis SSF6 has a high cellulose degradation capacity, with a filter paper assay (FPA) and an exoglucanase activity of 64.48 ± 0.28 and 78.59 ± 0.42 U/mL, respectively. Comparative genomic analysis depicted that B. velezensis SSF6 was richer in carbohydrate hydrolase gene. In conclusion, the cellulose-degrading ability of B. velezensis SSF6 was revealed by genome sequencing and the determination of cellulase activity, which laid a foundation for further cellulose degradation and bioconversion.

6.
Plants (Basel) ; 12(15)2023 Jul 26.
Artículo en Inglés | MEDLINE | ID: mdl-37570928

RESUMEN

Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for "Neiya No. 9", a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.

7.
Genome Biol Evol ; 15(3)2023 03 03.
Artículo en Inglés | MEDLINE | ID: mdl-36807517

RESUMEN

The yellow nutsedge (Cyperus esculentus L. 1753) is an unconventional oil plant with oil-rich tubers, and a potential alternative for traditional oil crops. Here, we reported the first high-quality and chromosome-level genome assembly of the yellow nutsedge generated by combining PacBio HiFi long reads, Novaseq short reads, and Hi-C data. The final genome size is 225.6 Mb with an N50 of 4.3 Mb. More than 222.9 Mb scaffolds were anchored to 54 pseudochromosomes with a BUSCO score of 96.0%. We identified 76.5 Mb (33.9%) repetitive sequences across the genome. A total of 23,613 protein-coding genes were predicted in this genome, of which 22,847 (96.8%) were functionally annotated. A whole-genome duplication event was found after the divergence of Carex littledalei and Rhynchospora breviuscula, indicating the rich genetic resources of this species for adaptive evolution. Several significantly enriched GO terms were related to invasiveness of the yellow nutsedge, which may explain its plastic adaptability. In addition, several enriched Kyoto Encyclopedia of Genes and Genomes pathways and expanded gene families were closely related with substances in tubers, partially explaining the genomic basis of characteristics of this oil-rich tuber.


Asunto(s)
Cyperus , Cyperus/genética , Cyperus/metabolismo , Cromosomas , Genómica , Genoma , Secuencias Repetitivas de Ácidos Nucleicos
8.
Food Chem ; 411: 135456, 2023 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-36669340

RESUMEN

Oat supplementation of the ruminant diet can improve growth performance and meat quality traits, but the role of muscle metabolites has not been evaluated. This study aimed to establish whether oat grass supplementation (OS) of Small-tail Han sheep improved growth performance and muscle tissue metabolites that are associated with better meat quality and flavor. After 90-day, OS fed sheep had higher live-weight and carcass-weight, and lower carcass fat. Muscle metabolomics analysis showed that OS fed sheep had higher levels of taurine, l-carnitine, inosine-5'-monophospgate, cholic acid, and taurocholic acid, which are primarily involved in taurine and hypotaurine metabolism, purine metabolism, and bile acid biosynthesis and secretion, decreased fat accumulation and they promote functional or flavor metabolites. OS also increased muscle levels of amino acids that are attributed to better quality and flavorsome mutton. These findings provided further evidence for supplementing sheep with oat grass to improve growth performance and meat quality.


Asunto(s)
Aminoácidos , Avena , Ovinos , Animales , Aminoácidos/análisis , Avena/metabolismo , Cola (estructura animal)/química , Cola (estructura animal)/metabolismo , Composición Corporal , Ácidos Grasos/análisis , Dieta/veterinaria , Músculos/metabolismo , Carne/análisis , Suplementos Dietéticos/análisis , Taurina/metabolismo , Taurina/farmacología , Alimentación Animal/análisis
9.
Molecules ; 27(14)2022 Jul 14.
Artículo en Inglés | MEDLINE | ID: mdl-35889364

RESUMEN

Curcumin and germacrone, natural products present in the Zingiberaceae family of plants, have several biological properties. Among these properties, the anti-NSCLC cancer action is noteworthy. In this paper, kinetics of the two compounds in rat liver microsomes (RLMs), human liver microsomes (HLMs), and cytochrome P450 (CYP) enzymes (CYP3A4, 1A2, 2E1, and 2C19) in an NADPH-generating system in vitro were evaluated by UP-HPLC-MS/MS (ultrahigh-pressure liquid chromatography-tandem mass spectrometry). The contents of four cytochrome P450 (CYP) enzymes, adjusting by the compounds were detected using Western blotting in vitro and in vivo. The t1/2 of curcumin was 22.35 min in RLMs and 173.28 min in HLMs, while 18.02 and 16.37 min were gained for germacrone. The Vmax of curcumin in RLMs was about 4-fold in HLMs, meanwhile, the Vmax of germacrone in RLMs was similar to that of HLMs. The single enzyme t1/2 of curcumin was 38.51 min in CYP3A4, 301.4 min in 1A2, 69.31 min in 2E1, 63.01 min in 2C19; besides, as to the same enzymes, t1/2 of germacrone was 36.48 min, 86.64 min, 69.31 min, and 57.76 min. The dynamic curves were obtained by reasonable experimental design and the metabolism of curcumin and germacrone were selected in RLMs/HLMs. The selectivities in the two liver microsomes differed in degradation performance. These results meant that we should pay more attention to drugs in clinical medication-drug and drug-enzyme interactions.


Asunto(s)
Curcumina , Microsomas Hepáticos , Animales , Curcumina/metabolismo , Curcumina/farmacología , Citocromo P-450 CYP3A/metabolismo , Sistema Enzimático del Citocromo P-450/metabolismo , Humanos , Microsomas Hepáticos/metabolismo , Ratas , Sesquiterpenos de Germacrano , Espectrometría de Masas en Tándem
11.
Front Microbiol ; 13: 1032622, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-36590432

RESUMEN

Supplementation of the sheep diet with oats (Avena sativa L.) improves animal growth and meat quality, however effects on intestinal microbes and their metabolites was not clear. This study aimed to establish the effect of dietary oat supplementation on rumen and colonic microbial abundance and explore the relationship with subsequent changes in digesta metabolites. Twenty Small-tail Han sheep were randomly assigned to a diet containing 30 g/100 g of maize straw (Control) or oat hay (Oat). After 90-days on experimental diets, rumen and colon digesta were collected and microbial diversity was determined by 16S rRNA gene Illumina NovaSeq sequencing and metabolomics was conducted using Ultra-high performance liquid chromatography Q-Exactive mass spectrometry (UHPLC-QE-MS). Compared to Control group, oat hay increased the abundance of Bacteroidetes and Fibrobacteres as well as known short-chain fatty acid (SCFA) producers Prevotellaceae, Ruminococcaceae and Fibrobacteraceae in rumen (p < 0.05). In rumen digesta, the Oat group showed had higher levels of (3Z,6Z)-3,6-nonadienal, Limonene-1,2-epoxide, P-tolualdehyde, and Salicylaldehyde compared to Control (p < 0.05) and these metabolites were positively correlated with the abundance of cecal Prevotellaceae NK3B31. In conclusion, supplementation of the sheep diet with oat hay improved desirable microbes and metabolites in the rumen, providing insight into mechanisms whereby meat quality can be improved by oat hay supplementation.

13.
J Equine Vet Sci ; 102: 103458, 2021 07.
Artículo en Inglés | MEDLINE | ID: mdl-34119210

RESUMEN

Having considered that the current methods are costly and time-consuming, we designed an only 3 pairs primer-based PCR test to accurately identify the species and gender in horses, donkeys, mules and hinnies. Through a thorough sequence comparison between horse and donkey's highly similar genomes, and a vast amount of preliminary confirmation, we found that three fragments, CNGB3 gene on an autosome, displacement loop region on mitochondrial DNA and SRY genes on chromosome Y, within these equine DNA, are enough to enable us achieving our goal. The PCR test described here would be an economical, fast and accurate alternative for the most commonly-used methods, polymerase chain reaction-restriction fragment length polymorphism, microsatellite assay, and sequencing.


Asunto(s)
Equidae , Cromosoma Y , Animales , Equidae/genética , Caballos/genética , Repeticiones de Microsatélite/genética , Reacción en Cadena de la Polimerasa/veterinaria , Polimorfismo de Longitud del Fragmento de Restricción
14.
Front Microbiol ; 11: 596394, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-33343537

RESUMEN

The community of microorganisms inhabiting the gastrointestinal tract of monogastric herbivores played critical roles in the absorption of nutrients and keeping the host healthy. However, its establishment at different age groups has not been quantitatively and functionally examined. The knowledge of microbial colonization and its function in the intestinal tract of different-age donkeys is still limited. By applying the V3-V4 region of the bacterial 16S rRNA gene and functional prediction on fecal samples from different-age donkeys, we characterized the gut microbiota during the different age groups. In contrast to the adult donkeys, the gut microbiota diversity and richness of the young donkeys showed significantly less resemblance. The microbial data showed that diversity and richness increased with age, but a highly individual variation of microbial composition was observed at month 1. Principal coordinate analysis (PCoA) revealed a significant difference across five time points in the feces. The abundance of Bacteroides, Lactobacillus, and Odoribacter tended to decrease, while the proportion of Streptococcus was significantly increased with age. For functional prediction, the relative abundance of pathways had a significant difference in the feces across different age groups, for example, Terpenoids and Polyketides and Folding, Sorting, and Degradation (P < 0.05 or P < 0.01). The analysis of beta diversity (PCoA and LEfSe) and microbial functions predicted with PICRUSt (NSTIs) clearly divided the donkeys into foals (≤3 months old) and adults (≥7 months old). Microbial community composition and structure had distinctive features at each age group, in accordance with functional stability of the microbiota. Our findings established a framework for understanding the composition and function of the fecal microbiota to differ between young and adult donkeys.

15.
Pharm Biol ; 58(1): 239-246, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32202453

RESUMEN

Context: Camellia nitidissima Chi (Theaceae) is an evergreen shrub, the leaves of which are used in many medicinal applications.Objective: To characterize the chemical composition of a 10% aqueous ethanol extract of C. nitidissima leaves (CNE), and to explore the protective effect of the extract against acute liver injury (ALI) in rats.Materials and methods: Male Sprague-Dawley rats were divided into six groups (n = 10): control and negative (0.5% CMC-Na, 5 mL/kg/d), thiopronin (20 mg/kg/d) and CNE (40, 80 and 160 mg/kg/d). All groups were treated for seven consecutive days, and then, except for the control, carbon tetrachloride was administered intraperitoneally. The biochemical parameters, mRNAs, and proteins were analyzed using enzyme-linked immunoassays kits, quantitative polymerase chain reaction and western blot. Chemical components were identified using mass spectroscopy, and the phenol and flavonoid content determined by ultraviolet spectrophotometry.Results: Pre-treatment with CNE (160 mg/kg) attenuated the pathological changes in liver tissues and decreased alanine transaminase (62 and 60%), aspartate transaminase (49 and 53%) and malondialdehyde (35 and 42%) levels in serum and liver tissues. Moreover, CNE reduced the concentrations of reactive oxygen species (55%), tumour necrosis factor-α (26%), interleukin-1ß (19%) and IL-6 (19%) and blocked the nuclear translocation of p65. Pre-treatment with CNE increased anti-heme oxygenase-1 (40%), superoxide dismutase (108%) and glutathione (97%) levels through upregulating nuclear factor erythroid-2-related factor 2. Twelve compounds were detected; the content of phenols and flavonoids was determined as 34.474 ± 1.026 and 15.228 ± 0.422 mg/g crude drug in CNE, respectively.Discussion and conclusions: These results suggested that CNE is a promising agent for functional food and hepatoprotective drug against ALI.


Asunto(s)
Camellia/química , Enfermedad Hepática Inducida por Sustancias y Drogas/prevención & control , Hígado/efectos de los fármacos , Factor 2 Relacionado con NF-E2/metabolismo , FN-kappa B/metabolismo , Extractos Vegetales/farmacología , Animales , Enfermedad Hepática Inducida por Sustancias y Drogas/etiología , Enfermedad Hepática Inducida por Sustancias y Drogas/metabolismo , Enfermedad Hepática Inducida por Sustancias y Drogas/patología , Modelos Animales de Enfermedad , Etanol/química , Hígado/metabolismo , Hígado/patología , Masculino , Extractos Vegetales/aislamiento & purificación , Hojas de la Planta/química , Ratas , Ratas Sprague-Dawley , Transducción de Señal
16.
Microbiologyopen ; 9(6): 1085-1101, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32153142

RESUMEN

The intestinal microbiota plays an important role in the health and metabolism of the host. Next-generation sequencing technology has enabled the characterization of the gut microbiota of several animal species. We analyzed the intestinal microbiota in six different parts of the gastrointestinal tracts (GITs) of five Mongolian horses by sequencing the 16S rRNA gene V3-V4 hypervariable region. All horses were kept in the natural habitat of the Inner Mongolia grassland. Significant differences were observed among the microbiota compositions of the distinct GIT regions. In addition, while the microbial community structures of the small and large intestine were significantly different, those of the cecum and colon were similar. In the foregut, Firmicutes (65%) and Proteobacteria (23%) were the most abundant, while Firmicutes (45%) and Bacteroidetes (42%) were the most common in the hindgut. At the level of family, Ruminococcaceae (p = .203), Lachnospiraceae (p = .157), Rikenellaceae (p = .122), and Prevotellaceae (p = .068) were predominant in the hindgut, while the relative abundance of the Akkermansia genus (5.7%, p = .039) was higher in the ventral colon. In terms of the putative functions, the ratio of microbial abundance in the different parts of the GIT was similar, the result can help characterize the gut microbial structure of different animals.


Asunto(s)
Akkermansia/clasificación , Bacteroidetes/clasificación , Clostridiales/clasificación , Firmicutes/clasificación , Microbioma Gastrointestinal/genética , Proteobacteria/clasificación , Akkermansia/genética , Akkermansia/aislamiento & purificación , Animales , Bacteroidetes/genética , Bacteroidetes/aislamiento & purificación , Ciego/microbiología , China , Clostridiales/genética , Clostridiales/aislamiento & purificación , Colon/microbiología , ADN Bacteriano/genética , Femenino , Firmicutes/genética , Firmicutes/aislamiento & purificación , Tracto Gastrointestinal/microbiología , Secuenciación de Nucleótidos de Alto Rendimiento , Caballos , Intestino Grueso/microbiología , Intestino Delgado/microbiología , Masculino , Proteobacteria/genética , Proteobacteria/aislamiento & purificación , ARN Ribosómico 16S/genética
17.
PLoS One ; 14(12): e0226186, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31834903

RESUMEN

Gastrointestinal microbiota has significant impact on the nutrition and health of monogastric herbivores animals including donkey. However, so far the microbiota in different gastrointestinal compartments of healthy donkey has not been described. Therefore, we investigated the abundance and function of microbiota at different sites of the gastrointestinal tract (GIT) (foregut: stomach, duodenum, jejunum and ileum; hindgut: cecum, ventral colon, dorsal colon, and rectum) of healthy adult donkeys mainly based on 16S rRNA gene sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis. Collectively, our results showed that donkey has a rich, diverse and multi-functional microbiota along the GIT. In general, the richness and diversity of the microbiota are much higher in the hindgut relative to that in the foregut; at phylum level, the Firmicutes is dominant in the foregut while both Firmicutes and Bacteroides are abundant in the hindgut; at the genus level, Lactobacillus was dominant in the foregut while Streptococcus was more dominant in the hindgut. Our further PICRUSt analysis showed that varying microbiota along the GIT is functionally compatible with the corresponding physiological function of different GIT sites. For example, the microbes in the foregut are more active at carbohydrate metabolism, and in the hindgut are more active at amino acid metabolism. This work at the first time characterized the donkey digestive system from the aspects of microbial composition and function, provided an important basic data about donkey healthy gastrointestinal microbiota, which may be utilized to evaluate donkey health and also offer clues to further investigate donkey digestive system, nutrition, even to develop the microbial supplements.


Asunto(s)
Bacterias/clasificación , ADN Bacteriano/análisis , Microbioma Gastrointestinal/genética , Tracto Gastrointestinal/microbiología , Animales , Bacterias/genética , ADN Bacteriano/genética , Equidae , Masculino , Filogenia , ARN Ribosómico 16S/análisis , ARN Ribosómico 16S/genética
18.
Front Plant Sci ; 10: 908, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31354775

RESUMEN

Dynamic global vegetation models (DGVMs) suffer insufficiencies in tracking biochemical cycles and ecosystem fluxes. One important reason for these insufficiencies is that DGVMs use fixed parameters (mostly traits) to distinguish attributes and functions of plant functional types (PFTs); however, these traits vary under different climatic conditions. Therefore, it is urgent to quantify trait covariations, including those among specific leaf area (SLA), area-based leaf nitrogen (N area), and leaf area index (LAI) (in 580 species across 218 sites in this study), and explore new classification methods that can be applied to model vegetation dynamics under future climate change scenarios. We use a redundancy analysis (RDA) to derive trait-climate relationships and employ a Gaussian mixture model (GMM) to project vegetation distributions under different climate scenarios. The results show that (1) the three climatic variables, mean annual temperature (MAT), mean annual precipitation (MAP), and monthly photosynthetically active radiation (mPAR) could capture 65% of the covariations of three functional traits; (2) tropical, subtropical and temperate forest complexes expand while boreal forest, temperate steppe, temperate scrub and tundra shrink under future climate change scenarios; and (3) the GMM classification based on trait covariations should be a powerful candidate for building new generation of DGVM, especially predicting the response of vegetation to future climate changes. This study provides a promising route toward developing reliable, robust and realistic vegetation models and can address a series of limitations in current models.

19.
Sci Rep ; 9(1): 5022, 2019 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-30903011

RESUMEN

P-element induced wimpy testis-interacting RNAs (piRNAs) are essential for testicular development and spermatogenesis in mammals. Comparative analyses of the molecular mechanisms of spermatogenesis among different organisms are therefore dependent on accurate characterizations of piRNAs. At present, little is known of piRNAs in non-model organisms. Here, we characterize piRNAs in the Mongolian horse, a hardy breed that reproduces under extreme circumstances. A thorough understanding of spermatogenesis and reproduction in this breed may provide insights for the improvement of fecundity and reproductive success in other breeds. We identified 4,936,717 piRNAs and 7,890 piRNA clusters across both testicular developmental stages. Of these, 2,236,377 putative piRNAs were expressed in the mature samples only, and 2,391,271 putative piRNAs were expressed in the immature samples only. Approximately 3,016 piRNA clusters were upregulated in the mature testes as compared to the immature testes, and 4,874 piRNA clusters were downregulated. Functional and pathway analyses indicated that the candidate generating genes of the predicted piRNAs were likely involved in testicular development and spermatogenesis. Our results thus provide information about differential expression patterns in genes associated with testicular development and spermatogenesis in a non-model animal.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Regulación del Desarrollo de la Expresión Génica , Caballos/genética , Familia de Multigenes , ARN Interferente Pequeño/genética , Testículo/metabolismo , Animales , Cruzamiento , China , Fertilidad/genética , Ontología de Genes , Caballos/crecimiento & desarrollo , Masculino , Transducción de Señal/genética , Espermatogénesis/genética , Testículo/crecimiento & desarrollo
20.
PLoS One ; 11(3): e0151858, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-27002822

RESUMEN

Casuarina equisetifolia is commonly planted and used in the construction of coastal shelterbelt protection in Hainan Island. Thus, it is critical to accurately estimate the tree biomass of Casuarina equisetifolia L. for forest managers to evaluate the biomass stock in Hainan. The data for this work consisted of 72 trees, which were divided into three age groups: young forest, middle-aged forest, and mature forest. The proportion of biomass from the trunk significantly increased with age (P<0.05). However, the biomass of the branch and leaf decreased, and the biomass of the root did not change. To test whether the crown radius (CR) can improve biomass estimates of C. equisetifolia, we introduced CR into the biomass models. Here, six models were used to estimate the biomass of each component, including the trunk, the branch, the leaf, and the root. In each group, we selected one model among these six models for each component. The results showed that including the CR greatly improved the model performance and reduced the error, especially for the young and mature forests. In addition, to ensure biomass additivity, the selected equation for each component was fitted as a system of equations using seemingly unrelated regression (SUR). The SUR method not only gave efficient and accurate estimates but also achieved the logical additivity. The results in this study provide a robust estimation of tree biomass components and total biomass over three groups of C. equisetifolia.


Asunto(s)
Biomasa , Magnoliopsida/fisiología , Bosque Lluvioso , Árboles/fisiología , China , Modelos Teóricos , Hojas de la Planta , Raíces de Plantas
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