Gut microbiota induced abnormal amino acids and their correlation with diabetic retinopathy.

AIM: To explore the correlation of gut microbiota and the metabolites with the progression of diabetic retinopathy (DR) and provide a novel strategy to elucidate the pathological mechanism of DR. METHODS: The fecal samples from 32 type 2 diabetes patients with proliferative retinopathy (PDR), 23 with non-proliferative retinopathy (NPDR), 27 without retinopathy (DM), and 29 from the sex-, age- and BMI- matched healthy controls (29 HC) were analyzed by 16S rDNA gene sequencing. Sixty fecal samples from PDR, DM, and HC groups were assayed by untargeted metabolomics. Fecal metabolites were measured using liquid chromatography-mass spectrometry (LC-MS) analysis. Associations between gut microbiota and fecal metabolites were analyzed. RESULTS: A cluster of 2 microbiome and 12 metabolites accompanied with the severity of DR, and the close correlation of the disease progression with PDR-related microbiome and metabolites were found. To be specific, the structure of gut microbiota differed in four groups. Diversity and richness of gut microbiota were significantly lower in PDR and NPDR groups, than those in DM and HC groups. A cluster of microbiome enriched in PDR group, including Pseudomonas, Ruminococcaceae-UCG-002, Ruminococcaceae-UCG-005, Christensenellaceae-R-7, was observed. Functional analysis showed that the glucose and nicotinate degradations were significantly higher in PDR group than those in HC group. Arginine, serine, ornithine, and arachidonic acid were significantly enriched in PDR group, while proline was enriched in HC group. Functional analysis illustrated that arginine biosynthesis, lysine degradation, histidine catabolism, central carbon catabolism in cancer, D-arginine and D-ornithine catabolism were elevated in PDR group. Correlation analysis revealed that Ruminococcaceae-UCG-002 and Christensenellaceae-R-7 were positively associated with L-arginine, ornithine levels in fecal samples. CONCLUSION: This study elaborates the different microbiota structure in the gut from four groups. The relative abundance of Ruminococcaceae-UCG-002 and Parabacteroides are associated with the severity of DR. Amino acid and fatty acid catabolism is especially disordered in PDR group. This may help provide a novel diagnostic parameter for DR, especially PDR.

Efficacy of machine learning assisted dental age assessment in local population.

INTRODUCTION: Although the dental age assessment is commonly applied in forensic and maturity evaluation, the long-standing dilemma from population differences has limited its application. OBJECTIVES: This study aimed to verify the efficacy of the machine learning (ML) to build up the dental age standard of a local population. METHODS: We retrospectively studied 2052 panoramic films retrieved from healthy Taiwanese children aged 2.6-17.7 years with comparable sizes in each age-group. The recently reported Han population-based standard (H method) served as the control condition. To develop and validate ML models, random divisions of the sample in an 80%-20% ratio repeated 20 times. The model performances were compared with the H method, Demirjian's method, and Willems's method. RESULTS: The ML-assisted models provided more accurate age prediction than those non-ML-assisted methods. The range of errors was effectively reduced to less than one per year in the ML models. Furthermore, the consistent agreements among the age groups from preschool to adolescence were reported for the first time. The Gaussian process regression was the best ML model; of the non-ML modalities, the H method was the most efficacious, followed by the Demirjian's method and Willems's methods. CONCLUSION: The ML-assisted dental age assessment is helpful to provide customized standards to a local population with more accurate estimations in preschool and adolescent age groups than do studied conventional methods. In addition, the earlier complete tooth developments were also observed in present study. To construct more reliable dental maturity models in the future, additional environment-related factors should be taken into account.

Progress in long non-coding RNAs in animals.

Long non-coding RNAs (lncRNAs) are important transcripts that are more than 200 nucleotides in length, and distribute extensively in animal and plant genomes. Accumulated studies demonstrate that lncRNAs play critical roles in biological processes related to embryogenesis, muscle development, lipid deposition and immune responses. They assist protein complexes in translocating to appropriate locations and participate in regulating gene activation and inactivation. Recently, rapid progress of lncRNA research is emerging, largely due to molecular biological technologies and information developed in the human genome project and the Encyclopedia of DNA Elements (ENCODE) project. For example, a dwarf open reading frame (DWORF) encoded by an annotated lncRNA was reported to activate the SERCA pump. Moreover, small regulatory polypeptide of amino acid response (SPAR) encoded by lncRNA LINC00961 was found to regulate muscle regeneration. These new results have revealed a novel model that lncRNA regulates biological processes using its small peptide product. In this review, we summarize the characteristics, databases, biological functions and molecular regulatory models, as well as research interests of lncRNAs in the future.

[Agricultural soil contamination from As and Cd and its responses to landscape heterogeneity at multiple scales in Guangzhou, China]. / 广州市农业土壤As和Cdæ±¡æŸ“åŠå ¶å¯¹æ™¯è§‚å¼‚è´¨æ€§çš„å¤šå°ºåº¦å“åº”.

Based on 641 agricultural top soil samples (0-20 cm) and land use map in 2005 of Guangzhou, we used single-factor pollution indices and Pearson/Spearman correlation and partial redundancy analyses and quantified the soil contamination with As and Cd and their relationships with landscape heterogeneity at three grid scales of 2 km×2 km, 5 km×5 km, and 10 km×10 km as well as the determinant landscape heterogeneity factors at a certain grid scale. 5.3% and 7.2% of soil samples were contaminated with As and Cd, respectively. At the three scales, the agricultural soil As and Cd contamination were generally significantly correlated with parent materials' composition, river/road density and landscape patterns of several land use types, indicating the parent materials, sewage irrigation and human activities (e.g., industrial and traffic activities, and the additions of pesticides and fertilizers) were possibly the main input pathways of trace metals. Three subsets of landscape heterogeneity variables (i.e., parent materials, distance-density variables, and landscape patterns) could explain 12.7%-42.9% of the variation of soil contamination with As and Cd, of which the explanatory power increased with the grid scale and the determinant factors varied with scales. Parent materials had higher contribution to the variations of soil contamination at the 2 and 10 km grid scales, while the contributions of landscape patterns and distance-density variables generally increased with the grid scale. Adjusting the distribution of cropland and optimizing the landscape pattern of land use types are important ways to reduce soil contamination at local scales, which urban planners and decision makers should pay more attention to.

Construct synthetic gene encoding artificial spider dragline silk protein and its expression in milk of transgenic mice.

Based on the known partial cDNA sequence of dragline silk protein an artificial gene monomer, a 360 bp sequence, was designed and polymerized to encode an analog of dragline silk protein. Six tandem copies of monomer were cloned into pBC1 vector and microinjected into the pronuclei of fertilized Kunming White eggs. Transgenic mice were screened by Polymerase Chain Reaction (PCR) and Southern blot which revealed that 10 mice (5 male, 5 female) among 58 mice were transgenic positive. Milk of five F0 mice and eight F1 mice was analyzed by Western blot, and two F0 mice and seven F1 mice expressed recombinant dragline silk protein. In transgenic mice milk a maximum of concentration of recombinant dragline silk protein was 11.7 mg/L by radioimmunoassay.

[Genetic diversity in Tibetan chicken].

Morphological traits and living habit of Tibetan chicken, which is an aboriginal chicken breed on plateau with its own characteristic populational genetic features, are in great common with the Red Jungle Fowl, the assumed ancestry of domestic chicken. To fully exploit this chicken resource, Multiplex PCR with semi-automated polyacrilamide gel electrophoresis (PAGE) using fluorescently labeled microsatellite primers was used to detect the polymorphism at 20 microsatellite loci. At the same time, we randomly test the individual morphology and performance. It showed that numbers of polymorphic alleles were 4 approximately 10, with mean value 7.25 per locus. Polymorphism Information Content (C(PI)) and Heterozygosity (H) had mean values 0.67 and 0.74, respectively. Macrochromosomes had relatively higher polymorphism than microchromosomes(P > 0.05). In all, high polymorphisms at microsatellite loci related to the uneven production performance and morphological discrepancy of population genetic characteristics in Tibetan chicken.

Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthio camelus) genome.

Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.

[Preliminary analysis on China Agricultural University chicken resource population based on genomic scanning].

Combining the technique of multiplex-PCR and the fluorescent semi-automated detection, a large-scale genome scanning was performed for 440 chickens, which was derived from China Agricultural University chicken resource families, within three generations. Fifty-five microsatellite markers were analyzed for this study. Those 55 microsatellite loci accorded with the characters of Mendelian co-inheritance. The heterozygosities ranged from zero to 0.89, with 72% of loci having a heterozygosity of more than 0.60. The polymorphism information content (PIC) ranged from 0 to 0.85, in which 70% of those loci had a PIC of more than 0.50 but their distribution varied in line A and line C. The allele frequency was significantly different between line A and line C at most loci (P < 0.01). At the same time, gene accordance inclination was found in line C. The Nei population resemble coefficient and standard genetic distance were 0.1002 and 0.8928.

[The factors affecting the efficiency of mutiplex PCR].

In the research,the outputs of different cycle parameters, PCR buffer and reaction volumes are compared. The results indicated that the annealing temperature, annealing time, elongated time and ingredient of PCR buffer affected mutiplex PCR, but the reaction volume and cycle number had few effect on it.