Shanghai Majorbio Bio pharm Technology Co.

Shanghai, China

Shanghai Majorbio Bio pharm Technology Co.

Shanghai, China
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Lou Q.,Fudan University | Lou Q.,Shanghai Agrobiological Gene Center | Chen L.,Shanghai Agrobiological Gene Center | Mei H.,Shanghai Agrobiological Gene Center | And 8 more authors.
Frontiers in Plant Science | Year: 2017

Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots. © 2017 Lou, Chen, Mei, Xu, Wei, Feng, Li, Pang, Shi, Luo and Zhong.


Li B.,University of Sichuan | Zhou X.,University of Sichuan | Wu P.,Shanghai Majorbio Bio pharm Technology Co. | Li M.,University of Sichuan | And 4 more authors.
FEMS Microbiology Letters | Year: 2017

The aims of this study were to investigate the effects of substrates (glass versus hydroxyapatite [HA]) and growth media (SHI medium versus a modified artificial saliva medium with cysteine) on the microbial community of saliva-derived biofilm in vitro. 16S rRNA gene sequencing technology was used to analyze the microbial community of saliva-derived biofilm cultured for 72 h anaerobically. The metagenomes of biofilms were predicted from the clusters of orthologous groups. No significant difference was found between the saliva-derived biofilms grown on HA and glass in ACE, Chao, Shannon and Simpson indices. The abundances of only a few bacteria on HA were significantly different from those on glass with a low relative abundance (<0.5%). Compared with the biofilms developed in a modified artificial saliva medium with cysteine, biofilms in SHI medium were significantly higher (P < 0.05) in diversity. Linear discriminant analysis coupled with effect size measurement showed that some obligate anaerobic genera (Lactobacillus, Veillonella, Porphyromonas and Leptotrichia) were more abundant in SHI medium biofilms. The biofilms grown in different media were also significantly different in predicted gene categories. In conclusion, the growth media, not the substrates, have significant effects on the microbial community of saliva-derived biofilm in vitro. © FEMS 2017. All rights reserved.


Wu S.,CAS Wuhan Institute of Hydrobiology | Ren Y.,Shanghai Majorbio Bio Pharm Technology Co. | Peng C.,CAS Wuhan Institute of Hydrobiology | Hao Y.,CAS Wuhan Institute of Hydrobiology | And 5 more authors.
FEMS Microbiology Ecology | Year: 2015

Despite the economic importance of fish, the ecology and metabolic capacity of fish microbiomes are largely unknown. Here, we sequenced the metatranscriptome of the intestinal microbiota of grass carp, Ctenopharyngodon idellus, a freshwater herbivorous fish species. Our results confirmed previous work describing the bacterial composition of the microbiota at the phylum level as being dominated by Firmicutes, Fusobacteria, Proteobacteria and Bacteriodetes. Comparative transcriptomes of the microbiomes of fish fed with different experimental diets indicated that the bacterial transcriptomes are influenced by host diet. Although hydrolases and cellulosome-based systems predicted to be involved in degradation of the main chain of cellulose, xylan, mannan and pectin were identified, transcripts with glycoside hydrolase modules targeting the side chains of noncellulosic polysaccharides were more abundant. Predominant 'COG' (Clusters of Orthologous Group) categories in the intestinal microbiome included those for energy production and conversion, as well as carbohydrate and amino acid transport and metabolism. These results suggest that the grass carp intestinal microbiome functions in carbohydrate turnover and fermentation, which likely provides energy for both host and microbiota. Grass carp intestinal microbiome thus reflects its evolutionary adaption for harvesting nutrients for an herbivore with a high-throughput nutritional strategy that is not dominated by cellulose digestion but rather the degradation of intracellular polysaccharides. © FEMS 2015.


Hov J.R.,University of Oslo | Zhong H.,BGI Shenzhen | Qin B.,BGI Shenzhen | Qin B.,Shanghai Majorbio Bio pharm Technology Co. | And 6 more authors.
PLoS ONE | Year: 2015

Multiple immune-related genes are encoded in the HLA complex on chromosome 6p21. The 8.1 ancestral haplotype (AH8.1) include the classical HLA alleles HLA-B∗08:01 and HLA-DRB1∗03:01, and has been associated with a large number of autoimmune diseases, but the underlying mechanisms for this association are largely unknown. Given the recently established links between the gut microbiota and inflammatory diseases, we hypothesized that the AH8.1 influences the host gut microbial community composition. To study this further, healthy individuals were selected from the Norwegian Bone Marrow Donor Registry and categorized as either I. AH8.1 homozygote (n=34), II. AH8.1 heterozygote (n=38), III. Non AH8.1 heterozygote or IV. HLA-DRB1 homozygote but non AH8.1 (n=15). Bacterial DNA from stool samples were subjected to sequencing of the V3-V5 region of the 16S rRNA gene on the 454 Life Sciences platform and data analyzed using Mothur and QIIME. The results showed that the abundances of different taxa were highly variable within all predefined AH8.1 genotype groups. Using univariate non-parametric statistics, there were no differences regarding alpha or beta diversity between AH8.1 carriers (categories I and II) and non-carriers (categories III and IV), however four different taxa (Prevotellaceae, Clostridium XVIII, Coprococcus, Enterorhabdus) had nominally significant lower abundances in AH8.1 carriers than non-carriers. After including possible confounders in a multivariate linear regression, only the two latter genera remained significantly associated. In conclusion, the overall contribution of the AH8.1 haplotype to the variation in gut microbiota profile of stool in the present study was small. ©2015 Hov et al.


Ren H.,Shanghai JiaoTong University | Ren H.,Shanghai Majorbio Bio pharm Technology Co. | Xiong S.,Shanghai JiaoTong University | Gao G.,Sinopec | And 4 more authors.
Frontiers in Microbiology | Year: 2015

Water flooding is widely used for oil recovery. However, how the introduction of bacteria via water flooding affects the subsurface ecosystem remains unknown. In the present study, the distinct bacterial communities of an injection well and six adjacent production wells were revealed using denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. All sequences of the variable region 3 of the 16S rRNA gene retrieved from pyrosequencing were divided into 543 operational taxonomic units (OTUs) based on 97% similarity. Approximately 13.5% of the total sequences could not be assigned to any recognized phylum. The Unifrac distance analysis showed significant differences in the bacterial community structures between the production well and injection water samples. However, highly similar bacterial structures were shown for samples obtained from the same oil-bearing strata. More than 69% of the OTUs detected in the injection water sample were absent or detected in low abundance in the production wells. However, the abundance of two OTUs reached as high as 17.5 and 26.9% in two samples of production water, although the OTUs greatly varied among all samples. Combined with the differentiated water flow rate measured through ion tracing, we speculated that the transportation of injected bacteria was impacted through the varied permeability from the injection well to each of the production wells. Whether the injected bacteria predominate the production well bacterial community might depend both on the permeability of the strata and the reservoir conditions. © 2015 Ren, Xiong, Gao, Song, Cao, Zhao and Zhang.


Zhang M.,East China Normal University | Jiang Z.,East China Normal University | Li D.,East China Normal University | Jiang D.,East China Normal University | And 4 more authors.
Microbial Ecology | Year: 2014

Antibiotic treatment eliminates commensal bacteria and impairs mucosal innate immune defenses in the gut. However, whether oral antibiotic treatment could alter the composition of the microbiota on the skin surface and influence innate immune responses remains unclear. To test this, mice were treated with vancomycin for 7 days and then wounds were made on the back skin of the mice. Five days later, scar tissue from each mouse was collected for bacterial enumeration, the bacterial composition on the scar and unwounded skin was determined using 16S RNA gene-based pyrosequencing analysis, and skin around wounds was collected for RNA extraction. Compared with the control group, the overall density and composition of skin bacteria were altered, and the proportion of Staphylococcus-related sequences was reduced in the vancomycin-treated group. Moreover, vancomycin treatment decreased the expression of RegIIIγ and interleukin (IL)-17 in the wounded skin. Taken together, our data demonstrate that antibiotic treatment decreases the bacterial density and alters the bacterial composition in skin wounds, followed by a decrease in RegIIIγ expression, which may contribute to the delayed wound repair. Our findings also indicate that antibiotic therapy should be carefully considered in the treatment of skin injury. © 2014, Springer Science+Business Media New York.


Jin M.-J.,Ningbo Fiber Inspection Institute | Ruan Y.,Ningbo Fiber Inspection Institute | Cai H.-K.,Shanghai Majorbio Bio pharm Technology Co. | Qian W.-J.,Ningbo Fiber Inspection Institute
Wool Textile Journal | Year: 2012

There are some differences in the DNA sequence among different species. Living environment, food chain and other factors can also caused genetic mutations. This paper analysed the mtDNA sequence, based on testing for different regions or kinds of cashmere and wool fibers, then gave the results as follows;the similarity of mtDNA sequence between cashmere and wool was more than 98% , but in specific locations there had their own characteristic base sequence; the characteristic base sequence of mtDNA of cashmere fiber, from different regions or kinds, was almost the same, and so did the wool.


Jin M.-J.,Ningbo Fiber Inspection Institute | Ruan Y.,Ningbo Fiber Inspection Institute | Yan B.-B.,Shanghai Majorbio Bio Pharm Technology Co. | Shi D.-H.,Ningbo Fiber Inspection Institute
Wool Textile Journal | Year: 2011

Extraction method of mtDNA is the key technical problem about research and development the DNA testing for animal fiber. This paper studys the extraction method of mtDNA for cashmere and wool, and validates through PCR enlarge. The results show that use the Promega kit, it is favorable to next step that makeing the sample powder as much as possible, and first remove the undissolved fibers through centrifugal after cracking, then the sampte gained can be met the ruquirments for PCR enlarge and DNA sequencing.


PubMed | Cornell University, Shanghai Majorbio Bio Pharm Technology Co. and CAS Wuhan Institute of Hydrobiology
Type: Journal Article | Journal: FEMS microbiology ecology | Year: 2015

Despite the economic importance of fish, the ecology and metabolic capacity of fish microbiomes are largely unknown. Here, we sequenced the metatranscriptome of the intestinal microbiota of grass carp, Ctenopharyngodon idellus, a freshwater herbivorous fish species. Our results confirmed previous work describing the bacterial composition of the microbiota at the phylum level as being dominated by Firmicutes, Fusobacteria, Proteobacteria and Bacteriodetes. Comparative transcriptomes of the microbiomes of fish fed with different experimental diets indicated that the bacterial transcriptomes are influenced by host diet. Although hydrolases and cellulosome-based systems predicted to be involved in degradation of the main chain of cellulose, xylan, mannan and pectin were identified, transcripts with glycoside hydrolase modules targeting the side chains of noncellulosic polysaccharides were more abundant. Predominant COG (Clusters of Orthologous Group) categories in the intestinal microbiome included those for energy production and conversion, as well as carbohydrate and amino acid transport and metabolism. These results suggest that the grass carp intestinal microbiome functions in carbohydrate turnover and fermentation, which likely provides energy for both host and microbiota. Grass carp intestinal microbiome thus reflects its evolutionary adaption for harvesting nutrients for an herbivore with a high-throughput nutritional strategy that is not dominated by cellulose digestion but rather the degradation of intracellular polysaccharides.

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