Comprehensive Evaluation and Application of Experimental Sources of Variation in Gut Microbiome Sequencing Studies / 中国生物化学与分子生物学报

Gut microbiome sequencing studies have great potential to translate microbial analysis outcomes into human health research. Sequencing strategies of 16S amplicon and whole-metagenome shotgun (WMS) are two main methods in microbiome research with respective advantages. However, how sample heterogeneity, sequencers and library preparation protocols affect the sequencing reproducibility of gut microbiome needs further investigation. This study aims to provide a reference for the selection of sequencing technologies by comparing differences in microbial composition from different sampling sites. The results of three widely adopted sequencers showed that the technical repetition correlation (r= 0. 94) was high in WMS method, while the biological repetition correlation (r = 0. 69) was low. Bray-Curtis distance identified that dissimilarity from biological replicates was larger than that of technical replicates (P<0. 001). In addition, dissimilarity and specific taxonomic profiles were observed between 16S and WMS datasets. Our results imply that homogenization is a necessary step before sample DNA extraction. The sequencers contributed less to taxonomic variation than the library preparation protocols. We developed an empirical Bayes approach that " borrowed information" in calculations and analyzed batch effect parameters using standardized data and prior distributions of (non-) parameters, which may improve population comparability between 16S and WMS and provide a basis for further application to fusion analysis of published 16S and microbial datasets.

Gene rearrangement analysis of papillary thyroid carcinoma / 中华耳鼻咽喉头颈外科杂志

<p><b>OBJECTIVE</b>To investigate the characteristics of RET/PTC and H47PTEN rearrangement and the association between gene rearrangement and clinicopathological properties of thyroid carcinoma.</p><p><b>METHODS</b>Rearrangement of RET/PTC-1, RET/PTC-2, RET/PTC-3, ELKS-RET and H4-PTEN (H4/PTEN and PTEN/H4) was analyzed in 139 thyroid tumor tissues by using RT-PCR and sequencing.</p><p><b>RESULTS</b>Twelve RET/PTC-1, 6 RET/PTC-3, 6 H4/PTEN and 7 PTEN/H4 were detected in 126 papillary thyroid carcinomas. In 3 cases, both RET/PTC and H4-PTEN were identified simultaneously. However, repeated experiments did not give the same results of H4-PTEN rearrangement. The overall frequency of rearrangement was 21.4% (27/126). The patients with gene rearrangement were younger (P = 0.02) and had a higher frequency of lymph node involvement (P = 0.02). High frequency of lateral neck lymph node involvement was detected in RET/PTC positive PTC (P < 0.01). PTEN/H4 rearrangement could also be detected in medullary thyroid carcinoma (2/5).</p><p><b>CONCLUSIONS</b>H4-PTEN rearrangement can occur simultaneously with RET/PTC rearrangement in PTC. High predisposition to gene rearrangement is a characteristic of PTC. The patients of PTC with gene rearrangement are younger and have a higher frequency of lymph node involvement.</p>

Differentially expressed genes between a fertile patient and an infertile patient in a large Chinese androgen insensitivity syndrome pedigree / 中国医学科学院学报

<p><b>OBJECTIVE</b>To screen and identify differentially expressed genes between a fertile patient and another infertile patient who belonged to a large Chinese pedigree affected with androgen insensitivity syndrome (AIS).</p><p><b>METHODS</b>We constructed the forward and reversed subtracted libraries using genital skin fibroblasts (GSF), which were obtained from the fertile patient MJ and infertile patient ZGJ, as tester respectively. Candidate clones were screened with colony in situ hybridization, dot blot, and Southern blot analysis step by step and conformed with Northern blot analysis. The potential positive clones were sequenced and the homology of the sequences was analyzed.</p><p><b>RESULTS</b>The forward and reversed subtracted libraries containing differentially expressed pattern of two GSF cell lines were constructed. Two positive clones identified by Northern blot were obtained in the reversed subtracted library. Eleven candidate clones from the two libraries that failed to hybridize with both RNA populations were obtained simultaneously, which might represent differentially expressed low abundance transcripts. Sequencing results and homology analysis demonstrated that the two positive clones were significantly homologous with the genes of autotaxin-t and calcium binding protein calcyclin (S100A6), respectively.</p><p><b>CONCLUSIONS</b>Two positive clones and eleven clones showing no hybridization signals may represent differentially expressed genes between the two GSFs. This finding may be useful to elucidate the molecular mechanisms leading to phenotypic variation and preserved fertility of the AIS pedigree.</p>