In the past ten years, the research and application of microbiome has continued to increase. The microbiome has gradually become the research focus in the fields of life science, environmental science, and medicine. Meanwhile, many countries and organizations around the world are launching their own microbiome projects and conducting a multi-faceted layout, striving to gain a strategic position in this promising field. In addition, whether it is scientific research or industrial applications, there has been a climax of research and a wave of investment and financing, accordingly, products and services related to the microbiome are constantly emerging. However, due to the rapid development of microbiome sequencing and analysis related technologies and methods, the research and application from various countries have not yet unified on the standards of technology, programs, and data. Domestic industry participants also have insufficient understanding of the microbiome. New methods, technologies, and theories have not yet been fully accepted and used. In addition, some of the existing standards and guidelines are too general with poor practicality. This not only causes obstacles in the integration of scientific research data and waste of resources, but also gives related companies unfair competition opportunity. More importantly, China still lacks national standards related to the microbiome, and the national microbiome project is still in the process of preparation. In this context, the experts and practitioners of the microbiome worked together and developed the consensus of experts. It can not only guide domestic scientific research and industrial institutions to regulate the production, learning and research of the microbiome, the application can also provide reference technical basis for the relevant national functional departments, protect the scale and standardized corporate company's interests, strengthen industry self-discipline, avoid unregulated enterprises from disrupting the market, and ultimately promote the benign development of microbiome-related industries.
China ; Consensus ; Humans ; Industry ; Microbiota

Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annota-tions. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are system-atically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to mas-sive RNA-seq data applied in genome annotation. Consequently, we incorporate the improvedannotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.

Objective To construct the UAS-Hey transgenic fly strains to provide a tool for researching the function of Hey gene in the fly development.Methods The Hey gene coding sequence was amplified by reverse transcription PCR and subcloned into pUAST expression vector.The pUAS-Hey recombinant plasmid was constructed and microinjected into the embryos of wild type flies.The UAS-Hey transgenic flies with red eyes were screened out with mini-white marker,then the balancing and mapping of these transgenic strains were performed.The identification was performed by using the PCR amplification method.Results The pUAS-Hey recombinant plasmid was successfully constructed,and seven independent transgenic strains were obtained by microinjection and transgenic fly screening and balance.PCR analysis confirmed that the P[mini-white,UAS-Hey] was integrated into genomes of transgenic strains and was in expressible region.Conclusion The UAS-Hey transgenic flies are successfully constructed,which lays the foundation for further studies of the function and regulation of Hey gene with GAL4/UAS system.

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of version-dependent annotation files and other compatible public dataset for downstream analysis. To handle these tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool (RGAAT), a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNA-seq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool (RATT), RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification, genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/ and https://github.com/wushyer/RGAAT_v2 at no cost.
Genome ; Genomics ; High-Throughput Nucleotide Sequencing ; methods ; standards ; Humans ; Reference Standards ; Sequence Analysis, DNA ; methods ; standards ; Software

Objective To study the relationship between erythromycin sensitivity and drug-resistance gene in Mycoplasma pneu-moniae(Mp).Methods In 46 erythromycin-resistant MP clinical isolates,domain Ⅴ of 23S rRNA was amplified by polymerase chain reaction(PCR),followed by direct automatic sequencing method.The DNA sequences were compared to find molecular mecha-nisms of drug resistance.Results Among the 46 erythromycin-resistant Mp clinical isolates,44(95.65%)harbored an A-to-G tran-sition mutation at position 2063 in the 23S rRNA gene and 2(4.35%)harbored an A-to-G transition mutation at position 2064,but no A-to-C transition mutation at position 2063 and C-to-G/A transition mutation at position 2617 were detected.Conclusion E-rythromycin-resistant of Mp clinical isolates were closely related to A-to-G transition mutation at position 2063/2064 in domain Ⅴof 23S rRNA genes and the most important was the A2063G transition mutation.Rapid and accurate identification of the genetic mutations in domain Ⅴ of 23S rRNA may be help to diagnose the infection of Mycoplasma pneumoniae,provide the drug-resistant information,and instruct the application of antibiotics reasonably and effectively.

China has entered a period of high incidence of colorectal cancer. The year of 2015 is the start of precision medicine. Colorectal cancer "precision medicine" is based on the analysis of the cancer genome sequencing and information analysis, interprets the mechanism of the occurrence, development, invasion, metastasis and recurrence of colorectal cancer, and helps to implement targeted individual treatment. The experts of the world's Colorectal Cancer Subtyping Consortium, integrated the past genetic testing based on the classification of colorectal cancer subtypes, refered to the indices of gene mutation, copy number, methylation, microRNA and proteomics, and coalesce the types of colorectal cancer into four consensus molecular subtypes(CMSs) with distinguishing features. CMSs may be the most powerful classification system of colorectal cancer because of its clear biological interpretation, and is expected to provide a reference basis for the establishment of clinical precision treatment system.
China ; Colorectal Neoplasms ; Humans ; Mutation ; Precision Medicine ; Proteomics ; Recurrence

Objective To summarize the experience in the diagnosis and treatment of symptomatic splanchnic artery dissection. Methods A total of 21 patients with symptomatic splanchnic artery dissection, who were admitted to the Affiliated First Hospital of China Medical University during the period from June 2006 to March 2014, were included in this study. Combined with the literature, the clinical data, including the diagnosis and treatment, were analyzed. Results Contrast-enhanced abdominal CT and CT angiography revealed superior mesenteric artery dissection in 15 cases, celiac artery dissection in 5 cases and splenic artery dissection in one case. Conservative therapy was employed in 5 patients; among them one was complicated with hepatic artery thrombosis. Of the 16 patients who received endovascular stent placement, additional intestinal resection was performed in 2 and transcatheter thrombolysis treatment in other 2. No procedure-related severe complications occurred in perioperative period. All the patients were followed up for 2-74 months (mean of 19.1 months). In patients who received endovascular stent placement, the abdominal pain and the bloody stool were relieved or disappeared, and no abdominal pain recurred. CT angiography showed that in-stent blood flow was fluent, the stent was in good position, and neither stenosis nor thrombosis was observed. One patient with superior mesenteric artery dissection died of stroke three months after the treatment. Conclusion It is very important to make early diagnosis and to adopt early treatment for symptomatic splanchnic artery dissection. CT angiography can confirm the diagnosis in most cases, but attention should be paid to some atypical manifestations. For the treatment of splanchnic artery dissection, endovascular stent placement is mini-invasive, safe and reliable.

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non-protein-coding RNAs (npcRNAs or ncRNAs). Among them, long npcRNAs or ncRNAs (lnpcRNAs or lncRNAs) represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in plants.

Objective To evaluate the technique and result of endovascular treatment for right subclavian artery stenosis or occlusion.Methods Seventeen patients [13 males,4 females ; (56 ± 11)years old] with right subclavian artery stenosis or occlusion were treated with endovascular surgery which included recanalization,balloon angioplasty and stenting via femoral or brachial artery route.Cerebral protection devices were used in 6 cases to avoid cerebral embolism.Results Sixteen of the seventeen patients acquired successful recanalization in 8 cases with subclavian artery stenosis (100％ technical success rate) and in other 8 cases with subclavian artery occlusion (88.9％ technical success rate).Five cases were treated with balloon angioplasty,and 11 cases were treated with balloon angioplasty combined with stenting.Good patency was seen in the 16 cases immediately after the procedure.The cerebral protection devices prevented all the cases from cerebral embolism and were retrieved suceessfully.Sixteen cases were followed up from 1 to 66 months [mean (24 ± 18) months].Restenosis was found in one case 10 months later and was successfully treated with re-PTA.One case with aortoarteritis died of cerebral infarction 18 months later.No symptom recurrence was found in other cases and ultrasound or CTA of followup showed excellent patency.Conclusions Balloon angioplasty and stenting are safe and effective for the treatment of right subclavian artery occlusion.

Histone H3 lysine 4 trimethylation (H3K4me3) is well known to occur in the promoter region of genes for transcription activation.However,when investigating the H3K4me3 profiles in the mouse cerebrum and testis,we discovered that H3K4me3 also has a significant enrichment at the 3' end of actively transcribed (sense) genes,named as 3′-H3K4me3.3′-H3K4me3 is associated with ～15％ of protein-coding genes in both tissues.In addition,we examined the transcriptional initiation signals including RNA polymerase II (RNAPII)binding sites and 5′-CAGE-tag that marks transcriptional start sites.Interestingly,we found that 3′-H3K4me3 is associated with the initiation of antisense transcription.Furthermore,3′-H3K4me3 modification levels correlate positively with the antisense expression levels of the associated sense genes,implying that 3′-H3K4me3 is involved in the activation of antisense transcription.Taken together,our findings suggest that H3K4me3 may be involved in the regulation of antisense transcription that initiates from the 3′ end of sense genes.In addition,a positive correlation was also observed between the expression of antisense and the associated sense genes with 3'-H3K4me3 modification.More importantly,we observed the 3'-H3K4me3 enrichment among genes in human,fruitfly and Arabidopsis,and found that the sequences of 3'-H3K4me3-marked regions are highly conserved and essentially indistinguishable from known promoters in vertebrate.Therefore,we speculate that these 3'-H3K4me3-marked regions may serve as potential promoters for antisense transcription and 3′-H3K4me3 appear to be a universal epigenetic feature in eukaryotes.Our results provide a novel insight into the epigenetic roles of H3K4me3 and the regulatory mechanism of antisense transcription.