Objective To build a literature database that systematically sorts out and integrates related knowledge of Yersinia pestis researches, which will improve the efficiency of future researches on Y.pestis.Methods EndNote X5 software was used as a literature collection tool in this research.Computer languages, including Perl and PHP, were employed to standardize the text data, establish the entity relationship model, code the webpage and build the basic literature database.The tool combination of Apache+PHP+MySQL that is usually used in development of small or medium-scale websites was selected to build a dynamic website.Results and Conclusion The Y.pestis literature database(YPKD) was constructed (accessed by http://101.201.51.148/ypkd/.), from which users can quickly search or browse the required literature, download the required full text, and obtain the latest online information on Y.pestis.The database can serve as a model for establishing literature databases of other crucial pathogens.

Anatomic structure in craniofacial region is very complicated and orthognathic surgery is difficultly performed.Therefore,it is necessary to generate virtual surgical model from CT scan data before operation on personal computer in order to make surgery more accurate.This technique has been increasingly interested in the field of orthognathic surgery both at home and abroad.The sample was scanned with thin-layer CT.CT image data (336 layer,1.0 mm slice thickness) were analyzed with the Mimics software.Simultaneously,three-dimensional model and virtual surgery of the facial cranium were established.The digitized virtual surgical platform of facial cranium was preliminarily created,and three common surgical methods in maxillofacial surgery,i.e.,LeFort Ⅰ osteotomy,mandibular angle osteotomy,and genioplasty,for maxillofacial surgery were simulated.The results showed that the digitized virtual surgical platform of facial cranium could be generated with the Mimics software on personal computer,which provides convenient and quick methods for research,teaching,and clinical surgery.More importantly,it creates theoretical basis for virtual surgical platform which can be widely used on personal computer.

Objective:To investigate the changes in adaptive phenotypes of Yersinia pestis ( Yp) during successive passages in macrophages. Methods:A Yp strain of 201-MI was induced by 50 successive passages of Yp 201 strain in Raw264.7 cells. Phenotypic characteristics of 201 and 201-MI strains were compared by analyzing their survival rates in macrophages, growth curves, biofilm formation abilities, acid and hydrogen peroxide-stress tolerance, and virulence to mammal cells (Raw264.7 and HeLa cells) and mice. Results:Comparing with 201 strain, 201-MI strain showed various phenotypic changes, including higher survival rate in Raw264.7 cells, faster growth in iron-deficient medium, higher tolerance to acid and hydrogen peroxide, decreased biofilm formation ability, and less damages to Raw264.7 and HeLa cells. More-over, 201-MI strain showed decreased virulence to mice in both subcutaneous and intraperitoneal challenges. Preliminary comparative genomics analysis revealed some indel and nonsense mutations in 201-MI strain, which might account for its phenotype changes.Conclusions:After successive passages in macrophages, Yp showed some phenotypic changes, which might reflect its adaptive evolution under the pressure of macrophages. Detailed multi-omics analysis would be of great help to understand the underlying genetic mechanisms of these changes, and the related Yp-macrophage interaction processes as well.

Population genomics, an interdiscipline of genomics and population genetics, is booming in recent years with the rapid growth number of deciphered genomes and revolutionizes the understanding of bacterial population diversity and evolution dynamics. It also largely improves the prevention and control of infectious disease through providing more accurate genotyping and source-tracing results and more comprehensive characteristics of emerging pathogens. In this review, taking one of the best characterized bacteria, Escherichia coli, as model, we reviewed the phylogenetic relationship across its five major populations (designated A, B1, B2, D and E); and summarized researches on molecular mutation rate, selection signals, and patterns of adaptive evolution. We also described the application of population genomics in responding against large-scale outbreaks of E. coli O157:H7 and E. coli O104:H4. These results indicated that, although being a novel discipline, population genomics has played an important role in deciphering bacterial population structures, exploring evolutionary patterns and combating emerging infectious diseases.

Population genomics, an interdiscipline of genomics and population genetics, is booming in recent years with the rapid growth number of deciphered genomes and revolutionizes the understanding of bacterial population diversity and evolution dynamics. It also largely improves the prevention and control of infectious disease through providing more accurate genotyping and source-tracing results and more comprehensive characteristics of emerging pathogens. In this review, taking one of the best characterized bacteria, Escherichia coli, as model, we reviewed the phylogenetic relationship across its five major populations (designated A, B1, B2, D and E); and summarized researches on molecular mutation rate, selection signals, and patterns of adaptive evolution. We also described the application of population genomics in responding against large-scale outbreaks of E. coli O157:H7 and E. coli O104:H4. These results indicated that, although being a novel discipline, population genomics has played an important role in deciphering bacterial population structures, exploring evolutionary patterns and combating emerging infectious diseases.

As the demand for high-performance computing continues to grow, traditional computing models are facing unprecedented challenges. Among the many emerging computing technologies, DNA computing has attracted much attention due to its low energy consumption and parallelism. The DNA circuit, which is the basis for DNA computing, is an important technology for the regulation and processing of the molecular information. This review highlights the basic principles of DNA computing, summarizes the latest research progress, and concludes with a discussion of the challenges of DNA computing. Such integrated molecular computing systems are expected to be widely used in the fields of aerospace, information security and defense system.
DNA/genetics*

Objective This study aimed to investigate the effects of P.odoratum extract on lactase activity and microflora diversity in mice with bacterial dysbacteriosis.Methods SPF male BALB/c mice were randomized into 4 groups:control,model,P.odoratum extract low dose(1.56 g·kg-1·d-1)and high dose(3.12 g·kg-1·d-1)treatment group.There were 8 mice in each group(5 in the blank group).In addition to the control group,after 7 days of intragastric administration of mixed antibiotics,the administration groups were given P.odoratum extract for 7 days,and the control group and the model group were given the same amount of sterile water.The changes of diarrhea,body weight and food intake of mice were recorded.The colon HE staining sections,ZO-1 protein,IL-6 expression,and serum LPS concentration were detected.Feces were collected for lactase activity and microbial diversity determination with 16S rRNA high-throughput sequencing technology.Results After 7 days of antibiotic intervention,compared with the control group,the mice in the model group had soft stool,weight loss,reduced food intake,and significantly reduced intestinal flora diversity.At the 14th day,in the model group,ulceration accompanied by slight interstitial congestion and edema was seen in the colon,ZO-1 expression was significantly reduced,IL-6 expression was significantly increased,serum LPS was significantly increased,lactase activity was significantly reduced,and intestinal flora diversity was still lower compared with the control group.After 7 days of administration,compared with the model group,P.odoratum reduced the diarrhea rate of mice,promoted a recovery of body weight and food intake,downregulated pathological colon tissue damage,significantly increased ZO-1 protein expression,and reduced colon factor IL-6 and serum LPS concentration.In addition,P.odoratum can significantly up-regulate lactase activity and improve the community richness and diversity of dysbacteriosis mice.It is shown that three phyla(up-regulated Firmicutes,down-regulated Proteobacteria and Bacteroidetes)and seven genera(up-regulated Rikenellaceae_RC9_gut_group,Rikenella,Colidextribacter,norank_f__Lachnospiraceae,norank_f__Oscillospiraceae,and Lachnospiraceae_NK4A136_group,down-regulated Alloprevotella),the abundance of which was significantly correlated with body weight and lactase activity,serum LPS,and colon factor IL-6.Conclusion P.odoratum can alleviate the gut barrier injury and dysfunction caused by antibiotic induced dysbiosis,and its mechanism may be achieved by regulating microflora structure.

BACKGROUNDOncofetal protein high-mobility-group AT-hook protein 2 (HMGA2) is reactivated in serous ovarian cancer (SOC) and its overexpression correlates with poor prognosis. To explore the mechanism, we investigated whether HMGA2 could avoid microRNA regulation due to gene truncation or 3' UTR shortening by alternative polyadenylation.

METHODSReal-time reverse transcription polymerase chain reaction (RT-PCR) was used to evaluate the abundance of different regions of HMGA2 mRNA in 46 SOC samples. Rapid amplification of cDNA 3' ends (3' RACE) and Southern blotting were used to confirm the shortening of 3' untranslated region (UTR). 5' RACE and Southern blotting were used to prove the mRNA decay.

RESULTSNo significant difference in the ratio of the stable coding region to the fragile region was observed between SOC and control normal fallopian tubes, indicating that the HMGA2 gene is not truncated in SOC. Varying degrees of 3' UTR shortening in SOC samples were observed by comparing the abundance of the proximal region and distal region of the HMGA2 3' UTR. The ratio of the proximal to the distal region of the 3' UTR correlated significantly with expression of the HMGA2 coding region in SOC (r = 0.579, P < 0.01). Moreover, although the abundance of the HMGA2 coding region varied, all samples, including the very low expressed samples, exhibit relatively high levels of the proximal 3' UTR region, suggesting a dynamic decay of HMGA2 mRNA from the 5' end. The shortening of 3' UTR and the decay from the 5' end were confirmed by 3' RACE, 5' RACE and subsequent Southern blotting.

CONCLUSIONHeterogeneous 3' UTR lengths render HMGA2 susceptible to different levels of negative regulation by microRNAs, which represents an important mechanism of HMGA2 reactivation in SOC.

3' Untranslated Regions ; genetics ; Cystadenocarcinoma, Serous ; genetics ; metabolism ; Female ; HMGA2 Protein ; genetics ; metabolism ; Humans ; Ovarian Neoplasms ; genetics ; metabolism ; Reverse Transcriptase Polymerase Chain Reaction