Not just a sponge: new functions of circular RNAs discovered

One of the most exciting findings in RNA biology is the discovery of numerous circular RNAs （circRNA） in mammalian genome. Once being considered as low abundance splicing byproducts, circRNAs are surprisingly abundant and can be generated by multiple pathways. The majority of circRNAs are generated from the RNA backsplicing in which an upstream 3＇ splicing site （ss） is joined with a downstream 5＇ ss. Several groups have independently demonstrated that the complementary paring of intronic sequences is sufficient to promote the biogenesis of circRNA via backsplicing. In addition, intronic circRNAs can also be generated through partial degradation of lariat RNAs that are splicing byproduct.

SMAD7 and SERPINE1 as novel dynamic network biomarkers detect and regulate the tipping point of TGF-beta induced EMT

Epithelial–mesenchymal transition(EMT) is a complex nonlinear biological process that plays essential roles in fundamental biological processes such as embryogenesis, wounding healing, tissue regeneration,and cancer metastasis. A hallmark of EMT is the switch-like behavior during state transition, which is characteristic of phase transitions. Hence, detecting the tipping point just before mesenchymal state transition is critical for understanding molecular mechanism of EMT. Through dynamic network biomarkers(DNB) model, a DNB group with 37 genes was identified which can provide the early-warning signals of EMT. Particularly, we found that two DNB genes, i.e., SMAD7 and SERPINE1 promoted EMT by switching their regulatory network which was further validated by biological experiments. Survival analyses revealed that SMAD7 and SERPINE1 as DNB genes further acted as prognostic biomarkers for lung adenocarcinoma.

Subtyping of type A influenza by sequencing the variable regions of HA gene specifically amplified with RT-PCR

The outbreak of a novel influenza A(H1N1) virus across the globe poses a threat to human health.It is of paramount importance to develop a rapid,reliable and inexpensive diagnostic procedure.Based on the bioinformatic information from public database,primers specific for influenza A virus surface protein haemagglutinin(HA) of several subtypes(including H1,H2,H3,H5,H7 and H9) were designed.Primer-specific PCR products were subjected to sequencing for accurately distinguishing H1 and H3 subtypes from others.This sequencing-based detection method will not only be applied to rapid detection and simultaneous subtype identification of new influenza A virus H1N1,but also provide the strategies to monitor other new types ofinfluenza virus with explosive potential.

The mutation network for the hemagglutinin gene from the novel influenza A (H1N1) virus

A mutation network for the hemagglutinin gene(HA) of the novel type A(H1N1) influenza virus was constructed.Sequence homology analysis indicated that one HA sequence type from the viruses mainly isolated from Mexico was likely the original type in this epidemic.Based on the 658A and 1408T mutations in HA,the viruses evolving into this epidemic were divided into three categories,the Mexico,the transitional and the New York type.The three groups of viruses presented distinctive clustering features in their geographic distributions.

Structure modeling and spatial epitope analysis for HA protein of the novel H1N1 influenza virus

In recent months,a novel influenza virus H1N1 broke out around the world.With bioinformatics technology,the 3D structure of HA protein was obtained,and the epitope residues were predicted with the method developed in our group for this novel flu virus.58 amino acids were identified as potential epitope residues,the majority of which clustered at the surface of the globular head of HA protein.Although it is located at the similar position,the epitope of HA protein for the novel H1N1 flu virus has obvious differences in the electrostatic potential compared to that of HA proteins from previous flu viruses.

One Yin-Yang Wu-Xing Model of TCM

Although Yin-Yang Wu-Xing （Yin-Yang and Five-Elements, subsystems of human body） has been the theoretical basis of traditional Chinese medicine （TCM） for more than 5 000 years, it has been primarily analytical or empirical in nature without a formal scientific foundation. Based on bipolar set theory, an equilibrium/non-equilibrium computational model of Yin-Yang Wu-Xing is proposed. The Yin-Yang Wu-Xing dynamical systems are formulated so that equilibrium and non-equilibrium conditions can be established and proved. Computer simulations of equilibrium and non-equilibrium processes show that this new approach can provide diagnostic decision support in TCM. Thus, this equilibrium-based approach provides a unique scientific basis for future research in TCM, Qi （vital energy）, QiGong, Meridians and Collaterals （acupuncture channels） and herbal treatment. On the other hand, it provides a basic Yin-Yang cellular network architecture for modem scientific research in genomics such that regulation mechanisms of the ubiquitous YY1 protein for cell processes can be explained.

How to Diagnose the State of a Dynamic System

When analyzing a system,it is not only the easily quantified parameters (like where an item,e.g.the location of a planet in the planetary system or the weight,the temperature。