Abstract:Themed in synthetic biology, supplemented with multiple inter-disciplines, International Genetically Engineered Machine (iGEM)Competition provides with a most influential and dynamic platform for young minds in the field of biology. Many college and high school teams not only achieved excellent results in this competition, but got academic breakthrough achievements as well in recent years. Hence, we launch this iGEM special editorial column, featured in latest domestic iGEM research projects. Simultaneously, we discuss, in this special issue, about the progress of iGEM in China, and its inspiration on development of research skills and scientific competence of collegiate students.

Abstract:Various genetic switches have been developed to let engineered cells perform designed functions. However, a sustained input is often needed to maintain the on/off state, which is energy-consuming and sensitive to perturbation. Therefore, we developed a set of transcriptional switches for cell states control that were constructed by the inversion effect of site-specific recombinases on terminators. Such a switch could respond to a pulse signal and maintain the new state by itself until the next input. With a bottom-up design principle, we first characterized the terminators and recombinases. Then the mutual interference was studied to select compatible pairs, which were used to achieve one-time and two-time state transitions. Finally, we constructed a biological seven-segment display as a demonstration to prove such switch’s immense potential for application.

Abstract:Transcriptional regulation is crucial for regulated gene expression. Due to the complexity, it has been difficult to engineer eukaryotic transcription factor (TF) and promoter pairs. The few availabilities of eukaryotic TF and promotor pairs limit their practical use for clinical or industrial applications. Here, we report a de novo construction of synthetic inhibitory transcription factor and promoter pairs for mammalian transcriptional regulation. The design of synthetic TF was based on the fusion of DNA binding domain and Kruppel associated box transcription regulating domain (KRAB). The synthetic promoter was constructed by inserting the corresponding TF response element after SV40 promoter. We constructed and tested five synthetic inhibitory transcription factor and promoter pairs in cultured mammalian cells. The inhibition capability and orthogonality were verified by flow cytometry. In summary, we demonstrate the feasibility of constructing mammalian inhibitory TF and promoter pairs, which could be standardized for advanced gene-circuit design and various applications in the mammalian synthetic biology.

Abstract:The exogenous gene expression and its impacts on the bacterial population are important to study quorum sensing systems and synthetic biology industry. However, the behavior of exogenous protein expressing bacteria remains poorly understood. To find out which factors are playing a critical role in the growth of population and exogenous gene expression, we measured Lux-type receptor-regulated exogenous gene expression under the induction of N-acyl homoserine lactone (N-AHL) signaling molecules and impacts on the bacterial population dynamics after such stimulation. To analyze the cause of fitness burden of bacteria, we set up a hypothetical mathematical model. Previous studies often arrogate this phenomenon to the synthesis cost and the toxicity of N-AHL signaling molecule. However, we suggested another possible cause of the fitness burden.

Abstract:Genetically engineered intestinal microbes could be powerful tools to detect and treat intestine inflammation due to their non-invasive character, low costs, and convenience. Intestinal inflammation is usually detected along with an increasing concentration of thiosulfate and tetrathionate molecules in the intestines. ThsSR and TtrSR are two-component biosensors to detect the presence of thiosulfate and tetrathionate molecules, respectively. In real-life intestinal inflammation detection, sophisticated instruments are needed if using fluorescent proteins as reporters. However, chromoproteins and other colored small molecules, which can be seen by the unaided eye, could extend the use of ThsSR and TtrSR biosensors to detect intestine inflammation. The feasibility of ThsSR and TtrSR systems was tested by monitoring the fluorescence intensity of sfGFP in response to the concentration of thiosulfate and tetrathionate, followed by the incorporation of the two systems into Escherichia coli Top10 and E. coli Nissle 1917. The potential for the real-life application of the two systems was further corroborated by substituting sfGFP with a series of chromoproteins and a protoviolaceinic acid synthesis cassette as reporter genes. The results indicated that signal expression of the new systems had a positive correlation with the concentration of tetrathionate and thiosulfate molecules. Thus, the modified ThsSR and TtrSR system may potentially be applied in the human body for the detection of intestinal inflammation.

Abstract:Synthetic biology is a fast moving interdisciplinary branch of biology and engineering. To educate the next generation of synthetic biology scientists, the International Genetically Engineered Machine (iGEM) competition was established. In the past eleven years, many Chinese teams have participated in this event, but no thorough review and analysis have been carried out. In this paper, we collected the data and information of the Chinese teams from the iGEM website and analyzed the number, distribution and performance of Chinese teams in iGEM competition. We also described contributions made by the Conference of China iGEMer Community (CCiC) organization. The contributions to China higher education made by the iGEM competition were also summarized. Finally, we proposed several suggestions for the development of the iGEM competition in China. We envision the iGEM competition will continue to promote the innovative education and cultivation of the next-generation synthetic biology scientists in China.

Abstract:In recent years, the International Genetically Engineered Machine (iGEM) competition has experienced rapid global development. In 2017 alone, the number of iGEM teams registered around the globe reached an unprecedented 313, with 98 iGEM teams from China having enrolled in the competition and obtained outstanding results. In contrast to the many college students’ innovation projects and scientific research training programs in China, iGEM’s organization mode is focused on student-centered research learning. Moreover, it achieved a rich educational effect, embodying a new educational idea, which gives it great significance for the extracurricular scientific research training of undergraduates in Chinese universities. In this article, we took Peking University’s participation in the iGEM competition as a starting point. The first part introduces the background and general situation of the iGEM competition. The second part reproduces the general procedure of one iGEM season and organization of Peking University’s team. The third part compares iGEM’s organization mode with those of other undergraduate research training courses and discusses them in detail. The fourth part sums up the experience with iGEM activities as well as explains its effect on developing the research capacity of undergraduate students as well as inspiring them to organize an undergraduate scientific research competition. This article aims to provide a reference for the organization of iGEM activities in domestic universities and for the reform of undergraduate education.

Abstract:African swine fever (ASF) is a hemorrhagic and devastating infectious disease of pigs caused by African swine fever virus (ASFV), with mortality up to 100%. The first ASF outbreak occurred in China in August 2018, followed by 69 cases of ASF in 18 provinces in more than three months, causing a heavy burden to the pig industry. Based on the global epidemic situation of ASF and the experience of prevention and control in other countries, the ASF control and eradication situation in China is extremely complex and serious. The availability of effective and safe ASF vaccines is an urgent requirement to reinforce control and eradication strategies. Therefore, this article starts with the latest findings of ASFV, summarizes the progress in prevention and control strategies and vaccine approaches for ASFV. We also discuss the challenges of preventing and controlling ASF, focusing on current vaccine strategies, the gaps, future research directions, and key scientific issues in commercial applications. We hope to provide basic information for the development of vaccines and prevention control strategies against this disease in China.

Abstract:The Bcr-Abl oncogene is produced by the reciprocal translocation between c-Abl gene on chromosome 9 and the Bcr gene on chromosome 22 in human genome. The encoded Bcr-Abl fusion protein is responsible for the pathogenesis of certain human leukemias. Abelson murine leukemia virus (A-MuLV) is a retrovirus that could lead to transformation of B lymphocyte in mice, and v-Abl is the oncogene of A-MuLV. Abl oncoproteins (such as Bcr-Abl and v-Abl) play critical roles in tumorigenesis of certain cell types. Several signal transduction pathways, including JAK/STAT/Pim, PI3K/AKT/mTOR and RAS/RAF/MEK signaling pathway, are involved in Abl-mediated tumorigenesis. In addition, Abl-mediated tumorigenesis is associated with mutation or abnormal modification of key signal molecules as well as dysregulation of some critical long noncoding RNAs (lncRNAs). Here, we review the molecular mechanisms by which Abl oncogenes activate three major signaling pathways, and provide a scientific basis for therapy of Abl oncoprotein-induced tumors.

Abstract:Heparinases can produce biologically active oligosaccharides by specifically cleaving the α-(1,4) glycosidic linkages of heparin and heparan sulphate. Heparinases are divided into heparinase and heparanase. Because heparinase is an effective biocatalyst, more and more researchers pay attention to the application of heparinase in medical field in the recent years. Combined with the related research work in our group, the application value of heparinase in the medical field was summarized, such as the determination of the structure of heparin, the preparation of low-molecular-weight heparin and ultra-low-molecular-weight heparin, tumor therapy and as a heparin antagonist. In addition, we summarized the definition, source of heparinase and its application in the medicine field. Heparinases have a great application prospect in the field of medicine.

Abstract:Animal infectious diseases pose a serious and continuing threat to the animal health and cause huge economic losses throughout the world. Vaccination is one of the most effective solutions to prevent and control animal infectious diseases. With the development of biotechnologies and the need for disease prevention and control, the focus of vaccine research has been shifted to the development of safe, efficient, broad-spectrum, low-dose and marker vaccines. Novel vaccines capable of inducing high levels of both humoral and cellular immune responses are promising to provide more efficient protection against animal infectious diseases. This minireview summarizes the development, applications, advantages and disadvantages of new-concept animal vaccines emerging in recent years, including mucosal vaccines, long-acting and fast-acting vaccines, chimeric vaccines, nanoparticle vaccines, and so on. Furthermore, we discuss future directions of the vaccines, in order to provide new insights for animal vaccine development.

Abstract:Conventional IgG is composed of heavy and light chains. The light chain has one variable region (VL) and one constant region (CL) domain, whereas the heavy chain has one variable region (VH) and three constant region domains (CH1, CH2 and CH3). Single domain antibody (sdAb) is a kind of antibody that is composed of a variable domain of heavy chain and devoid of the light chain completely. Due to its small size, it is also called as nanobody. Although the sdAb has a simple structure, it can exhibit a comparable even better antigen-binding affinity than conventional antibody. Compared with conventional antibody, the small size, high stability and simplicity in recombinant expression are representative advantages of sdAb. In recent years, scientists are becoming increasingly interested in the roles of sdAb in fundamental biomedical research and clinical application. In this review, we summarized the structural features, physicochemical properties, screening strategies and recent advances in application of sdAb.

Abstract:Several putative transcription factor binding sites (TFBSs) exist in the PCV2 rep gene promoter. To explore if porcine circovirus type 2 (PCV2) could regulate the viral replication by using these TFBSs, we conducted electrophoretic mobility shift assay (EMSA), DNA-pull down and liquid?chromatography-tandem?mass?spectrometric (LC-MS/MS) assays. EMSA confirmed the binding activity of the rep gene promoter with nuclear proteins of host cells. DNA-pull down and LC-MS/MS identified the porcine transcription factor AP-2δ (poTFAP2δ) could bind the PCV2 rep gene promoter. Dual-luciferase reporter assay, quantitative real-time PCR, Western blotting and indirect immunofluorescent assay demonstrated that poTFAP2δ could not only promote the activity of the rep gene promoter, but also enhance the transcription/translation activity of the rep/cap gene and the virus titer of PCV2 during the entire life cycle of PCV2 infection. This study revealed the molecular mechanism of PCV2 using host proteins to enhance the viral replication, provided a new perspective for studying the pathogenic mechanism of PCV2 from virus and host interactions, and provided a theoretical basis for developing highly effective PCV2 vaccines.

Abstract:Efficient utilization of cellulose and xylan is of importance in the bioethanol industry. In this study, a novel bifunctional xylanase/cellulase gene, Tcxyn10a, was cloned from Thermoascus crustaceus JCM12803, and the gene product was successfully overexpressed in Pichia pastoris GS115. The recombinant protein was then purified and characterized. The pH and temperature optima of TcXyn10A were determined to be 5.0 and 65?70 °C, respectively. The enzyme retained stable under acid to alkaline conditions (pH 3.0?11.0) or after 1-h treatment at 60 °C. The specific activities of TcXyn10A towards beechwood xylan, wheat arabinoxylan, sodium carboxymethyl cellulose and lichenan were (1 480±26) U/mg, (2 055±28) U/mg, (7.4±0.2) U/mg and (10.9±0.4) U/mg, respectively. Homologous modeling and molecular docking analyses indicated that the bifunctional TcXyn10A has a single catalytic domain, in which the substrate xylan and cellulose shared the same binding cleft. This study provides a valuable material for the study of structure and function relationship of bifunctional enzymes.

Abstract:To investigate the effect of INF-γ on the expression of programmed death ligand 1 (PD-L1), epithelial-mesenchymal transition (EMT) and the potential mechanism in breast cancer cell line MDA-MB-231, the cells were treated with different concentrations of INF-γ. The expressions of proteins, including PD-L1, cell-migration-related proteins (E-cadherin, N-cadherin and vimentin), ERK, p-ERK, Jak2, and p-Jak2 were detected by Western blotting analysis and immunofluorescent staining assay. Cell migration was studied through cell wound healing assay and transwell assay. IFN-γ could up-regulate the expressions of PD-L1 in MDA-MB-231 cells. The cell migration rate was significantly increased after adding IFN-γ. The expression levels of vimentin and N-cadherin were increased whereas the expression of E-cadherin was decreased after adding IFN-γ. The expression levels of ERK, p-ERK, Jak2 and p-Jak2 were significantly increased and this phenomenon was inhibited when adding ERK inhibitor U0126 or Jak2 inhibitor AG490. These results demonstrate that IFN-γ could up-regulate the expression of PD-L1, promote cell migration and transmission, and facilitate epithelial-mesenchymal transformation of breast cancer cells and this process may be related with ERK and Jak2-STAT signaling pathways.

Abstract:To screen the specific anti-human intercellular adhesion molecule-1 (ICAM-1) single chain fragment variable (scFv) using phage display library technology and to identify its biological activity. P1 peptide was used as antigen, and the phage antibodies against human ICAM-1 antigen were panned by four binding-eluting-amplifying cycles using Tomlinson I+J phage display library. After four rounds of selective enrichment screening, the positive clones were determined by PCR, enzyme linked immunosorbent assay (ELISA)-based antigenic cross reaction and Dot blotting. Then the binding specificity and biological activity of purified scFv were identified by Western blotting, competitive ELISA and cell adhesion inhibition assay respectively. Furthermore, four positive clones were first panned through P1 peptide coated-ELISA assay, and then J-A1 was obtained and identified by PCR, ELISA-based antigenic cross reaction and Dot blotting, which could show a specific binding between P1 peptide and human ICAM-1 protein antigen. Subsequently, the purified scFv showed a satisfactory specificity and anti-adhesive activity in competitive ELISA and the cell adhesion inhibition assay. The specific anti-human ICAM-1 scFv was prepared successfully from Tomlinson I+J phage display library, which pave the way for further application of anti-human ICAM-1 scFv for inflammation diseases therapeutics.

Abstract:Ebola virus (EBOV) is an extremely contagious pathogen first discovered in Africa associated with severe hemorrhagic disease in humans and nonhuman primates, which has resulted in at least 28 500 suspected cases and 11 300 confirmed deaths in 2014–2016 Ebola epidemic in West Africa. Rapid and sensitive detection of EBOV is the key to increasing the probability of survival and reducing infection rates in pandemic regions. Here, we report an ultrasensitive and instrument-free EBOV detection assay based on colloidal carbon immunochromatography. Carbon nanoparticle-labeled rabbit anti-EBOV-VP40 IgG were concentrated in the conjugate pad, monoclonal antibody (McAb, 4B7F9) against EBOV-VP40 and goat anti-rabbit IgG were immobilized on the nitrocellulose membrane with 2 μL/cm at a concentration of 1 mg/mL as test and control lines, respectively. Then the sample application pad, conjugate release pad, nitrocellulose membrane and absorbent pad were assembled into a lateral flow test strip. The test strip shows strong specificity against related viruses that share similar clinical symptoms and geographic range with EBOV, including marburg virus, influenza virus, yellow fever virus and dengue virus. In addition, 1 500 negative serums were tested with false-positive rate of 1.3‰ which significantly lower than that of ReEBOV? colloidal gold test kit recommended by World Health Organization (WHO). The sensitivity of this strip was analyzed using inactivated EBOV with detection limit of 100 ng/mL (106 copies/mL) which clearly higher than that of ReEBOV? dipstick (108 copies/mL). Furthermore, the strip showed excellent thermal stability characteristics in room temperature and could be as a point-of-care (POC), ultra-sensitive and specific promising candidate for EBOV serological screening in rural Africa or entry/exit ports.