2021, 10(5):1-11. DOI: doi: 10.12146/j.issn.2095-3135.20210304001
Abstract:TLR4 is an important pattern recognition receptor that plays important roles in innate immunity against infections. CD317 is a type Ⅱ transmembrane glycoprotein with unique structure that endows it viral tethering and signaling potential. However, it is not clear yet whether CD317 regulates TLR4-mediated signal transduction. Herein, we investigated the role of CD317 on TLR4 signal transduction by using primary peritoneal macrophages derived from CD317 knockout mice and THP-1-derived human macrophages, and found that the expression of CD317 could be induced by TLR4 agonist (Lipopolysaccharide), which, in a feedback loop, further enhanced the TLR4-mediated NF-κB activation and subsequent release of pro inflammatory cytokines (TNF-α, IL-1β and IL-6, etc.). CD317 knockdown or knockout markedly impaired the TLR4 signal transduction and cytokine production. By using co-immunoprecipitation, we found that CD317 could interact with both MyD88 and TRAF6, suggesting that CD317 probably enhanced the TLR- 4-mediated NF-κB activation through MyD88-TRAF6 signal transduction pathway. Conclusively, our study not only extends the understanding on the role of CD317 in innate immune regulation, but also provides new targets and theoretical guidance for the development of effective strategies for related diseases.
2021, 10(5):12-22. DOI: doi: 10.12146/j.issn.2095-3135.20210324001
Abstract:Vestibular nuclei (VN) is a sensorimotor structure controlling posture and balance. The anatomy and function of VN is closely related to diseases, such as motion sickness, vestibular migraine, vertigo, postural deficits, and Parkinson’s disease. It has been known that stress imposes effects on the function of VN and the progress of these diseases. Since the locus coeruleus-norepinephrine (LC-NE) system is activated by stress, it would be interesting to know whether there is a connection between LC and VN and its possible function. The experiment results showed that LC neurons project to the VN and they are tyrosine hydroxylase (TH)-positive. After subjected to sleep deprivation stress treatment, the mice showed higher cFos activation in the LC-NE neurons compared with the untreated control group, suggesting the important role LC-NE may play in stress-related VN malfunction. This study provides anatomical basis for further neural circuity studies of LC-VN in balance and then its possible involvement in diseases.
2021, 10(5):23-33. DOI: doi: 10.12146/j.issn.2095-3135.20210308001
Abstract:High-level action information, such as spatial feature of frames, temporal feature among frames, or human level skeleton features are usually used in existing video action recognition methods. However, these high-level features cannot effectively describe the action composition of human behavior, and thus reduce the ability of deep learning models to recognize confusing behaviors. In this work, video action recognition method based on human body parts is investigated. By learning the action representation of the fine-grained parts of the human body, the video representation of human action was learned from bottom to up level. Specifically, the method mainly includes three modules: (1) body part feature enhancement module, which enhances the image-based human body part feature, (2) body part feature fusion module, which fuses the features of various parts of the human body to form human feature, and (3) body feature enhancement module, which is responsible for enhancing the human body features of all people in the video. The popular datasets of UCF101 and HMDB51 were used for experiments. And the results showed that, the video action recognition method based on human body parts is complementary with current methods, and can effectively improve the accuracy of human action recognition.
2021, 10(5):34-42. DOI: doi: 10.12146/j.issn.2095-3135.20210315001
Abstract:Convolutional neural network is widely used in the field of object detection. In this paper, a novel anchor-free two-stage object detection algorithm is investigated. Region proposals are produced via corner points extracted based on CornerNet. In order to improve the inception ability to the internal information of the object, central pooling is introduced in the algorithm to enhance the features of interal regions for internal feature point detection. A large number of false-positive proposals can be filtered out by checking whether the internal key points exist in the internal area. The remaining proposals are fed into a multivariate classifier to obtain the final result. The proposed algorithm has been tested on the data set of
2021, 10(5):43-56. DOI: doi: 10.12146/j.issn.2095-3135.20210510001
Abstract:Living systems are extremely sophisticated and difficult to accurately describe and predict, posing challenges in designing synthetic biological systems. Therefore, massively parallel trial-and-error processes are often required to optimize synthetic biological systems. In recent years, intelligent technology has experienced rapid development and has demonstrated continual learning capacity from massive data and intelligent exploring ability in unknown space, which perfectly meets the needs of the current trial-and error platform of synthetic biology engineering and shows great potential in mining complex biological patterns and in designing biosystems. This article reviews the progresses of applying artificial intelligence (AI) in the fields of synthetic biological parts engineering, circuit engineering, metabolic engineering, and genome engineering. This article also analyzes a series of challenges in data standardization, platform intellectualization, experimental automation, and accurate prediction of cross-over studies between AI and synthetic biology. By solving these challenges, the entire workflow of “design-build-test-learn” in synthetic biology is expected to be revolutionized by AI, and creating an “AI synthetic biologist” would in turn lead to the technological advances in AI.
2021, 10(5):57-66. DOI: doi: 10.12146/j.issn.2095-3135.20210427013
Abstract:Population of cells, growing under constant conditions, is a mixture of cells at different stages of the cell cycle. To study specific stage of the cell cycle, synchronization methods are required to make cells grow synchronously. Physical or chemical methods can be used to isolate subpopulation of cells at distinct cell cycle stages or to block cells at certain stage. Via synchronization methods, cell population can grow and divide synchronously during the subsequent culture and maintain 2-3 cycles. As a direct and powerful method, cell cycle synchronization attracts great interests of scientists in the field of bacterial cell cycle researches. Although there are many kinds of synchronization methods, different methods have their own advantages and disadvantages in terms of the degree of synchronization, yield, ease of operation steps, and the degree of interference to the cell cycle. This paper aims to introduce the cell cycle synchronization methods used in the bacterial cell cycle studies and what advantages or disadvantages they have.
2021, 10(5):67-71. DOI: doi: 10.12146/j.issn.2095-3135.20210427006
Abstract:Electroporation technology can penetrate the cell membrane by reversibly applying a certain electric field, forming holes or pathways in the cell membrane, so that the genetic material can be transferred into the cell. Traditional electroporation devices often require several hundred to several thousand volts and are very dangerous to operate. In this study, an electrically insulated polyvinyl chloride (PVC) film was used to make a small distance electroporation device with the electrodes’ distance of 80 μm, which can undertake high flux operation. The experiments show that the proposed small distance electroporation device facilitates cell electroporation with the voltage one order of magnitude lower than the 1 mm standard shock cup, greatly enhance the safety of the experimental operation, high flux also greatly improves the efficiency of experimental operation. But the electroporation efficiency is one order of magnitude lower, and experimental parameters need to be further optimized.
2021, 10(5):72-79. DOI: doi: 10.12146/j.issn.2095-3135.20210427005
Abstract:To find possible reactions that exist in metabolic networks is essential for metabolic engineering. The K-shortest path (KSP) algorithm is a traditional method that is usually used to identify alternative metabolic pathways. To improve the computation efficiency of conventional KSP method, an efficient KSP-based searching method is proposed in this paper. The basic idea is to introduce the critical edge to reduce the redundant calculation. A web-platform is constructed to design metabolic pathways. The parallel computing technique is introduced to improve the computing efficiency. The proposed method is validated on the KEGG metabolic pathways map, and the results show that the proposed method improve the computation efficiency by 5-9 times, compared with the traditional KSP algorithm.
2021, 10(5):80-95. DOI: doi: 10.12146/j.issn.2095-3135.20210427002
Abstract:Comparing with genome sequencing, which facilitates the digitization of life, synthetic biology has enabled human beings to explore the nature of life and promote the cross-disciplinary applications in medicine, chemical industry, agriculture and IT technologies. Since DNA synthesis serves as the fundamental technology of synthetic biology. This paper makes a systematic review of DNA synthesis technology and its instrumental development. In addition, the current technical bottlenecks and potential approaches for breaking through are also discussed.
2021, 10(5):96-103. DOI: doi: 10.12146/j.issn.2095-3135.20210427015
Abstract:The β-carotene ketolase gene (bkt) and β-carotene hydroxylase gene (crtR-B) from Haematococcus pluvialis were codon-optimized and transferred to Synechocystis sp. PCC 6803 genome by natural transformation method. High performance liquid chromatography analysis showed that cells transfected with bkt gene produced canthaxanthin, while echinone decreased; the cells with crtR-B gene produced adonixanthin, while zeaxanthin was reduced. The results showed that the exogenous β-carotene ketolase converted echinone to canthaxanthin and the exogenous β-carotene hydroxylase converted zeaxanthin into adonixanthin. In this paper, the pathway of astaxanthin biosynthesis in Synechocystis sp. PCC 6803 was constructed by metabolic engineering strategy, which laid a foundation for astaxanthin production in Synechocystis sp. PCC 6803 with metabolic engineering.
2021, 10(5):104-116. DOI: doi: 10.12146/j.issn.2095-3135.20210511001
Abstract:As a multidisciplinary approach, synthetic biology has been developing for almost two decades. It involves almost all fields of biological research, combines the modules of engineering and abstract concepts, introduces new quantitative research methods, and improves people’s understanding of life system. Unlike traditional basic science or single technology, the complexity of synthetic biology significantly increases people’s capacity to apply biology and distribute it among different applications. At present, synthetic biology has made remarkable achievements in the development of enable technology, the establishment of synthetic biology platform, and the application in medical treatment, agriculture and food, and bio-based goods, promoting the development of the blue ocean market. Based on the concept of synthetic biology, numerous companies have emerged in many industrial areas recently. Some startups have thrived, and dominant companies have commercialized the technology through cost advantages. Based on this, the paper briefly introduces and analyzes the development of the synthetic biology industry, combining enterprise type, technology platform and financing conditions to provide reference for the development of technology, industry and investment in synthetic biology.
2021, 10(5):117-127. DOI: doi: 10.12146/j.issn.2095-3135.20210427009
Abstract:Synthetic biology is experiencing rapid growth and commercialization in the second decade of the 21st century, after an earlier groundbreaking technological innovation and initial exploration of commercialization. This paper combs and analyzes the current situation of global synthetic biology industry from three aspects: market scale, industry financing and industry development. The analysis shows, in terms of market scale, the synthetic biology market is growing rapidly, but there is an obvious gap in its scale in different geographical regions and industrial fields; in terms of industry financing, the investment and financing trend of synthetic biology industry shows an obvious upward trend. In 2020, the number and amount of investment and financing events in synthetic biology industry reached a historical record, but the development between different geographical regions is still unbalanced; in terms of industry development, the landing application scenarios of synthetic biology are very diverse, have taken root in all walks of life, and show great application potential.