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Pichia as yeast cell factory for production of industrially important bio-products:Current trends,challenges,and future prospects

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生物质资源与工程(英文) 2023年第2期8卷 108-124页

作者： Akansha Shrivastava Mamta Pal Rakesh Kumar Sharma Department of Biosciences Manipal University JaipurJaipur 303007India Sardar Swaran Singh National Institute of Bio-Energy Jalandhar 144601India

Yeast has been used as a cell factory for thousands of years to produce a wide variety of com-plex biofuels,bioproducts,biochemicals,food ingredients,and pharmaceuticals.For a variety of biotechnological production hosts,a few specific genera of yeast have proven themselves.Rapid developments in metabolic engineering and synthetic biology provide a workable long-term supply solution for these substances.In this review,we have covered recent advances in the design of yeast cell factories for the synthesis of terpenoids,alkaloids,phenylpropanoids,and other natural chemicals,primarily focusing on Pichia species.Cutting-edge solutions involving genetic and process engineering have also been discussed.Overall,the review summarized recent advancements and challenges in synthetic and systems biology,as well as initiatives in metabolic engineering aimed at commercializing non-conventional yeasts like Pichia.The processes used in non-traditional yeasts to produce enzymes,therapeutic proteins,lipids,and metabolic products for industrial applications were thoroughly elaborated.

关键词： Natural product Pichia Non-conventional yeast Biosynthesis system biology Synthetic biology

A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis

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Synthetic and systems Biotechnology 2023年第1期8卷 97-106页

作者： Yiming Huang Nishant Sinha Anil Wipat Jaume Bacardit Interdisciplinary Computing and Complex Biosystems(ICOS)Group School of ComputingNewcastle UniversityUK Department of Neurology Perelman School of MedicineUniversity of PennsylvaniaUSA

One challenge in the engineering of biological systems is to be able to recognise the cellular stress states of bacterial hosts,as these stress states can lead to suboptimal growth and lower yields of target products.To enable the design of genetic circuits for reporting or mitigating the stress states,it is important to identify a relatively reduced set of gene biomarkers that can reliably indicate relevant cellular growth states in bacteria.Recent advances in high-throughput omics technologies have enhanced the identification of molecular biomarkers specific states in bacteria,motivating computational methods that can identify robust biomarkers for experimental characterisation and verification.Focused on identifying gene expression biomarkers to sense various stress states in Bacillus subtilis,this study aimed to design a knowledge integration strategy for the selection of a robust biomarker panel that generalises on external datasets and experiments.We developed a recommendation system that ranks the candidate biomarker panels based on complementary information from machine learning model,gene regulatory network and co-expression network.We identified a recommended biomarker panel showing high stress sensing power for a variety of conditions both in the dataset used for biomarker identification(mean f1-score achieved at 0.99),as well as in a range of independent datasets(mean f1-score achieved at 0.98).We discovered a significant correlation between stress sensing power and evaluation metrics such as the number of associated regulators in a B.subtilis gene regulatory network(GRN)and the number of associated modules in a B.subtilis co-expression network(CEN).GRNs and CENs provide information relevant to the diversity of biological processes encoded by biomarker genes.We demonstrate that quantitatively relating meaningful evaluation metrics with stress sensing power has the potential for recognising biomarkers that show better sensitivity and robustness to an extended set of stress conditions and enable a more

关键词： Transcriptomics analysis system biology Biomarker discovery Machine learning

Deciphering Ascorbic Acid Regulatory Pathways in Ripening Tomato Fruit Using a Weighted Gene Correlation Network Analysis Approach

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Journal of Integrative Plant biology 2013年第11期55卷 1080-1091页

作者： Chao Gao Zheng Ju Shan Li Jinhua Zuo Daqi Fu Huiqin Tian Yunbo Luo Benzhong Zhu Laboratory of Fruit biology College of Food Science and Nutritional Engineering China Agricultural University Laboratory of Postharvest Storage and Processing of Vegetables National Engineering Research Center for Vegetables

Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid （AsA）, which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato （Solanum lycopersicum L.） fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty- four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.

关键词： Gene co-expression L-ascorbic acid network system biology weighted gene correlation network analysis approach.

Stochastic Simulation of the Cell Cycle Model for Budding Yeast

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Communications in Computational Physics 2011年第2期9卷 390-405页

作者： Di Liu Department of Mathematics Michigan State UniversityEast LansingMI 48824USA

We use the recently proposed Nested Stochastic Simulation Algorithm(Nested SSA)to simulate the cell cycle model for budding yeast.The results show that Nested SSA is able to significantly reduce the computational cost... 详细信息

关键词： Stochastic simulation algorithm stochastic process bio-chemical reacting network system biology

Suprabiology 2014： Promoting UK-China collaboration on systems biology and High Performance Computing

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Frontiers of Electrical and Electronic Engineering in China 2015年第1期10卷 46-53页

作者： Ettore Murabito Riccardo Colombo Chengkun Wu Malkhey Verma Samrina Rehman Jacky Snoep Shao-Liang Peng Naiyang Guan Xiangke Liao Hans V. Westerhoff Manchester Institute of Biotechnology School of Computer Science Faculty of Engineering and Physical Sciences Manchester Centre for Integrative Systems Biology The University of Manchester Manchester M139PL United Kingdom. Department of Informatics Systems and Communication University of Milan-Bicocca Milan 20126 Italy. SYSBIO - Centre of systems biology Milan 20126 Italy. Manchester Institute of Biotechnology School of Chemical Engineering and Analytical Sciences Manchester Centre forIntegrative Systems Biology The University of Manchester Manchester M139PL United Kingdom. School of Computer Science National University of Defence Technology Changsha 410073China

In the second half of 2014 the Manchester Institute of Biotechnology, based in Manchester （UK）, hosted the first Suprabiology congress, an event attended by representa- tives of different academic institutions and industry based in both the UK and China. The congress was aimed to serve as a platform to discuss and promote potential collaborations between the UK and China on the subject of systems biology and High Performance Computing. The event, sponsored by the ＂BBSRC China Partnering Awards＂ and ISBE, was organised as a sequence of talks addressing the different aspects of systems biology that can benefit from High Performance Computing. A general discussion session followed where the scientific, techni- cal, and logistic aspects of the prospected UK-China collaborations were examined.

关键词： system biology High Performance Computing Flux Balance Analysis Nonnegative Matrix Factorization Biochemical Network

Strategies for Revitalization of Traditional Medicine

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Chinese Herbal Medicines 2010年第1期2卷 1-15,83页

作者： MUKHERJEE Pulok K PITCHAIRAJAN Venkatesh MURUGAN Venkatesh SIVASANKARAN Ponnusankar KHAN Yaseen School of Natural Product Studies Department of Pharmaceutical TechnologyJadavpur University

Traditional medicine (TM) plays an inevitable role in drug discovery and development. Most of the therapeutically useful molecules used in the present day are inspired from TM. Herbal drugs are the oldest forms of medicines used for the treatment of various ailments and the TM of every country has a long history of their usage. To develop more data on their quality, safety, and efficacy, so also to improve the consumer’s need of modern days several thrust areas of research are to be focused on the development of TM. Based on the above concept, a paradigm shift is required for the revitalization of TM. These facts along with the modern scientific approaches, molecular tools, and strategies make it necessary for TM to be revitalized. Confluencing several strategies with the technological and scientific developments including pharmacogenomics, nutrigenomics, system biology, and related approaches, the scientific potential of TM can be explored further with international coordination and collaborations.

关键词： alternative medicine Ayurveda Chinese medicine drug discovery herbal resurgence Indian medicine Omic technology system biology traditional medicines

A Patient with End-stage Respiratory Failure Gets Recovery from Mechanical Ventilation by Utilization of Chinese Traditional Medicine

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World Journal of Integrated Traditional and Western Medicine 2020年第6期6卷 40-46页

作者：方辉泮辉肖党生 Department of Internal Medicine the First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou 310000China Department of Lung Transplantation the First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou 310000China VIP Ward the First Affiliated HospitalCollege of MedicineZhejiang UniversityHangzhou 310000China

Ventilator-assisted ventilation and lung transplantation are the final treatments for the patients with end-stage respiratory failure.A patient,who has been diagnosed as end-stage respiratory failure and received tracheal intubation with mechanical ventilation,received the treatment of Chinese herbal medicine on the principle of TCM and got some recovery gradually.After two months,the patient got rid of mechanical ventilation successfully.This case implies that TCM will be an alternative treatment for the patients with the similar conditions.

关键词： Respiratory failure Mechanical ventilation system biology Herbal medicine Traditional Chinese Medicine

Omics Studies and systems biology Perspective towards Abiotic Stress Response in Plants

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American Journal of Plant Sciences 2020年第12期11卷 2172-2194页

作者： Jyoti Prakash Sahoo Laxmipreeya Behera Siddhartha Shankar Sharma Jannila Praveena Suman Kumari Nayak Kailash Chandra Samal Department of Agricultural Biotechnology Odisha University of Agriculture and Technology Bhubaneswar India Department of Genetics and Plant Breeding Uttar Banga Krishi Viswavidyalaya Cooch Behar India Department of Fruit Science and Horticulture Technology Odisha University of Agriculture and Technology Bhubaneswar India Department of Plant Physiology Odisha University of Agriculture and Technology Bhubaneswar India

Plant abiotic stress responses are vital yield-restricting aspect in agriculture. Recent technology in plant biology allows research of such stress responses at a molecular scale in plants. Network analysis provides in-depth knowledge regarding omics information visualisation as it reduces the intrinsic intricacy of such data. The use of integrated functional genomics helps to understand the relationship between the genomic profile and the phenotypic profile in different environmental conditions of an organism. Plants’ responses to abiotic stress are often considered as a complex process. systems biology approaches allow visualising and understanding how plant life works to overcome abiotic stress. The combination of integrated functional genomics along with bioinformatics will put a hand in additional in-depth research knowledge on stress tolerance to plants by exploiting available genetic information and continuously improving techniques and strategies. Most of the omics technologies are high throughput with very rapid data generation rates and humongous outputs. These technologies have made noticeable contributions to the modern-day improvements in our knowledge of plant biology. So, in this review, omics studies and the system biology approach towards abiotic stress tolerance in plants are highlighted.

关键词： Genomics Proteomics Transcriptomics system biology Abiotic Stress Plants

The systemic hallmarks of cancer

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Journal of Cancer Metastasis and Treatment 2020年第1期6卷 314-344页

作者： Doru Paul Medical Oncology Weill Cornell MedicineNew YorkNY 10021USA

Cancer is not just a lump of cells that divide,invade,and spread randomly,but rather a multi-layered precisely tuned process that requires the participation of the whole organism.There is an urgent need to zoom-out from the cellular and the local stromal view and broaden our perspective by including the whole organism level.Geographically separated cancer tissues communicate between themselves,forming a system that interacts with the rest of the organism through cancer induced systemic pathogenic networks.In the present paper,I introduce six systemic hallmarks of cancer that emerge as a result of these interactions.I also describe several potential therapeutic approaches that can be developed using the cancer system concept.Overall,I argue that the tumoricentric paradigm should be replaced with a broader approach that brings into focus the“cancerized”organism.

关键词： Cancer system metastasis cancer hallmarks organism tissue system of cancer systemic networks system biology