Article
Biochemistry & Molecular Biology
Xiaofan Feng, Mario Andrea Marchisio
Summary: New synthetic constitutive promoters for Saccharomyces cerevisiae were constructed and optimized by utilizing foreign core promoters as templates and manipulating the TATA box composition, leading to an expanded pool of yeast promoters.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Plant Sciences
L. K. Savinkova, E. B. Sharypova, N. A. Kolchanov
Summary: For the initiation of transcription by RNA polymerase II (Pol II), the assembly of a basal transcription machinery on the core promoter is required in all eukaryotes. The interaction between the TATA-binding protein (TBP) and the TATA box triggers the assembly of the preinitiation complex on TATA-containing promoters. However, the interaction of TBP with TATA boxes in plants, specifically Arabidopsis thaliana, has not been extensively studied. This review examines the roles of general transcription factors and the functions of TATA boxes in A. thaliana, highlighting their involvement in transcription machinery assembly and adaptation to environmental conditions.
Article
Multidisciplinary Sciences
Jan Zrimec, Xiaozhi Fu, Azam Sheikh Muhammad, Christos Skrekas, Vykintas Jauniskis, Nora K. Speicher, Christoph S. Boerlin, Vilhelm Verendel, Morteza Haghir Chehreghani, Devdatt Dubhashi, Verena Siewers, Florian David, Jens Nielsen, Aleksej Zelezniak
Summary: Designing de novo synthetic regulatory DNA is a promising approach for controlling gene expression in biotechnology and medicine. In this study, the researchers developed ExpressionGAN, a generative adversarial network that uses genomic and transcriptomic data to generate regulatory DNA sequences with predefined target mRNA levels.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Clarice K. Y. Hong, Barak A. Cohen
Summary: In gene regulation, enhancers provide specificity while core promoters provide a modular site for the assembly of the basal transcriptional machinery. The activities of different core promoters are preserved across genomic locations, suggesting that they are modular regulatory elements independently scaled up or down by different genomic environments.
Article
Agronomy
Yu Tian, Delin Li, Xueqing Wang, Hao Zhang, Jiajun Wang, Lijie Yu, Changhong Guo, Xiaoyan Luan, Xinlei Liu, Hongjie Li, Jochen C. Reif, Ying-hui Li, Li-juan Qiu
Summary: In this study, through pedigree analysis and SNP markers, important genomic fragments related to soybean cyst nematode (SCN) resistance were identified. A total of 23 genomic loci underlying resistance to SCN were found, and a causative SNP in the Glyma.08G096500 gene, encoding a predicted TIFY5b-related protein, was highly correlated with SCN resistance. These findings provide valuable information for gene cloning and the development of resistant soybean cultivars.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Juan F. Santana, Geoffrey S. Collins, Mrutyunjaya Parida, Donal S. Luse, David H. Price
Summary: The effects of depleting different components of RNA polymerase II general transcription factors vary in their impact on promoter activity and are regulated by both core promoter elements and the recruitment of TFIID.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Rene Dreos, Anna Sloutskin, Nati Malachi, Diana Ideses, Philipp Bucher, Tamar Juven-Gershon
Summary: This study identified preferred downstream positions in human promoters resembling the fruit fly DPE, supporting the presence of Inr+DPE-containing promoters in human genes. Functional characterization of these positions also suggests a spacing dependency on the Inr, indicating the likelihood of common canonical Inr+DPE promoters in metazoan species.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Jacqueline M. Dresch, Regan D. Conrad, Daniel Klonaros, Robert A. Drewell
Summary: This study examines the sequence variation of core promoter elements in Drosophila melanogaster and reveals the importance of considering detailed sequence composition features for accurate bioinformatic predictions.
Article
Chemistry, Multidisciplinary
Akkinepally Vanaja, Venkata Rajesh Yella
Summary: This study analyzed and categorized the core promoters of multiple eukaryotic genomes based on DNA sequence and structural properties. The results revealed distinct patterns for different core promoter classes and conserved DNA structural signals. The findings provide insights into the chromatin configuration and transcription process.
Article
Biochemistry & Molecular Biology
Yong Zhang, Muhammad Faseeh Iqbal, Yulong Wang, Kaiyun Qian, Jinxia Xiang, Guohua Xu, Xiaorong Fan
Summary: This study demonstrated that the TATA-box is the key cis-regulatory element for the transcription of OsNRT2.3 into specific isoforms, and the binding protein OsTBP2.1 can promote rice growth and increase yield.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Green & Sustainable Science & Technology
Lorenc Malka, Alban Kuriqi, Adhurim Haxhimusa
Summary: This study highlights the importance of thermal insulation in buildings and proposes a method to optimize insulation thickness using linearization and correction factors. Simulation results in Albania show that using a standardized corrected insulation thickness can significantly reduce energy consumption and CO2 emissions, while also providing economic benefits.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Construction & Building Technology
Akos Lakatos, Zsolt Kovacs
Summary: In order to reduce the energy use of buildings, the use of insulation materials is a possible solution to improve energy efficiency. However, as regulations become stricter, thicker insulation materials are required. Research has started to focus on decreasing the thickness and thermal conductivity of materials, leading to the development of new types of insulation materials with lower thermal conductivity.
ENERGY AND BUILDINGS
(2021)
Article
Chemistry, Analytical
Casey J. Toft, Alanna E. Sorenson, Patrick M. Schaeffer
Summary: This review highlights the important properties of the Tus-Ter complex and its exploitation for the development of diverse and novel ultrasensitive detection devices as well as innovative genomic and proteomic platform technologies. Various ex vivo and in vivo bioanalytical applications, including immuno-PCR diagnostics, bioassays, and protein array technologies, are discussed. A perspective on future research and applications is provided.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemistry & Molecular Biology
Xiaoxia Ni, Zhengyang Liu, Jintang Guo, Genlin Zhang
Summary: A novel bifunctional element with promoter and terminator functions was created by fusing a termination signal with a promoter sequence. The strength of this synthetic element was regulated by different sequences, resulting in optimized promoter-like and terminator-like bifunctional elements with significantly increased strengths. These bifunctional elements effectively improved pathway assembly efficiency and could be a useful tool for yeast synthetic biology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Pediatrics
Vikrant Sood, Bikrant Bihari Lal, Shvetank Sharma, Rajeev Khanna, Manish K. Siloliya, Seema Alam
Summary: There is limited literature on Gilbert's syndrome in children with persistent unconjugated hyperbilirubinemia from the Indian subcontinent. The majority of patients were diagnosed in the adolescent age group, with fluctuating levels of serum total bilirubin accompanied by other associated conditions in some cases. Gilbert's syndrome may complicate the clinical and laboratory picture and lead to higher levels of hyperbilirubinemia than typically described.
INDIAN JOURNAL OF PEDIATRICS
(2021)
Review
Biochemistry & Molecular Biology
Yadan Zhang, Mario Andrea Marchisio
Summary: The CRISPR-Cas system in prokaryotes serves as an adaptive and inheritable immune response against invading DNA, while anti-CRISPR proteins act as inhibitors of this system. Over the past decade, CRISPR-Cas systems have been harnessed as a genetic-engineering tool, with the type II CRISPR-Cas system being the most popular in biotechnology.
Review
Biotechnology & Applied Microbiology
Michael Dare Asemoloye, Mario Andrea Marchisio, Vijai Kumar Gupta, Lorenzo Pecoraro
Summary: The ability of fungi to produce ligninolytic enzymes for various industrial applications is limited by their natural production levels, but recent advances in synthetic biology and computational design have shown promise in enhancing enzyme synthesis. Different protein engineering methods such as rational, semi-rational, and directed evolution approaches have been utilized to enhance the production of ligninolytic enzymes in fungi. Techniques like metabolic pathway engineering and synthetic biology have been instrumental in optimizing enzyme production and improving their properties for industrial use. The CRISPR-Cas protein systems have emerged as a promising biotechnology for large-scale production of ligninolytic enzymes in fungi.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemical Research Methods
Xingyu Xu, Zhen Zhu, Yingying Wang, Yangye Geng, Feng Xu, Mario A. Marchisio, Zixin Wang, Dejing Pan
Summary: Microfluidic methodologies for replicative lifespan determination of budding yeast cells are highly impacted by the robustness of experimental conditions, especially the design of yeast-trapping structures. In this study, an optimized design, the yeast rotation (YRot) trap, was proposed and validated for stable retention of mother cells and hydrodynamic rotation of buds. The integration of denser YRot traps in microchannels could potentially improve experimental conditions for precise RLS determination in yeast aging studies.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Yadan Zhang, Mario Andrea Marchisio
Summary: Type II CRISPR-(d)SpCas9 and anti-CRISPR proteins (AcrIIs) exhibit evidence of coevolution and competition between bacteria and phages. In Saccharomyces cerevisiae, using bare dSpCas9 in conjunction with scaffold gRNA (scRNA) appears to be the most efficient activation system. Among the AcrIIs studied, AcrIIA4 demonstrated the highest inhibition strength at low concentrations, while the fusion of activation domains with dSpCas9 limited their interaction with AcrIIs, highlighting the superiority of bare dSpCas9 for building synthetic genetic networks in yeast.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Xuekun Wang, Mario Andrea Marchisio
Summary: This study highlights the importance of coordinated, high-level, and stable expression of multiple genes for engineering biosynthetic circuits and metabolic pathways. The use of IRES and 2 A peptides allows for co-expression of various genes in polycistronic vectors, enabling reliable expression in eukaryotic cells. Ribosome-skipping events mediated by 2 A peptides facilitate the generation of multiple independent proteins from a single open reading frame.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Yingying Wang, Zhen Zhu, Ke Liu, Qin Xiao, Yangye Geng, Feng Xu, Shuiping Ouyang, Ke Zheng, Yimin Fan, Nan Jin, Xiangwei Zhao, Mario A. Marchisio, Dejing Pan, Qing-An Huang
Summary: In this study, a high-throughput microfluidic chip for diploid yeast long-term culturing, optical inspection, and cell-aging analysis was developed. The chip features delicate microstructures to ensure cell stability and alleviate stress. Using this chip, the researchers were able to track the replicative lifespan and budding time interval of diploid yeast cells and observe cell desynchronization during aging.
JOURNAL OF NANOBIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Biruck Woldai Abraha, Mario Andrea Marchisio
Summary: This article presents a method for the visual design and modular modeling of synthetic gene circuits using SBML Level 3. It demonstrates the wet-lab implementation of Boolean NOT gates using the bacterial ClpX-ClpP system for protein degradation. The study serves as the starting point for the development of new software for modular design of eukaryotic gene circuits and provides an alternative approach to building genetic Boolean gates.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yadan Zhang, Huanhuan Ge, Mario Andrea Marchisio
Summary: CRISPR-Cas systems are powerful tools for genetic manipulation and gene expression regulation. In this study, Nme1Cas9 was mutated to d(16A)Nme1Cas9, which retained the active HNH domain and functioned as a functional RNase in vivo. However, LwaCas13a and RfxCas13d did not show functional activity in Saccharomyces cerevisiae.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Environmental Sciences
Michael Dare Asemoloye, Mario Andrea Marchisio
Summary: Fungal laccase (Lac) has become an important biocatalyst in various industries, and in this study, engineered yeast strains showed significant response to different carbon and nitrogen sources, as well as efficient degradation of complex hydrocarbon mixtures.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Review
Chemistry, Multidisciplinary
Tsigereda Weldemichael, Michael Dare Asemoloye, Mario Andrea Marchisio
Summary: Feedforward loops (FFLs) are simple network motifs composed of three genes, and they have been found in many organisms. FFLs enable cells to survive critical environmental conditions. The most common types are coherent 1 and incoherent 1 FFLs, which have different functions. Only a few synthetic FFLs have been engineered so far, and they differ greatly from natural FFLs.
APPLIED SCIENCES-BASEL
(2022)
Article
Biophysics
Michael Dare Asemoloye, Mario Andrea Marchisio
Summary: Yeast-based biosensors have the potential for various applications, and this work contributes to the understanding of detectable chemicals and the development of modular yeast biosensors. By using bacterial transcription factors, transducer circuits were built in Saccharomyces cerevisiae for the detection of specific chemicals. These engineered strains showed fast response time and strong signal output to a wide range of chemical concentrations, and were capable of operating in complex media.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Biochemistry & Molecular Biology
Lifang Yu, Mario Andrea Marchisio
Summary: This study presents an efficient tool to induce mRNA degradation in yeast using CRISPR-(d)Cas system, specifically (d)Cas12a. The study highlights the potential of V-A Cas proteins in yeast and demonstrates their applications in constructing Boolean logic gates.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Tian Zhou, Zhiying Liang, Mario Andrea Marchisio
Summary: In this study, the working of a ss-estradiol-sensing device was optimized by engineering both the chimeric activator and the reporter protein expression cassette. The researchers found a configuration that functions as a highly sensitive biosensor and a sharp switch depending on the concentration of the chimeric activator and the strength of its activation domain.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Xuekun Wang, Ximing Tian, Mario Andrea Marchisio
Summary: Gene digital circuits have various applications and are the subject of many studies in Synthetic Biology. They utilize small genetic components that mimic Boolean gates to perform complex logic functions. In this study, three bacterial repressors (TetR, LexA, and LacI) were coexpressed in the yeast Saccharomyces cerevisiae using synthetic polycistronic cassettes based on 2A peptide sequences. By modifying the original 2A peptides, we successfully constructed single and two-input Boolean gates, and eventually developed a tricistronic vector that enabled the implementation of three-input circuits containing AND and OR gates. Overall, polycistronic constructs simplify the cloning and coexpression of multiple proteins, reducing the complexity of gene digital circuits.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Lifang Yu, Yadan Zhang, Mario Andrea Marchisio
Summary: Synthetic gene Boolean gates and digital circuits have diverse applications, and the discovery of CRISPR-Cas systems and their natural inhibitors-Acrs-provides a new tool for designing and implementing in vivo gene digital circuits. This article presents a protocol for establishing small transcriptional networks in Saccharomyces cerevisiae using dCas9/dCas12a and their corresponding Acrs. The results highlight the properties of these Cas proteins as transcription factors and demonstrate how to build Boolean gates based on the CRISPR-dCas-Acr interaction.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)