Article
Biochemistry & Molecular Biology
Anissia Ait Saada, Alex B. Costa, Ziwei Sheng, Wenying Guo, James E. Haber, Kirill S. Lobachev
Summary: This study elucidates the mechanisms of palindromic sequence fragility in Saccharomyces cerevisiae, including the involvement of specific nucleases and transcription status, the restriction condition with loops, the impact of RPA on secondary structure stability, and a new fragility pathway during the G2 phase.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Polina Govorkova, Chee Ka Candice Lam, Kevin Truong
Summary: This paper developed a method to design shorter synthetic mammalian promoters for endogenous genes and found that these synthetic promoters had higher palindromic density than expected. By applying this method, they successfully expressed fluorescent proteins, and the synthetic promoters contained important expression sites.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Mathematics
Jan Petr, Jan Soukup
Summary: In a recent paper, the question of palindromic subwords of finite binary words was posed, with a conjecture that the longest palindrome is at least n/2, which was disproved in the study. Sequences of words were constructed to show that the longest palindromes have a size of 15n/32 + o(n), and it was also proven that the longest palindromes have a size of at least 3n/8.
DISCRETE MATHEMATICS
(2021)
Article
Astronomy & Astrophysics
Metha Prathaban, Will Handley
Summary: We explore the linearly quantized primordial power spectra associated with palindromic universes and improve the modeling of recombination to achieve consistent predictions with observational data.
Article
Mathematics, Applied
Phakhinkon Napp Phunphayap, Prapanpong Pongsriiam
Summary: In this article, we conclude the comparative study of functions Ab(n) and Ab1(n), providing a complete understanding of their asymptotic difference behavior.
Article
Biophysics
Rui Yuan, Wanyan Tang, Hong Zhang, Wenxin You, Xiaolin Hu, Haiwei Zhang, Ling Chen, Weiqi Nian, Shijia Ding, Yang Luo
Summary: The PASTA strategy for detecting circulating EGFR exon mutations achieved high accuracy and sensitivity, and can be applied to molecular subtyping in clinical lung cancer patients.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Genetics & Heredity
Agnes Thierry, Varun Khanna, Bernard Dujon
Summary: Novel, large-scale structural mutations were discovered in engineered Saccharomyces cerevisiae strains, including giant chromosomes, complex segmental rearrangements, and the formation of neochromosomes. These mutations involved short repeated sequences and novel junctions between unrelated sequences in the genome, leading to an increase in chromosome number and stability.
Article
Biophysics
Dan Mark Alon, Karin Mittelman, Eytan Stibbe, Stefanie Countryman, Louis Stodieck, Shankini Doraisingam, Dylan Mikeala Leal Martin, Eliran Raphael Hamo, Gur Pines, David Burstein
Summary: Monitoring astronauts' health in space is challenging, but CRISPR-Cas12a has shown promise for rapid genetic diagnostics. We tested the efficiency and sensitivity of CRISPR-based diagnostics in microgravity using recombinase polymerase amplification (RPA). Coupling RPA with Cas12a allowed us to detect genetic targets in attomolar concentrations. This research demonstrates the potential of CRISPR-based detection for on-site genetic diagnostics in microgravity.
BIOSENSORS & BIOELECTRONICS
(2023)
Article
Biochemistry & Molecular Biology
Anissia Ait Saada, Wenying Guo, Alex B. Costa, Jiaxin Yang, Jianrong Wang, Kirill S. Lobachev
Summary: DNA inverted repeats (IRs) are common in eukaryotic genomes and can cause chromosome instability leading to human diseases. This study shows that structural constraints are overcome when the repeats interact in single-stranded DNA (ssDNA). Using a yeast system, it is found that spaced Alu-IRs in ssDNA have high levels of genomic rearrangements, while high heterology suppresses IR-induced instability. Mechanistically, rearrangements occur through cis-interaction of IRs, resulting in DNA fold-back and dicentric chromosome formation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Guoqiao Huang, Jing Zhang, Yinghao Cheng, Chan Li, Qiufeng Song, Chang Xue, Zai-sheng Wu, Zhifa Shen
Summary: An intelligent DNA machine called S-nanoprobe was designed for the detection of miRNA-21. The S-nanoprobe demonstrated high efficiency in detecting target miRNA and exhibited a high specificity. It could be used to detect down to 1 fM of target and could discriminate target miRNA from homologous miRNAs. The S-nanoprobe also showed promising results in detecting tumor-associated biomarkers in early diagnosis.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Chemistry, Multidisciplinary
Hongyan Yu, Zhi Weng, Xi Zhou, Dan Bai, Wang Luo, Xiaole Han, Lin Song, Qian Liu, Junjie Li, Yujun Yang, Yongcan Guo, Ke Lv, Guoming Xie
Summary: In this study, a hairpin probe-mediated exponential amplification reaction (HEAR) strategy is proposed, which combines DNA strand displacement with a who triggers, who gets generated mode, providing excellent single-base discrimination and reduced background signal. The detection limit is 19 aM, reduced by 3 orders of magnitude compared to traditional exponential amplification approaches. This one-pot strategy also exhibits a wide dynamic range, high specificity, and short detection time, and is expected to become a powerful tool for clinical diagnosis.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Min Qing, Sheng Liang Chen, Zhe Sun, Yi Fan, Hong Qun Luo, Nian Bing Li
Summary: The study introduced the CRISPR/Cas system into an electrochemical biosensing platform for sensitive and specific detection of disease-related molecules. By utilizing modular rolling circle amplification and CRISPR/Cas12a, signal amplification was achieved. The flexibility and programmability of this strategy allow for the detection of various targets.
ANALYTICAL CHEMISTRY
(2021)
Article
Physics, Multidisciplinary
Jean-Marc Girault, Sebastien Menigot
Summary: The analysis of symmetry in biological sequences, particularly palindromic analysis, is essential in studying the properties of these sequences. In addition to mirror symmetry, other types of symmetry like those found in friezes can provide alternative perspectives for analyzing binary sequences. New tools based on different types of palindromes, such as symmetropy and symmentropy, offer improved discrimination capabilities compared to traditional methods like Lempel-Ziv complexity. These new types of palindromes also demonstrate better discrimination abilities for binarized DNA sequences.
Review
Biochemistry & Molecular Biology
Jiezhong Shi, Ben Zhang, Tianyi Zheng, Tong Zhou, Min Guo, Ying Wang, Yuanchen Dong
Summary: Due to the specific base-pairing recognition, clear nanostructure, programmable sequence and responsiveness of the DNA molecule, DNA materials have attracted extensive attention and been widely used in controlled release, drug delivery and tissue engineering. Generally, the strategies for preparing DNA materials are based on the assembly of multiple DNA strands. However, using only one DNA strand for material construction can save time, cost and avoid defects, promoting large-scale production and practical application. This review introduces the development of DNA assembly and mainly summarizes the current reported materials formed by one DNA strand.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Shuai Chen, Jianghong Cheng, Yanhong Zhong, Ruimin Liu, Zhongxian Lu, Xianyang Luo
Summary: The deletion of the Gab2 gene has a preventive effect on chronic liver inflammation and hepatocellular carcinoma. Gab2 can accelerate tumor growth and progression in hepatocarcinogenesis by activating IL-6 and MDSCs. This study provides novel insights into the role of Gab2 in autoimmune tolerance during hepatocarcinogenesis.
Meeting Abstract
Biotechnology & Applied Microbiology
Anita Slavica, Bojan Zunar, Ivan Kresimir Svetec, Tonci Rezic, Srdan Novak, Bozidar Santek
JOURNAL OF BIOTECHNOLOGY
(2015)
Meeting Abstract
Biotechnology & Applied Microbiology
Marina Svetec Miklenic, Bojan Zunar, Ana Loncar, Davor Nestic, Anamarija Stafa, Ivan Kresimir Svetec
JOURNAL OF BIOTECHNOLOGY
(2016)
Meeting Abstract
Biotechnology & Applied Microbiology
Bojan Zunar, Andrea Pranklin, Ana Loncar, Davor Nestic, Marina Svetec Miklenic, Anamarija Stafa, Bozidar Santek, Ivan Kresimir Svetec
JOURNAL OF BIOTECHNOLOGY
(2016)
Meeting Abstract
Biotechnology & Applied Microbiology
Bojan Zunar, Marina Svetec Miklenic, Davor Nestic, Ana Loncar, Anamarija Stafa, Bozidar Santek, Ivan Kresimir Svetec
JOURNAL OF BIOTECHNOLOGY
(2016)
Meeting Abstract
Biotechnology & Applied Microbiology
Anamarija Stafa, Andrea Pranklin, Antonio Zandona, Bojan Zunar, Marina Svetec Miklenic, Bozidar Santek, Ivan Kresimir Svetec
JOURNAL OF BIOTECHNOLOGY
(2017)
Meeting Abstract
Biotechnology & Applied Microbiology
Bojan Zunar, Marina Svetec Miklenic, Anamarija Stafa, Kristian Arambasic, Bozidar Santek, Ivan Kresimir Svetec
JOURNAL OF BIOTECHNOLOGY
(2017)
Article
Genetics & Heredity
Anamarija Stafa, Marina Miklenic, Bojan Zunar, Berislav Lisnic, Lorraine S. Symington, Ivan-Kresimir Svetec
Article
Biotechnology & Applied Microbiology
Marina Miklenic, Anamarija Stafa, Ana Bajic, Bojan Zunar, Berislav Lisnic, Ivan-Kresimir Svetec
JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
(2013)
Article
Biotechnology & Applied Microbiology
Bojan Zunar, Antonija Trontel, Marina Svetec Miklenic, Juliana Lana Prah, Anamarija Stafa, Nenad Mardetko, Mario Novak, Bozidar Santek, Ivan Kresimir Svetec
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2020)
Article
Microbiology
Angela Matanovic, Kristian Arambasic, Bojan Zunar, Anamarija Stafa, Marina Svetec Miklenic, Bozidar Santek, Ivan-Kresimir Svetec
Summary: Non-conventional yeasts are increasingly being used in biotechnological processes, but many lack the basic tools for genetic engineering. This study constructed integrative and replicative plasmids that can be used in different yeasts and demonstrated their successful use in transforming Schwanniomyces species. It also discovered a replicative plasmid that can be used in these species. This research provides a solid starting point for further study and application of genetic transformation in yeasts.
Article
Biotechnology & Applied Microbiology
Ante Tomasovic, Damir Stanzer, Ivan Kresimir Svetec, Marina Svetec Miklenic
Summary: Research reveals that COVID19-positive women have milder symptoms and lower fatality rates, potentially due to estrogen affecting SARS-CoV2 S protein infectivity. A potential estrogen binding site on S protein was identified, prompting the need for further comprehensive study.
FOOD TECHNOLOGY AND BIOTECHNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Anamarija Stafa, Bojan Zunar, Andrea Pranklin, Antonio Zandona, Marina Svetec Miklenic, Bozidar Santek, Ivan Kresimir Svetec
FOOD TECHNOLOGY AND BIOTECHNOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Anamarija Stafa, Marina Svetec Miklenic, Antonio Zandona, Bojan Zunar, Neza Cadez, Hrvoje Petkovic, Ivan Kresimir Svetec
FEMS YEAST RESEARCH
(2017)
Article
Biotechnology & Applied Microbiology
Marina Miklenic, Bojan Zunar, Anamarija Stafa, Ivan-Kresimir Svetec
FEMS YEAST RESEARCH
(2015)