Article
Chemistry, Physical
Songcheng Yu, Shengnan Cao, Sitian He, Kaixiang Zhang
Summary: DNA methylation is an important epigenetic characteristic that can result in heritable and revisable changes in phenotype without altering the DNA sequence. Aberrant methylation at specific loci has been linked to various diseases. The use of Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems as biosensors has shown potential for detecting locus-specific DNA methylation.
Review
Chemistry, Multidisciplinary
Seungheon Lee, Shivudu Godhulayyagari, Shadler T. Nguyen, Jasmine K. Lu, Sasha B. Ebrahimi, Devleena Samanta
Summary: The use of DNA-based nanostructures as probes has led to significant advances in chemical and biological sensing, allowing the detection of analytes in complex media, the understanding of fundamental biological processes, and the ability to diagnose diseases based on molecular signatures.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Analytical
Lin Zhou, Nahoko Kasai, Hizuru Nakajima, Shungo Kato, Sifeng Mao, Katsumi Uchiyama
Summary: Metabolism and responses of single cells are influenced by the microenvironment, and real-time monitoring can provide insights into cell behavior. The study adopts a liquid transfer-based approach for detecting lactate response from a single cell.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Xiangnan Wang, Xin Yi, Zhimei Huang, Jianjun He, Zhenkun Wu, Xia Chu, Jian-Hui Jiang
Summary: In this study, a repaired and activated DNAzyme (RADzyme) was developed by incorporating single methyl lesions at designated positions. This technology allowed the development of a fluorogenic RADzyme sensor for monitoring DNA repair, facilitating evaluation of repair activity in different cells and under drug treatment. This strategy provides a simple and versatile tool for the study of DNA repair biology, clinical diagnosis, and therapeutic assessment.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Peng Ni, Neng Huang, Fan Nie, Jun Zhang, Zhi Zhang, Bo Wu, Lu Bai, Wende Liu, Chuan-Le Xiao, Feng Luo, Jianxin Wang
Summary: DeepSignal-plant is a deep learning tool that accurately detects genome-wide 5mCs of all three contexts in plants from Nanopore reads, providing more comprehensive information on the epigenetic mechanisms of different biological processes.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Hongxu Ding, Ioannis Anastopoulos, Andrew D. Bailey, Joshua Stuart, Benedict Paten
Summary: This study introduces a deep learning framework that can predict the characteristic ionic currents of nucleotides to enable novel detection of nucleotide modifications, particularly methylated cytosine and guanine, without the need for controls.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Zaka Wing-Sze Yuen, Akanksha Srivastava, Runa Daniel, Dennis McNevin, Cameron Jack, Eduardo Eyras
Summary: The study evaluated the performance of multiple tools in detecting CpG methylation from Nanopore sequencing, revealing a tradeoff between false positives and false negatives. The authors proposed a consensus approach, METEORE, to improve prediction accuracy, and provided Snakemake pipelines for reproducibility.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Vahid Akbari, Jean-Michel Garant, Kieran O'Neill, Pawan Pandoh, Richard Moore, Marco A. Marra, Martin Hirst, Steven J. M. Jones
Summary: This study used nanopore sequencing data to map the imprinted intervals in the human genome. It successfully phased the human methylome and detected both known and novel imprinted DMRs. The study also found several conserved imprinted DMRs in mouse, rhesus monkey, and chimpanzee. These findings expand our understanding of imprinting and demonstrate the potential of nanopore sequencing in identifying imprinting regions.
Article
Materials Science, Multidisciplinary
Mohammad Mosarof Hossain, Babar Shabbir, Jingying Liu, Zhichen Wan, Sumeet Walia, Qiaoliang Bao, Tuncay Alan, Sudha Mokkapati
Summary: Bisphenol A exposure is associated with increased risk of various diseases. Monitoring BPA exposure is important for human healthcare. A microfluidic device based on MoS2 field-effect transistor has been developed to detect biomolecules at low concentrations. The functionalized MoS2 FET sensors show high sensitivity and can detect BPA concentration as low as 1 pg mL(-1).
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Review
Chemistry, Multidisciplinary
Simona Ranallo, Sara Bracaglia, Daniela Sorrentino, Francesco Ricci
Summary: This Perspective provides a critical overview of recent research efforts on the development and characterization of synthetic antigen-conjugated DNA strands responsive to specific antibodies. These systems have potential applications in sensing, drug-delivery, and antibody-antigen binding characterization. The examples demonstrate how synthetic nucleic acids can be used to create innovative analytical tools and target-responsive systems.
Article
Medicine, General & Internal
Huanwen Wu, Shiwei Guo, Xiaoding Liu, Yatong Li, Zhixi Su, Qiye He, Xiaoqian Liu, Zhiwen Zhang, Lianyuan Yu, Xiaohan Shi, Suizhi Gao, Huan Wang, Yaqi Pan, Chengcheng Ma, Rui Liu, Menghua Dai, Gang Jin, Zhiyong Liang
Summary: A non-invasive test for early detection of pancreatic ductal adenocarcinoma (PDAC) was developed by capturing the methylation signature of circulating tumor DNA (ctDNA) in blood. The test showed high accuracy in classifying PDAC plasma samples using a 56-marker classifier, and performed better than CA19-9 in detecting early and CA19-9-negative PDAC. The study highlights the effectiveness of methylation haplotype analyses in discovering robust cancer markers.
Article
Multidisciplinary Sciences
Gaolian Xu, Hao Yang, Jiani Qiu, Julien Reboud, Linqing Zhen, Wei Ren, Hong Xu, Jonathan M. M. Cooper, Hongchen Gu
Summary: The authors propose a method called STEM-PCR for rapid and facile detection of specific nucleic acid modifications. This method utilizes a simple and widely accessible PCR-based workflow, and exhibits sensitivity 20 times greater than current gold-standard techniques by using a bisulfite-free process. They successfully demonstrate the clinical applicability of this method by detecting methylation of SEPTIN9 and SFRP2 genes, which are key biomarkers in tumor prognosis and diagnosis.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Noor Mohammad, Shrinivas S. Katkam, Qingshan Wei
Summary: This study demonstrates a novel CRISPR-Cas12a-based sensing platform for detecting single-stranded DNA targets by quantifying the size reduction of double-stranded DNA as report molecules. It is simple, inexpensive, non-optical, and exhibits high sensitivity compared to fluorescent methods.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Computer Science, Information Systems
Zengri Zeng, Baokang Zhao, Han-Chieh Chao, Ilsun You, Kuo-Hui Yeh, Weizhi Meng
Summary: In recent years, frequent network attacks have posed serious threats to human interests and security. Although many detection methods have been studied, the development of network interconnection technology has led to the generation of massive amounts of network data with considerable redundant information. Additionally, the constantly changing types of cyberattacks have created difficulties in collecting samples, resulting in imbalanced datasets. Existing methods fail to solve these problems effectively.
ACM TRANSACTIONS ON MULTIMEDIA COMPUTING COMMUNICATIONS AND APPLICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Sara Bracaglia, Simona Ranallo, Francesco Ricci
Summary: Research scientists have developed programmable antigen-conjugated gene circuits that can detect target antibodies and trigger the production of detectable RNA sequences using a disposable electrochemical sensor. This cell-free electrochemical biosensor enables sensitive, specific, selective, and multiplexed detection of different antibodies in blood serum.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Agricultural Engineering
Mahmoud Osanloo, Amir Amani, Hassan Sereshti, Mohammad Reza Abai, Fariba Esmaeili, Mohammad Mehdi Sedaghat
INDUSTRIAL CROPS AND PRODUCTS
(2017)
Article
Chemistry, Applied
Mosayeb Azizi, Fariba Esmaeili, Alireza Partoazar, Shahram Ejtemaei Mehr, Amir Amani
JOURNAL OF MICROENCAPSULATION
(2017)
Article
Biotechnology & Applied Microbiology
Fariba Dehghanian, Zohreh Hojati, Fariba Esmaeili, Ali Masoudi-Nejad
Article
Nanoscience & Nanotechnology
Aref Teimouri, Sanaz Jafarpour Azami, Hossein Keshavarz, Fariba Esmaeili, Rasoul Alimi, Sara Ayazian Mavi, Saeedeh Shojaee
INTERNATIONAL JOURNAL OF NANOMEDICINE
(2018)
Article
Nanoscience & Nanotechnology
Sanaz Jafarpour Azami, Aref Teimouri, Hossein Keshavarz, Amir Amani, Fariba Esmaeili, Hamid Hasanpour, Samira Elikaee, Hamid Salehiniya, Saeedeh Shojaee
INTERNATIONAL JOURNAL OF NANOMEDICINE
(2018)
Article
Pharmacology & Pharmacy
Zahra Ghiasi, Fariba Esmaeli, Mahdi Aghajani, Mahmoud Ghazi-Khansari, Mohammad Ali Faramarzi, Amir Amani
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2019)
Article
Integrative & Complementary Medicine
Maryam Maghbool, Tomaj Khosravi, Salman Vojdani, Mahsa Rostami Chaijan, Fariba Esmaeili, Amir Amani, Fatemeh Rezayat, Ramin Nasimi Doost Azgomi, Shadan S. Mehraban, Mohammad Hashem Hashempur
COMPLEMENTARY THERAPIES IN MEDICINE
(2020)
Article
Materials Science, Biomaterials
Akram Hasanpour, Fariba Esmaeili, Hossein Hosseini, Amir Amani
Summary: Streptokinase, a clot-dissolving agent, is encapsulated in mPEG-PLGA nanoparticles to improve its biological activity and prolong circulation time, with no significant adverse effects on blood and tissues.
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS
(2021)
Review
Engineering, Biomedical
Mahdi Aghajani, Fariba Esmaeili
Summary: Protein/cell interactions at the blood-biomaterial interface play a crucial role in controlling the efficiency of biomedical devices. Various mechanisms, such as resistance to proteins and hydrophilic coatings, have been shown to decrease cell adhesion, with layer-by-layer deposition being a promising method to manipulate protein and cell adhesion behavior.
JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION
(2021)
Article
Engineering, Electrical & Electronic
Fariba Esmaeili, Mahdi Aghajani, Ali Rashti, Mohammad Abdollahi, Reza Faridi-Majidi, Hossein Ghanbari, Amir Amani
Summary: In this study, alendronate-loaded chitosan/hydroxypropyl-methylcellulose/tripolyphosphate nanoparticles were prepared using ionic gelation method combined with electrospray. The influence of factors on the size of nanoparticles was identified using an artificial neural networks (ANNs) model, revealing a strong dependence on TPP and poloxamer concentrations. The presented method shows promise for preparing nanoparticles for mucoadhesive oral drug delivery applications.
JOURNAL OF ELECTROSTATICS
(2021)
Review
Chemistry, Applied
Fariba Esmaili, Alireza Sanei-Dehkordi, Fatemeh Amoozegar, Mahmoud Osanloo
Summary: Mosquito-borne diseases cause one million deaths per year worldwide, and preventing these diseases is possible and more manageable than treating patients. Essential oils formulated into nanoformulations are appropriate alternatives for synthetic insecticides, but their practical usage is still being questioned due to volatility and lower efficiency.
BIOINTERFACE RESEARCH IN APPLIED CHEMISTRY
(2021)
Article
Materials Science, Biomaterials
Elham Zarenezhad, Abbas Abdollahi, Fariba Esmaeili, Saha Satvati, Mahmoud Osanloo
Article
Public, Environmental & Occupational Health
Mahmoud Osanloo, Mohammad Mehdi Sedaghat, Fariba Esmaeili, Amir Amani
JOURNAL OF ARTHROPOD-BORNE DISEASES
(2018)
Article
Nanoscience & Nanotechnology
Morteza Abyadeh, Esmaeil Sadroddiny, Ammar Ebrahimi, Fariba Esmaeili, Farzaneh Saeedi Landi, Amir Amani
INTERNATIONAL NANO LETTERS
(2017)
Article
Nanoscience & Nanotechnology
Farzaneh Saeedi Landi, Babak Negahdari, Fariba Esmaeili, Sedigheh Kolivand, Amir Amani
Summary: Electrospray technique was used to transfer chitosan-pDNA nanoparticles with an N/P ratio of 5 to HEK293T cells, and physicochemical characterization and transfection efficiency studies showed higher efficiency compared to calcium phosphate method in gene transfection.
JOURNAL OF NANO RESEARCH
(2021)