Article
Biology
Brianna Bibel, Elad Elkayam, Steve Silletti, Elizabeth A. Komives, Leemor Joshua-Tor
Summary: Argonaute (Ago) proteins play a crucial role in post-transcriptional gene regulation through RNA interference. Phosphorylation by CK1 alpha can alleviate miRNA-mediated repression by promoting target release, allowing Ago to target additional mRNAs.
Article
Biochemistry & Molecular Biology
Zhao Wang, Gui-Yun Long, Dao-Chao Jin, Hong Yang, Cao Zhou, Xi-Bin Yang
Summary: The study revealed that SfTre1 and SfTre2 play crucial roles in the growth and development of S. furcifera, with RNA interference affecting their expression and causing malformed phenotypes and high mortality rates.
Review
Biotechnology & Applied Microbiology
Congting Guo, Xiaoteng Ma, Fei Gao, Yuxuan Guo
Summary: Gene editing involves precise changes to specific nucleic acid sequences. The CRISPR/Cas9 system has revolutionized gene editing, making it efficient, convenient, and programmable. However, off-target effects remain a major concern, leading to unexpected alterations in the genome. Various methods have been developed to detect and mitigate these off-target effects, advancing the precision of CRISPR/Cas9 derivatives. This review summarizes these technological advancements and discusses the challenges in managing off-target effects for future gene therapy.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Martin Pacesa, Chun-Han Lin, Antoine Clery, Aakash Saha, Pablo R. Arantes, Katja Bargsten, Matthew J. Irby, Frederic H. -T. Allain, Giulia Palermo, Peter Cameron, Paul D. Donohoue, Martin Jinek
Summary: The crystallographic structures of Cas9 bound to off-target substrates reveal that noncanonical base-pairing interactions within the guide:off-target heteroduplex enable off-target binding. Single-nucleotide deletions in off-target substrates are accommodated by base skipping or multiple noncanonical base pairs. PAM-distal mismatches result in duplex unpairing and induce a conformational change in the Cas9 REC lobe. These insights contribute to the improved rational design of guide RNAs and off-target prediction algorithms.
Article
Parasitology
Wan Chen, Kathryn Bartley, Francesca Nunn, Alan S. Bowman, Jeremy M. Sternberg, Stewart T. G. Burgess, Alasdair J. Nisbet, Daniel R. G. Price
Summary: This study identified core RNAi pathway genes in the D. gallinae genome and developed a robust RNAi methodology for targeting genes in D. gallinae, which will be valuable for studying genes of unknown function and validating potential control targets in D. gallinae.
PARASITES & VECTORS
(2021)
Article
Biochemistry & Molecular Biology
Jens Hoer, Jakob Jung, Svetlana Durica-Mitic, Lars Barquist, Joerg Vogel
Summary: INRI-seq is an in vitro method for analyzing the translational landscape of a synthetic transcriptome in a comprehensive manner. It eliminates the need for extracting ribosomes from living cells and allows for the analysis of translation initiation sites and the effects of translation inhibitors.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biology
Emily Nicole Powers, Charlene Chan, Ella Doron-Mandel, Lidia Llacsahuanga Allcca, Jenny Kim Kim, Marko Jovanovic, Gloria Ann Brar
Summary: Targeted selection-based genome-editing approaches have enabled many fundamental discoveries and are used routinely with high precision. However, this study found that replacing one gene with a common selection cassette in yeast led to reduced expression and function of a neighboring gene, a phenomenon known as the neighboring gene effect (NGE). The study revealed that the bidirectionality of promoters drives a divergent transcript that represses the neighboring gene through transcriptional interference and translational repression. Insertion of transcription terminator sequences into the cassette can eliminate these off-target effects.
Article
Nanoscience & Nanotechnology
Liuwei Zhang, Jingyun Wang, Hongyan Cui, Haonan Zheng, Xiaolan Yin, Jiaqi Lin, Yue Wang, Yan Zhao, Haidong Li, Qixian Chen
Summary: Tumors that can escape immune clearance can be effectively treated by a chemotherapeutic nanomedicine that targets the tumors and delivers siRNA payloads to knock down immune suppressive molecules, resulting in the reactivation of anti-tumor immunities. This study demonstrated significant anti-tumor effects in triple-negative breast tumors by using a chemotherapeutic nanomedicine that combines targeted delivery and RNA interference.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Nanoscience & Nanotechnology
Liuwei Zhang, Jingyun Wang, Hongyan Cui, Haonan Zheng, Xiaolan Yin, Jiaqi Lin, Yue Wang, Yan Zhao, Haidong Li, Qixian Chen
Summary: Targeted therapy, inhibition of immune suppressive molecules, and the use of chemotherapy drugs can improve anti-tumor outcomes.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemistry & Molecular Biology
Jiasheng Chen, Yingchuan Peng, Hainan Zhang, Kangxu Wang, Chunqing Zhao, Guanheng Zhu, Subba Reddy Palli, Zhaojun Han
Summary: Research has identified rules governing the specificity of dsRNA triggering RNAi against target genes, and by designing dsRNA that meets certain conditions, specificity and efficiency can be optimized, paving the way for the rational application of RNAi in pest control.
Article
Multidisciplinary Sciences
William T. Garrood, Nace Kranjc, Karl Petri, Daniel Y. Kim, Jimmy A. Guo, Andrew M. Hammond, Ioanna Morianou, Vikram Pattanayak, J. Keith Joung, Andrea Crisanti, Alekos Simoni
Summary: The study shows that off-target mutations induced by CRISPR-Cas9 in mosquitoes can be reduced to undetectable levels, with judicious design of the guide RNA and strict temporal control of Cas9 expression in the germline being key factors.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Entomology
Clauvis Nji Tizi Taning, Shunhua Gui, Kristof De Schutter, Mona Jahani, Nathaly Lara Castellanos, Olivier Christiaens, Guy Smagghe
Summary: This study confirmed the susceptibility of bumblebees to ingested dsRNA targeting specific genes, and found no significant off-target effects on gene expression in bumblebees following exposure to a fusion dsRNA product designed for pest control.
JOURNAL OF PEST SCIENCE
(2021)
Article
Medicine, Research & Experimental
Atsushi Shibata, Hisao Shirohzu, Yusuke Iwakami, Tomoaki Abe, Chisato Emura, Eriko Aoki, Tadaaki Ohgi
Summary: Recently, a novel class of RNA interference (RNAi) reagent, called enforced strand bias (ESB) RNA, has been developed. ESB RNA functions in a Dicer-independent manner and effectively triggers RNAi without causing off-target effects. It also exhibits a unique target sequence preference and can efficiently silence target sequences that cannot be effectively suppressed by siRNA. These findings suggest that ESB RNA has the potential to be an effective RNAi reagent, even in cases where the target sequence is not suitable for siRNA.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Endocrinology & Metabolism
Siuming-Francis Chan, Qi-Qiao Wen, Chun-Mei Ao, Wei Wang, Cheng-Gui Wang, Yan-Fei Zhao
Summary: Ecdysis triggering hormone (ETH) plays a crucial role in molting, reproduction, and courtship behavior in crabs. This study revealed the potential downstream pathways and genes of ETH in Scylla paramamosain, providing valuable insights into the regulation of crustacean molting.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Immunology
Junna Jiao, Zhuangwei Lv, Yurong Wang, Liye Fan, Angang Yang
Summary: Activation-induced cytidine deaminase (AID) plays a crucial role in promoting B cell diversification through somatic hypermutation (SHM) and class switch recombination (CSR). Apart from its physiological function of humoral immune response, AID has been linked to the initiation and progression of lymphomas. This review proposes an alternative role for AID and explores its off-target effects in regulating tumorigenesis.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Chian Teng Ong, Elizabeth M. Ross, Gry B. Boe-Hansen, Conny Turni, Ben J. Hayes, Ala E. Tabor
Summary: This study compares the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. It finds that ONT adaptive sequencing yields a higher amount of metagenomic data per 1 Gb of sequence data and has increased sequencing efficiency and long read continuity. This method improves the amount and accuracy of metagenomic data for samples with high host-to-microbe DNA ratio.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Gongjun Shi, Gayan Kariyawasam, Sanzhen Liu, Yueqiang Leng, Shaobin Zhong, Shaukat Ali, Paula Moolhuijzen, Caroline S. Moffat, Jack B. Rasmussen, Timothy L. Friesen, Justin D. Faris, Zhaohui Liu
Summary: This study reports the genetic mapping, molecular cloning, and functional analysis of the ToxC1 gene in Pyrenophora tritici-repentis, which is required for Ptr ToxC production. This finding is a major step towards revealing the biosynthetic pathway of Ptr ToxC and studying its molecular interactions with host factors.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Parasitology
Muhammad Noman Naseem, Ali Raza, Geoffry Fordyce, Michael McGowan, Constantin Constantinoiu, Conny Turni, Rachel Allavena, Ala E. Tabor, Peter James
Summary: Buffalo flies are a major concern for health and production in north Australian beef herds. They can cause skin lesions and transmit nematodes, but the role of nematodes in lesion development is unclear. This study investigated the distribution of Stephanofilaria nematodes in buffalo flies and lesions in different regions of Queensland. The results showed that Stephanofilaria was present in most regions, but its presence did not always correlate with lesion development. Using surface swabs for sampling lesions proved to be a quicker and less invasive method than dermal biopsies. Understanding the pathogenesis of buffalo fly lesions is important for developing effective treatment and control strategies.
VETERINARY PARASITOLOGY
(2022)
Article
Microbiology
Chian Teng Ong, Gry Boe-Hansen, Elizabeth M. Ross, Patrick J. Blackall, Conny Turni, Ben J. Hayes, Ala E. Tabor
Summary: This study compared the effectiveness of different host depletion and DNA extraction methods for bovine vaginal metagenomic samples. The findings indicated that Soft-spin and QIAamp were the most effective methods in reducing host DNA contamination and increasing sequencing depth for microbial reads. Thus, a combination of these methods provided the most robust representation of the vaginal microbial community in cattle.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biotechnology & Applied Microbiology
Wenying Zhang, Cong Tan, Haifei Hu, Rui Pan, Yuhui Xiao, Kai Ouyang, Gaofeng Zhou, Yong Jia, Xiao-Qi Zhang, Camilla Beate Hill, Penghao Wang, Brett Chapman, Yong Han, Le Xu, Yanhao Xu, Tefera Angessa, Hao Luo, Sharon Westcott, Darshan Sharma, Eviatar Nevo, Roberto A. Barrero, Matthew Bellgard, Tianhua He, Xiaohai Tian, Chengdao Li
Summary: Divergent selection in different environments leads to functional genomic divergence. This study examined the genomic differentiation and gene expression patterns in two populations of wild barley under abiotic stress. The researchers identified structural variants and single nucleotide polymorphisms (SNPs) that may be associated with well-differentiated phenotypes and local adaptation. The findings provide new insights into the genomic basis of local adaptation and have implications for the genetic improvement of cultivated barley.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Genetics & Heredity
Paula M. Moolhuijzen, Pao Theen See, Gongjun Shi, Harold R. Powell, James Cockram, Lise N. Jorgensen, Hamida Benslimane, Stephen E. Strelkov, Judith Turner, Zhaohui Liu, Caroline S. Moffat
Summary: This study conducted a pan genomic analysis of a globally significant crop fungal pathogen, Pyrenophora tritici-repentis (Ptr), and identified potential variations involved in pathogenicity. The results provide a new resource for searching natural homologues and monitoring pathogenicity-related variations.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Ziheng Zhou, Cong Tan, Matthew Hoi Kin Chau, Xiaosen Jiang, Ziyuan Ke, Xiaoyan Chen, Ye Cao, Yvonne K. Kwok, Matthew Bellgard, Tak Yeung Leung, Kwong Wai Choy, Zirui Dong
Summary: In this study, we curated and analyzed sequencing data from multiple developmental periods of humans and various model organisms, providing insights into gene expression, chromatin accessibility, and gene-gene regulation interactions. The findings contribute to our understanding of the roles of genes in tissue/organ development and disease mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Orthopedics
X. Wu, C. Liyanage, M. Plan, T. Stark, T. McCubbin, R. A. Barrero, J. Batra, R. Crawford, Y. Xiao, I. Prasadam
Summary: This study aims to identify the changes in energy metabolism in osteoarthritis (OA) cartilage. Metabolomics, proteomics, and transcriptomics analyses were conducted to investigate the global alterations in OA metabolism. The results showed increased lactate production and decreased mitochondrial respiratory rates in OA chondrocytes. This study provides a basis for targeting metabolism as a therapeutic approach for OA.
OSTEOARTHRITIS AND CARTILAGE
(2023)
Article
Microbiology
Amanda D. Barbosa, Michelle Long, Wenna Lee, Jill M. Austen, Mike Cunneen, Andrew Ratchford, Brian Burns, Prasad Kumarasinghe, Rym Ben-Othman, Tobias R. Kollmann, Cameron R. Stewart, Miles Beaman, Rhys Parry, Roy Hall, Ala Tabor, Justine O'Donovan, Helen M. Faddy, Marjorie Collins, Allen C. Cheng, John Stenos, Stephen Graves, Charlotte L. Oskam, Una M. Ryan, Peter J. Irwin
Summary: There is a lack of data about tick-related illnesses in Australia, especially the Debilitating Symptom Complexes Attributed to Ticks (DSCATT). This research plan aims to investigate the causes, pathophysiology, and clinical outcomes of tick-associated disease in Australia, using prospective data collection, matched control groups, and integrative data analysis. The study includes laboratory analyses, such as metagenomics, to explore potential pathogen transmission during tick bites, as well as multi-omics technology to investigate links between immune responses and disease causations. Psychometric profiling will also be used to examine the influence of psychological attributes on symptom development. The research will contribute to a better understanding of tick-borne diseases and improve diagnostic outcomes and treatment for patients bitten by ticks in Australia.
Article
Plant Sciences
Paula Moolhuijzen, Lilian M. V. P. Sanglard, David J. Paterson, Sean Gray, Karina Khambatta, Mark J. Hackett, Ayalsew Zerihun, Mark R. Gibberd, Fatima Naim
Summary: In susceptible wheat cultivars infected with Pyrenophora tritici-repentis, calcium oscillations are modified, resulting in frozen host defence signals and silencing of recognition and defence mechanisms. In contrast, resistant cultivars show heightened defence response and calcium accumulation at later stages of disease development. By using gene expression data and high-resolution elemental imaging, the study provides insights into spatial and temporal changes in the asymptomatic green region, highlighting the benefits of spatially resolved molecular analysis and nutrient mapping in understanding complex plant-pathogen interactions.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Selvam Paramasivan, Janna L. Morrison, Mitchell C. Lock, Jack R. T. Darby, Roberto A. Barrero, Paul C. Mills, Pawel Sadowski
Summary: Sequential window acquisition of all theoretical mass spectra-mass spectrometry, supported by advanced bioinformatics, provides a comprehensive framework for proteome analysis and biomarker discovery. However, the lack of a generic sample preparation platform for heterogeneous materials from different sources limits its broad application. We developed universal and fully automated workflows using a robotic sample preparation platform, enabling in-depth and reproducible proteome coverage of bovine and ovine specimens. The high correlation between sheep proteomics and transcriptomics datasets validates this development and suggests the potential for various clinical applications across different animal species and disease models.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Agronomy
Paula Moolhuijzen, Cynthia Ge, Elzette Palmiero, Simon R. R. Ellwood
Summary: Gene expression analysis revealed that RBgh2 plays a role in cAMP/G-protein-coupled signalling and innate immunity in barley powdery mildew adult plant resistance. RBgh2 is a major effect adult plant resistance gene in barley powdery mildew, showing different underlying genetic factors compared to conventional resistance genes. The resistance mechanism of RBgh2 involves temporary genome-wide gene expression changes and constitutive changes, especially at the RBgh2 locus, inducing defence-related genes associated with innate immunity and pathogen recognition.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Oncology
Chameera Ekanayake Weeramange, Kai Dun Tang, Roberto A. Barrero, Gunter Hartel, Zhen Liu, Rahul Ladwa, Julian Langton-Lockton, Ian Frazer, Lizbeth Kenny, Sarju Vasani, Chamindie Punyadeera
Summary: This study found that salivary microRNAs could be used for early detection and prognosis of oropharyngeal cancer, specifically the HPV-associated fraction. A panel of nine microRNAs was identified to effectively distinguish HPV-positive oropharyngeal cancer from HPV-positive controls, and a panel of six microRNAs was identified to distinguish oropharyngeal cancer from controls regardless of HPV status. Additionally, downregulation of hsa-miR-7-5p was associated with poor overall survival of oropharyngeal cancer patients, and a panel of nine microRNAs was identified to predict overall survival.
Article
Agriculture, Dairy & Animal Science
Muhammad Noman Naseem, Ali Raza, Muhammad Kamran, Rachel Allavena, Constantin Constantinoiu, Michael McGowan, Conny Turni, Ala E. E. Tabor, Peter James
Summary: Skin lesions in cattle associated with feeding by Haematobia fly species are a significant health issue in northern Australian cattle. This study found that differences in the hypersensitivity response to buffalo fly antigens is a key factor underlying the variation amongst the cattle in susceptibility-to-lesion development. Further understanding of the skin response could lead to the identification of biomarkers for selecting cattle with increased resistance to buffalo fly lesion development.
