by Yu-Hui Wang, Dina Espinoza Rivera, William Klobasa, Marcé D. Lorenzen The corn planthopper, Peregrinus maidis, is an economically important pest of corn and sorghum. Here we report the initial steps towards developing a CRISPR-based control method, precision guided sterile insect technique (pgSIT), for this hemipteran pest. Specifically, we evaluated the potential of transformer-2 (tra-2) as a target for sterilizing insects. First, we identified tra-2 transcripts within our P. maidis transcriptome database and performed RNA interference (RNAi) to confirm functional conservation. RNAi-mediat ..read more

by Mohammad J. Hossain, Tamara J. O’Connor The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) are widely used for genome editing in cultured cell lines. However, the implementation of genome editing is still challenging due to the complex and often costly multi-step process associated with this technique. Moreover, the efficiency of genome editing varies across cell types, often limiting utility. Herein, we describe pCRISPR-EASY, a vector for simplified cloning of single guide RNAs (sgRNAs) and its simultaneous introduction with CRISPR ..read more

by Alejandro Miguel Cisneros-Martínez, Ulises E. Rodriguez-Cruz, Luis D. Alcaraz, Arturo Becerra, Luis E. Eguiarte, Valeria Souza Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed virus-host prediction tools on a dataset of 1,046 virus-host pairs and then apply the best-performing tools to a metageno ..read more

by Aidan O’Brien, Denis C. Bauer, Gaetan Burgio Genome editing through the development of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat)–Cas technology has revolutionized many fields in biology. Beyond Cas9 nucleases, Cas12a (formerly Cpf1) has emerged as a promising alternative to Cas9 for editing AT-rich genomes. Despite the promises, guide RNA efficiency prediction through computational tools search still lacks accuracy. Through a computational meta-analysis, here we report that Cas12a target and off-target cleavage behavior are a factor of nucleotide bias combined with n ..read more

by Shubhada Shenai, Gita Nataraj, Minal Jinwal, Akhil S. Thekke Purakkal, Rajashree Sen, Nayana Ingole, Trupti Mathure, Sanjay Sarin, Sarabjit S. Chadha Background Tata MD CHECK SARS-CoV-2 kit 1.0, a CRISPR based reverse transcription PCR (TMC-CRISPR) test was approved by Indian Council of Medical Research (ICMR) for COVID-19 diagnosis in India. To determine the potential for rapid roll-out of this test, we conducted performance characteristic and an operational feasibility assessment (OFA) at a tertiary care setting. Intervention The study was conducted at an ICMR approved COVID-19 RT-PCR lab ..read more

by Omer Benjakob, Olha Guley, Jean-Marc Sevin, Leo Blondel, Ariane Augustoni, Matthieu Collet, Louise Jouveshomme, Roy Amit, Ariel Linder, Rona Aviram Rapid developments and methodological divides hinder the study of how scientific knowledge accumulates, consolidates and transfers to the public sphere. Our work proposes using Wikipedia, the online encyclopedia, as a historiographical source for contemporary science. We chose the high-profile field of gene editing as our test case, performing a historical analysis of the English-language Wikipedia articles on CRISPR. Using a mixed-method approa ..read more

by Daniel A. Kuppers, Jonathan Linton, Sergio Ortiz Espinosa, Kelly M. McKenna, Anthony Rongvaux, Patrick J. Paddison Human CD34+ hematopoietic stem and progenitor cells (HSPCs) are a standard source of cells for clinical HSC transplantations as well as experimental xenotransplantation to generate “humanized mice”. To further extend the range of applications of these humanized mice, we developed a protocol to efficiently edit the genomes of human CD34+ HSPCs before transplantation. In the past, manipulating HSPCs has been complicated by the fact that they are inherently difficult to transduce ..read more

by Mohammadreza Paraan, Mohamed Nasef, Lucy Chou-Zheng, Sarah A. Khweis, Allyn J. Schoeffler, Asma Hatoum-Aslan, Scott M. Stagg, Jack A. Dunkle Type III CRISPR-Cas systems employ multiprotein effector complexes bound to small CRISPR RNAs (crRNAs) to detect foreign RNA transcripts and elicit a complex immune response that leads to the destruction of invading RNA and DNA. Type III systems are among the most widespread in nature, and emerging interest in harnessing these systems for biotechnology applications highlights the need for detailed structural analyses of representatives from diverse org ..read more

by Ikuko Nakajima, Hiroyuki Kawahigashi, Chikako Nishitani, Akifumi Azuma, Takashi Haji, Seiichi Toki, Masaki Endo Transposition of transposable elements affect expression levels, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus. For example, in grape, presence of the Gret1 retrotransposon in the promoter region of the VvMYBA1a allele at the VvMYBA1 locus suppress the expression of the VvMYBA1 transcription factor gene for the anthocyanin biosynthesis and this transposon insertion is responsible for the green berry skin color of Vitis labras ..read more

by Aya Bridgeland, Sudip Biswas, Nikolaos Tsakirpaloglou, Michael J. Thomson, Endang M. Septiningsih Cowpea (Vigna unguiculata) is a legume staple widely grown across Sub-Saharan Africa and other tropical and sub-tropical regions. Considering projected climate change and global population increases, cowpea’s adaptation to hot climates, resistance to drought, and nitrogen-fixing capabilities make it an especially attractive crop for facing future challenges. Despite these beneficial traits, efficient varietal improvement is challenging in cowpea due to its recalcitrance to transformation and lo ..read more