DNA sequencing in the classroom: complete genome sequence of two earwig (Dermaptera; Insecta) species

CRISPR/Cas9 gene targeting plus nanopore DNA sequencing with the plasmid pBR322 in the classroom

Both nanopore-based DNA sequencing and CRISPR/Cas-based gene editing represent groundbreaking innovations in molecular biology and genomics, offering unprecedented insights into and tools for working with genetic information. For students, reading, editing, and even writing DNA will be part of their everyday life. We have developed a laboratory procedure that includes (i) the biosynthesis of a guide RNA for, (ii) targeting Cas9 to specifically linearize the pBR322 plasmid, and (iii) the identification of the cutting site through nanopore DNA sequencing. The protocol is intentionally kept simple and requires neither living organisms nor biosafety laboratories. We divided the experimental procedures into separate activities to facilitate customization. Assuming access to a well-equipped molecular biology laboratory, an initial investment of approximately $2,700 is necessary. The material costs for each experiment group amount to around $130. Furthermore, we have developed a freely accessible website (https://dnalesen.hs-mittweida.de) for sequence read analysis and visualization, lowering the required computational skills to a minimum. For those with strong computational skills, we provide instructions for terminal-based data processing. With the presented activities, we aim to provide a hands-on experiment that engages students in modern molecular genetics and motivates them to discuss potential implications. The complete experiment can be accomplished within half a day and has been successfully implemented by us at high schools, in teacher training, and at universities. Our tip is to combine CRISPR/Cas gene targeting with nanopore-based DNA sequencing. As a tool, we provide a website that facilitates sequence data analysis and visualization.

Molecular identification of Hymenopteran insects collected by using Malaise traps from Hazarganji Chiltan National Park Quetta, Pakistan

The order Hymenoptera holds great significance for humans, particularly in tropical and subtropical regions, due to its role as a pollinator of wild and cultivated flowering plants, parasites of destructive insects and honey producers. Despite this importance, limited attention has been given to the genetic diversity and molecular identification of Hymenopteran insects in most protected areas. This study provides insights into the first DNA barcode of Hymenopteran insects collected from Hazarganji Chiltan National Park (HCNP) and contributes to the global reference library of DNA barcodes. A total of 784 insect specimens were collected using Malaise traps, out of which 538 (68.62%) specimens were morphologically identified as Hymenopteran insects. The highest abundance of species of Hymenoptera (133/538, 24.72%) was observed during August and least in November (16/538, 2.97%). Genomic DNA extraction was performed individually from 90/538 (16.73%) morphologically identified specimens using the standard phenol-chloroform method, which were subjected separately to the PCR for their molecular confirmation via the amplification of cytochrome c oxidase subunit 1 (cox1) gene. The BLAST analyses of obtained sequences showed 91.64% to 100% identities with related sequences and clustered phylogenetically with their corresponding sequences that were reported from Australia, Bulgaria, Canada, Finland, Germany, India, Israel, and Pakistan. Additionally, total of 13 barcode index numbers (BINs) were assigned by Barcode of Life Data Systems (BOLD), out of which 12 were un-unique and one was unique (BOLD: AEU1239) which was assigned for Anthidium punctatum. This indicates the potential geographical variation of Hymenopteran population in HCNP. Further comprehensive studies are needed to molecularly confirm the existing insect species in HCNP and evaluate their impacts on the environment, both as beneficial (for example, pollination, honey producers and natural enemies) and detrimental (for example, venomous stings, crop damage, and pathogens transmission).

The Molecular Resistance Mechanisms of European Earwigs from Apple Orchards Subjected to Different Management Strategies

To date, apple orchards are among the most treated crops in Europe with up to 35 chemical treatments per year. Combining control methods that reduce the number of pesticide treatments is essential for agriculture and more respectful of the environment, and the use of predatory insects such as earwigs may be valuable to achieve this goal. European earwigs, Forficula auricularia (Dermaptera: Forficulidae) are considered beneficial insects in apple orchards where they can feed on many pests like aphids. The aim of this study was to investigate the potential impact of orchards' insecticide treatments on resistance-associated molecular processes in natural populations of earwigs. Because very few molecular data are presently available on earwigs, our first goal was to identify earwig resistance-associated genes and potential mutations. Using earwigs from organic, integrated pest management or conventional orchards, we identified mutations in acetylcholinesterase 2, α1 and β2 nicotinic acetylcholine receptors. In addition, the expression level of these targets and of some essential detoxification genes were monitored using RT-qPCR. Unexpectedly, earwigs collected in organic orchards showed the highest expression for acetylcholinesterase 2. Four cytochromes P450, one esterase and one glutathione S-transferases were over-expressed in earwigs exposed to various management strategies in orchards. This first study on resistance-associated genes in Forficula auricularia paves the way for future experimental studies aimed at better understanding the potential competition between natural enemies in apple orchards in order to optimize the efficiency of biocontrol.