@article{coates_walden_lata_vellichirammal_mitchell_andersson_mckay_lorenzen_grubbs_wang_et al._2023, title={A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect}, volume={24}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-022-08990-y}, DOI={10.1186/s12864-022-08990-y}, abstractNote={Abstract}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Coates, Brad S. and Walden, Kimberly K. O. and Lata, Dimpal and Vellichirammal, Neetha Nanoth and Mitchell, Robert F. and Andersson, Martin N. and McKay, Rachel and Lorenzen, Marcé D. and Grubbs, Nathaniel and Wang, Yu-Hui and et al.}, year={2023}, month={Jan} }
 @article{chu_wu_pinzi_grubbs_cohen_lorenzen_2023, title={An Optimized Small-Scale Rearing System to Support Embryonic Microinjection Protocols for Western Corn Rootworm, Diabrotica virgifera virgifera}, volume={14}, ISSN={2075-4450}, url={http://dx.doi.org/10.3390/insects14080683}, DOI={10.3390/insects14080683}, abstractNote={Western corn rootworm (WCR), a major pest of corn, has been reared in laboratories since the 1960s. While established rearing methods are appropriate for maintaining WCR colonies, they are not optimal for performing germline transformation or CRISPR/Cas9-based genome editing. Here we report the development of an optimized rearing system for use in WCR functional genomics research, specifically the development of a system that facilitates the collection of preblastoderm embryos for microinjection as well as gathering large larvae and pupae for downstream phenotypic screening. Further, transgenic-based experiments require stable and well-defined survival rates and the ability to manipulate insects at every life stage. In our system, the WCR life cycle (egg to adult) takes approximately 42 days, with most individuals eclosing between 41 and 45 days post oviposition. Over the course of one year, our overall survival rate was 67%. We used this data to establish a quality control system for more accurately monitoring colony health. Herein, we also offer detailed descriptions for setting up single-pair crosses and conducting phenotypic screens to identify transgenic progeny. This study provides a model for the development of new rearing systems and the establishment of highly controlled processes for specialized purposes.}, number={8}, journal={Insects}, publisher={MDPI AG}, author={Chu, Fu-Chyun and Wu, Pei-Shan and Pinzi, Sofia and Grubbs, Nathaniel and Cohen, Allen Carson and Lorenzen, Marcé D.}, year={2023}, month={Aug}, pages={683} }
 @article{klobasa_chu_huot_grubbs_rotenberg_whitfield_lorenzen_2021, title={Microinjection of Corn Planthopper, <em>Peregrinus maidis</em>, Embryos for CRISPR/Cas9 Genome Editing}, volume={3}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/62417}, DOI={10.3791/62417}, abstractNote={The corn planthopper, Peregrinus maidis, is a pest of maize and a vector of several maize viruses. Previously published methods describe the triggering of RNA interference (RNAi) in P. maidis through microinjection of double-stranded RNAs (dsRNAs) into nymphs and adults. Despite the power of RNAi, phenotypes generated via this technique are transient and lack long-term Mendelian inheritance. Therefore, the P. maidis toolbox needs to be expanded to include functional genomic tools that would enable the production of stable mutant strains, opening the door for researchers to bring new control methods to bear on this economically important pest. However, unlike the dsRNAs used for RNAi, the components used in CRISPR/Cas9-based genome editing and germline transformation do not easily cross cell membranes. As a result, plasmid DNAs, RNAs, and/or proteins must be microinjected into embryos before the embryo cellularizes, making the timing of injection a critical factor for success. To that end, an agarose-based egg-lay method was developed to allow embryos to be harvested from P. maidis females at relatively short intervals. Herein are provided detailed protocols for collecting and microinjecting precellular P. maidis embryos with CRISPR components (Cas9 nuclease that has been complexed with guide RNAs), and results of Cas9-based gene knockout of a P. maidis eye-color gene, white, are presented. Although these protocols describe CRISPR/Cas9-genome editing in P. maidis, they can also be used for producing transgenic P. maidis via germline transformation by simply changing the composition of the injection solution.}, number={169}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Klobasa, William and Chu, Fu-Chyun and Huot, Ordom and Grubbs, Nathaniel and Rotenberg, Dorith and Whitfield, Anna E. and Lorenzen, Marcé D.}, year={2021}, month={Mar} }
 @article{german_lorenzen_grubbs_whitfield_2020, title={New Technologies for Studying Negative-Strand RNA Viruses in Plant and Arthropod Hosts}, volume={33}, ISSN={0894-0282 1943-7706}, url={http://dx.doi.org/10.1094/MPMI-10-19-0281-FI}, DOI={10.1094/MPMI-10-19-0281-FI}, abstractNote={ The plant viruses in the phylum Negarnaviricota, orders Bunyavirales and Mononegavirales, have common features of single-stranded, negative-sense RNA genomes and replication in the biological vector. Due to the similarities in biology, comparative functional analysis in plant and vector hosts is helpful for understanding host–virus interactions for negative-strand RNA viruses. In this review, we will highlight recent technological advances that are breaking new ground in the study of these recalcitrant virus systems. The development of infectious clones for plant rhabdoviruses and bunyaviruses is enabling unprecedented examination of gene function in plants and these advances are also being transferred to study virus biology in the vector. In addition, genome and transcriptome projects for critical nonmodel arthropods has enabled characterization of insect response to viruses and identification of interacting proteins. Functional analysis of genes using genome editing will provide future pathways for further study of the transmission cycle and new control strategies for these viruses and their vectors. }, number={3}, journal={Molecular Plant-Microbe Interactions®}, publisher={Scientific Societies}, author={German, Thomas L. and Lorenzen, Marcé D. and Grubbs, Nathaniel and Whitfield, Anna E.}, year={2020}, month={Mar}, pages={382–393} }
 @article{adedipe_grubbs_coates_wiegmman_lorenzen_2019, title={Structural and functional insights into the Diabrotica virgifera virgifera ATP-binding cassette transporter gene family}, volume={20}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-019-6218-8}, DOI={10.1186/s12864-019-6218-8}, abstractNote={Abstract}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Adedipe, Folukemi and Grubbs, Nathaniel and Coates, Brad and Wiegmman, Brian and Lorenzen, Marcé}, year={2019}, month={Nov} }
 @article{evans_mckenna_scully_cook_dainat_egekwu_grubbs_lopez_lorenzen_reyna_et al._2018, title={Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory}, volume={7}, ISSN={2047-217X}, url={http://dx.doi.org/10.1093/gigascience/giy138}, DOI={10.1093/gigascience/giy138}, abstractNote={Abstract Background The small hive beetle (Aethina tumida; ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. We have sequenced and annotated the ATUMI genome, providing the first genomic resources for this species and for the Nitidulidae, a beetle family that is closely related to the extraordinarily species-rich clade of beetles known as the Phytophaga. ATUMI thus provides a contrasting view as a neighbor for one of the most successful known animal groups. Results We present a robust genome assembly and a gene set possessing 97.5% of the core proteins known from the holometabolous insects. The ATUMI genome encodes fewer enzymes for plant digestion than the genomes of wood-feeding beetles but nonetheless shows signs of broad metabolic plasticity. Gustatory receptors are few in number compared to other beetles, especially receptors with known sensitivity (in other beetles) to bitter substances. In contrast, several gene families implicated in detoxification of insecticides and adaptation to diverse dietary resources show increased copy numbers. The presence and diversity of homologs involved in detoxification differ substantially from the bee hosts of ATUMI. Conclusions Our results provide new insights into the genomic basis for local adaption and invasiveness in ATUMI and a blueprint for control strategies that target this pest without harming their honey bee hosts. A minimal set of gustatory receptors is consistent with the observation that, once a host colony is invaded, food resources are predictable. Unique detoxification pathways and pathway members can help identify which treatments might control this species even in the presence of honey bees, which are notoriously sensitive to pesticides.}, number={12}, journal={GigaScience}, publisher={Oxford University Press (OUP)}, author={Evans, Jay D and McKenna, Duane and Scully, Erin and Cook, Steven C and Dainat, Benjamin and Egekwu, Noble and Grubbs, Nathaniel and Lopez, Dawn and Lorenzen, Marcé D and Reyna, Steven M and et al.}, year={2018}, month={Dec} }
 @article{chu_wu_pinzi_grubbs_lorenzen_2018, title={Microinjection of Western Corn Rootworm, <em>Diabrotica virgifera virgifera</em>, Embryos for Germline Transformation, or CRISPR/Cas9 Genome Editing}, ISSN={1940-087X}, url={http://dx.doi.org/10.3791/57497}, DOI={10.3791/57497}, abstractNote={The western corn rootworm (WCR) is an important pest of corn and is well known for its ability to rapidly adapt to pest management strategies. Although RNA interference (RNAi) has proved to be a powerful tool for studying WCR biology, it has its limitations. Specifically, RNAi itself is transient (i.e. does not result in long-term Mendelian inheritance of the associated phenotype), and it requires knowing the DNA sequence of the target gene. The latter can be limiting if the phenotype of interest is controlled by poorly conserved, or even novel genes, because identifying useful targets would be challenging, if not impossible. Therefore, the number of tools in WCR's genomic toolbox should be expanded by the development of methods that could be used to create stable mutant strains and enable sequence-independent surveys of the WCR genome. Herein, we detail the methods used to collect and microinject precellular WCR embryos with nucleic acids. While the protocols described herein are aimed at the creation of transgenic WCR, CRISPR/Cas9-genome editing could also be performed using the same protocols, with the only difference being the composition of the solution injected into the embryos.}, number={134}, journal={Journal of Visualized Experiments}, publisher={MyJove Corporation}, author={Chu, Fu-Chyun and Wu, Pei-Shan and Pinzi, Sofia and Grubbs, Nathaniel and Lorenzen, Marcé D.}, year={2018}, month={Apr} }
 @article{scott_gould_lorenzen_grubbs_edwards_o’brochta_2017, title={Agricultural production: assessment of the potential use of Cas9-mediated gene drive systems for agricultural pest control}, volume={5}, ISSN={2329-9460 2329-9037}, url={http://dx.doi.org/10.1080/23299460.2017.1410343}, DOI={10.1080/23299460.2017.1410343}, abstractNote={ABSTRACTTo highlight how gene drives could be useful for control of agricultural insect pests, we selected species that are pests of animals (New World screwworm), plants (spotted wing Drosophila, ...}, number={sup1}, journal={Journal of Responsible Innovation}, publisher={Informa UK Limited}, author={Scott, Maxwell J. and Gould, Fred and Lorenzen, Marcé and Grubbs, Nathaniel and Edwards, Owain and O’Brochta, David}, year={2017}, month={Dec}, pages={S98–S120} }
 @article{chu_klobasa_grubbs_lorenzen_2017, title={Development and use of a piggyBac
-based jumpstarter system in Drosophila suzukii}, volume={97}, ISSN={0739-4462}, url={http://dx.doi.org/10.1002/arch.21439}, DOI={10.1002/arch.21439}, abstractNote={Abstract}, number={3}, journal={Archives of Insect Biochemistry and Physiology}, publisher={Wiley}, author={Chu, Fu-Chyun and Klobasa, William and Grubbs, Nathaniel and Lorenzen, Marcé D.}, year={2017}, month={Dec}, pages={e21439} }
 @article{chu_klobasa_wu_pinzi_grubbs_gorski_cardoza_lorenzen_2017, title={Germline transformation of the western corn rootworm, Diabrotica virgifera virgifera}, volume={26}, ISSN={0962-1075}, url={http://dx.doi.org/10.1111/imb.12305}, DOI={10.1111/imb.12305}, abstractNote={Abstract}, number={4}, journal={Insect Molecular Biology}, publisher={Wiley}, author={Chu, F. and Klobasa, W. and Wu, P. and Pinzi, S. and Grubbs, N. and Gorski, S. and Cardoza, Y. and Lorenzen, M. D.}, year={2017}, month={Apr}, pages={440–452} }
 @article{grubbs_haas_beeman_lorenzen_2015, title={The ABCs of Eye Color in Tribolium castaneum: Orthologs of the Drosophila white, scarlet, and brown Genes}, volume={199}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.114.173971}, abstractNote={Abstract}, number={3}, journal={GENETICS}, author={Grubbs, Nathaniel and Haas, Sue and Beeman, Richard W. and Lorenzen, Marce D.}, year={2015}, month={Mar}, pages={749-+} }
 @article{grubbs_leach_su_petrisko_rosario_mahaffey_2013, title={New Components of Drosophila Leg Development Identified through Genome Wide Association Studies}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0060261}, abstractNote={The adult Drosophila melanogaster body develops from imaginal discs, groups of cells set-aside during embryogenesis and expanded in number during larval stages. Specification and development of Drosophila imaginal discs have been studied for many years as models of morphogenesis. These studies are often based on mutations with large developmental effects, mutations that are often lethal in embryos when homozygous. Such forward genetic screens can be limited by factors such as early lethality and genetic redundancy. To identify additional genes and genetic pathways involved in leg imaginal disc development, we employed a Genome Wide Association Study utilizing the natural genetic variation in leg proportionality found in the Drosophila Genetic Reference Panel fly lines. In addition to identifying genes already known to be involved in leg development, we identified several genes involved in pathways that had not previously been linked with leg development. Several of the genes appear to be involved in signaling activities, while others have no known roles at this time. Many of these uncharacterized genes are conserved in mammals, so we can now begin to place these genes into developmental contexts. Interestingly, we identified five genes which, when their function is reduced by RNAi, cause an antenna-to-leg transformation. Our results demonstrate the utility of this approach, integrating the tools of quantitative and molecular genetics to study developmental processes, and provide new insights into the pathways and networks involved in Drosophila leg development.}, number={4}, journal={PLOS ONE}, author={Grubbs, Nathaniel and Leach, Megan and Su, Xin and Petrisko, Tiffany and Rosario, Juan B. and Mahaffey, James W.}, year={2013}, month={Apr} }
 @misc{heffer_grubbs_mahaffey_pick_2013, title={The evolving role of the orphan nuclear receptor ftz-f1, a pair-rule segmentation gene}, volume={15}, ISSN={["1525-142X"]}, DOI={10.1111/ede.12050}, abstractNote={SUMMARY}, number={6}, journal={EVOLUTION & DEVELOPMENT}, author={Heffer, Alison and Grubbs, Nathaniel and Mahaffey, James and Pick, Leslie}, year={2013}, month={Nov}, pages={406–417} }
 @article{patel_farzana_robertson_hutchinson_grubbs_shepherd_mahaffey_2007, title={The appendage role of insect disco genes and possible implications on the evolution of the maggot larval form}, volume={309}, ISSN={["0012-1606"]}, DOI={10.1016/j.ydbio.2007.06.017}, abstractNote={Though initially identified as necessary for neural migration, Disconnected and its partially redundant paralog, Disco-related, are required for proper head segment identity during Drosophila embryogenesis. Here, we present evidence that these genes are also required for proper ventral appendage development during development of the adult fly, where they specify medial to distal appendage development. Cells lacking the disco genes cannot contribute to the medial and distal portions of ventral appendages. Further, ectopic disco transforms dorsal appendages toward ventral fates; in wing discs, the medial and distal leg development pathways are activated. Interestingly, this appendage role is conserved in the red flour beetle, Tribolium (where legs develop during embryogenesis), yet in the beetle we found no evidence for a head segmentation role. The lack of an embryonic head specification role in Tribolium could be interpreted as a loss of the head segmentation function in Tribolium or gain of this function during evolution of flies. However, we suggest an alternative explanation. We propose that the disco genes always function as appendage factors, but their appendage nature is masked during Drosophila embryogenesis due to the reduction of limb fields in the maggot style Drosophila larva.}, number={1}, journal={DEVELOPMENTAL BIOLOGY}, author={Patel, Mukund and Farzana, Laila and Robertson, Lisa K. and Hutchinson, Jennifer and Grubbs, Nathaniel and Shepherd, Mark N. and Mahaffey, James W.}, year={2007}, month={Sep}, pages={56–69} }