@article {69594, title = {Activity of nested neural circuits drives different courtship songs in Drosophila.}, journal = {Nat Neurosci}, year = {2024}, month = {2024 Aug 28}, abstract = {

Motor systems implement diverse motor programs to pattern behavioral sequences, yet how different motor actions are controlled on a moment-by-moment basis remains unclear. Here, we investigated the neural circuit mechanisms underlying the control of distinct courtship songs in Drosophila. Courting males rapidly alternate between two types of song: pulse and sine. By recording calcium signals in the ventral nerve cord in singing flies, we found that one neural population is active during both songs, whereas an expanded neural population, which includes neurons from the first population, is active during pulse song. Brain recordings showed that this nested activation pattern is present in two descending pathways required for singing. Connectomic analysis reveals that these two descending pathways provide structured input to ventral nerve cord neurons in a manner consistent with their activation patterns. These results suggest that nested premotor circuit activity, directed by distinct descending signals, enables rapid switching between motor actions.

}, issn = {1546-1726}, doi = {10.1038/s41593-024-01738-9}, url = {https://doi.org/10.1038/s41593-024-01738-9}, author = {Shiozaki, Hiroshi M and Wang, Kaiyu and Lillvis, Joshua L and Xu, Min and Dickson, Barry J and Stern, David L} } @article {49128, title = {Accurate and sensitive quantification of protein-DNA binding affinity.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, year = {2018}, month = {2018 Apr 02}, pages = {E3692-701}, abstract = {

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

}, issn = {1091-6490}, doi = {10.1073/pnas.1714376115}, author = {Rastogi, Chaitanya and Rube, H Tomas and Kribelbauer, Judith F and Crocker, Justin and Loker, Ryan E and Martini, Gabriella D and Laptenko, Oleg and Freed-Pastor, William A and Prives, Carol and Stern, David L and Mann, Richard S and Bussemaker, Harmen J} } @article {45724, title = {Aphids evolved novel secreted proteins for symbiosis with bacterial endosymbiont.}, journal = {Proc Biol Sci}, volume = {280}, year = {2013}, month = {2013 Jan 7}, pages = {20121952}, abstract = {

Aphids evolved novel cells, called bacteriocytes, that differentiate specifically to harbour the obligatory mutualistic endosymbiotic bacteria Buchnera aphidicola. The genome of the host aphid Acyrthosiphon pisum contains many orphan genes that display no similarity with genes found in other sequenced organisms, prompting us to hypothesize that some of these orphan genes are related to lineage-specific traits, such as symbiosis. We conducted deep sequencing of bacteriocytes mRNA followed by whole mount in situ hybridizations of over-represented transcripts encoding aphid-specific orphan proteins. We identified a novel class of genes that encode small proteins with signal peptides, which are often cysteine-rich, that are over-represented in bacteriocytes. These genes are first expressed at a developmental time point coincident with the incorporation of symbionts strictly in the cells that contribute to the bacteriocyte and this bacteriocyte-specific expression is maintained throughout the aphid{\textquoteright}s life. The expression pattern suggests that recently evolved secretion proteins act within bacteriocytes, perhaps to mediate the symbiosis with beneficial bacterial partners, which is reminiscent of the evolution of novel cysteine-rich secreted proteins of leguminous plants that regulate nitrogen-fixing endosymbionts.

}, keywords = {Amino Acid Sequence, Animals, Aphids, Buchnera, DNA, Complementary, Evolution, Molecular, High-Throughput Nucleotide Sequencing, In Situ Hybridization, Insect Proteins, Protein Sorting Signals, RNA, Messenger, Sequence Alignment, Sequence Analysis, RNA, Symbiosis}, issn = {1471-2954}, doi = {10.1098/rspb.2012.1952}, author = {Shigenobu, Shuji and Stern, David L} } @article {45737, title = {Aphids.}, journal = {Curr Biol}, volume = {18}, year = {2008}, month = {2008 Jun 24}, pages = {R504-5}, abstract = {

Mammalian herbivores profoundly influence plant-dwelling insects [1]. Most studies have focused on the indirect effect of herbivory on insect populations via damage to the host plant [2,3]. Many insects, however, are in danger of being inadvertently ingested during herbivore feeding. Here, we report that pea aphids (Acyrthosiphon pisum) are able to sense the elevated heat and humidity of the breath of an approaching herbivore and thus salvage most of the colony by simultaneously dropping off the plant in large numbers immediately before the plant is eaten. Dropping entails the risk of losing the host plant and becoming desiccated or preyed upon on the ground [4,5], yet pea aphids may sporadically drop when threatened by insect enemies [6]. The immediate mass dropping, however, is an adaptation to the potential destructive impact of mammalian herbivory on the entire aphid colony. The combination of heat and humidity serves as a reliable cue to impending mammalian herbivory, enabling the aphids to avoid unnecessary dropping. No defensive behavior against incidental predation by herbivores has ever been demonstrated. The pea aphids{\textquoteright} highly adaptive escape behavior uniquely demonstrates the strength of the selective pressure large mammalian herbivores impose on insect herbivores.

}, keywords = {Animals, Aphids, Female, Genome, Insect, Insect Vectors, Male, Peas, Plant Diseases, Plant Tumors, Styrax}, issn = {0960-9822}, doi = {10.1016/j.cub.2008.03.034}, author = {Stern, David L} }