BBE Publications October - December 2023 - Biology and Biological Engineering

Zhang, Yameng; Pool, Allan-Hermann; et el. (2023) Parallel neural pathways control sodium consumption and taste valence; Cell; Vol. 186; No. 26; 5751-5765.e16; 10.1016/j.cell.2023.10.020
Nava, Stephanie; Palma, Wilber; et el. (2023) A cGAL-UAS bipartite expression toolkit for Caenorhabditis elegans sensory neurons; Proceedings of the National Academy of Sciences; Vol. 120; No. 51; e2221680120; 10.1073/pnas.2221680120
Osorio-Rodriguez, Daniela; Metcalfe, Kyle S.; et el. (2023) Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation; Proceedings of the National Academy of Sciences; Vol. 120; No. 51; e2302156120; 10.1073/pnas.230215612
Guo, Hongsun; Salahshoor, Hossein; et el. (2023) Effects of focused ultrasound in a "clean" mouse model of ultrasonic neuromodulation; PMCID PMC10690554; 10.1016/j.isci.2023.108372
Sperling, Alexis L. and Glover, David M. (2023) Protocol for screening facultative parthenogenesis in Drosophila; STAR Protocols; Vol. 4; No. 4; 102585; PMCID PMC10520562; 10.1016/j.xpro.2023.102585
Schwartz, Hillel T.; Tan, Chieh-Hsiang; et el. (2023) Molecular identification of a peroxidase gene controlling body size in the entomopathogenic nematode Steinernema hermaphroditum; Genetics; 10.1093/genetics/iyad209
Zhang, Bao; He, Peng; et el. (2023) A human embryonic limb cell atlas resolved in space and time; Nature; 10.1038/s41586-023-06806-x
Zernicka-Goetz, Magdalena (2023) The evolution of embryo models; Nature Methods; 10.1038/s41592-023-02077-6
Sader, John E.; Stassi, Stefano; et el. (2023) Effect of intramodal and intermodal nonlinearities on the flexural resonant frequencies of cantilevered beams; Physical Review B; Vol. 108; No. 22; 224303; 10.1103/physrevb.108.224303
Lau, Kasey Y. C.; Amadei, Gianluca; et el. (2023) Assembly of complete mouse embryo models from embryonic and induced stem cell types in vitro; Nature Protocols; Vol. 18; No. 12; 3662-3689; 10.1038/s41596-023-00891-y
Shao, Shuai; Meister, Markus; et el. (2023) Efficient population coding of sensory stimuli; Physical Review Research; Vol. 5; No. 4; 043205; 10.1103/physrevresearch.5.043205
Nemet, Ina; Funabashi, Masanori; et el. (2023) Microbe-derived uremic solutes enhance thrombosis potential in the host; mBio; Vol. 14; No. 6; e01331-23; 10.7907/ha07h-ryw11
Bult, Carol J. and Sternberg, Paul W. (2023) The alliance of genome resources: transforming comparative genomics; Mammalian Genome; Vol. 34; No. 4; 531-544; PMCID PMC10628019; 10.1007/s00335-023-10015-2
Tropini, Carolina; Finlay, B. Brett; et el. (2023) Time to rethink academic publishing: the peer reviewer crisis; mBio; Vol. 14; No. 6; e01091-23; 10.1128/mbio.01091-23
Griggs, Whitney S.; Norman, Sumner L.; et el. (2023) Decoding motor plans using a closed-loop ultrasonic brain–machine interface; Nature Neuroscience; 10.1038/s41593-023-01500-7
Dam, Kim-Marie A.; Fan, Chengcheng; et el. (2023) Intermediate conformations of CD4-bound HIV-1 Env heterotrimers; Nature; Vol. 623; No. 7989; 1017-1025; 10.1038/s41586-023-06639-8
Sperling, A. L. and Glover, D. M. (2023) Aneuploidy during development in facultative parthenogenetic Drosophila; Heredity; 10.1038/s41437-023-00664-z
Shin, Boyoung; Zhou, Wen; et el. (2023) Author Correction: Runx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms; Nature Immunology; Vol. 24; 1458–1472; 10.1038/s41590-023-01716-6
Tsypin, Lev M. Z.; Saunders, Scott H.; et el. (2023) Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation; 10.1101/2023.11.14.567096
Godneeva, Baira; Ninova, Maria; et el. (2023) SUMOylation of Bonus, the Drosophila homolog of Transcription Intermediary Factor 1, safeguards germline identity by recruiting repressive chromatin complexes to silence tissue-specific genes; eLife; Vol. 12; RP89493; PMCID PMC10672805; 10.7554/elife.89493
Banerjee, Navonil; Rojas Palato, Elisa J.; et el. (2023) Distinct neurogenetic mechanisms establish the same chemosensory valence state at different life stages in Caenorhabditis elegans; G3: Genes, Genomes, Genetics; 10.1093/g3journal/jkad271
Tropini, Carolina; Finlay, B. Brett; et el. (2023) Time to rethink academic publishing: the peer reviewer crisis; 10.1128/mbio.01091-23
Stevens, Taylor Anthony; Pinton Tomaleri, Giovani; et el. (2023) A nanobody-based strategy for rapid and scalable purification of human protein complexes; Nature Protocols; 10.1038/s41596-023-00904-w
Prakash, Sharan J.; Van Auken, Kimberly M.; et el. (2023) Semantic representation of neural circuit knowledge in Caenorhabditis elegans; Brain Informatics; Vol. 10; 30; PMCID PMC10638142; 10.1186/s40708-023-00208-5
Xiong, Lingyun; Liu, Jing; et el. (2023) Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney; Developmental Cell; Vol. 58; No. 21; 2338-2358.e5; 10.1016/j.devcel.2023.08.010
Spolski, Rosanne; Li, Peng; et el. (2023) Distinct use of super-enhancer elements controls cell type–specific CD25 transcription and function; Science Immunology; Vol. 8; No. 89; eadi8217; 10.1126/sciimmunol.adi8217
Mao, Runze; Taylor, Doris Mia; et el. (2023) Biocatalytic, stereoconvergent alkylation of (Z/E)-trisubstituted silyl enol ethers; Nature Synthesis; 10.1038/s44160-023-00431-2
Salahshoor, Hossein; Yao, Yuxing; et el. (2023) Geometric effects in gas vesicle buckling under ultrasound; Biophysical Journal; Vol. 121; No. 21; 4221-4228; PMCID PMC9674984; 10.1016/j.bpj.2022.09.004
Gorin, Gennady; Yoshida, Shawn; et el. (2023) Assessing Markovian and Delay Models for Single-Nucleus RNA Sequencing; Bulletin of Mathematical Biology; Vol. 85; No. 11; 114; 10.1007/s11538-023-01213-9
Moyers, Belle A.; Partridge, E. Christopher; et el. (2023) Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells; Genome Research; Vol. 33; No. 11; 1879-1892; PMCID PMC10760452; 10.1101/gr.278205.123
Godneeva, Baira; Fejes Toth, Katalin; et el. (2023) Impact of Germline Depletion of Bonus on Chromatin State in Drosophila Ovaries; Cells; Vol. 12; No. 22; 2629; PMCID PMC10670193; 10.3390/cells12222629
Sun, Jingjing; Zhang, Chen; et el. (2023) Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm; Cell Reports; Vol. 42; No. 10; 113289; PMCID PMC10704487; 10.1016/j.celrep.2023.113289
Guna, Alina; Page, Katharine R.; et el. (2023) A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens; BMC Genomics; Vol. 24; 651; PMCID PMC10614335; 10.1186/s12864-023-09754-y
Mah-Som, Annelise Y.; Daw, Jil; et el. (2023) An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP; American Journal of Human Genetics; 10.1016/j.ajhg.2023.10.007
Henrickson, Amy; Ding, Xiaozhe; et el. (2023) Characterization and quantification of adeno-associated virus capsid-loading states by multi-wavelength analytical ultracentrifugation with UltraScan; Nanomedicine; 10.2217/nnm-2023-0156
Jacobs-Li, Jessica; Tang, Weiyi; et el. (2023) Single-cell profiling coupled with lineage analysis reveals vagal and sacral neural crest contributions to the developing enteric nervous system; eLife; Vol. 12; e79156; PMCID PMC10627514; 10.7554/elife.79156
Luo, Yicheng; He, Peng; et el. (2023) Maternally inherited siRNAs initiate piRNA cluster formation; Molecular Cell; 10.1016/j.molcel.2023.09.033
Kahan, Anat; Mahe, Karan; et el. (2023) Immediate responses to ambient light in vivo reveal distinct subpopulations of suprachiasmatic VIP neurons; iScience; Vol. 26; No. 10; 107865; PMCID PMC10520357; 10.1016/j.isci.2023.107865
Gorin, Gennady; Vastola, John J.; et el. (2023) Studying stochastic systems biology of the cell with single-cell genomics data; Cell Systems; Vol. 14; No. 10; 822-843.e22; PMCID PMC10725240; 10.1016/j.cels.2023.08.004
Yang, Zheng and Chan, David C. (2023) Control of mitochondrial dynamics by a fusogenic lipid; Trends in Cell Biology; 10.1016/j.tcb.2023.10.006
Wang, Renée Z.; Lonergan, Zachery R.; et el. (2023) Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N₂O under anoxia; PMCID PMC10592819; 10.1101/2023.10.13.562248
Mohanty, Atish; Nam, Arin; et el. (2023) Acquired resistance to KRAS G12C small-molecule inhibitors via genetic/nongenetic mechanisms in lung cancer; Science Advances; Vol. 9; No. 41; eade3816; PMCID PMC10575592; 10.1126/sciadv.ade3816
Wu-Woods, Natalie J.; Barlow, Jacob T.; et el. (2023) Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples; Nature Methods; 10.1038/s41592-023-02025-4
Hung, Shao-Min; Adams, Sara W.; et el. (2023) Practice makes imperfect: stronger implicit interference with practice in individuals at high risk of developing Alzheimer's disease; GeroScience; 10.1007/s11357-023-00953-9
Albright, Thomas D.; Baltimore, David; et el. (2023) Science, evidence, law, and justice; Proceedings of the National Academy of Sciences; Vol. 120; No. 41; e2312529120; PMCID PMC10576109; 10.1073/pnas.2312529120
Cohen, Alexander A.; van Doremalen, Neeltje; et el. (2023) Mosaic RBD nanoparticles protect against multiple sarbecovirus challenges in animal models; PMCID PMC8978945; 10.1101/2022.03.25.485875
Afik, Eldad; Liu, Toni J. B.; et el. (2023) Macroscopic waves, biological clocks and morphogenesis driven by light in a giant unicellular green alga; Nature Communications; Vol. 14; 6204; PMCID PMC10550971; 10.1038/s41467-023-41813-6
Blumenfeld, Zack; Bera, Kallol; et el. (2023) Antidepressants enter cells, organelles, and membranes; Neuropsychopharmacology; 10.1038/s41386-023-01725-x
Lamanna, Francesco; Hervas-Sotomayor, Francisca; et el. (2023) A lamprey neural cell type atlas illuminates the origins of the vertebrate brain; Nature Ecology & Evolution; Vol. 7; No. 10; 1714-1728; PMCID PMC10555824; 10.1038/s41559-023-02170-1
Venkei, Zsolt G.; Gainetdinov, Ildar; et el. (2023) A maternally programmed intergenerational mechanism enables male offspring to make piRNAs from Y-linked precursor RNAs in Drosophila; Nature Cell Biology; Vol. 25; No. 10; 1495-1505; PMCID PMC10567549; 10.1038/s41556-023-01227-4
Tu, Jiaobing; Min, Jihong; et el. (2023) A wireless patch for the monitoring of C-reactive protein in sweat; Nature Biomedical Engineering; Vol. 7; No. 10; 1293-1306; PMCID PMC10592261; 10.1038/s41551-023-01059-5
Chuapoco, Miguel R.; Flytzanis, Nicholas C.; et el. (2023) Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain; Nature Nanotechnology; Vol. 18; No. 10; 1241-1251; PMCID PMC10575780; 10.1038/s41565-023-01419-x
Schiava, Marianela; Ikenaga, Chiseko; et el. (2023) Clinical Classification of Variants in the Valosin-Containing Protein Gene Associated With Multisystem Proteinopathy; Neurology Genetics; Vol. 9; No. 5; e200093; 10.1212/nxg.0000000000200093
Ji, Jenny; Viloria Winnett, Alexander; et el. (2023) Index cases first identified by nasal-swab rapid COVID-19 tests had more transmission to household contacts than cases identified by other test types; PLOS ONE; Vol. 18; No. 10; e0292389; PMCID PMC10553276; 10.1371/journal.pone.0292389