Journal: Neuron

Article Title: Amygdalostriatal transition zone neurons encode sustained cue responses to guide defensive behaviors

doi: 10.1016/j.neuron.2026.08.012

Figure Lengend Snippet: (A) Target regions for single-nucleus RNA sequencing (snRNA-seq). (B) Two-dimensional uniform manifold approximation projection (UMAP) of all sequenced nuclei passing quality filters ( n = 97,434 nuclei, see also ), colored by region of origin. Arrows indicate distinct ASt subclusters within the GABAergic Drd1a + and Drd2 + clusters. (C) Two-dimensional UMAP, colored by broad cellular identity assigned by graph-based clustering of neuronal and non-neuronal cells (GABA-D1, GABAergic neurons expressing Drd1a cluster; GABA-D2, GABAergic neurons expressing Drd2 cluster; OLGs, oligodendrocytes; NFOL, newly formed oligodendrocytes; OPCs, oligodendrocyte precursor cells). (D) Cell-type-specific expression of canonical marker genes indicating broad cellular identity in the brain. Dot size is proportional to the percentage of nuclei expressing the marker, with the color scale representing normalized expression level. (E) Dendrogram of cell-type classification and proportion of cells of each class in the ASt and other target regions. (F) Difference in overall proportion of each cell type in the ASt compared with the CeA, TS, and DS. (G) Total proportion of cells of each identified type in each target region. (H) All nuclei, colored by expression levels of Drd1a (top) or Drd2 (bottom), with cells identified as part of the major Drd1a + or Drd2 + clusters highlighted. (I) Drd1a + cluster (top) or Drd2 + cluster (bottom) neurons, with individual nuclei colored by region of origin. (J) Relative proportion of nuclei classified in Drd1a + or Drd2 + clusters in each striatal target region. Nuclei in the Drd1a + cluster that also expressed Drd2 , or in the Drd2 + cluster that expressed Drd1a , were classified as “dual expressing.” ASt Drd1a + :Drd2 + proportions were significantly different from those in the TS or DS (χ 2 tests, Holm-corrected: ASt vs. TS, χ 2 (1) = 1,329, p = 1.4 × 10 −290 , V = 0.26; ASt vs. DS, χ 2 (1) = 1,866, p = 3.6 × 10 −407 , V = 0.24). Due to the high N, the TS vs. DS also differed significantly (TS vs. DS, χ 2 (1) = 15.9, p = 6.7 × 10 −5 , V = 0.02) but had an effect size an order of magnitude smaller than either ASt comparison. ASt: 7,941; TS: 13,214; DS: 25,791 nuclei. *** p < 0.001. (K) Representative images of in situ RNAscope labeling of Drd1a RNA (green) and Drd2 RNA (red) in striatal target regions. Bottom panel shows ASt with increased contrast to visualize labeled neurons. (L) Relative proportion of cells in each target region positively labeled for Drd1a RNA, Drd2 RNA, or both (dual expressing). Drd1a +: Drd2 + proportions compared by paired t tests on per-animal log-ratios, Holm-corrected for 3 pairwise comparisons: ASt vs. TS, t(6) = 5.51, p = 0.0039; ASt vs. DS, t(7) = 5.17, p = 0.0039; TS vs. DS, t(6) = 2.22, p = 0.068. DS: n = 8 mice, 11,673 cells; TS: n = 7 mice, 11,758 cells; ASt: n = 8 mice, 1,689 cells. ** p < 0.01.

Article Snippet: Fluorescence in situ hybridization was performed using the Advanced Cell Diagnostics bio V2 RNAscope kit and protocol (Advanced Cell Diagnostics, Newark, CA) using the RNAscope Multiplex Fluorescent Reagent Kit V2 (Catalog #323100), Fluorescent Multiplex Detection Reagents (#323110), probes for Drd1a (#406491-C1 and #406491-C3), Drd2 (#406501-C3 and #406501-C1), Cdh6 (#519441-C2), Slit2 (#449691-C1), and VGlut1 (#501101-C1), and the Perkin Elmer TSA Plus Fluorescence Palette Kit (NEL760001KT).

Techniques: RNA Sequencing, Expressing, Marker, Comparison, In Situ, RNAscope, Labeling

Journal: Neuron

Article Title: Amygdalostriatal transition zone neurons encode sustained cue responses to guide defensive behaviors

doi: 10.1016/j.neuron.2026.08.012

Figure Lengend Snippet:

Article Snippet: Fluorescence in situ hybridization was performed using the Advanced Cell Diagnostics bio V2 RNAscope kit and protocol (Advanced Cell Diagnostics, Newark, CA) using the RNAscope Multiplex Fluorescent Reagent Kit V2 (Catalog #323100), Fluorescent Multiplex Detection Reagents (#323110), probes for Drd1a (#406491-C1 and #406491-C3), Drd2 (#406501-C3 and #406501-C1), Cdh6 (#519441-C2), Slit2 (#449691-C1), and VGlut1 (#501101-C1), and the Perkin Elmer TSA Plus Fluorescence Palette Kit (NEL760001KT).

Techniques: Virus, Plasmid Preparation, Recombinant, RNAscope, Multiplex Assay, Electron Microscopy, Software, Optogenetics, Microscopy, Data-independent acquisition, Imaging

Journal: eLife

Article Title: Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci

doi: 10.7554/eLife.111773

Figure Lengend Snippet: ( A ) AlphaFold protein models for D. melanogaster Kraken (AF- O18391 -F1-model_v4) and Alkbh7 (AF- Q9VTP1 -F1-model_v4) ( ; ), highlighting a conserved putative catalytic serine in the active site in Kraken, and the mitochondrial targeting sequence in Alkbh7 (predicted by MitoFates; ). See also . ( B ) Tissue-specific expression of D. melanogaster kraken and Alkbh7 from bulk RNA-sequencing data from the Fly Atlas 2.0 . ( C ) tSNE plots illustrating D. melanogaster kraken expression in single-cell transcriptomes of the Malpighian tubules and gut from the Fly Cell Atlas (Stringent 10× datasets) . ( D ) Left: RNAscope detection of kraken (green) transcripts in the gut and Malpighian tubules, with nuclei counterstained with DAPI (blue). Right: higher-magnification images showing kraken transcript expression in the indicated tissues. Scale bars, 200 μm. This expression pattern was observed in tissues from >20 individuals. ( E ) Expression levels of the kraken and Alkbh7 in the indicated laboratory strains (left panel) and wild-caught strains (right panel) ( ; ) of adult female D. sechellia and D. simulans measured by quantitative PCR (qPCR) . Expression is represented as calibrated and normalized relative quantities (CNRQ). Significance was assessed using the unpaired t-test correcting for multiple testing and represented using letter codes. ( F ) Expression levels of kraken and Alkbh7 in the indicated strains and species at larval or adult stages as indicated from published RNA-sequencing data (References: 1, ; 2 ; 3 ). Significance was assessed using the unpaired t-test correcting for multiple testing and represented using letter codes when multiple replicates were present in the original data. ( G ) Expression levels of the candidate genes at generations 0, 25, and 50 of the experimentally evolved D. simulans populations measured by qPCR . Significance was assessed using the paired t-test correcting for multiple testing and represented using letter codes. Panels E and F were created with BioRender.com . Figure 4—source data 1. Quantitative PCR (qPCR) expression of kraken and Alkbh7 in different strains.

Article Snippet: To detect kraken mRNA in situ, we used the RNAscope Multiplex Fluorescence Detection Reagents v2 (Advanced Cell Diagnostics, 323110) and RNAscope H 2 O 2 and Protease Reagents (Advanced Cell Diagnostics, 322381).

Techniques: Sequencing, Expressing, RNA Sequencing, Single Cell, RNAscope, Real-time Polymerase Chain Reaction

Journal: eLife

Article Title: Intersecting experimental evolution and CRISPR screens to identify novel toxin resistance loci

doi: 10.7554/eLife.111773

Figure Lengend Snippet: ( A ) Bar plots showing the expression levels of kraken and Alkbh7 across various adult Drosophila tissues and species. Data from . ( B ) Bar plots showing the expression levels of kraken and Alkbh7 across various larval Drosophila tissues and species. Data from (‘medium diet’ condition). ( C ) Bar plots showing the effect of exposure to 9 μl octanoic acid (OA) (in the tube assay) on kraken and Alkbh7 expression in D. sechellia and three evolved ( G50 ) D. simulans populations. ( D ) Left: RNAscope detection of kraken (green) and Rpl32 (magenta) transcripts in the gut and Malpighian tubules. Right: higher-magnification showing kraken transcript expression in the indicated tissues. Scale bars, 200 μm. This expression pattern was observed in tissues from >10 individuals.

Article Snippet: To detect kraken mRNA in situ, we used the RNAscope Multiplex Fluorescence Detection Reagents v2 (Advanced Cell Diagnostics, 323110) and RNAscope H 2 O 2 and Protease Reagents (Advanced Cell Diagnostics, 322381).

Techniques: Expressing, RNAscope

Journal: Cell Genomics

Article Title: Single-cell transcriptomics provides insights into the stress-immune interplay and informs disease risk

doi: 10.1016/j.xgen.2026.101330

Figure Lengend Snippet:

Article Snippet: In situ hybridization was performed using ACD Bio’s RNAScope technology per the kit instructions (Multiplex Fluorescent Detection Kit, ACD Bio, #323110).

Techniques: Recombinant, Electron Microscopy, Selection, cDNA Synthesis, RNAscope, Multiplex Assay, Single Cell, Software