A 3D searchable database of transgenic zebrafish gal4 and cre lines for functional neuroanatomy studies

Citation: Marquart, G. D., Tabor, K. M., Brown, M., Strykowski, J. L., Varshney, G. K., LaFave, M. C., . . . Burgess, H. A. (2015). A 3D searchable database of transgenic zebrafish gal4 and cre lines for functional neuroanatomy studies. Frontiers in Neural Circuits, 9(November), 1-17. doi:10.3389/fncir.2015.00078Transgenic methods enable the selective manipulation of neurons for functional mapping of neuronal circuits. Using confocal microscopy, we have imaged the cellular-level expression of 109 transgenic lines in live 6 day post fertilization larvae, including 80 Gal4 enhancer trap lines, 9 Cre enhancer trap lines and 20 transgenic lines that express fluorescent proteins in defined gene-specific patterns. Image stacks were acquired at single micron resolution, together with a broadly expressed neural marker, which we used to align enhancer trap reporter patterns into a common 3-dimensional reference space. To facilitate use of this resource, we have written software that enables searching for transgenic lines that label cells within a selectable 3-dimensional region of interest (ROI) or neuroanatomical area. This software also enables the intersectional expression of transgenes to be predicted, a feature which we validated by detecting cells with co-expression of Cre and Gal4. Many of the imaged enhancer trap lines show intrinsic brain-specific expression. However, to increase the utility of lines that also drive expression in non-neuronal tissue we have designed a novel UAS reporter, that suppresses expression in heart, muscle, and skin through the incorporation of microRNA binding sites in a synthetic 3? untranslated region. Finally, we mapped the site of transgene integration, thus providing molecular identification of the expression pattern for most lines. Cumulatively, this library of enhancer trap lines provides genetic access to 70% of the larval brain and is therefore a powerful and broadly accessible tool for the dissection of neural circuits in larval zebrafish. © 2015 Marquart, Tabor, Brown, Strykowski, Varshney, LaFave, Mueller, Burgess, Higashijima and Burgess

Prepontine Non-giant Neurons Drive Flexible Escape Behavior in Zebrafish

Many species execute ballistic escape reactions to avoid imminent danger. Despite fast reaction times, responses are often highly regulated, reflecting a trade-off between costly motor actions and perceived threat level. However, how sensory cues are integrated within premotor escape circuits remains poorly understood. Here, we show that in zebrafish, less precipitous threats elicit a delayed escape, characterized by flexible trajectories, which are driven by a cluster of 38 prepontine neurons that are completely separate from the fast escape pathway. Whereas neurons that initiate rapid escapes receive direct auditory input and drive motor neurons, input and output pathways for delayed escapes are indirect, facilitating integration of cross-modal sensory information. These results show that rapid decision-making in the escape system is enabled by parallel pathways for ballistic responses and flexible delayed actions and defines a neuronal substrate for hierarchical choice in the vertebrate nervous system

Randomized, placebo controlled trial of experimental hookworm infection for improving gluten tolerance in Celiac disease

INTRODUCTION: Celiac disease is an autoimmune disorder where intestinal immunopathology arises after gluten consumption. Previous studies suggested that hookworm infection restores gluten tolerance; however, these studies were small (n = 12) and not placebo controlled. METHODS: We undertook a randomized, placebo-controlled trial of hookworm infection in 54 people with celiac disease. The 94-week study involved treatment with either 20 or 40 Necator americanus third-stage larvae (L3-20 or L3-40) or placebo, followed by escalating gluten consumption (50 mg/d for 12 weeks, 1 g intermittent twice weekly for 12 weeks, 2 g/d sustained for 6 weeks, liberal diet for 1 year). RESULTS: Successful study completion rates at week 42 (primary outcome) were similar in each group (placebo: 57%, L3-20: 37%, and L3-40: 44%; P = 0.61), however gluten-related adverse events were significantly reduced in hookworm-treated participants: Median (range) adverse events/participant were as follows: placebo, 4 (1–9); L3-20, 1 (0–9); and L3-40, 0 (0–3) (P = 0.019). Duodenal villous height:crypt depth deteriorated similarly compared with their enrolment values in each group (mean change [95% confidence interval]: placebo, −0.6 [−1.3 to 0.2]; L3-20, −0.5 [−0.8 to 0.2]; and L3-40, −1.1 [−1.8 to 0.4]; P = 0.12). A retrospective analysis revealed that 9 of the 40 L3-treated participants failed to establish hookworm infections. Although week 42 completion rates were similar in hookworm-positive vs hookworm-negative participants (48% vs 44%, P = 0.43), quality of life symptom scores were lower in hookworm-positive participants after intermittent gluten challenge (mean [95% confidence interval]: 38.9 [33.9–44] vs 45.9 [39.2–52.6]). DISCUSSION: Hookworm infection does not restore tolerance to sustained moderate consumption of gluten (2 g/d) but was associated with improved symptom scores after intermittent consumption of lower, intermittent gluten doses

Decision Making and Behavioral Choice during Predator Avoidance

One of the most important decisions animals have to make is how to respond to an attack from a potential predator. The response must be prompt and appropriate to ensure survival. Invertebrates have been important models in studying the underlying neurobiology of the escape response due to their accessible nervous systems and easily quantifiable behavioral output. Moreover, invertebrates provide opportunities for investigating these processes at a level of analysis not available in most other organisms. Recently, there has been a renewed focus in understanding how value-based calculations are made on the level of the nervous system, i.e., when decisions are made under conflicting circumstances, and the most desirable choice must be selected by weighing the costs and benefits for each behavioral choice. This article reviews samples from the current literature on anti-predator decision making in invertebrates, from single neurons to complex behaviors. Recent progress in understanding the mechanisms underlying value-based behavioral decisions is also discussed

High precision registration between zebrafish brain atlases using symmetric diffeomorphic normalization

AbstractAtlases provide a framework for information from diverse sources to be spatially mapped and integrated into a common reference space. In particular, brain atlases allow regional annotation of gene expression, cell morphology, connectivity and activity. In larval zebrafish, advances in genetics, imaging and computational methods have enabled the collection of large datasets providing such information on a whole-brain scale. However, datasets from different sources may not be aligned to the same spatial coordinate system, because technical considerations may necessitate use of different reference templates. Two recent brain atlases for larval zebrafish exemplify this problem. The Z-Brain atlas contains information on gene expression, neural activity and neuroanatomical segmentation acquired using immunohistochemical staining of fixed tissue. In contrast, the Zebrafish Brain Browser (ZBB) atlas was constructed from live scans of fluorescent reporter genes in transgenic larvae. Although different reference brains were used, the two atlases included several transgene patterns in common that provided potential 'bridges' for transforming each into the other’s coordinate space. We therefore tested multiple bridging channels and registration algorithms. The symmetric diffeomorphic normalization (SyN) algorithm in ANTs improved the precision of live brain registration while better preserving cell morphology than the previously used B-spline elastic registration algorithm. SyN could also be calibrated to correct for tissue distortion introduced during fixation and permeabilization. Finally, multi-reference channel optimization provided a transformation matrix that enabled Z-Brain and ZBB to be co-aligned with acceptable precision and minimal perturbation of cell and tissue morphology. This study demonstrates the feasibility of integrating whole brain datasets, despite disparate acquisition protocols and reference templates, when sufficient information is present for bridging.Anatomical abbreviationsacanterior commissureDTThalamusGTGriseum tectaleHaHabenulaHcHypothalamus caudal zoneHiHypothalamus intermediate zoneMOMedulla oblongataNXmVagus motor neuronsOBOlfactory bulbOEOlfactory epitheliumIOInferior oliveLCLocus coeruleusMNMauthner neuronMOMedulla oblongataPalPalliumpcposterior commissurePrPretectumSRSuperior rapheTegTegmentumTeOnOptic tectum neuropilTGTrigeminal ganglionTLTorus longitudinalis</jats:sec

Prepontine non-giant neurons drive flexible escape behavior in zebrafish.

Many species execute ballistic escape reactions to avoid imminent danger. Despite fast reaction times, responses are often highly regulated, reflecting a trade-off between costly motor actions and perceived threat level. However, how sensory cues are integrated within premotor escape circuits remains poorly understood. Here, we show that in zebrafish, less precipitous threats elicit a delayed escape, characterized by flexible trajectories, which are driven by a cluster of 38 prepontine neurons that are completely separate from the fast escape pathway. Whereas neurons that initiate rapid escapes receive direct auditory input and drive motor neurons, input and output pathways for delayed escapes are indirect, facilitating integration of cross-modal sensory information. These results show that rapid decision-making in the escape system is enabled by parallel pathways for ballistic responses and flexible delayed actions and defines a neuronal substrate for hierarchical choice in the vertebrate nervous system

Prepontine non-giant neurons drive flexible escape behavior in zebrafish

AbstractMany species execute ballistic escape reactions to avoid imminent danger. Despite fast reaction times, responses are often highly regulated, reflecting a trade-off between costly motor actions and perceived threat level. However, how sensory cues are integrated within premotor escape circuits remains poorly understood. Here we show that in zebrafish, less precipitous threats elicit a delayed escape, characterized by flexible trajectories, that are driven by a cluster of 38 prepontine neurons that are completely separate from the fast escape pathway. Whereas neurons that initiate rapid escapes receive direct auditory input and drive motor neurons, input and output pathways for delayed escapes are indirect, facilitating integration of cross-modal sensory information. Rapid decision making in the escape system is thus enabled by parallel pathways for ballistic responses and flexible delayed actions.</jats:p

Generation and characterization of Kctd15 mutations in zebrafish.

Potassium channel tetramerization domain containing 15 (Kctd15) was previously found to have a role in early neural crest (NC) patterning, specifically delimiting the region where NC markers are expressed via repression of transcription factor AP-2a and inhibition of Wnt signaling. We used transcription activator-like effector nucleases (TALENs) to generate null mutations in zebrafish kctd15a and kctd15b paralogs to study the in vivo role of Kctd15. We found that while deletions producing frame-shift mutations in each paralog showed no apparent phenotype, kctd15a/b double mutant zebrafish are smaller in size and show several phenotypes including some affecting the NC, such as expansion of the early NC domain, increased pigmentation, and craniofacial defects. Both melanophore and xanthophore pigment cell numbers and early markers are up-regulated in the double mutants. While we find no embryonic craniofacial defects, adult mutants have a deformed maxillary segment and missing barbels. By confocal imaging of mutant larval brains we found that the torus lateralis (TLa), a region implicated in gustatory networks in other fish, is absent. Ablation of this brain tissue in wild type larvae mimics some aspects of the mutant growth phenotype. Thus kctd15 mutants show deficits in the development of both neural crest derivatives, and specific regions within the central nervous system, leading to a strong reduction in normal growth rates

Optogenetic prepontine neuron stimulation elicits C-start behavior.

(A) Schematic of optogenetic stimulation and two-photon calcium imaging: a DMD was used to spatially restrict 460-nm LED excitation (green box) within the brain of head-embedded larvae (blue box) mounted on a stage with a speaker for acoustic/vibratory stimulation, an infrared light source for tail illumination, and a high-speed camera for behavioral readout (orange box). (B) Two-photon optical section of mCherry expression in y293-Gal4, UAS:ChEF-2a-mCherry larva with the area around one prepontine cluster (asterisks) stimulated by the DMD outlined in blue. Scale bar 40 μm. (C) C-start and swim-like (C') behaviors elicited by unilateral optogenetic stimulation of prepontine neurons in y293-Gal4, UAS:ChEF-positive larvae. Scale bars 500 μm. (D) Percent of behaviors elicited by illumination of larvae expressing ChEF (ChEF+; 229 trials, n = 8 larvae) and nonexpressing sibling controls (ChEF−; 63 trials, n = 7 larvae). C-start-like responses (“C,” green), swim-like bouts (“Sw,” red), other responses (blue), nr (gray). (E) Number of C-start responses made ipsilateral (“IPSI”) and contralateral (“CON”) to the side of optogenetic stimulation, color-coded for each of the 8 larvae tested. χ2 = 15.25, *p S1 Data. DMD, digital mirror device; LED, light-emitting diode; mCherry, monomeric Cherry; nr, no response.</p