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Hypoxia causes critical cellular injury both in early human development and in adulthood, leading to cerebral palsy, stroke, and myocardial infarction. Interestingly, a remarkable phenomenon known as hypoxic preconditioning arises when a brief hypoxia exposure protects target organs against subsequent, severe hypoxia. Although hypoxic preconditioning has been demonstrated in several model organisms and tissues including the heart and brain, its molecular mechanisms remain poorly understood. Accordingly, we used embryonic and larval zebrafish to develop a novel vertebrate model for hypoxic preconditioning, and used this model to identify conserved hypoxia-regulated transcripts for further functional study as published in Manchenkov et al. (2015) in G3: Genes | Genomes | Genetics. In this Brief article, we provide extensive annotation for the most strongly hypoxia-regulated genes in zebrafish, including their human orthologs, and describe in detail the methods used to identify, filter, and annotate hypoxia-regulated transcripts for downstream functional and bioinformatic assays using the source data provided in Gene Expression Omnibus Accession GSE68473.

Animal locomotion requires coordination between the central and peripheral nervous systems, between sensory inputs and motor outputs, and between nerves and muscles. Analysis of locomotion thus provides a comprehensive and sensitive readout of nervous system function and dysfunction. Tardigrades, the smallest known walking animals, coordinate movement of their eight legs with a relatively simple nervous system, and are a promising model for neuronal control of limb-driven locomotion. Here, we developed open-source tools for automated tracking of tardigrade locomotion in an unconstrained two-dimensional environment, for measuring multiple parameters of individual leg movements, and for quantifying interleg coordination. We used these tools to analyze >13,000 complete strides in >100 tardigrades, and identified preferred walking speeds and distinct step coordination patterns associated with those speeds. In addition, the rear legs of tardigrades, although they have distinct anatomy and step kinematics, were nonetheless incorporated into overall patterns of interleg coordination. Finally, comparisons of tardigrade locomotion across lifespan, between species, and upon disulfiram treatment suggested that neuronal regulation of high-level aspects of walking (e.g. speed, turns, walking bout initiation) operate independently from circuits controlling individual leg movements and interleg coordination., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Anderson et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cattle change their behaviour in response to hot temperatures, including by engaging in stepping that indicates agitation. The automated recording of these responses would be helpful in the timely diagnosis of animals experiencing heat loading. Behavioural responses of beef cattle to hot environmental conditions were studied to investigate whether it was possible to assess behavioural responses by video-digitised image analysis. Open-source automated behavioural quantification software was used to record pixel changes in 13 beef cattle videorecorded in a climate-controlled chamber during exposure to a simulated typical heat event in Queensland, Australia. Increased digitised movement was observed during the heat event, which was related to stepping and grooming/scratching activities in standing animals. The 13 cattle were exposed in two cohorts, in which the first group of cattle ( n = 6) was fed a standard finisher diet based on a high percentage of cereal grains, and the second group of cattle ( n = 7) received a substituted diet in which 8% of the grains were replaced by lucerne hay. The second group displayed a smaller increase in digitised movements on exposure to heat than the first, suggesting less discomfort under hot conditions. The results suggest that cattle exposed to heat display increased movement that can be detected automatically by video digitisation software, and that replacing some cereal grain with forage in the diet of feedlot cattle may reduce the measured activity responses to the heat., Competing Interests: The authors declare no conflicts of interest.

Connexins are transmembrane proteins that form hemichannels allowing the exchange of molecules between the extracellular space and the cell interior. Two hemichannels from adjacent cells dock and form a continuous gap junction pore, thereby permitting direct intercellular communication. Connexin 36 (Cx36), expressed primarily in neurons, is involved in the synchronous activity of neurons and may play a role in aberrant synchronous firing, as seen in seizures. To understand the reciprocal interactions between Cx36 and seizure-like neural activity, we examined three questions: (a) does Cx36 deficiency affect seizure susceptibility, (b) does seizure-like activity affect Cx36 expression patterns, and (c) does acute blockade of Cx36 conductance increase seizure susceptibility. We utilize the zebrafish pentylenetetrazol [PTZ; a GABA(A) receptor antagonist] induced seizure model, taking advantage of the compact size and optical translucency of the larval zebrafish brain to assess how PTZ affects brain-wide neuronal activity and Cx36 protein expression. We exposed wild-type and genetic Cx36-deficient ( cx35.5-/- ) zebrafish larvae to PTZ and subsequently mapped neuronal activity across the whole brain, using phosphorylated extracellular-signal-regulated kinase (pERK) as a proxy for neuronal activity. We found that cx35.5-/- fish exhibited region-specific susceptibility and resistance to PTZ-induced hyperactivity compared to wild-type controls, suggesting that genetic Cx36 deficiency may affect seizure susceptibility in a region-specific manner. Regions that showed increased PTZ sensitivity include the dorsal telencephalon, which is implicated in human epilepsy, and the lateral hypothalamus, which has been underexplored. We also found that PTZ-induced neuronal hyperactivity resulted in a rapid reduction of Cx36 protein levels within 30 min. This Cx36 reduction persists after 1-h of recovery but recovered after 3-6 h. This acute downregulation of Cx36 by PTZ is likely maladaptive, as acute pharmacological blockade of Cx36 by mefloquine results in increased susceptibility to PTZ-induced neuronal hyperactivity. Together, these results demonstrate a reciprocal relationship between Cx36 and seizure-associated neuronal hyperactivity: Cx36 deficiency contributes region-specific susceptibility to neuronal hyperactivity, while neuronal hyperactivity-induced downregulation of Cx36 may increase the risk of future epileptic events., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Brunal, Clark, Ma, Woods and Pan.)

Identity-by-descent (IBD) segments are a useful tool for applications ranging from demographic inference to relationship classification, but most detection methods rely on phasing information and therefore require substantial computation time. As genetic datasets grow, methods for inferring IBD segments that scale well will be critical. We developed IBIS, an IBD detector that locates long regions of allele sharing between unphased individuals, and benchmarked it with Refined IBD, GERMLINE, and TRUFFLE on 3,000 simulated individuals. Phasing these with Beagle 5 takes 4.3 CPU days, followed by either Refined IBD or GERMLINE segment detection in 2.9 or 1.1 h, respectively. By comparison, IBIS finishes in 6.8 min or 7.8 min with IBD2 functionality enabled: speedups of 805-946× including phasing time. TRUFFLE takes 2.6 h, corresponding to IBIS speedups of 20.2-23.3×. IBIS is also accurate, inferring ≥7 cM IBD segments at quality comparable to Refined IBD and GERMLINE. With these segments, IBIS classifies first through third degree relatives in real Mexican American samples at rates meeting or exceeding other methods tested and identifies fourth through sixth degree pairs at rates within 0.0%-2.0% of the top method. While allele frequency-based approaches that do not detect segments can infer relationship degrees faster than IBIS, the fastest are biased in admixed samples, with KING inferring 30.8% fewer fifth degree Mexican American relatives correctly compared with IBIS. Finally, we ran IBIS on chromosome 2 of the UK Biobank dataset and estimate its runtime on the autosomes to be 3.3 days parallelized across 128 cores., (Copyright © 2020 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.)

Hypoxia causes critical cellular injury both in early human development and in adulthood, leading to cerebral palsy, stroke, and myocardial infarction. Interestingly, a remarkable phenomenon known as hypoxic preconditioning arises when a brief hypoxia exposure protects target organs against subsequent, severe hypoxia. Although hypoxic preconditioning has been demonstrated in several model organisms and tissues including the heart and brain, its molecular mechanisms remain poorly understood. Accordingly, we used embryonic and larval zebrafish to develop a novel vertebrate model for hypoxic preconditioning, and used this model to identify conserved hypoxia-regulated transcripts for further functional study as published in Manchenkov et al. (2015) in G3: Genes | Genomes | Genetics. In this Brief article, we provide extensive annotation for the most strongly hypoxia-regulated genes in zebrafish, including their human orthologs, and describe in detail the methods used to identify, filter, and annotate hypoxia-regulated transcripts for downstream functional and bioinformatic assays using the source data provided in Gene Expression Omnibus Accession GSE68473.

Differences in nervous system function can result in differences in behavioral output. Measurements of animal locomotion enable the quantification of these differences. Automated tracking of animal movement is less labor-intensive and bias-prone than direct observation, and allows for simultaneous analysis of multiple animals, high spatial and temporal resolution, and data collection over extended periods of time. Here, we present a new video-tracking system built on Python-based software that is free, open source, and cross-platform, and that can analyze video input from widely available video capture devices such as smartphone cameras and webcams. We validated this software through four tests on a variety of animal species, including larval and adult zebrafish (Danio rerio), Siberian dwarf hamsters (Phodopus sungorus), and wild birds. These tests highlight the capacity of our software for long-term data acquisition, parallel analysis of multiple animals, and application to animal species of different sizes and movement patterns. We applied the software to an analysis of the effects of ethanol on thigmotaxis (wall-hugging) behavior on adult zebrafish, and found that acute ethanol treatment decreased thigmotaxis behaviors without affecting overall amounts of motion. The open source nature of our software enables flexibility, customization, and scalability in behavioral analyses. Moreover, our system presents a free alternative to commercial video-tracking systems and is thus broadly applicable to a wide variety of educational settings and research programs.

Loss of neurons that express the neuropeptide hypocretin (Hcrt) has been implicated in narcolepsy, a debilitating disorder characterized by excessive daytime sleepiness and cataplexy. Cell replacement therapy, using Hcrt-expressing neurons generated in vitro, is a potentially useful therapeutic approach, but factors sufficient to specify Hcrt neurons are unknown. Using zebrafish as a high-throughput system to screen for factors that can specify Hcrt neurons in vivo, we identified the LIM homeobox transcription factor Lhx9 as necessary and sufficient to specify Hcrt neurons. We found that Lhx9 can directly induce hcrt expression and we identified two potential Lhx9 binding sites in the zebrafish hcrt promoter. Akin to its function in zebrafish, we found that Lhx9 is sufficient to specify Hcrt-expressing neurons in the developing mouse hypothalamus. Our results elucidate an evolutionarily conserved role for Lhx9 in Hcrt neuron specification that improves our understanding of Hcrt neuron development., (© 2015. Published by The Company of Biologists Ltd.)