Biology subjects

Johnson, A. R.

Publications and source records attributed to Johnson, A. R..

8 recordsLinked to original sources

bioRxiv2026

In transected nerves, distal repair Schwann cells are required at the injury site to direct and accelerate axonal regrowth

In vertebrate peripheral nerves, damaged axons can regrow after injury, but the outcomes of regeneration are variable and often incomplete. Schwann cells in injured nerves are important for repair, but their actions at different positions and stages of nerve repair are not well understood. We have investigated the roles of Schwann cells in a larval zebrafish nerve injury model, in which nerves are visible in living animals during development, the initial injury response, and regrowth of the transected axons. After mechanical injury, distal Schwann cells adopt a repair phenotype characterized by changes in marker expression, elongation, and ability to guide axons across the injury site. In contrast, proximal Schwann cells are not sufficient to guide axons across the injury site, and they associate with axons that regrow along aberrant paths. In erbb2 mutants lacking Schwann cells, developmental axon growth is normal, but after transection, axonal regrowth is greatly slowed and often misdirected. By examining animals with nerves partially populated by Schwann cells, we find that axons can regrow through regions devoid of Schwann cells, provided that at least one distal Schwann cell is at the injury site. Timelapse imaging reveals that distal Schwann cells extend processes toward the injury site, which contact and guide axons regrowing from the proximal nerve stump. In irf8 mutants lacking macrophages, debris from transected axons is cleared on schedule, and axonal regrowth is normal. Our studies demonstrate that Schwann cells immediately distal to the injury site have a unique and essential role in axonal regrowth. Main PointsO_LIAfter nerve transection in larval zebrafish, proximal and distal Schwann cells have distinct functions at injury site C_LIO_LIA single distal repair Schwann cell is sufficient for axonal regrowth C_LIO_LIAxonal regrowth is normal in mutants without macrophages C_LI

neuroscience↗

bioRxiv2024

Transcriptional dissection of petty spurge (Euphorbia peplus L.) reproductive structures supports the Euphorbia cyathium as an inflorescence rather than a complete flower

The unique reproductive structure of Euphorbia species, the cyathium, is an inflorescence that resembles a single complete flower. This structure has not yet been investigated using transcriptomics at a genomic scale. Enabled by the petty spurge (Euphorbia peplus L.) genome and guided by the ABCDE model of floral development, we dissected petty spurge cyathia and carried out a transcriptomic analysis of the different organs. We also constructed gene phylogenies and performed dN/dS analysis on select floral genes. Unlike in model species in the Asteraceae, which also have pseudanthia (false flowers), we did not find evidence for lineage-specific duplications of E class genes in Euphorbia. Rather, our transcriptomic and genomic analyses indicate that SEP1 paralogs have distinct expression patterns within the cyathium. E. peplus filiform structures (sterile organs within the cyathium) show upregulation of B and E class genes and transcriptomic signatures of heterochromatin formation, consistent with some form of floral identity and potentially consistent with their being reduced flowers in an inflorescence. The gene CRABS CLAW (CRC), which is involved in nectary development in both arabidopsis and petunia, is not upregulated in E. peplus nectaries, indicating an alternative nectary development pathway in Euphorbia. Finally, Euphorbia homologs for the inflorescence/floral meristem genes UFO and LFY and the B class genes AP3 and PI have highly diverged sequences relative to other Euphorbiaceae species.

plant biology↗

bioRxiv2024

Myoglobin Inhibits Breast Cancer Cell Fatty Acid Oxidation and Migration via Heme-Dependent Oxidant Production and Not Fatty Acid Binding

The monomeric heme protein myoglobin (Mb), traditionally thought to be expressed exclusively in cardiac and skeletal muscle, is now known to be expressed in approximately 40% of breast tumors. While Mb expression is associated with better patient prognosis, the molecular mechanisms by which Mb limits cancer progression are unclear. In muscle, Mbs predominant function is oxygen storage and delivery, which is dependent on the proteins heme moiety. However, prior studies demonstrate that the low levels of Mb expressed in cancer cells preclude this function. Recent studies propose a novel fatty acid binding function for Mb via a lysine residue (K46) in the heme pocket. Given that cancer cells can upregulate fatty acid oxidation (FAO) to maintain energy production for cytoskeletal remodeling during cell migration, we tested whether Mb-mediated fatty acid binding modulates FAO to decrease breast cancer cell migration. We demonstrate that the stable expression of human Mb in MDA-MB-231 breast cancer cells decreases cell migration and FAO. Site-directed mutagenesis of Mb to disrupt Mb fatty acid binding did not reverse Mb-mediated attenuation of FAO or cell migration in these cells. In contrast, cells expressing Apo-Mb, in which heme incorporation was disrupted, showed a reversal of Mb-mediated attenuation of FAO and cell migration, suggesting that Mb attenuates FAO and migration via a heme-dependent mechanism rather than through fatty acid binding. To this end, we show that Mbs heme-dependent oxidant generation propagates dysregulated gene expression of migratory genes, and this is reversed by catalase treatment. Collectively, these data demonstrate that Mb decreases breast cancer cell migration, and this effect is due to heme-mediated oxidant production rather than fatty acid binding. The implication of these results will be discussed in the context of therapeutic strategies to modulate oxidant production and Mb in tumors. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=137 HEIGHT=200 SRC="FIGDIR/small/591659v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@84f5f9org.highwire.dtl.DTLVardef@130b7eeorg.highwire.dtl.DTLVardef@17b96faorg.highwire.dtl.DTLVardef@f517a5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract:C_FLOATNO Mb-dependent oxidant generation (but not fatty acid binding) dysregulates mitochondrial respiration and migratory gene expression, leading to decreased cell migration. Created with BioRender. C_FIG HighlightsO_LIMyoglobin (Mb) expression in MDA-MB-231 breast cancer cells slows migration. C_LIO_LIMb expression decreases mitochondrial respiration and fatty acid oxidation. C_LIO_LIMb-dependent fatty acid binding does not regulate cell migration or respiration. C_LIO_LIMb-dependent oxidant generation decreases mitochondrial metabolism and migration. C_LIO_LIMb-derived oxidants dysregulate migratory gene expression. C_LI

cancer biology↗

bioRxiv2022

Chromosome-level genome assembly of Euphorbia peplus, a model system for plant latex, reveals that relative lack of Ty3 transposons contributed to its small genome size

Euphorbia peplus (petty spurge) is a small, fast-growing plant that is native to Eurasia and has become a naturalized weed in North America and Australia. E. peplus is not only medicinally valuable, serving as a source for the skin cancer drug ingenol mebutate, but also has great potential as a model for latex production owing to its small size, ease of manipulation in the laboratory, and rapid reproductive cycle. To help establish E. peplus as a new model, we generated a 267.2 Mb HiC-anchored PacBio HiFi nuclear genome assembly with an embryophyta BUSCO score of 98.5%, a genome annotation based on RNA-seq data from six tissues, and publicly accessible tools including a genome browser and an interactive organ-specific expression atlas. Chromosome number is highly variable across Euphorbia species. Using a comparative analysis of our newly sequenced E. peplus genome with other Euphorbiaceae genomes, we show that variation in Euphorbia chromosome number is likely due to fragmentation and rearrangement rather than aneuploidy. Moreover, we found that the E. peplus genome is relatively compact compared to related members of the genus in part due to restricted expansion of the Ty3 transposon family. Finally, we identify a large gene cluster that contains many previously identified enzymes in the putative ingenol mebutate biosynthesis pathway, along with additional gene candidates for this biosynthetic pathway. The genomic resources we have created for E. peplus will help advance research on latex production and ingenol mebutate biosynthesis in the commercially important Euphorbiaceae family. Significance statementEuphorbia is one of the five largest genera in the plant kingdom. Despite an impressive phenotypic and metabolic diversity in this genus, only one Euphorbia genome has been sequenced so far, restricting insights into Euphorbia biology. Euphorbia peplus has excellent potential as a model species due to its latex production, fast growth rate and production of the anticancer drug ingenol mebutate. Here, we present a chromosome-level E. peplus genome assembly and publicly accessible resources to support molecular research for this unique species and the broader genus. We also provide an explanation of one reason the genome is so small, and identify more candidate genes for the anticancer drug and related compounds.

plant biology↗

bioRxiv2022

Schedule-dependent production of stereotyped sequences of actions

Concatenating actions into automatic routines is evolutionarily advantageous as it allows organisms to efficiently use time and energy under predictable conditions. However, over reliance on inflexible behaviors can be life-threatening in a changing environment and can become pathological in disease states such as obsessive-compulsive disorder (OCD) and substance use disorder (SUD). Understanding the conditions under which stereotypical sequences of actions are produced is crucial to studying how these behaviors can become maladaptive. Here, we investigated the ability of operant conditioning schedules and contingencies to promote reproducible sequences of five lever presses. We found that signaling reinforcer delivery with a visual cue was effective at increasing learning rates but resulted in mice pressing the lever in fast succession until the cue turned on, rather than pressing it five times. We also found that requiring mice to collect their reinforcer between sequences had little effect on both rate of behavior and on quantitative metrics of reproducibility such as interresponse interval (IRI) variance, and that a training strategy that directly reinforced sequences with low variance IRIs was not more effective than a traditional fixed ratio schedule at promoting reproducible action execution. Together, our findings provide insights into the parameters of behavioral training that promote reproducible sequences and serve as a roadmap to investigating the neural substrates of automatic behaviors.

animal behavior and cognition↗

bioRxiv2019

An optimized procedure for robust volitional drug intake in mice

Substance use disorder is a behavioral disorder characterized by volitional drug consumption, compulsive behavior, drug seeking, and relapse. Mouse models of substance use disorder allow for the use of molecular, genetic, and circuit level tools, which provide enormous potential for defining the underlying mechanisms of this disorder. However, the relevance of results depends entirely on the validity of the mouse models used. Self-administration models have long been considered the gold standard of preclinical addiction models, as they allow for volitional drug use, this providing strong face validity. In a series of experiments, we show that traditional mouse models of self-administration, where behavior is maintained on a fixed-ratio one schedule of reinforcement, show similar levels of responding in the presence and absence of drug delivery - demonstrating that it is impossible to determine when intake is and is not volitional. Further, when assessing inclusion criteria, we find a sex-bias in exclusion criteria where females that acquired food self-administration were eliminated when traditional criteria were applied. To address these issues, we have developed a novel mouse self-administration procedure where animals do not need to be pre-trained on food and behavior is maintained on a variable ratio schedule of reinforcement. This procedure increases rates of reinforcement behavior, increases levels of drug intake, and eliminates sex bias in inclusion criteria. Together, these data highlight a major issue with fixed-ratio models in mice that complicates subsequent analysis and provide a simple and novel approach to minimize these confounds with escalating variable-ratio schedules of reinforcement.

neuroscience↗

bioRxiv2019

A novel multidimensional reinforcement task in mice elucidates sex-specific behavioral strategies

BackgroundSex is a critical biological variable in the neuropathology of psychiatric disease, and in many cases, women represent a vulnerable population. It has been hypothesized that sex differences in neuropsychiatric disorders are manifestations of differences in basic reward processing. However, preclinical models often present rewards in isolation, ignoring that ethologically, reward seeking requires the consideration of potential aversive outcomes.\n\nMethodsWe developed a Multidimensional Cue Outcome Action Task (MCOAT) to dissociate motivated action from cue learning and valence. Mice are trained in a series of operant tasks. In phase 1, mice acquire positive and negative reinforcement in the presence of discrete discriminative stimuli. In phase 2, both discriminative stimuli are presented concurrently allowing us to parse innate behavioral strategies based on reward seeking and shock avoidance. Phase 3 is punished responding where a discriminative stimulus predicts that nose-poking for sucrose occurs concurrently with footshock, allowing for the assessment of how positive and negative outcomes are relatively valued.\n\nResultsFemales prioritize avoidance of negative outcomes over seeking positive, while males have the opposite strategy. In cases where rules are uncertain, males and females employ different strategies, with females demonstrating bias for shock avoidance.\n\nConclusionsThe MCOAT has broad utility for neuroscience research where pairing this task with recording and manipulation techniques will allow for the definition of the discrete information encoded within cellular populations. Ultimately, we show that making conclusions from unidimensional data leads to inaccurate generalizations about sex-specific behaviors that do not accurately represent ground truth.

animal behavior and cognition↗

bioRxiv2019

Silencing cryptic specialized metabolism in Streptomyces by the nucleoid-associated protein Lsr2

Lsr2 is a nucleoid-associated protein conserved throughout the actinobacteria, including the antibiotic-producing Streptomyces. Streptomyces species encode paralogous Lsr2 proteins (Lsr2 and Lsr2-like, or LsrL), and we show here that of the two, Lsr2 has greater functional significance. We found that Lsr2 binds AT-rich sequences throughout the chromosome, and broadly represses gene expression. Strikingly, specialized metabolic clusters were over-represented amongst its targets, and the cryptic nature of many of these clusters appears to stem from Lsr2-mediated repression. Manipulating Lsr2 activity in model species and uncharacterized isolates resulted in the production of new metabolites not seen in wild type strains. Our results suggest that the transcriptional silencing of biosynthetic clusters by Lsr2 may protect Streptomyces from the inappropriate expression of specialized metabolites, and provide global control over Streptomyces arsenal of signalling and antagonistic compounds.

microbiology↗