Publications

Submitted
Harris RM, Kao HY, Alarcón JM, Fenton AA, Hofmann HA. Transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory. bioRxiv [Internet]. Submitted. Publisher's VersionAbstract
typical protein kinase C isoform PKC ι/λ for acquisition of the conditioned behavior, whereas persistent activation of the other atypical PKC, protein kinase M zeta (PKMζ) is necessary for maintaining the memory for at least a month. It nonetheless remains unclear what other molecules and their interactions maintain active place avoidance long-term memory, and the candidate molecule approach is both impractical and inadequate to identify new candidates since there are so many to survey. Here we use a complementary approach to identify candidates by transcriptional profiling of hippocampus subregions after formation of the long-term active place avoidance memory. Interestingly, 24-h after conditioning and soon after expressing memory retention, immediate early genes were upregulated in the dentate gyrus but not Ammon’s horn of the memory expressing group. In addition to determining what genes are differentially regulated during memory maintenance, we performed an integrative, unbiased survey of the genes with expression levels that covary with behavioral measures of active place avoidance memory persistence. Gene Ontology analysis of the most differentially expressed genes shows that active place avoidance memory is associated with activation of transcription and synaptic differentiation in dentate gyrus but not CA3 or CA1, whereas hypothesis-driven candidate molecule analyses identified insignificant changes in the expression of many LTP-associated molecules in the various hippocampal subfields, nor did they covary with active place avoidance memory expression, ruling out strong transcriptional regulation but not translational regulation, which was not investigated. These findings and the data set establish an unbiased resource to screen for molecules and evaluate hypotheses for the molecular components of a hippocampus-dependent, long-term active place avoidance memory.
Chan ME, Bhamidipati PS, Goldsby HJ, Hintze A, Hofmann HA, Young RL. Comparative transcriptomics reveal distinct patterns of gene expression conservation through vertebrate embryogenesis. bioRxiv [Internet]. Submitted;840801. Publisher's VersionAbstract
Despite life’s diversity, studies of variation across animals often remind us of our shared evolutionary past. Abundant genome sequencing over the last ~25 years reveals remarkable conservation of genes and recent analyses of gene regulatory networks illustrate that not only genes but entire pathways are conserved, reused, and elaborated in the evolution of diversity. Predating these discoveries, 19th-century embryologists observed that though morphology at birth varies tremendously, certain stages of embryogenesis appear remarkably similar across vertebrates. Specifically, while early and late stages are variable across species, anatomy of mid-stages embryos (the ‘phylotypic’ stage) is conserved. This model of vertebrate development and diversification has found mixed support in recent analyses comparing gene expression across species possibly owing to differences across studies in species, embryonic stages, and gene sets compared. Here we perform a comparative analysis using 186 microarray and RNA-seq expression data sets covering embryogenesis in six vertebrate species spanning ~420 million years of evolution. We use an unbiased clustering approach to group stages of embryogenesis by transcriptomic similarity and ask whether gene expression similarity of clustered embryonic stages deviates from the null hypothesis of no relationship between timing and diversification. We use a phylogenetic comparative approach to characterize expression conservation pattern (i.e., early conservation, hourglass, inverse hourglass, late conservation, or no relationship) of each gene at each evolutionary node. Across vertebrates, we find an enrichment of genes exhibiting early conservation, hourglass, late conservation patterns and a large depletion of gene exhibiting no distinguishable pattern of conservation in both microarray and RNA-seq data sets. Enrichment of genes showing patterned conservation through embryogenesis indicates diversification of embryogenesis may be temporally constrained. However, the circumstances (e.g., gene groups, evolutionary nodes, species) under which each pattern emerges remain unknown and require both broad evolutionary sampling and systematic examination of embryogenesis across species.
2021
Arasappan D, Eickhoff SB, Nemeroff CB, Hofmann HA, Jabbi M. Transcription factor motifs associated with anterior insula gene-expression underlying mood disorder phenotypes. Molecular Neurobiology [Internet]. 2021. Publisher's VersionAbstract

Background Mood disorders represent a major cause of morbidity and mortality worldwide but the brain-related molecular pathophysiology in mood disorders remains largely undefined.

Methods Because the anterior insula is reduced in volume in patients with mood disorders, RNA was extracted from postmortem mood disorder samples and compared with unaffected control samples for RNA-sequencing identification of differentially expressed genes (DEGs) in a) bipolar disorder (BD; n=37) versus (vs.) controls (n=33), and b) major depressive disorder (MDD n=30) vs controls, and c) low vs. high Axis-I comorbidity (a measure of cumulative psychiatric disease burden). Given the regulatory role of transcription factors (TFs) in gene expression via specific-DNA-binding domains (motifs), we used JASPAR TF binding database to identify TF-motifs.

Results We found that DEGs in BD vs. controls, MDD vs. controls, and high vs. low Axis-I comorbidity were associated with TF-motifs that are known to regulate expression of toll-like receptor genes, cellular homeostatic-control genes, and genes involved in embryonic, cellular/organ and brain development.

Discussion Robust imaging-guided transcriptomics (i.e., using meta-analytic imaging results to guide independent post-mortem dissection for RNA-sequencing) was applied by targeting the gray matter volume reduction in the anterior insula in mood disorders, to guide independent postmortem identification of TF motifs regulating DEG. TF motifs were identified for immune, cellular, embryonic and neurodevelopmental processes.

Conclusion Our findings of TF-motifs that regulate the expression of immune, cellular homeostatic-control, and developmental genes provides novel information about the hierarchical relationship between gene regulatory networks, the TFs that control them, and proximate underlying neuroanatomical phenotypes in mood disorders.

arasappan_etal_2021_transcriptionfactormotifsassoc.pdf
Hernandez Scudder ME, Young RL, Thompson LM, Kore P, Crews D, Hofmann HA, Gore AC. Prenatal exposure to EDCs dis-integrates and reconstitutes neuromolecular-behavioral relationships in adult rats. Journal of the Endocrine Society [Internet]. 2021. Publisher's VersionAbstract
Exposure to endocrine-disrupting chemicals (EDCs) is ubiquitous in all species, including humans. Previous studies have shown behavioral deficits caused by EDCs that have implications for social competence and sexual selection. The neuromolecular mechanisms for these behavioral changes induced by EDCs have not been thoroughly explored. Here, we tested the hypothesis that EDCs administered to rats during a critical period of embryonic brain development would lead to disruption of normal social preference behavior, and that this involves a network of underlying gene pathways in brain regions that regulate these behaviors. Rats were exposed prenatally to human-relevant concentrations of EDCs [polychlorinated biphenyls (PCB), an industrial chemical mixture; vinclozolin (VIN), a fungicide], or vehicle. In adulthood, a sociosexual preference test (choice between hormone-primed and hormone-depleted opposite-sex rats) was administered. We profiled gene expression of in three brain regions involved in these behaviors [preoptic area (POA), medial amygdala (MeA), ventromedial nucleus (VMN)]. Prenatal PCBs impaired sociosexual preference in both sexes, and VIN disrupted this behavior in males. Each brain region (POA, MeA, VMN) had unique sets of genes altered in a sex- and EDC-specific manner. Sexually dimorphic gene expression disruption was particularly prominent for gene modules pertaining to sex steroid hormones and nonapeptides in the MeA. EDC exposure also changed the relationships between gene expression and behavior in the mate preference test, a pattern we refer to as dis-integration and reconstitution. These findings underscore the profound effects that developmental exposure to EDCs can have on adult social behavior, highlight sex-specific and individual variation in responses, and provide a foundation for further work on the disruption of mate preference behavior after prenatal exposure to EDCs.
Wallace KJ, Hofmann HA. Equal performance but distinct behaviors: sex differences in a novel object recognition task and spatial maze in a highly social cichlid fish. Animal Cognition [Internet]. 2021. Publisher's VersionAbstract

Sex differences in behavior and cognition can be driven by differential selection pressures from the environment and in the underlying neuromolecular mechanisms of decision-making. The highly social cichlid fish Astatotilapia burtoni exhibits dynamic and complex social hierarchies, yet explicit cognitive testing (outside of social contexts) and investigations of sex differences in cognition have yet to be fully explored. Here we assessed male and female A. burtoni in two cognitive tasks: a novel object recognition task and a spatial task. We hypothesized that males outperform females in a spatial learning task and exhibit more neophilic/exploratory behavior in across both tasks. In the present study we find that both sexes prefer the familiar object in a novel object recognition task, but the time at which they exhibit this preference differs between the sexes. Females more frequently learned the spatial task, exhibiting longer decision latencies and quicker error correction, suggesting a potential speed-accuracy tradeoff.

Furthermore, the sexes differ in space use in both tasks and in a principal component analysis of the spatial task. A model selection analysis finds that preference, approach, and interaction duration in the novel object recognition task that reach a threshold of importance averaged across all models. This work highlights the need to explicitly test for sex differences in cognition to better understand how individuals navigate dynamic social environments.

wallacehofmann_2021.pdf
Whitaker KW, Alvarez M, Preuss T, Cummings ME, Hofmann HA. Courting danger: Socially dominant cichlid fish adjust their startle-escape behavior to compensate for increased visual conspicuousness to avian predators. Hydrobiologia [Internet]. 2021. Publisher's Version whitaker_et_al-2021-hydrobiologia.pdf
2020
DeAngelis R, Hofmann HA. Neural and molecular mechanisms underlying female mate choice decisions in vertebrates. Journal of Experimental Biology [Internet]. 2020;223 :jeb207324. Publisher's VersionAbstract
Female mate choice is a dynamic process that allows individuals to selectively mate with those of the opposite sex that display a preferred set of traits. Because in many species males compete with each other for fertilization opportunities, female mate choice can be a powerful agent of sexual selection, often resulting in highly conspicuous traits in males. Although the evolutionary causes and consequences of the ornamentation and behaviors displayed by males to attract mates have been well studied, embarrassingly little is known about the proximate neural mechanisms through which female choice occurs. In vertebrates, female mate choice is inherently a social behavior, and although much remains to be discovered about this process, recent evidence suggests the neural substrates and circuits underlying other fundamental social behaviors (such as pair bonding, aggression and parental care) are likely similarly recruited during mate choice. Notably, female mate choice is not static, as social and ecological environments can shape the brain and, consequently, behavior in specific ways. In this Review, we discuss how social and/or ecological influences mediate female choice and how this occurs within the brain. We then discuss our current understanding of the neural substrates underlying female mate choice, with a specific focus on those that also play a role in regulating other social behaviors. Finally, we propose several promising avenues for future research by highlighting novel model systems and new methodological approaches, which together will transform our understanding of the causes and consequences of female mate choice.
deangelis_hofmann_2020.pdf
Harris RM, Kao H-Y, Alarcón JM, Fenton AA, Hofmann HA. Transcriptome analysis of hippocampal subfields identifies gene expression profiles associated with long-term active place avoidance memory. Hippocampus [Internet]. 2020. Publisher's VersionAbstract
The hippocampus plays a critical role in storing and retrieving spatial information. By targeting the dorsal hippocampus and manipulating specific “candidate” molecules using pharmacological and genetic manipulations, we have previously discovered that long-term active place avoidance memory requires transient activation of particular molecules in dorsal hippocampus. These molecules include amongst others, the persistent kinases Ca-calmodulin kinase II (CaMKII) and the atypical protein kinase C isoform PKC ι/λ for acquisition of the conditioned behavior, whereas persistent activation of the other atypical PKC, protein kinase M zeta (PKMζ) is necessary for maintaining the memory for at least a month. It nonetheless remains unclear what other molecules and their interactions maintain active place avoidance long-term memory, and the candidate molecule approach is both impractical and inadequate to identify new candidates since there are so many to survey. Here we use a complementary approach to identify candidates by transcriptional profiling of hippocampus subregions after formation of the long-term active place avoidance memory. Interestingly, 24-h after conditioning and soon after expressing memory retention, immediate early genes were upregulated in the dentate gyrus but not Ammon’s horn of the memory expressing group. In addition to determining what genes are differentially regulated during memory maintenance, we performed an integrative, unbiased survey of the genes with expression levels that covary with behavioral measures of active place avoidance memory persistence. Gene Ontology analysis of the most differentially expressed genes shows that active place avoidance memory is associated with activation of transcription and synaptic differentiation in dentate gyrus but not CA3 or CA1, whereas hypothesis-driven candidate molecule analyses identified insignificant changes in the expression of many LTP-associated molecules in the various hippocampal subfields, nor did they covary with active place avoidance memory expression, ruling out strong transcriptional regulation but not translational regulation, which was not investigated. These findings and the data set establish an unbiased resource to screen for molecules and evaluate hypotheses for the molecular components of a hippocampus-dependent, long-term active place avoidance memory.
harris_etal_2020.pdf
Jabbi M, Arasappan D, Eickhoff SB, Strakowski M, Nemeroff CB, Hofmann HA. Neuro-transcriptomic signatures for mood disorder morbidity and suicide mortality. Journal of Psychiatric Research [Internet]. 2020;127 :62-74. Publisher's VersionAbstract

Suicidal behaviors are strongly linked with mood disorders, but the specific neurobiological and functional gene-expression correlates for this linkage remain elusive. We performed neuroimaging-guided RNA-sequencing in two studies to test the hypothesis that imaging-localized gray matter volume (GMV) loss in mood disorders, harbors gene-expression changes associated with disease morbidity and related suicide mortality in an independent postmortem cohort. To do so, first, we conducted study 1 using an anatomical likelihood estimation (ALE) MRI meta-analysis including a total of 47 voxel-based morphometry (VBM) publications (i.e. 26 control versus (vs) major depressive disorder (MDD) studies, and 21 control vs bipolar disorder (BD) studies) in 2387 (living) participants. Study 1 meta-analysis identified a selective anterior insula cortex (AIC) GMV loss in mood disorders. We then used this results to guide study 2 postmortem tissue dissection and RNA-Sequencing of 100 independent donor brain samples with a life-time history of MDD (N = 30), BD (N = 37) and control (N = 33). In study 2, exploratory factor-analysis identified a higher-order factor representing number of Axis-1 diagnoses (e.g. substance use disorders/psychosis/anxiety, etc.), referred to here as morbidity and suicide-completion referred to as mortality. Comparisons of case-vs-control, and factor-analysis defined higher-order-factor contrast variables revealed that the imaging-identified AIC GMV loss sub-region harbors differential gene-expression changes in high morbidity-&-mortality versus low morbidity-&-mortality cohorts in immune, inflammasome, and neurodevelopmental pathways. Weighted gene co-expression network analysis further identified co-activated gene modules for psychiatric morbidity and mortality outcomes. These results provide evidence that AIC anatomical signature for mood disorders are possible correlates for gene-expression abnormalities in mood morbidity and suicide mortality.

    jabbi_et_al._2020.pdf
    Eastman G, Valiño G, Radío S, Young RL, Quintana L, Zakon HH, Hofmann HA, Sotelo-Silveira J, Silva A. Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression. Scientific Reports [Internet]. 2020;10 (9496). Publisher's VersionAbstract
    Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression

    Scientific Reports volume 10, Article number: 9496 (2020) Cite this article

    Abstract

    Differences in social status are often mediated by agonistic encounters between competitors. Robust literature has examined social status-dependent brain gene expression profiles across vertebrates, yet social status and reproductive state are often confounded. It has therefore been challenging to identify the neuromolecular mechanisms underlying social status independent of reproductive state. Weakly electric fish, Gymnotus omarorum, display territorial aggression and social dominance independent of reproductive state. We use wild-derived G. omarorum males to conduct a transcriptomic analysis of non-breeding social dominance relationships. After allowing paired rivals to establish a dominance hierarchy, we profiled the transcriptomes of brain sections containing the preoptic area (region involved in regulating aggressive behaviour) in dominant and subordinate individuals. We identified 16 differentially expressed genes (FDR < 0.05) and numerous genes that co-varied with behavioural traits. We also compared our results with previous reports of differential gene expression in other teleost species. Overall, our study establishes G. omarorum as a powerful model system for understanding the neuromolecular bases of social status independent of reproductive state.

    eastman_etal_2020.pdf
    Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, et al. Behavior-related gene regulatory networks: A new level of organization in the brain. Proceedings of the National Academy of Sciences USA [Internet]. 2020. Publisher's VersionAbstract
    Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain—the gene regulatory network (GRN)—that orchestrates expression levels of hundreds to thousands of genes in a behavior-related manner. We examine emerging insights into the relationships between these two types of networks and discuss their interplay in spatial as well as temporal dimensions, across multiple scales of organization. We discuss properties expected of behavior-related GRNs by drawing inspiration from the rich literature on GRNs related to animal development, comparing and contrasting these two broad classes of GRNs as they relate to their respective phenotypic manifestations. Developmental GRNs also represent a third layer of network biology, playing out over a third timescale, which is believed to play a crucial mediatory role between neuronal networks and behavioral GRNs. We end with a special emphasis on social behavior, discuss whether unique GRN organization and cis-regulatory architecture underlies this special class of behavior, and review literature that suggests an affirmative answer.
    sinha_etal_2020.pdf
    Rodriguez-Santiago M, Nührenberg P, Derry J, Deussen O, Francisco FA, Garrison LK, Garza SF, Hofmann HA, Jordan A. Behavioral traits that define social dominance are the same that reduce social influence in a consensus task. Proceedings of the National Academy of Sciences USA [Internet]. 2020. Publisher's VersionAbstract
    Dominant individuals are often most influential in their social groups, affecting movement, opinion, and performance across species and contexts. Yet, behavioral traits like aggression, intimidation, and coercion, which are associated with and in many cases define dominance, can be socially aversive. The traits that make dominant individuals influential in one context may therefore reduce their influence in other contexts. Here, we examine this association between dominance and influence using the cichlid fish Astatotilapia burtoni, comparing the influence of dominant and subordinate males during normal social interactions and in a more complex group consensus association task. We find that phenotypically dominant males are aggressive, socially central, and that these males have a strong influence over normal group movement, whereas subordinate males are passive, socially peripheral, and have little influence over normal movement. However, subordinate males have the greatest influence in generating group consensus during the association task. Dominant males are spatially distant and have lower signal-to-noise ratios of informative behavior in the association task, potentially interfering with their ability to generate group consensus. In contrast, subordinate males are physically close to other group members, have a high signal-to-noise ratio of informative behavior, and equivalent visual connectedness to their group as dominant males. The behavioral traits that define effective social influence are thus highly context specific and can be dissociated with social dominance. Thus, processes of hierarchical ascension in which the most aggressive, competitive, or coercive individuals rise to positions of dominance may be counterproductive in contexts where group performance is prioritized.
    rodriguez_santiago_et_al_2020.pdf
    2019
    Yin W, Borniger JC, Wang X, Maguire SM, Munselle ML, Bezner KS, Tesfamariam HM, Liang J, Garcia AN, Hofmann HA, et al. Estradiol treatment improves biological rhythms in a preclinical rat model of menopause. Neurobiology of Aging. 2019.Abstract
    The perimenopausal transition at middle age is often associated with hot flashes and sleep disruptions, metabolic changes, and other symptoms. Whereas the mechanisms for these processes are incompletely understood, both aging and a loss of ovarian estrogens play contributing roles. Furthermore, the timing of when estradiol treatment should commence, and for how long, are key clinical questions in the management of symptoms. Using a rat model of surgical menopause, we determined the effects of regimens of estradiol treatment with differing time at onset and duration of treatment on diurnal rhythms of activity and core temperature, and on food intake and body weight. Reproductively mature (MAT, ∼4 mo.) or aging (AG, ∼11 mo.) female rats were ovariectomized, implanted intraperitoneally with a telemetry device, and given either a vehicle (V) or estradiol (E) subcutaneous capsule implantation. Rats were remotely recorded for 10 days per month for 3 (MAT) or 6 (AG) months. To ascertain whether delayed onset of treatment affected rhythms, a subset of AG-V rats had their capsules switched to E at the end of 3 months. Another set of AG-E rats had their capsules removed at 3 months to determine whether beneficial effects of E would persist. Overall, activity and temperature mesor, robustness, and amplitude declined with aging. Compared to V treatment, E treated rats showed: 1) better maintenance of body weight and food intake; 2) higher, more consolidated activity and temperature rhythms; and 3) higher activity and temperature robustness and amplitude. In the AG arm of the study, switching treatment from V to E or E to V quickly reversed these patterns. Thus, the presence of E was the dominant factor in determining stability and amplitude of locomotor activity and temperature rhythms. As a whole the results show benefits of E treatment, even with a delay, on biological rhythms and physiological functions.
    yin-noa_2019-e2_biological_rhythms_in_rat.pdf
    Rubenstein DR, Agren JA, Carbone L, Hoekstra HE, Kapheim KM, Keller L, Moreau CS, Toth AL, Yeaman S, Hofmann HA. Coevolution of genome architecture and social behavior. Trends in Ecology and Evolution [Internet]. 2019;34 (9) :844-855. Publisher's VersionAbstract
    Although social behavior can have a strong genetic component, it can also result in selection on genome structure and function, thereby influencing the evolution of the genome itself. Here we explore the bidirectional links between social behavior and genome architecture by considering variation in social and/or mating behavior among populations (social polymorphisms) and across closely related species. We propose that social behavior can influence genome architecture via associated demographic changes due to social living. We establish guidelines to exploit emerging whole-genome sequences using analytical approaches that examine genome structure and function at different levels (regulatory vs structural variation) from the perspective of both molecular biology and population genetics in an ecological context.
    rubenstein_et_al_2019.pdf
    Still MB, Lea AM, Hofmann HA, Ryan MJ. Multimodal stimuli regulate reproductive behavior and physiology in male túngara frogs. Hormones and Behavior [Internet]. 2019. Publisher's VersionAbstract
    Unlike in terrestrial animals, the boundary between internal (e.g., hormones) and external (e.g., social) stimulation can be blurred for aquatic and amphibious species. When chemicals such as hormones and glandular secretions leach into the water, they can further interact with other signaling systems, creating multimodal stimuli. It is unclear, however, whether water-borne chemical secretions from courting male frogs affect the physiology and behavior of their rivals. In order to address this question we first established non-invasive, continuous sampling methods for simultaneously measuring both hormones and behavior in amphibious species. Then, we examined whether interactions between water-borne chemical secretions and conspecific calls affect reproductive behavior and physiology (testosterone and corticosterone) of courting male túngara frogs. Our results demonstrate that conspecific acoustic stimulation alone increases locomotor activity, decreases latency to call, and increases calling behavior but does not alter the amount of hormones excreted. In response to water containing chemical secretions from rivals, but in the absence of calls from other males, males excrete more testosterone. Interestingly, the combined acoustic and chemical stimulus causes a multiplicative increase in both calling behavior and hormonal excretion. Taken together, our results suggest that a multimodal chemical-acoustic stimulus physiologically primes males for aggressive behavior.
    still_et_al_2019.pdf
    Northcutt AJ, Kick DR, Otopalik AG, Goetz BM, Harris RM, Santin JM, Hofmann HA, Marder E, Schulz DJ. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences USA [Internet]. 2019. Publisher's VersionAbstract
    Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: if cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell type classification, we performed two forms of transcriptional profiling – RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from two small crustacean networks: the stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally-defined neuron types can be classified by expression profile alone. Our results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post-hoc grouping so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between two or more cell types. Therefore, our study supports the general utility of cell identification by transcriptional profiling, but adds a caution: it is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology or innervation target can neuronal identity be unambiguously determined.
    northcutt_et_al._2019.pdf
    Harris RM, Kao H-Y, Alarcon JM, Hofmann HA, Fenton AA. Hippocampal transcriptomic responses to enzyme-mediated cellular dissociation. Hippocampus [Internet]. 2019 :1-7. Publisher's VersionAbstract

    Single-neuron gene expression studies may be especially important for understanding nervous system structure and function because of the neuron-specific functionality and plasticity that defines functional neural circuits. Cellular dissociation is a prerequi- site technical manipulation for single-cell and single cell-population studies, but the extent to which the cellular dissociation process affects neural gene expression has not been determined. This information is necessary for interpreting the results of experi- mental manipulations that affect neural function such as learning and memory. The goal of this research was to determine the impact of cellular dissociation on brain transcriptomes. We compared gene expression of microdissected samples from the dentate gyrus (DG), CA3, and CA1 subfields of the mouse hippocampus either prepared by a standard tissue homogenization protocol or subjected to enzymatic digestion used to dissociate cells within tissues. We report that compared to homoge- nization, enzymatic dissociation alters about 350 genes or 2% of the hippocampal transcriptome. While only a few genes canonically implicated in long-term potentiation and fear memory change expression levels in response to the dissociation procedure, these data indicate that sample preparation can affect gene expression profiles, which might confound interpretation of results depending on the research question. This study is important for the investigation of any complex tissues as research effort moves from subfield level analysis to single cell analysis of gene expression.

    harris_et_al-2019-hippocampus.pdf
    Friesen CN, Hofmann HA. Molecular origins and outcomes of status and stress in primates. Proceedings of the National Academy of Sciences USA [Internet]. 2019;116 (4) :1081-1083. Publisher's Version friesenhofmann_2019.pdf
    Solomon-Lane TK, Hofmann HA. Early-life social environment alters juvenile behavior and neuroendocrine function in a highly social cichlid fish. Hormones and Behavior [Internet]. 2019;115. Publisher's VersionAbstract
    Early-life experiences can shape adult behavior, with consequences for fitness and health, yet fundamental questions remain unanswered about how early-life social experiences are translated into variation in brain and behavior. The African cichlid fish Astatotilapia burtoni, a model system in social neuroscience, is well known for its highly plastic social phenotypes in adulthood. Here, we rear juveniles in either social groups or pairs to investigate the effects of early-life social environments on behavior and neuroendocrine gene expression. We find that both juvenile behavior and neuroendocrine function are sensitive to early-life effects. Behavior robustly co-varies across multiple contexts (open field, social cue investigation, and dominance behavior assays) to form a behavioral syndrome, with pair-reared juveniles towards the end of syndrome that is less active and socially interactive. Pair-reared juveniles also submit more readily as subordinates. In a separate cohort, we measured whole brain expression of stress and sex hormone genes. Expression of glucocorticoid receptor 1a was elevated in group-reared juveniles, supporting a highly-conserved role for the stress axis mediating early-life effects. The effect of rearing environment on androgen receptor α and estrogen receptor α expression was mediated by treatment duration (1 vs. 5 weeks). Finally, expression of corticotropin-releasing factor and glucocorticoid receptor 2 decreased significantly over time. Rearing environment also caused striking differences in gene co-expression, such that expression was tightly integrated in pair-reared juveniles but not group-reared or isolates. Together, this research demonstrates the important developmental origins of behavioral phenotypes and identifies potential behavioral and neuroendocrine mechanisms.
    solomon-lane_and_hofmann_2019.pdf
    Young RL, Ferkin MH, Ockendon NF, Orr VN, Phelps SM, Pogány Á, Richards-Zawacki CL, Summers K, Székely T, Trainor BC, et al. Conserved transcriptomic profiles underpin monogamy across vertebrates. Proc. Natl. Acad. Sci. USA [Internet]. 2019;116 (4) :1331-1336. Publisher's VersionAbstract
    Social monogamy, typically characterized by the formation of a pair bond, increased territorial defense, and often biparental care, has evolved numerous times in animals. Despite the independent evolutionary origins of monogamous mating systems, several homologous brain regions and neuroendocrine pathways play conserved roles in regulating social affiliation and parental care, but little is known about the evolution of the neuromolecular mechanisms underlying monogamy. Here, we show that shared transcriptomic profiles are associated with monogamy across vertebrates and discuss the importance of our discovery for understanding the origins of behavioral diversity. We compare neural transcriptomes of reproductive males in monogamous and nonmonogamous species pairs of mice, voles, parid songbirds, frogs, and cichlid fishes. Our results provide evidence of a universal transcriptomic code underlying monogamy in vertebrates.
    young_etal_2019_pnas.pdf youngetal2019_pnas_supportinginfo.pdf young_et_al_correction.pdf jiang_and_zhang_letter.pdf reply_to_jiang_and_zhang.pdf

    Pages