The Norway rat, from an obnoxious pest to a laboratory pet

Host population structure and rare dispersal events drive leptospirosis transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, such as rats, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of leptospirosis in urban settings. We investigated leptospirosis among brown rats in Boston, Massachusetts and hypothesized that rat dispersal in this urban setting influences the movement, persistence, and diversity of Leptospira . We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016-2022); 59 rats representing 12 of 17 sites were positive for Leptospira . We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira isolates obtained from frozen and fresh tissue from some of the 59 Leptospira -positive rat kidneys. When isolates were not obtained, we attempted Leptospira genomic DNA capture and enrichment, which yielded 14 additional Leptospira genomes from rats. We also generated an enriched Leptospira genome from a 2018 human case in Boston. We found evidence of high genetic structure and limited dispersal among rat populations that is likely influenced by major roads and/or other unknown dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats, with specific clades tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and movement of leptospirosis in this urban rat community is driven by rat dispersal. Finally, our genomic analyses of the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other urban settings.

A strategy to improve rodent control while reducing rodenticide release into the environment

In addition to having a negative impact on the health of people and domestic animals, rodents often cause enormous damage to the environment by disrupting natural biodiversity. The negative impacts of rodents in urban and rural areas have required intensive use of rodentcides in spite of the proven risk of secondary poisoning of non-target predators and scavengers. Continuous and intensive use of rodenticides has led to environmental pollution through their retention in the environment. Commensal rodents are predominantly managed with anticoagulant rodenticides, which are very persistent in the environment and move up the food chain and accumulate in the bodies of predators and scavengers. Generally, the use of anticoagulant rodenticides continues, and there is a need to take appropriate measures to reduce their harmful impact. The efficacy of second generation anticoagulants (bromadiolone, difenacoum and brodifacoum), combined either mutually or with chlorophacinone at reduced doses (0.001 % and 0.0008 %), in controlling brown rats (Rattus norvegicus) was tested in a four-day no-choice feeding test. Combinations of second generation anticoagulants were more effective than the combination of chlorophacinone and second generation anticoagulants. The results indicate that combinations of different anticoagulants at multifold lower doses than the standard may provide a successful tool for brown rat control and a more environment-friendly method of rodent control and protection of non-target animals.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

The crucial role of diverse animal models to investigate cochlear aging and hearing loss

Age-related hearing loss affects a large and growing segment of the population, with profound impacts on quality of life. Age-related pathology of the cochlea-the mammalian hearing organ-underlies age-related hearing loss. Because investigating age-related changes in the cochlea in humans is challenging and often impossible, animal models are indispensable to investigate these mechanisms as well as the complex consequences of age-related hearing loss on the brain and behavior. In this review, we advocate for a comparative and interdisciplinary approach while also addressing the challenges of comparing age-related hearing loss across species with varying lifespans. We describe the experimental advantages and limitations as well as areas for future research in well-established models of age-related hearing loss, including mice, rats, gerbils, chinchillas, and birds. We also indicate the need to expand characterization of age-related hearing loss in other established animal models, especially guinea pigs, cats, and non-human primates, in which auditory function is well characterized but age-related cochlear pathology is understudied. Finally, we highlight the potential of emerging animal models for advancing our understanding of age-related hearing loss, including deer mice, with their notably extended lifespans and preserved hearing, naked mole rats, with their exceptional longevity and extensive vocal communications, as well as zebrafish, which offer genetic tractability and suitability for drug screening. Ultimately, a comparative and interdisciplinary approach in auditory research, combining insights from various animal models with human studies, is key to robust and reliable research outcomes that better advance our understanding and treatment of age-related hearing loss.

Functional anatomy of mystacial active sensing in rats

Rats' whisking motion and objects' palpation produce tactile signals sensed by mechanoreceptors at the vibrissal follicles. Rats adjust their whisking patterns to target information type, flow, and resolution, adapting to their behavioral needs and the changing environment. This coordination requires control over the activity of the mystacial pad's intrinsic and extrinsic muscles. Studies have relied on muscle recording and stimulation techniques to describe the roles of individual muscles. However, these methods lack the resolution to isolate the mystacial pad's small and compactly arranged muscles. Thus, we propose functional anatomy as a complementary approach for studying the individual and coordinated effects of the mystacial pad muscles on vibrissae movements. Our functional analysis addresses the kinematic measurements of whisking motion patterns recorded in freely exploring rats. Combined with anatomical descriptions of muscles and fascia elements of the mystacial pad in situ, we found: (1) the contributions of individual mystacial pad muscles to the different whisking motion patterns; (2) active touch by microvibrissae, and its underlying mechanism; and (3) dynamic position changes of the vibrissae pivot point, as determined by the movements of the corium and subcapsular fibrous mat. Finally, we hypothesize that each of the rat mystacial pad muscles is specialized for a particular function in a way that matches the architecture of the fascial structures. Consistent with biotensegrity principles, the muscles and fascia form a network of structural support and continuous tension that determine the arrangement and motion of the embedded individual follicles.

RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research

The animal models used in biomedical research cover virtually every human disease. RatDEGdb, a knowledge base of the differentially expressed genes (DEGs) of the rat as a model object in biomedical research is a collection of published data on gene expression in rat strains simulating arterial hypertension, age-related diseases, psychopathological conditions and other human afflictions. The current release contains information on 25,101 DEGs representing 14,320 unique rat genes that change transcription levels in 21 tissues of 10 genetic rat strains used as models of 11 human diseases based on 45 original scientific papers. RatDEGdb is novel in that, unlike any other biomedical database, it offers the manually curated annotations of DEGs in model rats with the use of independent clinical data on equal changes in the expression of homologous genes revealed in people with pathologies. The rat DEGs put in RatDEGdb were annotated with equal changes in the expression of their human homologs in affected people. In its current release, RatDEGdb contains 94,873 such annotations for 321 human genes in 836 diseases based on 959 original scientific papers found in the current PubMed. RatDEGdb may be interesting first of all to human geneticists, molecular biologists, clinical physicians, genetic advisors as well as experts in biopharmaceutics, bioinformatics and personalized genomics. RatDEGdb is publicly available at https://www.sysbio.ru/RatDEGdb.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.

On the basis of sex: male vs. female rat adenosine A1/A2A receptor affinity

OBJECTIVE

To ensure reproducibility in biomedical research, the biological variable sex must be reported; yet a reason for using male (instead of female) rodents is seldom given. In our search for novel adenosine receptor ligands, our research group routinely determines a test compound's binding affinities at male Sprague-Dawley rat (r) adenosine A1 and A2A receptors via in vitro radioligand binding studies. This pilot study compared the binding affinities of four adenosine receptor ligands (frequently used as reference standards) at male and female adenosine rA1 and rA2A receptors.

RESULTS

The inhibition constant (Ki) values determined using female rats correspond well to the values obtained using male rats and no markable difference could be observed in affinity and selectivity of reference standards. For example, DPCPX the selective adenosine A1 receptor antagonist: male rA1Ki: 0.5 ± 0.1 nM versus female rA1Ki: 0.5 ± 0.03 nM; male rA2AKi: 149 ± 23 nM versus female rA2AKi: 135 ± 29 nM. From the limited data at hand, we conclude that even when using female rats for in vitro studies without regard for the oestrous cycle, the obtained data did not vary much from their male counterparts.

Going beyond established model systems of Alzheimer's disease: companion animals provide novel insights into the neurobiology of aging

Alzheimer's disease (AD) is characterized by brain plaques, tangles, and cognitive impairment. AD is one of the most common age-related dementias in humans. Progress in characterizing AD and other age-related disorders is hindered by a perceived dearth of animal models that naturally reproduce diseases observed in humans. Mice and nonhuman primates are model systems used to understand human diseases. Still, these model systems lack many of the biological characteristics of Alzheimer-like diseases (e.g., plaques, tangles) as they grow older. In contrast, companion animal models (cats and dogs) age in ways that resemble humans. Both companion animal models and humans show evidence of brain atrophy, plaques, and tangles, as well as cognitive decline with age. We embrace a One Health perspective, which recognizes that the health of humans is connected to those of animals, and we illustrate how such a perspective can work synergistically to enhance human and animal health. A comparative biology perspective is ideally suited to integrate insights across veterinary and human medical disciplines and solve long-standing problems in aging.

Ghost rodents: Albinism in Australian rodent species

While almost half of all mammal species are rodents, records of albinism in free‐ranging rodents are very rare. Australia has a large and diverse assemblage of native rodent species, but there are no records of free‐ranging albino rodents in the published literature. In this study, we aim to improve our understanding of the occurrence of albinism in Australian rodent species by collating contemporary and historic records of this condition and providing an estimate of its frequency. We found 23 records of albinism (i.e., a complete loss of pigmentation), representing eight species, in free‐ranging rodents native to Australia, with the frequency of albinism being generally <0.1%. Our findings bring the total number of rodent species in which albinism has been recorded globally to 76. While native Australian species represent only 7.8% of the world's murid rodent diversity, they now account for 42.1% of murid rodent species known to exhibit albinism. We also identified multiple concurrent albino records from a small island population of rakali (Hydromys chrysogaster) and discuss the factors that may contribute to the relatively high frequency (2%) of the condition on this island. We suggest that the small number of native albino rodents recorded in mainland Australia over the last 100 years means that traits associated with the condition are likely deleterious within populations and are thus selected against.

Non-Lethal Dose-Response Models Replace Lethal Bioassays for Predicting the Hazard of Para-Aminopropiophenone to Australian Wildlife

Para-aminopropiophenone (PAPP) is a potent methaemoglobin (MetHb) forming agent used for the lethal control of exotic carnivores and mustelids. To assess the sensitivity of Australian wildlife to PAPP we developed an in vivo assay that did not use death as an endpoint. Sub-lethal dose-response data were modelled to predict PAPP doses required to achieve an endpoint set at 80% MetHb (MetHb₈₀). The comparative sensitivity of non-target mammals referenced to this endpoint was found to be highly variable, with southern brown bandicoots (Isoodon obesulus) the most sensitive species (MetHb₈₀ = 6.3 mg kg^-1) and bush rats (Rattus fuscipes) the most tolerant (MetHb₈₀ = 1035 mg kg^-1). Published LD₅₀ estimates were highly correlated with PAPP doses modelled to achieve the MetHb₈₀ endpoint (r² = 0.99, p < 0.001). Most dose-response data for native mammals were collected in the field or in semi-natural enclosures, permitting PAPP and placebo dosed animals to be fitted with tracking transmitters and transponders and released at their point of capture. A protracted morbidity and mortality was observed only in Australian ravens (Corvus coronoides). The combination of sub-lethal dose-response assay and survival data collected in the field provided more relevant information about the actual hazard of pest control agents to non-target wildlife species than laboratory-based lethal-dose bioassays. We discuss the need to replace lethal-dose data with biologically meaningful insights able to define a continuum of toxicological hazards that better serve the needs of conservation and veterinary scientists and wildlife managers.

Assessing animal welfare impact of fourteen control and dispatch methods for house mouse (Mus musculus), Norway rat (Rattus norvegicus) and black rat (Rattus rattus)

Population control of the house mouse (Mus musculus), Norway rat (Rattus norvegicus) and black rat (Rattus rattus) is common practice worldwide. Our objective was to assess the impact on animal welfare of lethal and non-lethal control methods, including three dispatch methods. We used the Sharp and Saunders welfare assessment model with eight experts scoring eleven control methods and three dispatch methods used on the three species. We presumed the methods were performed as prescribed, only taking into account the effect on the target animal (and not, for example, on non-target catches). We did not assess population control efficacy of the methods. Methods considered to induce the least suffering to the target animal were captive-bolt traps, electrocution traps and cervical dislocation, while those with the greatest impact were anticoagulants, cholecalciferol and deprivation. Experts indicated considerable uncertainty regarding their evaluation of certain methods, which emphasises the need for further scientific research. In particular, the impact of hydrogen cyanide, chloralose and aluminium phosphide on animal welfare ought to be investigated. The experts also stressed the need to improve Standard Operating Procedures and to incorporate animal welfare assessments in Integrated Pest Management (IPM). The results of our study can help laypeople, professionals, regulatory agencies and legislators making well-informed decisions as to which methods to use when controlling commensal rodents.

Rat's response to a novelty and increased complexity of the environment resulting from the introduction of movable vs. stationary objects in the free exploration test

Most animals, including rats, show a preference for more complex environments. This is demonstrated particularly well when complexity increases due to the addition of new elements to the environment. The aim of the study was to investigate the reaction to novelty, understood as a change in environmental properties that involve both changes in complexity and controllability. Controllability may allow for dealing with challenges of an environment of low predictability in a way that the animal's own activity reduces the uncertainty of environmental events. In our study, the animals underwent a spontaneous exploration test in low-stress conditions. After a period of habituation to the experimental arena, additional stationary (increased complexity) and/or movable (increased complexity and controllability) tunnels were introduced, and the reaction of the rats to the novel objects was measured. The results of the study confirmed that an increase in the complexity of the environment through the addition of objects triggers a more intensive exploratory activity in rats. However, an increased spatial complexity combined with the movability of the novel objects seems to result in increased caution towards the novelty after an initial inspection of the changed objects. It suggests that the complexity of the novelty may trigger both neophilia and neophobia depending on the level of the predictability of the novel environment and that the movability of newly introduced objects is not independent of other parameters of the environment.

Expanding the frame around social dynamics and glucocorticoids: From hierarchies within the nest to competitive interactions among species

The effect of the social environment on individual state or condition has largely focused on glucocorticoid levels (GCs). As metabolic hormones whose production can be influenced by nutritional, physical, or psychosocial stressors, GCs are a valuable (though singular) measure that may reflect the degree of "stress" experienced by an individual. Most work to date has focused on how social rank influences GCs in group-living species or how predation risk influences GCs in prey. This work has been revealing, but a more comprehensive assessment of the social environment is needed to fully understand how different features of the social environment influence GCs in both group living and non-group living species and across life history stages. Just as there can be intense within-group competition among adult conspecifics, it bears appreciating there can also be competition among siblings from the same brood, among adult conspecifics that do not live in groups, or among heterospecifics. In these situations, dominance hierarchies typically emerge, albeit, do dominants or subordinate individuals or species have higher GCs? We examine the degree of support for hypotheses derived from group-living species about whether differential GCs between dominants and subordinates reflect the "stress of subordination" or "costs of dominance" in these other social contexts. By doing so, we aim to test the generality of these two hypotheses and propose new research directions to broaden the lens that focuses on social hierarchies and GCs.

Bisphenols impact hormone levels in animals: A meta-analysis

Bisphenols are used in the manufacture of plastics and are endocrine disrupting compounds detectable in free living organisms and environments globally. The original bisphenol, bisphenol A (BPA), is best known as a xenoestrogen, but it also disrupts other steroid hormones and other classes of hormones including thyroid and pituitary hormones. When its toxicity became better known, BPA was replaced by presumably less toxic alternatives, including bisphenols S, F, and AF. However, recent data suggest that all bisphenols can have endocrine disrupting effects, although their impacts remain unresolved particularly in non-human animals. Our aim was to establish the current state-of-knowledge of the effects of different bisphenols on circulating hormone levels in non-human animals. Our meta-analysis showed that a diverse range of hormones (including thyroid hormones, corticosterone, follicle stimulating hormone, luteinizing hormone, and estradiol) are strongly impacted by exposure to any bisphenol type, and that in laboratory rats (Rattus norvegicus) the effect was modified by life-stage. Although there were qualitative differences, BPA alternatives had as great or greater effects on hormone levels as BPA. However, data coverage across hormones was uneven, and most studies measured the effects of BPA on vertebrate reproductive hormones. Similarly, taxonomic coverage was poor. Over 80% of data originated from laboratory rats and zebrafish (Danio rerio) and there are no data for whole classes of invertebrates and vertebrates (e.g., amphibians). Our results show that all bisphenols alter circulating levels of a broad range of hormones. However, the current state-of-knowledge is incomplete so that the ecological impacts of bisphenols are difficult to gauge, although based on the available data bisphenols are likely to be detrimental to a broad range of taxa and ecosystems.

Whisker trimming during infanthood modifies the development of spike-wave discharges and behavioral sequences in IntelliCage impulsivity paradigm in adult WAG/Rij rats

Whisker system in rats undergoes rapid development during the first postnatal weeks. Neonatal whisker trimming increases excitability in the somatosensory cortex and affects exploratory behavior at adult ages. WAG/Rij rats are genetically predisposed to develop absence seizures in adulthood, and whisker trimming during three postnatal weeks aggravates epileptic activity in these rats. It is assumed that behavioral performance in adult WAG/Rij rats is influenced (1) by absence epilepsy and (2) by whisker trimming during the short period around the onset of active whisker movements, PN9-16. We examined the effect of whisker trimming in WAG/Rij rats during PN9-16 on spike-wave discharges (SWD, EEG hallmark of absence epilepsy). We found that 77% of WAG/Rij rats showed pronounced SWD (epileptic phenotype), and the rest did not (non-epileptic phenotype). At the age of 5 m, epileptic trimmed rats showed more SWD than epileptic control rats. Age-related increase of SWD was found only in the control group, suggesting that whisker trimming during PN9-16 led to an earlier maturation of SWD. Goal-directed behavior was examined in all rats at the age of 4-4.5 m using IntelliCage impulsivity paradigm. In order to optimize the analysis of behavioral data, we combined several Python packages into a single processing pipeline. Early life whisker trimming altered behavioral sequences and strategy of exploration in adulthood, suggesting reduced whisker sensitivity in the trimmed rats. Epileptic WAG/Rij rats at 4-4.5 months showed only a slight learning impairment during later stages of IntelliCage impulsivity paradigm, which may be associated with the early stage of development of SWD.

Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology

The profound impact of the gut microbiome on host health has led to a revolution in biomedical research, motivating researchers from disparate fields to define the specific molecular mechanisms that mediate host-beneficial effects. The advent of genomic technologies allied to the use of model microbiomes in gnotobiotic mouse models has transformed our understanding of intestinal microbial ecology and the impact of the microbiome on the host. However, despite incredible advances, our understanding of the host-microbiome dialogue that shapes host physiology is still in its infancy. Progress has been limited by challenges associated with developing model systems that are both tractable enough to provide key mechanistic insights while also reflecting the enormous complexity of the gut ecosystem. Simplified model microbiomes have facilitated detailed interrogation of transcriptional and metabolic functions of the microbiome but do not recapitulate the interactions seen in complex communities. Conversely, intact complex communities from mice or humans provide a more physiologically relevant community type, but can limit our ability to uncover high-resolution insights into microbiome function. Moreover, complex microbiomes from lab-derived mice or humans often do not readily imprint human-like phenotypes. Therefore, improved model microbiomes that are highly defined and tractable, but that more accurately recapitulate human microbiome-induced phenotypic variation are required to improve understanding of fundamental processes governing host-microbiome mutualism. This improved understanding will enhance the translational relevance of studies that address how the microbiome promotes host health and influences disease states. Microbial exposures in wild mice, both symbiotic and infectious in nature, have recently been established to more readily recapitulate human-like phenotypes. The development of synthetic model communities from such "wild mice" therefore represents an attractive strategy to overcome the limitations of current approaches. Advances in microbial culturing approaches that allow for the generation of large and diverse libraries of isolates, coupled to ever more affordable large-scale genomic sequencing, mean that we are now ideally positioned to develop such systems. Furthermore, the development of sophisticated in vitro systems is allowing for detailed insights into host-microbiome interactions to be obtained. Here we discuss the need to leverage such approaches and highlight key challenges that remain to be addressed.

Managing the Health of Captive Herds of Exotic Companion Mammals

Common medical problems diagnosed and treated in individual companion exotic mammals are relevant in a herd-health setting. Many of these problems are often associated with poor husbandry and/or inappropriate nutrition. Rabbits, ferrets, chinchillas, and rodents have been domesticated alongside humans and an understanding of their ethology gives veterinarians a base knowledge in making recommendations for animals in their care. This article briefly reviews the ethology and husbandry in such species, but detailed needs are beyond the scope of this article.

Let's get wild: A review of free-ranging rat assays as context-enriched supplements to traditional laboratory models

More than 24,000 rodent studies are published annually, with the vast majority of these studies focused on genetically undiverse animals in highly-controlled laboratory settings. However, findings from the laboratory have become increasingly unreliable for predicting outcomes in field and clinical settings, leading to a perceived crisis in translational research. One cause of this disparity might be that most human societies, in contrast to laboratory rodents, are genetically diverse and live in super-enriched environments. Methods for importing wild rats into the laboratory, and also exporting laboratory-style chambers into natural environments are not well-known outside their respective disciplines. Therefore, we have reviewed the current status of supplements to the laboratory rodent assay. We progress logically from highly-controlled experiments with natural breeding colonies to purely naturalistic approaches with free-ranging rats. We then highlight a number of approaches that allow genetically-diverse wild rats to be utilized in context-enriched paradigms. While considering the benefits and shortcomings of each available approach, we detail protocols for random sampling, remote-sensing, and deployment of laboratory chambers in the field. As supplements to standardized laboratory trials, some of these assays could offer key insights to help unify outcomes between laboratory and field studies. However, we note several outstanding questions that must be addressed such as: the trade-off between control and context, possible reductions in sample size, ramifications for the 'standardization fallacy', and ethical dilemmas of working with wild animals. Given these challenges, further innovation will be required before supplemental assays can be made broadly-accessible and thus, transferrable across disciplines.

Coding variants in mouse and rat model organisms: mousepost and ratpost

Mice and rats are the most commonly used vertebrate model organisms in biomedical research. The availability of a reference genome in both animals combined with the deep sequencing of several doze of popular inbred lines also provides rich sequence variation data in these species. In some cases, such sequence variants can be linked directly to a distinctive phenotype. In previous work, we created the mouse and rat online searchable databases ("Mousepost" and "Ratpost") where small variant information for protein coding transcripts in mouse and rat inbred strains can be easily retrieved at the amino acid level. These tools are directly useful in forward genetics strategies or as a repository of existing sequence variations. Here, we perform a comparison between the "Mousepost" and "Ratpost" databases and we couple these two tools to a database of human sequence variants ClinVar. We investigated the level of redundancy and complementarity of known variants in protein coding transcripts and found that the large majority of variants is species-specific. However, a small set of positions is conserved in an inbred line between both species. We conclude that both databases are highly complementary, but this may change with further sequencing efforts in both species.

The genome sequence of the Norway rat, Rattus norvegicus Berkenhout 1769

We present a genome assembly from an individual male Rattus norvegicus (the Norway rat; Chordata; Mammalia; Rodentia; Muridae). The genome sequence is 2.44 gigabases in span. The majority of the assembly is scaffolded into 20 chromosomal pseudomolecules, with both X and Y sex chromosomes assembled. This genome assembly, mRatBN7.2, represents the new reference genome for R. norvegicus and has been adopted by the Genome Reference Consortium.

Response to novelty induced by change in size and complexity of familiar objects in Lister-Hooded rats, a follow-up of 2019 study

This study examines the relationship between the change in size and change in complexity of well-known/familiarized objects and exploratory activity regulation in rats. In our experiment, the rats were exposed to three types of environmental novelty in a well-familiarized chamber: (1) addition of new tunnels to the chamber, (2) increased size of a familiarized tunnel, and (3) increased complexity of the existing tunnels. The animals responded to the addition of new tunnels with a significant behavioural shift involving increased exploration of the newly installed tunnels. This effect was stable across all three test trials. The rats exposed to a change in size of the familiar object initially reacted with a behavioural shift towards the enlarged tunnel but then re-focused on the unchanged one. There was also a significant increase in the frequency of moving between the zones of the chamber. The experimental group exposed to an increased complexity of familiar objects responded with a pronounced behavioural shift towards the complex tunnel and then slightly intensified their exploration of the unchanged one. A decrease was also observed in the frequency of moving between the zones of the chamber in the first and second test trials. In the effect size analysis, no differences were found in any of the three groups, which suggests that all manipulations had similar impact. The data obtained in this study supports the view that in rats, curiosity is at least two-dimensional: activational and cognitive. The activational aspect of curiosity may be explained by novelty-related arousal processes, while the cognitive processes are activated at longer time intervals in response to more complex stimulation. The validation of this hypothesis requires further research involving manipulations with a recently standardized protocol for measuring free exploration.

Sex differences in the auditory functions of rodents

BACKGROUND

In humans, it is well known that females have better hearing than males. The mechanism of this influence of sex on auditory function in humans is not well understood. Testing the hypothesis of underlying mechanisms often relies on preclinical research, a field in which sex bias still exists unconsciously. Rodents are popular research models in hearing, thus it is crucial to understand the sex differences in these rodent models when studying health and disease in humans.

OBJECTIVES

This review aims to summarize the existing sex differences in the auditory functions of rodent species including mouse, rat, Guinea pig, Mongolian gerbil, and chinchilla. In addition, a concise summary of the hearing characteristics and the advantages and the drawbacks of conducting auditory experiments in each rodent species is provided.

DESIGNS

Manuscripts were identified in PubMed and Ovid Medline for the queries "Rodent", "Sex Characteristics", and "Hearing or Auditory Function". Manuscripts were included if they were original research, written in English, and use rodents. The content of each manuscript was screened for the sex of the rodents and the discussion of sex-based results.

CONCLUSIONS

The sex differences in auditory function of rodents are prevalent and influenced by multiple factors including physiological mechanisms, sex-based anatomical variations, and stimuli from the external environment. Such differences may play a role in understanding and explaining sex differences in hearing of humans and need to be taken into consideration for developing clinical therapies aim to improve auditory performances.

Ratpost: a searchable database of protein-inactivating sequence variations in 40 sequenced rat-inbred strains

Rat-inbred strains are essential as scientific tools. We have analyzed the publicly available genome sequences of 40 rat-inbred strains and provide an overview of sequence variations leading to amino acid changes in protein-coding genes, premature STOP codons or loss of STOP codons, and short in-frame insertions and deletions of all protein-coding genes across all these inbred lines. We provide an overview of the predicted impact on protein function of all these affected proteins in the database, by comparing their sequence with the sequences of the rat reference strain BN/SsNHsdMcwi. We also investigate the flaws of the protein-coding sequences of this reference strain itself, by comparing them with a consensus genome. These data can be retrieved via a searchable website (Ratpost.be) and allow a global, better interpretation of genetic background effects and a source of naturally defective alleles in these 40 sequenced classical and high-priority rat-inbred strains.

Genome-to-phenome research in rats: progress and perspectives

Because of their relatively short lifespan (<4 years), rats have become the second most used model organism to study health and diseases in humans who may live for up to 120 years. First-, second- and third-generation sequencing technologies and platforms have produced increasingly greater sequencing depth and accurate reads, leading to significant advancements in the rat genome assembly during the last 20 years. In fact, whole genome sequencing (WGS) of 47 strains have been completed. This has led to the discovery of genome variants in rats, which have been widely used to detect quantitative trait loci underlying complex phenotypes based on gene, haplotype, and sweep association analyses. DNA variants can also reveal strain, chromosome and gene functional evolutions. In parallel, phenome programs have advanced significantly in rats during the last 15 years and more than 10 databases host genome and/or phenome information. In order to discover the bridges between genome and phenome, systems genetics and integrative genomics approaches have been developed. On the other hand, multiple level information transfers from genome to phenome are executed by differential usage of alternative transcriptional start (ATS) and polyadenylation (APA) sites per gene. We used our own experiments to demonstrate how alternative transcriptome analysis can lead to enrichment of phenome-related causal pathways in rats. Development of advanced genome-to-phenome assays will certainly enhance rats as models for human biomedical research.