Genetic manipulations in the rat: progress and prospects

Detrimental effects of chronic sugar-sweetened carbonated soft drink consumption on inflammatory response and the size of apical periodontitis: An animal-based study

AIM

This study aimed to evaluate the effects of chronic consumption of two sugar-sweetened carbonated soft drinks - one containing caffeine (Coca-Cola®) and one without (Sprite®) - on the progression of periapical lesions and the levels of pro-inflammatory cytokines in rats.

METHODOLOGY

Twelve Wistar rats were divided into three groups (n = 4): Control group, Coca-Cola group and Sprite group. The rats in Coca-Cola and Sprite groups were given ad libitum access to their respective soft drinks for 3 months, while the Control group received filtered water. After 2 months of consumption, the pulps of the lower left first molars were exposed for 28 days to induce periapical lesions. Following euthanasia, the jaws were removed, and the periapical lesions were assessed using micro-computed tomography imaging. Blood samples were collected to analyse the pro-inflammatory cytokines IL-1β, IL-6, IL-2, IL-17 and TNF-α via Luminex assay. Non-parametric data were analysed using the Kruskal-Wallis test followed by Dunn's test, while parametric data were analysed using one-way ANOVA followed by Tukey's test (p < 0.05).

RESULTS

Both the Coca-Cola and Sprite groups exhibited periapical lesions with significantly greater volume and diameter compared to the Control group (p < 0.05). Additionally, both soft drink groups had significantly higher levels of IL-1β, IL-6 and IL-2 compared to the Control group (p < 0.05). The Sprite group displayed significantly higher levels of IL-1β than the Coca-Cola group (p < 0.05), while the Coca-Cola group showed significantly elevated TNF-α levels compared to both the Control and Sprite groups (p < 0.05). No significant differences in IL-17 levels were observed among the groups (p > 0.05).

CONCLUSIONS

The chronic consumption of sugar-sweetened carbonated soft drinks, regardless of caffeine content, has detrimental effects on the inflammatory response and progression of apical periodontitis in rats.

Diagnosis of Indian Big Four and monocled Cobra snakebites in envenomed plasma using smartphone-based digital imaging colourimetry method

BACKGROUND

Venomous or dry bites can result from snake envenomation. Therefore, developing a detection test for venomous snakebites in envenomed patients can prevent from unnecessary antivenom therapy for dry bites, thereby, saving them from adverse effects and cost of antivenom therapy.

METHODOLOGY

This study demonstrates a method for the diagnosis of medically significant 'Big Four' Indian snake venoms (Naja naja, Bungarus caeruleus, Daboia russelii, Echis carinatus) in the plasma of experimentally envenomed animals (envenomed under laboratory conditions). Rabbit polyclonal antibodies (PAbs) were produced by generating modified bespoke peptides identified by computational analysis from the antigenic sites of the main toxins found in the proteome of India's 'Big Four' venomous snakes. The polyclonal antibody formulation (FPAb) prepared by mixing the five representative PAbs in the ratio of 1:1:1:1:1 demonstrated synergistic immune recognition of the 'Big Four' snakes and Naja kaouthia venoms. The recognition for these venoms under in vitro and in vivo conditions by FPAb was significantly higher (p<0.05) than commercial polyvalent antivenom produced against native venom toxins. The FPAb was tested to detect the venoms in subcutaneously envenomed rat plasmas until 240 minutes post-injection. Fourier-transform infrared spectroscopy, zeta potential, transmission electron microscopy, and atomic force microscopy characterised gold nanoparticles (AuNP) conjugated with FPAb. The FPAb-conjugated AuNP demonstrated aggregation upon interaction with venom toxins, changing the colour from red through burgundy to blue, monitored using a smartphone. From the digital image colourimetry analysis of the images, calibration curves for venoms were obtained, and each venom in the envenomed plasma at different time intervals was quantified using these curves.

CONCLUSION

A method for detection of venomous snakebites has been reported. The formulation of polyclonal antibodies generated against toxins of 'Big Four' venomous snakes of India immune-recognise venoms of 'Big Four' venomous snakes of India and N. kaouthia venoms under both in vitro and in vivo conditions. The antibody formulation conjugated to AuNP detected the venoms in envenomed plasma. This method of detection has potential to be useful for snakebite management in clinical settings.

Rat Models of Breast Cancer

As the first mammal to be domesticated for research purposes, rats served as the primary animal model for various branches of biomedical research, including breast cancer studies, up until the late 1990s and early 2000s. During this time, genetic engineering of mice, but not rats, became routine, and mice gradually supplanted rats as the preferred rodent model. But recent advances in creating genetically engineered rat models, especially with the assistance of CRISPR/Cas9 technology, have rekindled the significance of rats as a critical model in exploring various facets of breast cancer research. This is particularly pronounced in the study of the formation and progression of the estrogen receptor-positive subtype, which remains challenging to model in mice. In this chapter, we embark on a historical journey through the evolution of rat models in biomedical research and provide an overview of the general and histological characteristics of rat mammary glands. Next, we critically review major rat models for breast cancer research, including those induced by carcinogens, hormones, radiation, germline transgenes, germline knockouts, and intraductal injection of retrovirus/lentivirus to deliver oncogenic drivers into mature mammary glands. We also discuss the advances in building rat models using somatic genome editing powered by CRISPR/Cas9. This chapter concludes with our forward-looking perspective on future applications of advanced rat models in critical areas of breast cancer research that have continued to challenge the mouse model community.

Implementation of the Methyl-Seq platform to identify tissue- and sex-specific DNA methylation differences in the rat epigenome

Epigenomic annotations for the rat lag far behind those of human and mouse, despite the rat's immense utility in pharmacological and behavioral studies and the need to understand their epigenetic mechanisms. We have designed a targeted-enrichment method followed by next-generation sequencing (Methyl-Seq) to identify DNA methylation (DNAm) signatures across the rat genome. The design reflected an attempt to create a more comprehensive investigation of the rat epigenome, as it included promoters, CpG islands, and island shores of all RefSeq genes. In this study, we implemented the rat Methyl-Seq platform and tested its ability to distinguish differentially methylated regions (DMRs) among three different tissue types, three distinct brain regions, and, in the hippocampus, between males and females. These comparisons yielded DNAm differences of differing magnitudes, many of which were independently validated by bisulfite pyrosequencing, including autosomal regions that were predicted to show the least degree of difference in DNAm between males and females. Quantitative reverse transcription PCR revealed that most genes associated with the DMRs showed tissue-, brain region-, and sex-specific differences in expression. In particular, we found evidence for sex-specific DNAm and expression differences at Tubb6, Lrrn2, Tex26, and Sox5l1, all of which play important roles in neurodevelopment and have been implicated in studies examining sex differences. Our results demonstrate the utility of the rat Methyl-Seq platform and suggest the presence of DNAm differences between the male and female hippocampus. The rat Methyl-Seq has the potential to provide epigenomic insights into pharmacological and behavioral studies performed in the rat.

Genome-scale screening in a rat haploid system identifies Thop1 as a modulator of pluripotency exit

OBJECTIVES

The rats are crucial animal models for the basic medical researches. Rat embryonic stem cells (ESCs), which are widely studied, can self-renew and exhibit pluripotency in long-term culture, but the mechanism underlying how they exit pluripotency remains obscure. To investigate the key modulators on pluripotency exiting in rat ESCs, we perform genome-wide screening using a unique rat haploid system.

MATERIALS AND METHODS

Rat haploid ESCs (haESCs) enable advances in the discovery of unknown functional genes owing to their homozygous and pluripotent characteristics. REX1 is a sensitive marker for the naïve pluripotency that is often utilized to monitor pluripotency exit, thus rat haESCs carrying a Rex1-GFP reporter are used for genetic screening. Genome-wide mutations are introduced into the genomes of rat Rex1-GFP haESCs via piggyBac transposon, and differentiation-retarded mutants are obtained after random differentiation selection. The exact mutations are elucidated by high-throughput sequencing and bioinformatic analysis. The role of candidate mutation is validated in rat ESCs by knockout and overexpression experiments, and the phosphorylation of ERK1/2 (p-ERK1/2) is determined by western blotting.

RESULTS

High-throughput sequencing analysis reveals numerous insertions related to various pathways affecting random differentiation. Thereafter, deletion of Thop1 (one candidate gene in the screened list) arrests the differentiation of rat ESCs by inhibiting the p-ERK1/2, whereas overexpression of Thop1 promotes rat ESCs to exit from pluripotency.

CONCLUSIONS

Our findings provide an ideal tool to study functional genomics in rats: a homozygous haploid system carrying a pluripotency reporter that facilitates robust discovery of the mechanisms involved in the self-renewal or pluripotency of rat ESCs.

A Study to Assess the Quality of Reporting of Animal Research Studies Published in PubMed Indexed Journals: A Retrospective, Cross-Sectional Content Analysis

Objectives: A complete and concise pre-clinical experimental research gives detailed information about the disease-specific model, prevents duplication, and saves animal life, money, as well as time. It will also allow readers to effectively interpret and evaluate the work and ensure that others can replicate the experiments described. The present study was conducted to assess the adequacy of animal details provided in published experimental animal studies.

Methods: All in vivo studies published as full-text articles in two PubMed indexed journals (one Indian and one international) from January 2011 to December 2019 and satisfying the inclusion norms were included. A checklist consisting of 27 discrete items subdivided under three domains, viz. animal details, disease model, and guidelines, was used. Every article was assessed by two investigators independently for determining the reporting quality.

Results: One hundred and seventy-seven studies satisfied the inclusion criteria. Age or age range was reported in 20.34% of the articles in the Indian journal and 5.88% articles in the international journal (p=0.019). Housing and husbandry details were reported in all the articles published in the international journal and 82.7% of the articles in the Indian journal (p=0.001). The disease/pathology studied was given in 70.62% of articles published in the Indian journal and 86.27% of articles published in the international journal (p=0.029). None of the studies provided details of genetic modification, health status, sample size calculation, steps taken to minimize bias, and implementation of randomization.

Conclusion: There is a need for optimal reporting of certain relevant animal details, disease models, experimental procedures, sample size calculation, and adherence to guidelines by the researchers for which the reporting was found to be sub-par to improve reproducibility and validity of animal research.

The Mononuclear Phagocyte System of the Rat

The laboratory rat continues to be the model of choice for many studies of physiology, behavior, and complex human diseases. Cells of the mononuclear phagocyte system (MPS; monocytes, macrophages, and dendritic cells) are abundant residents in every tissue in the body and regulate postnatal development, homeostasis, and innate and acquired immunity. Recruitment and proliferation of MPS cells is an essential component of both initiation and resolution of inflammation. The large majority of current knowledge of MPS biology is derived from studies of inbred mice, but advances in technology and resources have eliminated many of the advantages of the mouse as a model. In this article, we review the tools available and the current state of knowledge of development, homeostasis, regulation, and diversity within the MPS of the rat.

Advances in Genome Editing and Application to the Generation of Genetically Modified Rat Models

The rat has been extensively used as a small animal model. Many genetically engineered rat models have emerged in the last two decades, and the advent of gene-specific nucleases has accelerated their generation in recent years. This review covers the techniques and advances used to generate genetically engineered rat lines and their application to the development of rat models more broadly, such as conditional knockouts and reporter gene strains. In addition, genome-editing techniques that remain to be explored in the rat are discussed. The review also focuses more particularly on two areas in which extensive work has been done: human genetic diseases and immune system analysis. Models are thoroughly described in these two areas and highlight the competitive advantages of rat models over available corresponding mouse versions. The objective of this review is to provide a comprehensive description of the advantages and potential of rat models for addressing specific scientific questions and to characterize the best genome-engineering tools for developing new projects.

TP53-Deficient Angiosarcoma Expression Profiling in Rat Model

Sarcomas are a heterogeneous group of malignant tumors, that develop from mesenchymal cells. Sarcomas are tumors associated with poor prognosis and expected short overall survival. Efforts to improve treatment efficacy and treatment outcomes of advanced and metastatic sarcoma patients have not led to significant improvements in the last decades. In the Tp53^C273X/C273X rat model we therefore aimed to characterize specific gene expression pattern of angiosarcomas with a loss of TP53 function. The presence of metabolically active tumors in several locations including the brain, head and neck, extremities and abdomen was confirmed by magnetic resonance imaging (MRI) and positron emission tomography (PET) examinations. Limb angiosarcoma tumors were selected for microarray expression analysis. The most upregulated pathways in angiosarcoma vs all other tissues were related to cell cycle with mitosis and meiosis, chromosome, nucleosome and telomere maintenance as well as DNA replication and recombination. The downregulated genes were responsible for metabolism, including respiratory chain electron transport, tricarboxylic acid (TCA) cycle, fatty acid metabolism and amino-acid catabolism. Our findings demonstrated that the type of developing sarcoma depends on genetic background, underscoring the importance of developing more malignancy susceptibility models in various strains and species to simulate the study of the diverse genetics of human sarcomas.

Animal Use in Neurobiological Research

The fact that neurobiological research is reliant upon laboratory-reared rodents is well known. The following paper discusses this topic broadly, but also aims to highlight other species used in the study of the nervous system and the evolution of animal species usage from the end of World War II through recent investigations. Attention is drawn to the dramatic reduction in the diversity of species used in neuroscience, with a significant shift toward two species, the mouse (Mus musculus) and rat (Rattus norvegicus). Such a limitation in animal species causes many difficulties in the development of new therapies for various neuropsychiatric diseases. Based on numerous scientific publications, the advantages of using a greater diversity of species in neuroscience and the disadvantages of focusing on mice and rats are presented.

Transchromosomic technology for genomically humanized animals

"Genomically" humanized animals are invaluable tools for generating human disease models and for biomedical research. Humanized animal models have generally been developed via conventional transgenic technologies; however, conventional gene delivery vectors such as viruses, plasmids, bacterial artificial chromosomes, P1 phase-derived artificial chromosomes, and yeast artificial chromosomes have limitations for transgenic animal creation as their loading gene capacity is restricted, and the expression of transgenes is unstable. Transchromosomic (Tc) techniques using mammalian artificial chromosomes, including human chromosome fragments, human artificial chromosomes, and mouse artificial chromosomes, have overcome these limitations. These tools can carry multiple genes or Mb-sized genomic loci and their associated regulatory elements, which has facilitated the creation of more useful and complex transgenic models for human disease, drug development, and humanized animal research. This review describes the history of Tc animal development, the applications of Tc animals, and future prospects.

Aging Reduces the Functional Brain Networks Strength-a Resting State fMRI Study of Healthy Mouse Brain

Resting-state functional magnetic resonance imaging (rsfMRI) is increasingly used to unravel the functional neuronal networks in health and disease. In particular, this technique of simultaneously probing the whole brain has found high interest in monitoring brain wide effects of cerebral disease and in evaluating therapeutic strategies. Such studies, applied in preclinical experimental mouse models, often require long-term observations. In particular during regeneration studies, easily several months of continuous monitoring are required to detect functional improvements. These long periods of following the functional deficits during disease evolution as well as the functional recoveries during therapeutic interventions represent a substantial fraction of the life span of the experimental animals. We have therefore aimed to decipher the role of healthy aging alone for changes in functional neuronal networks in mice, from developmental adolescence via adulthood to progressing aging. For this purpose, four different groups of C57Bl6 mice of varying age between 2 and 13 months were studied twice with 4 weeks separation using resting state fMRI at 9.4T. Dedicated data analysis including both Independent Component Analysis (ICA) followed by seed-based connectivity matrix compilation resulted in an inverse U-shape curve of functional connectivity (FC) strength in both the sensorimotor and default mode network (DMN). This inverse U-shape pattern presented a distinct maximum of FC strength at 8–9 months of age, followed by a continuous decrease during later aging phases. At progressed aging at 12–13 months, the reduction of connectivity strength varied between 25% and 70% with most connectivities showing a reduction in strength by approximately 50%. We recommend that these substantial age-dependent changes in FC strength must be considered in future longitudinal studies to discriminate focused disease-based functional deficits and therapy-related functional improvements from underlying independent age effects.

Targeted Manipulation of Brain Serotonin: RNAi-Mediated Knockdown of Tryptophan Hydroxylase 2 in Rats

Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in the biosynthesis of the biogenic monoamine serotonin (5-hydroxytryptamine, 5-HT). Two existing TPH isoforms are responsible for the generation of two distinct serotonergic systems in vertebrates. TPH1, predominantly expressed in the gastrointestinal tract and pineal gland, mediates 5-HT biosynthesis in non-neuronal tissues, while TPH2, mainly found in the raphe nuclei of the brain stem, is accountable for the production of 5-HT in the brain. Neuronal 5-HT is a key regulator of mood and behavior and its deficiency has been implicated in a variety of neuropsychiatric disorders, e.g., depression and anxiety. To gain further insights into the complexity of central 5-HT modulations of physiological and pathophysiological processes, a new transgenic rat model, allowing an inducible gene knockdown of Tph2, was established based on doxycycline-inducible shRNA-expression. Biochemical phenotyping revealed a functional knockdown of Tph2 mRNA expression following oral doxycycline administration, with subsequent reductions in the corresponding levels of TPH2 enzyme expression and activity. Transgenic rats showed also significantly decreased tissue levels of 5-HT and its degradation product 5-Hydroxyindoleacetic acid (5-HIAA) in the raphe nuclei, hippocampus, hypothalamus, and cortex, while peripheral 5-HT concentrations in the blood remained unchanged. In summary, this novel transgenic rat model allows inducible manipulation of 5-HT biosynthesis specifically in the brain and may help to elucidate the role of 5-HT in the pathophysiology of affective disorders.

The challenges of modeling hormone receptor-positive breast cancer in mice

Estrogen receptor-positive (ER+) tumors account for 70-80% of all breast cancer (BC) cases and are characterized by estrogen dependency for their growth. Endocrine therapies using estrogen receptor antagonists or aromatase inhibitors represent a key component of the standard of care for these tumors. The occurrence of de novo or acquired resistance to estrogen withdrawal represents an important clinical problem, impacting on patient survival. In addition, despite an initially favorable outcome, a part of ER+ BC patients present with disease recurrence locally or at distant sites years or even decades after apparent remission. In vivo models that closely mimic human disease are urgently needed to study the biology of these tumors, investigate the molecular mechanisms underlying endocrine resistance and identify patients at risk of recurrence. Despite the similarities in the overall hormonal regulation of mammary gland development between mice and humans, the majority of the mammary carcinomas occurring in genetically engineered mouse models (GEMMs) are ER negative and most xenograft models are based on few ER+ cancer cell lines. We recently showed that the microenvironment is critical for ER+ cancer cells and discuss in this review the potential of intraductal xenograft model for basic and preclinical research.

Canine mammary tumors as a model for human disease

Animal models for examining human breast cancer (HBC) carcinogenesis have been extensively studied and proposed. With the recent advent of immunotherapy, significant attention has been focused on the dog as a model for human cancer. Dogs develop mammary tumors and other cancer types spontaneously with an intact immune system, which exhibit a number of clinical and molecular similarities to HBC. In addition to the spontaneous tumor presentation, the clinical similarities between human and canine mammary tumors (CMT) include the age at onset, hormonal etiology and course of the diseases. Furthermore, factors that affect the disease outcome, including tumor size, stage and lymph node invasion, are similar in HBC and CMT. Similarly, the molecular characteristics of steroid receptor, epidermal growth factor, proliferation marker, metalloproteinase and cyclooxygenase expression, and the mutation of the p53 tumor suppressor gene in CMT, mimic HBC. Furthermore, ductal carcinomas in situ in human and canine mammary glands are particularly similar in their pathological, molecular and visual characteristics. These CMT characteristics and their similarities to HBC indicate that the dog could be an excellent model for the study of human disease. These similarities are discussed in detail in the present review, and are compared with the in vitro and other in vivo animal models available.

Production of immunodeficient rabbits by multiplex embryo transfer and multiplex gene targeting

Immunodeficient mice have been used predominantly in biomedical research. Realizing that large animal species may have an enhanced ability to predict clinical outcome relative to mice, we worked to develop immunodeficient rabbits by CRISPR/Cas9. We first demonstrated that multiplex embryo transfer efficiently produced multiple lines of single-gene mutant (SGM) founders. Embryos microinjected with single sgRNA targeting FOXN1, RAG2, IL2RG or PRKDC were pooled for embryo transfer. As few as three recipients were used to produce twenty SGM founders for four genes. We then demonstrated the powerful multiplex targeting capacity of CRISPR/Cas9. First, two genes on the same chromosome were targeted simultaneously, resulting in three RAG1/RAG2 double-gene mutant (DGM) founders. Next we microinjected forty-five embryos each with five sgRNAs targeting FOXN1, RAG1, RAG2, IL2RG and PRKDC, and transferred them to two recipients. Five founders were produced: one SGM, two DGM, one triple-gene mutant and one quadruple-gene mutant. The present work demonstrates that multiplex embryo transfer and multiplex gene targeting can be used to quickly and efficiently generate mutant rabbit founders. Four lines of SGM (e.g. FOXN1, RAG2, IL2RG, and PRKDC) immunodeficient rabbits, as well as multigenic mutant immunodeficient rabbits have been produced. These animals may prove useful for biomedical research.

Applications of the CRISPR-Cas9 system in kidney research

The recently discovered clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) is an RNA-guided DNA nuclease, and has been harnessed for the development of simple, efficient, and relatively inexpensive technologies to precisely manipulate the genomic information in virtually all cell types and organisms. The CRIPSR-Cas9 systems have already been effectively used to disrupt multiple genes simultaneously, create conditional alleles, and generate reporter proteins, even in vivo. The ability of Cas9 to target a specific genomic region has also been exploited for various applications, such as transcriptional regulation, epigenetic control, and chromosome labeling. Here we first describe the molecular mechanism of the RNA-guided DNA targeting by the CRISPR-Cas9 system and then outline the current applications of this system as a genome-editing tool in mice and other species, to better model and study human diseases. We also discuss the practical and potential uses of the CRISPR-Cas9 system in kidney research and highlight the further applications of this technology beyond genome editing. Undoubtedly, the CRISPR-Cas9 system holds enormous potential for revolutionizing and accelerating kidney research and therapeutic applications in the future.

Targets, models and challenges in osteoarthritis research

Osteoarthritis is a chronic degenerative disorder of the joint and represents one of the most common diseases worldwide. Its prevalence and severity are increasing owing to aging of the population, but treatment options remain largely limited to painkillers and anti-inflammatory drugs, which only provide symptomatic relief. In the late stages of the disease, surgical interventions are often necessary to partially restore joint function. Although the focus of osteoarthritis research has been originally on the articular cartilage, novel findings are now pointing to osteoarthritis as a disease of the whole joint, in which failure of different joint components can occur. In this Review, we summarize recent progress in the field, including data from novel ‘omics’ technologies and from a number of preclinical and clinical trials. We describe different in vitro and in vivo systems that can be used to study molecules, pathways and cells that are involved in osteoarthritis. We illustrate that a comprehensive and multisystem approach is necessary to understand the complexity and heterogeneity of the disease and to better guide the development of novel therapeutic strategies for osteoarthritis.

Animal models of bronchopulmonary dysplasia. The term rat models

Bronchopulmonary dysplasia (BPD) is the chronic lung disease of prematurity that affects very preterm infants. Although advances in perinatal care have enabled the survival of infants born as early as 23-24 wk of gestation, the challenge of promoting lung growth while protecting the ever more immature lung from injury is now bigger. Consequently, BPD remains one of the most common complications of extreme prematurity and still lacks specific treatments. Progress in our understanding of BPD and the potential of developing therapeutic strategies have arisen from large (baboons, sheep, and pigs) and small (rabbits, rats, and mice) animal models. This review focuses specifically on the use of the rat to model BPD and summarizes how the model is used in various research studies and the advantages and limitations of this particular model, and it highlights recent therapeutic advances in BPD by using this rat model.

Generation of TALEN-mediated GRdim knock-in rats by homologous recombination

Transcription Activator-Like Effector Nucleases (TALEN) are potential tools for precise genome engineering of laboratory animals. We report the first targeted genomic integration in the rat using TALENs (Transcription Activator-Like Effector Nucleases) by homology-derived recombination (HDR). We assembled TALENs and designed a linear donor insert targeting a pA476T mutation in the rat Glucocorticoid Receptor (Nr3c1) namely GR(dim), that prevents receptor homodimerization in the mouse. TALEN mRNA and linear double-stranded donor were microinjected into rat one-cell embryos. Overall, we observed targeted genomic modifications in 17% of the offspring, indicating high TALEN cutting efficiency in rat zygotes.

Immune reconstitution and graft-versus-host reactions in rat models of allogeneic hematopoietic cell transplantation

Allogeneic hematopoietic cell transplantation (alloHCT) extends the lives of thousands of patients who would otherwise succumb to hematopoietic malignancies such as leukemias and lymphomas, aplastic anemia, and disorders of the immune system. In alloHCT, different immune cell types mediate beneficial graft-versus-tumor (GvT) effects, regulate detrimental graft-versus-host disease (GvHD), and are required for protection against infections. Today, the “good” (GvT effector cells and memory cells conferring protection) cannot be easily separated from the “bad” (GvHD-causing cells), and alloHCT remains a hazardous medical modality. The transplantation of hematopoietic stem cells into an immunosuppressed patient creates a delicate environment for the reconstitution of donor blood and immune cells in co-existence with host cells. Immunological reconstitution determines to a large extent the immune status of the allo-transplanted host against infections and the recurrence of cancer, and is critical for long-term protection and survival after clinical alloHCT. Animal models continue to be extremely valuable experimental tools that widen our understanding of, for example, the dynamics of post-transplant hematopoiesis and the complexity of immune reconstitution with multiple ways of interaction between host and donor cells. In this review, we discuss the rat as an experimental model of HCT between allogeneic individuals. We summarize our findings on lymphocyte reconstitution in transplanted rats and illustrate the disease pathology of this particular model. We also introduce the rat skin explant assay, a feasible alternative to in vivo transplantation studies. The skin explant assay can be used to elucidate the biology of graft-versus-host reactions, which are known to have a major impact on immune reconstitution, and to perform genome-wide gene expression studies using controlled combinations of minor and major histocompatibility between the donor and the recipient.

Genome resource banking of biomedically important laboratory animals

Genome resource banking is the systematic collection, storage, and redistribution of biomaterials in an organized, logistical, and secure manner. Genome cryobanks usually contain biomaterials and associated genomic information essential for progression of biomedicine, human health, and research. In that regard, appropriate genome cryobanks could provide essential biomaterials for both current and future research projects in the form of various cell types and tissues, including sperm, oocytes, embryos, embryonic or adult stem cells, induced pluripotent stem cells, and gonadal tissues. In addition to cryobanked germplasm, cryobanking of DNA, serum, blood products, and tissues from scientifically, economically, and ecologically important species has become a common practice. For revitalization of the whole organism, cryopreserved germplasm in conjunction with assisted reproductive technologies, offer a powerful approach for research model management, as well as assisting in animal production for agriculture, conservation, and human reproductive medicine. Recently, many developed and developing countries have allocated substantial resources to establish genome resources banks which are responsible for safeguarding scientifically, economically, and ecologically important wild type, mutant, and transgenic plants, fish, and local livestock breeds, as well as wildlife species. This review is dedicated to the memory of Dr. John K. Critser, who has made profound contributions to the science of cryobiology and establishment of genome research and resources centers for mice, rats, and swine. Emphasis will be given to application of genome resource banks to species with substantial contributions to the advancement of biomedicine and human health.

Retake the center stage--new development of rat genetics

The rat is a powerful model for the study of human physiology and diseases, and is preferred by physiologists, neuroscientists and toxicologists. However, the lack of robust genetic modification tools has severely limited the generation of rat genetic models over the last two decades. In the last few years, several gene-targeting strategies have been developed in rats using N-ethyl-N-nitrosourea (ENU), transposons, zinc-finger nucleases (ZFNs), bacterial artificial chromosome (BAC) mediated transgenesis, and recently established rat embryonic stem (ES) cells. The development and improvement of these approaches to genetic manipulation have created a bright future for the use of genetic rat models in investigations of gene function and human diseases. Here, we summarize the strategies used for rat genetic manipulation in current research. We also discuss BAC transgenesis as a potential tool in rat transgenic models.

Modeling human neurodegenerative diseases in transgenic systems

Transgenic systems are widely used to study the cellular and molecular basis of human neurodegenerative diseases. A wide variety of model organisms have been utilized, including bacteria (Escherichia coli), plants (Arabidopsis thaliana), nematodes (Caenorhabditis elegans), arthropods (Drosophila melanogaster), fish (zebrafish, Danio rerio), rodents (mouse, Mus musculus and rat, Rattus norvegicus) as well as non-human primates (rhesus monkey, Macaca mulatta). These transgenic systems have enormous value for understanding the pathophysiological basis of these disorders and have, in some cases, been instrumental in the development of therapeutic approaches to treat these conditions. In this review, we discuss the most commonly used model organisms and the methodologies available for the preparation of transgenic organisms. Moreover, we provide selected examples of the use of these technologies for the preparation of transgenic animal models of neurodegenerative diseases, including Alzheimer's disease (AD), frontotemporal lobar degeneration (FTLD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD) and Parkinson's disease (PD) and discuss the application of these technologies to AD as an example of how transgenic modeling has affected the study of human neurodegenerative diseases.

Following the genes: a framework for animal modeling of psychiatric disorders

The number of individual cases of psychiatric disorders that can be ascribed to identified, rare, single mutations is increasing with great rapidity. Such mutations can be recapitulated in mice to generate animal models with direct etiological validity. Defining the underlying pathogenic mechanisms will require an experimental and theoretical framework to make the links from mutation to altered behavior in an animal or psychopathology in a human. Here, we discuss key elements of such a framework, including cell type-based phenotyping, developmental trajectories, linking circuit properties at micro and macro scales and definition of neurobiological phenotypes that are directly translatable to humans.