Model For Biomedical Research Research Articles

Gastric emphysema and pneumatosis intestinalis in two common marmosets with duodenal dilation syndrome

BackgroundCommon marmosets (Callithrix jacchus) are widely used as primate experimental models in biomedical research. Duodenal dilation with chronic vomiting in captive common marmosets is a recently described life-threatening syndrome that is problematic for health control. However, the pathogenesis and cause of death are not fully understood.Case presentationWe report two novel necropsy cases in which captive common marmosets were histopathologically diagnosed with gastric emphysema (GE) and pneumatosis intestinalis (PI). Marmoset duodenal dilation syndrome was confirmed in each case by clinical observation of chronic vomiting and by gross necropsy findings showing a dilated, gas-filled and fluid-filled descending duodenum that adhered to the ascending colon. A diagnosis of GE and PI was made on the basis of the bubble-like morphology of the gastric and intestinal mucosa, with histological examination revealing numerous vacuoles diffused throughout the lamina propria mucosae and submucosa. Immunostaining for prospero homeobox 1 and CD31 distinguished gas cysts from blood and lymph vessels. The presence of hepatic portal venous gas in case 1 and possible secondary bacteremia-related septic shock in case 2 were suggested to be acute life-threatening abdominal processes resulting from gastric emphysema and pneumatosis intestinalis.ConclusionsIn both cases, the gross and histopathological findings of gas cysts in the GI tract walls matched the features of human GE and PI. These findings contribute to clarifying the cause of death in captive marmosets that have died of gastrointestinal diseases.

Biomedical Researchers Should be Taught Statistics Differently than Biostatisticians in Training: Illustration of a Module within a Clinical Research Seminar Course

The predominant model for biomedical research is team science. Two critical members of the team are the clinical investigator and the biostatistician. Typically, the biostatistician performs statistical analyses and the clinical investigator interprets the results. Clinical investigators have different background and interests than biostatisticians, and should be taught statistics differently. Concepts should be phrased in plain language, illustrations should replace mathematical derivations, and underlying statistical concepts should be explicitly named. Consistent with basic principles of constructivism, clinical investigators and biostatisticians will (and should) have different but overlapping mental maps of statistics. Our approach is illustrated through the description of a module within a research seminar course for clinical investigators.

Genetic characterization of a captive marmoset (Callithrix jacchus) colony using genotype-by-sequencing.

The marmoset is a fundamental nonhuman primate model for the study of aging, neurobiology, and many other topics. Genetic management of captive marmoset colonies is complicated by frequent chimerism in the blood and other tissues, a lack of tools to enable cost-effective, genome-wide interrogation of variation, and historic mergers and migrations of animals between colonies. We implemented genotype-by-sequencing (GBS) of hair follicle derived DNA (a minimally chimeric DNA source) of 82 marmosets housed at the Southwest National Primate Research Center (SNPRC). Our primary goals were the genetic characterization of our marmoset population for pedigree verification and colony management and to inform the scientific community of the functional genetic makeup of this valuable resource. We used the GBS data to reconstruct the genetic legacy of recent mergers between colonies, to identify genetically related animals whose relationships were previously unknown due to incomplete pedigree information, and to show that animals in the SNPRC colony appear to exhibit low levels of inbreeding. Of the >99,000 single-nucleotide variants (SNVs) that we characterized, >9800 are located within gene regions known to harbor pathogenic variants of clinical significance in humans. Overall, we show the combination of low-resolution (sparse) genotyping using hair follicle DNA is a powerful strategy for the genetic management of captive marmoset colonies and for identifying potential SNVs for the development of biomedical research models.

Complete Genomic Assembly of Mauritian Cynomolgus Macaque Killer Ig-like Receptor and Natural Killer Group 2 Haplotypes.

Mauritian-origin cynomolgus macaques (MCMs) serve as a powerful nonhuman primate model in biomedical research due to their unique genetic homogeneity, which simplifies experimental designs. Despite their extensive use, a comprehensive understanding of crucial immune-regulating gene families, particularly killer Ig-like receptors (KIR) and NK group 2 (NKG2), has been hindered by the lack of detailed genomic reference assemblies. In this study, we employ advanced long-read sequencing techniques to completely assemble eight KIR and seven NKG2 genomic haplotypes, providing an extensive insight into the structural and allelic diversity of these immunoregulatory gene clusters. Leveraging these genomic resources, we prototype a strategy for genotyping KIR and NKG2 using short-read, whole-exome capture data, illustrating the potential for cost-effective multilocus genotyping at colony scale. These results mark a significant enhancement for biomedical research in MCMs and underscore the feasibility of broad-scale genetic investigations.

Ultrasonography of the neotropical primate female reproductive system.

The Neotropical (e. g., Aotus sp., Callithrix jacchus, Saguinus sp., Saimiri sp., and Sapajus sp.) primates are important models for biomedical research and studies on reproductive physiology and biotechnology. Consequently, studies about gynecological and obstetric ultrasonography are crucial. B-mode ultrasonography is a non-invasive imaging technique that provides real-time bidimensional or three-dimensional/four-dimensional B-mode images. In association with Doppler ultrasonography, B-mode ultrasonography can also be used to monitor the mammalian blood flow to the reproductive tract during important events such as ovulation and gestation. Thus, gynecological and obstetric ultrasonography is essential for establishing the female reproductive anatomical and physiological ovarian and uterine health status, gestational diagnosis, and fetal growth monitoring. For instance, the paper presents and discusses the state-of-the-art gynecological and obstetric ultrasonography in the Neotropical primates, species that are models for biomedical research, and some recent studies on species targets for conservation strategies for wild animal populations.

Gen expression of Bax and Bcl-2 in Cynomolgus monkeys (Macaca fascicularis) as animal model for Papillomavirus study

Cervical cancer is one of the fourth cancers in the world that occurs in women. Papillomavirus infection has been reported as one of the causative agents of cervical cancer. Apoptotic mechanism is one of the signs of cancer. Cynomolgus monkeys have been widely used as animal models in biomedical research because they are similar to humans in terms of genetics, anatomy, and physiology compared to other animals. Previous studies reported that cynomolgus monkeys have undergone spontaneous infection by papillomavirus, but this infection did not show the phenomenon of cervical cancer. This study aimed to evaluate the prediction of papillomavirus-infected cervical cancer through apoptotic mechanisms regulated by Bax and Bcl-2 genes. Gene expression was performed in this study using Real-Time PCR technique. The results showed an increase in Bax and Bcl-2 gene expression in positive group cynomolgus monkeys with papillomavirus infection. Bcl-2 as anti-apoptotic gene expression increased significantly higher than Bax as pro-apoptotic gene. Bax and Bcl-2 have potential as biomarkers to predict the phenomenon of cervical cancer in cynomolgus monkeys with papillomavirus infection.

Alternatives of Animal Models for Biomedical Research: a Comprehensive Review of Modern Approaches.

Biomedical research has long relied on animal models to unravel the intricacies of human physiology and pathology. However, concerns surrounding ethics, expenses, and inherent species differences have catalyzed the exploration of alternative avenues. The contemporary alternatives to traditional animal models in biomedical research delve into three main categories of alternative approaches: in vitro models, in vertebrate models, and in silico models. This unique approach to artificial intelligence and machine learning has been a keen interest to be used in different biomedical research. The main goal of this review is to serve as a guide to researchers seeking novel avenues for their investigations and underscores the importance of considering alternative models in the pursuit of scientific knowledge and medical breakthroughs, including showcasing the broad spectrum of modern approaches that are revolutionizing biomedical research and leading the way toward a more ethical, efficient, and innovative future. Models can insight into cellular processes, developmental biology, drug interaction, assessing toxicology, and understanding molecular mechanisms.

Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds

BackgroundDomesticated pigs serve as an ideal animal model for biomedical research and also provide the majority of meat for human consumption in China. Porcine intramuscular fat content associates with human health and diseases and is essential in pork quality. The molecular mechanisms controlling lipid metabolism and intramuscular fat accretion across tissues in pigs, and how these changes in response to pig breeds, remain largely unknown.ResultsWe surveyed the tissue-resident cell types of the porcine jejunum, colon, liver, and longissimus dorsi muscle between Lantang and Landrace breeds by single-cell RNA sequencing. Combining lipidomics and metagenomics approaches, we also characterized gene signatures and determined key discriminating markers of lipid digestibility, absorption, conversion, and deposition across tissues in two pig breeds. In Landrace, lean-meat swine mainly exhibited breed-specific advantages in lipid absorption and oxidation for energy supply in small and large intestinal epitheliums, nascent high-density lipoprotein synthesis for reverse cholesterol transport in enterocytes and hepatocytes, bile acid formation, and secretion for fat emulsification in hepatocytes, as well as intestinal-microbiota gene expression involved in lipid accumulation product. In Lantang, obese-meat swine showed a higher synthesis capacity of chylomicrons responsible for high serum triacylglycerol levels in small intestinal epitheliums, the predominant characteristics of lipid absorption in muscle tissue, and greater intramuscular adipcytogenesis potentials from muscular fibro-adipogenic progenitor subpopulation.ConclusionsThe findings enhanced our understanding of the cellular biology of lipid metabolism and opened new avenues to improve animal production and human diseases.D7xkEMpXE5aNHjWuhXhcDpVideo

A review of the reproductive biology of mormyroidfishes: An emerging model for biomedical research.

Mormyroidea is a superfamily of weakly electric African fishes with great potential as a model in a variety of biomedical research areas including systems neuroscience, muscle cell and craniofacial development, ion channel biophysics, and flagellar/ciliary biology. However, they are currently difficult to breed in the laboratory setting, which is essential for any tractable model organism. As such, there is a need to better understand the reproductive biology of mormyroids to breed them more reliably in the laboratory to effectively use them as a biomedical research model. This review seeks to (1)briefly highlight the biomedically relevant phenotypes of mormyroids and (2) compile information about mormyroid reproduction including sex differences, breeding season, sexual maturity, gonads, gametes, and courtship/spawning behaviors. We also highlight areas of mormyroid reproductive biology that are currently unexplored and/or have the potential for further investigation that may provide insights into more successful mormyroid laboratory breeding methods.

Importance of Zebrafish as a Non-Mammalian Vertebrate Model for Studying Neurodegenerative Disorders Using Ayurvedic Medicinal Plants: A Review

Alzheimer's disease and Parkinson's disease are debilitating neurodegenerative disorders that impose a significant burden on the affected individuals and the society as a whole. Despite extensive research efforts, effective treatments for these diseases remain elusive till date. Ayurveda, a traditional system of medicinal practice which originated in ancient India, has long touted the potential of various plants possessing neuroprotective properties. The effects of a few relevant Ayurvedic plants viz. Guduchi, Kapikachhu, Shankhapushpi, Turmeric, Mandukparni, Ashwagadha, Brahmi, Jatamansi etc. on several non-human primates and rodents have been reported. The therapeutic potential of those plants to mitigate the pathological hallmarks associated with Alzheimer's disease and Parkinson's disease was assessed. We have outlined the most recent research on Ayurveda's effects on neurodegenerative brain illnesses in this review article, with an emphasis on Alzheimer's disease and Parkinson's disease. As the zebrafish (Danio rerio Hamilton) has emerged as a useful, non-mammalian vertebrate model organism for studying a wide range of diseases, the effect of few other medicinal plants on zebrafish was also mentioned. Powerful live imaging and genetic tools which is currently available for zebrafish has transformed this fish to a top model in biomedical research and toxicity testing. However, further research is needed to elucidate the precise mechanisms of action and to translate these promising results into clinical applications. The exploration of traditional medicinal systems, in conjunction with modern scientific methodologies using novel model organisms, such as zebrafish offers a valuable avenue for the development of innovative treatments for neurodegenerative disorders.

Establishment of a Practical Sperm Cryopreservation Pathway for the Axolotl (Ambystoma mexicanum): A Community-Level Approach to Germplasm Repository Development.

The axolotl (Ambystoma mexicanum) draws great attention around the world for its importance as a biomedical research model, but housing and maintaining live animals is increasingly expensive and risky as new transgenic lines are developed. The goal of this work was to develop an initial practical pathway for sperm cryopreservation to support germplasm repository development. The present study assembled a pathway through the investigation of axolotl sperm collection by stripping, refrigerated storage in various osmotic pressures, cryopreservation in various cryoprotectants, and in vitro fertilization using thawed sperm. By the stripping of males, 25-800 µL of sperm fluid was collected at concentrations of 1.6 × 106 to 8.9 × 107 sperm/mL. Sperm remained motile for 5 d in Hanks' Balanced Salt Solution (HBSS) at osmolalities of 100-600 mOsm/kg. Sperm cryopreserved in 0.25 mL French straws at 20 °C/min in a final concentration of 5% DMFA plus 200 mM trehalose and thawed at 25 °C for 15 s resulted in 52 ± 12% total post-thaw motility. In six in vitro fertilization trials, 20% of eggs tested with thawed sperm continued to develop to stage 7-8 after 24 h, and a third of those embryos (58) hatched. This work is the first report of successful production of axolotl offspring with cryopreserved sperm, providing a general framework for pathway development to establish Ambystoma germplasm repositories for future research and applications.

Morphometric Analysis of Growth in Captive-bred Pig-tailed macaque (Macaca nemestrina Linnaeus 1766)

ABSTRACT
 The pig-tailed macaque has a high vulnerability to human infectious disease pathogens as well as nonhuman primate viruses, making it a good animal model for biomedical research. The goals of this research are to better understand the morphometric and growth rate variations between male and female pig-tailed macaques living in tropical captivity as their natural climate, which will be useful in developing research techniques as well as modifying and developing equipment and instruments.
 The research was carried out on captive pig-tailed macaques born and kept at the Research Animal Facility in Lodaya (RAF-L) Primate Research Center IPB University (PRC-IPB). The characteristics were separated into four categories: head size, torso, upper limb, and lower limb. During the study period, 70 animals were measured, 32 males and 38 females. The repetition of measurements at distinct timepoints according to body development varies for each individual depending on the animal's situation at that time.
 There was no visible difference in body and extremity sizes between male and female animals between the ages of 1 and 4 years. Males' head proportions appear to expand consistently in height and width after they are beyond 2 years old, in contrast to females. The growth trend of females tends to decrease from one year of age until sexual maturity, in contrast to males which show a growth spurt at the ages of 1 and 4 years. Differences in size and growth rate indicating sexual dimorphism are visible after the female reaches sexual maturity.

Identification of novel mammalian viruses in tree shrews ( Tupaia belangeri chinensis).

The Chinese tree shrew ( Tupaia belangeri chinensis), a member of the mammalian order Scandentia, exhibits considerable similarities with primates, including humans, in aspects of its nervous, immune, and metabolic systems. These similarities have established the tree shrew as a promising experimental model for biomedical research on cancer, infectious diseases, metabolic disorders, and mental health conditions. Herein, we used meta-transcriptomic sequencing to analyze plasma, as well as oral and anal swab samples, from 105 healthy asymptomatic tree shrews to identify the presence of potential zoonotic viruses. In total, eight mammalian viruses with complete genomes were identified, belonging to six viral families, including Flaviviridae, Hepeviridae, Parvovirinae, Picornaviridae, Sedoreoviridae, and Spinareoviridae. Notably, the presence of rotavirus was recorded in tree shrews for the first time. Three viruses - hepacivirus 1, parvovirus, and picornavirus - exhibited low genetic similarity (<70%) with previously reported viruses at the whole-genome scale, indicating novelty. Conversely, three other viruses - hepacivirus 2, hepatovirus A and hepevirus - exhibited high similarity (>94%) to known viral strains. Phylogenetic analyses also revealed that the rotavirus and mammalian orthoreovirus identified in this study may be novel reassortants. These findings provide insights into the diverse viral spectrum present in captive Chinese tree shrews, highlighting the necessity for further research into their potential for cross-species transmission.

Understanding zebrafish sleep and wakefulness physiology as an experimental model for biomedical research.

Sleep is a globally observable fact, or period of reversible distracted rest, that can be distinguished from arousal by various behavioral criteria. Although the function of sleep is an evolutionarily conserved behavior, its mechanism is not yet clear. The zebrafish (Danio rerio) has become a valuable model for neurobehavioral studies such as studying learning, memory, anxiety, and depression. It is characterized by a sleep-like state and circadian rhythm, making it comparable to mammals. Zebrafish are a good model for behavioral studies because they share genetic similarities with humans. A number of neurotransmitters are involved in sleep and wakefulness. There is a binding between melatonin and the hypocretin system present in zebrafish. The full understanding of sleep and wakefulness physiology in zebrafish is still unclear among researchers. Therefore, to make a clear understanding of the sleep/wake cycle in zebrafish, this article covers the mechanism involved behind it, and the role of the neuromodulator system followed by the mechanism of the HPA axis.

Using Electroporation to Improve and Accelerate Zebrafish Embryo Toxicity Testing.

Zebrafish have emerged as a useful model for biomedical research and have been used in environmental toxicology studies. However, the presence of the chorion during the embryo stage limits cellular exposure to toxic elements and creates the possibility of a false-negative or reduced sensitivity in fish embryo toxicity testing (FET). This paper presents the use of electroporation as a technique to improve the delivery of toxic elements inside the chorion, increasing the exposure level of the toxins at an early embryo stage (<3 h post-fertilization). A custom-made electroporation device with the required electrical circuitry has been developed to position embryos between electrodes that provide electrical pulses to expedite the entry of molecules inside the chorion. The optimized parameters facilitate material entering into the chorion without affecting the survival rate of the embryos. The effectiveness of the electroporation system is demonstrated using Trypan blue dye and gold nanoparticles (AuNPs, 20-40 nm). Our results demonstrate the feasibility of controlling the concentration of dye and nanoparticles delivered inside the chorion by optimizing the electrical parameters, including pulse width, pulse number, and amplitude. Next, we tested silver nanoparticles (AgNPs, 10 nm), a commonly used toxin that can lower mortality, affect heart rate, and cause phenotypic defects. We found that electroporation of AgNPs reduces the exposure time required for toxicity testing from 4 days to hours. Electroporation for FET can provide rapid entry of potential toxins into zebrafish embryos, reducing the time required for toxicity testing and drug delivery experiments.

Book Review: Zebrafish Model for Biomedical Research

Book Review: Zebrafish Model for Biomedical Research

Towards a framework for interoperability and reproducibility of predictive models

The development and deployment of machine learning (ML) models for biomedical research and healthcare currently lacks standard methodologies. Although tools for model replication are numerous, without a unifying blueprint it remains difficult to scientifically reproduce predictive ML models for any number of reasons (e.g., assumptions regarding data distributions and preprocessing, unclear test metrics, etc.) and ultimately, questions around generalizability and transportability are not readily answered. To facilitate scientific reproducibility, we built upon the Predictive Model Markup Language (PMML) to capture essential information. As a key component of the PREdictive Model Index and Exchange REpository (PREMIERE) platform, we present the Automated Metadata Pipeline (AMP) for conversion of a given predictive ML model into an extended PMML file that autocompletes an ML-based checklist, assessing model elements for interoperability and reproducibility. We demonstrate this pipeline on multiple test cases with three different ML algorithms and health-related datasets, providing a foundation for future predictive model reproducibility, sharing, and comparison.

Sterility testing of germ-free mouse colonies.

In biomedical research, germ-free and gnotobiotic mouse models enable the mechanistic investigation of microbiota-host interactions and their role on (patho)physiology. Throughout any gnotobiotic experiment, standardized and periodic microbiological testing of defined gnotobiotic housing conditions is a key requirement. Here, we review basic principles of germ-free isolator technology, the suitability of various sterilization methods, and the use of sterility testing methods to monitor germ-free mouse colonies. We also discuss their effectiveness and limitations, and share the experience with protocols used in our facility. In addition, possible sources of isolator contamination are discussed and an overview of reported contaminants is provided.

Psychedelic Research and Therapeutic Practices: Embracing Communities, Groups, and Traditional Knowledge

ABSTRACTThe global prevalence of substance abuse and mental disorders continues to challenge healthcare systems, with one in eight individuals affected. The therapeutic potential of psychedelics is recognized not only for treating mental disorders but also for enhancing well-being and promoting pro-social behaviors. Conventional biomedical research models fall short in addressing the broader health needs of populations and poorly suited for overcoming barriers to service delivery. This special issue includes six articles that explore alternative approaches to psychedelic research and practice, emphasizing collaboration with diverse actors, including indigenous communities, and incorporating traditional knowledge systems into contemporary psychedelic research. They underscore the need for innovative research methods that engage multidisciplinary approaches while promoting culturally relevant outcome measures. They emphasize the importance of shifting from punitive drug policies to those grounded in public health and human rights, allowing for multi-country studies and the development of evidence-based care models for community mental health. Incorporating traditional knowledge and community-based methodologies into psychedelic science is vital for its evolution beyond biomedical research for widespread dissemination, offering new avenues for improved health outcomes and promotion of human flourishing.

Swine global genomic resources: insights into wild and domesticated populations.

Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.