iMarmot: an integrative platform for comparative and functional genomics of marmots.

BACKGROUND: Marmots are large Holarctic rodents with unique biological features, making them potential animal models in various research fields. Due to the rapid accumulation of the genetic data in marmots, a highly integrative database is urgent needed. DESCRIPTION: iMarmot is freely available on the web at http://www.marmotdb.org/ and currently contains the biological information of 14 marmots, genomic sequence of 6 marmots, syntenic relationship and orthologs among 3 marmots, and expression profiles of several hibernators and plague hosts. To assist with the genomic and transcriptomic analysis, we also integrated a set of analysis and visualization tools, such as KEGG or GO enrichment analysis, PCA, Blast, Muscle, GeneWise, Lastz, and JBrowse. Particularly, one DEGs (differentially expressed genes) module has been implemented in this database to visualize the gene expression changes in hibernators and plague hosts. CONCLUSION: This database will provide comprehensive information and analysis platform for researchers interested in understanding the biological features of marmots.

Genetic and molecular features for hepadnavirus and plague infections in the Himalayan marmot.

The Himalayan marmot (Marmota himalayana), a natural host and transmitter of plague, is also susceptible to the hepadnavirus infection. To reveal the genetic basis of the hepadnavirus susceptibility and the immune response to plague, we systematically characterized the features of immune genes in Himalayan marmot with those of human and mouse. We found that the entire major histocompatibility complex region and the hepatitis B virus pathway genes of the Himalayan marmot were conserved with those of humans. A Trim (tripartite motif) gene cluster involved in immune response and antiviral activity displays dynamic evolution, which is reflected by the duplication of Trim5 and the absence of Trim22 and Trim34. Three key regions of Ntcp, which is critical for hepatitis B virus entry, had high identity among seven species of Marmota. Moreover, we observed a severe alveolar hemorrhage, inflammatory infiltrate in the infected lungs and livers from Himalayan marmots after infection of EV76, a live attenuated Yersinia pestis strain. Lots of immune genes were remarkably up-regulated, which several hub genes Il2rγ, Tra29, and Nlrp7 are placed at the center of the gene network. These findings suggest that Himalayan marmot is a potential animal model for study on the hepadnavirus and plague infection.

Unique microbial communities of parasitic fleas on wild animals from the Qinghai-Tibet Plateau.

Fleas, one of the most significant ectoparasites, play a crucial role as vectors in spreading zoonotic diseases globally. The Qinghai Province, as part of the Qinghai-Tibet Plateau, is one of the provinces in China with the largest number of flea species. In this study, we characterized the microbial communities of eighty-five adult fleas, belonging to nineteen species within four families (Ceratophyllidae, Ctenophthalmidae, Leptopsyllidae, and Pulicidae). We identified a total of 1162 unique operational taxonomic units at the genus level, with flea-borne pathogens such as Wolbachia, Bartonella, Rickettsia being the members of top abundant taxa. Except for comparison between Ctenophthalmidae and Leptopsyllidae families, the analyses of both alpha- and beta- diversity indicators suggested that bacterial diversity varied among flea families. This could be attributed to flea phylogeny, which also influenced by their geographical sites and animal hosts. Results of Linear discriminant analysis effect size (LEfSe) indicated that 29 genera in Ceratophylloidea, 11 genera in Ctenophthalmidae, 15 genera in Leptopsyllidae, and 22 genera in Pulicidae were significantly responsible for explaining the differences among the four flea families (linear discriminant analysis score > 2, P < 0.05). Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) analyses showed that the functional pathways varied significantly across flea families, which was supported by the significant correlation between the functional pathways and the microbial communities.

Molecular characterization of the type I IFN receptor in two woodchuck species and detection of its expression in liver samples from woodchucks infected with woodchuck hepatitis virus (WHV).

Type I interferons (IFN-α/ß) serve as the first line of defense against viral infection and share the same type I IFN receptor (IFNAR) complex, which is composed of IFNAR1 and -2. The Eastern woodchuck (Marmota monax) and Chinese woodchuck (Marmota himalayana) are suitable for studying hepatitis B virus (HBV) infection. Here, the complete or partial sequences of the IFNARs of both species were obtained and analyzed. Small interference RNAs targeting wIFNAR1 and -2 specifically down-regulated the expression of wIFNAR1 and -2 and the IFN-stimulated gene MxA in a woodchuck cell line, respectively. IFNAR2 was significantly up-regulated in primary woodchuck hepatocytes stimulated with IFN-α or -γ. The expression of woodchuck IFNAR1 and -2 was decreased in woodchucks chronically infected with woodchuck hepatitis virus (WHV). These results are essential for studying type I IFN-related innate immunity and therapy in hepadnaviral infection in the woodchuck model.

Evaluation of mitochondrial toxicity in Marmota himalayana treated with metacavir, a novel 2',3'-dideoxyguanosine prodrug for treatment of hepatitis B Virus.

Metacavir (PNA) is a novel synthetic nucleoside analogue for the treatment of hepatitis B virus (HBV). Our recent studies showed that PNA, a prodrug of 2',3'-dideoxyguanosine (ddG), exhibited lower mitochondrial toxicity in long-term cultures of HepG2 cells. In the current study, we examined the long-term effects of PNA on mitochondrial toxicity in Marmota himalayana (Himalayan marmot). Himalayan marmots were treated daily with oral PNA (50 or 100 mg/kg), ziduvidine (AZT) (100 mg/kg), or water (control) for 90 days. PNA treatment did not alter the body weight or plasma lactate acid level. In livers from the animals treated with PNA at 100 mg/kg/day, histopathology showed mild steatosis or small focal liver cell necrosis. Electron microscopy also showed minor proliferation and partial mitochondrial swelling with crista reduction. Measurement of respiratory chain complex enzyme activity and mitochondrial DNA (mtDNA) content revealed no significant differences in skeletal muscle, liver, and kidney tissues between animals treated with PNA and controls. In contrast, in Himalayan marmots treated with AZT we observed delayed toxicity, including lactic acidosis, severe hepatic steatosis, obvious mitochondrial damage, and significant decreases in respiratory chain complex enzyme activity and mtDNA content. This is similar to the delayed toxicity syndrome observed previously in animals and humans. In summary, PNA treatment did not alter mitochondrial enzyme activity or mtDNA content. This suggests that PNA could pose a very low risk for adverse mitochondrion-related effects. However, long-term hepatotoxic effects of PNA were observed, and this indicates a need for continued monitoring of PNA-associated hepatotoxicity in clinical trials.

Establishing a new animal model for hepadnaviral infection: susceptibility of Chinese Marmota-species to woodchuck hepatitis virus infection.

Hepatitis B virus infection (HBV) is a major medical problem in China. The lack of a suitable infection model in China is recognized as an obstacle for research on HBV in China. Chinese Marmota-species is phylogenetically closely related to Marmota monax, thus, it might be suitable to serve as an animal model for HBV infection. Therefore, we attempted to prove the claim about the existence of woodchuck hepatitis virus (WHV)-like viruses in Chinese Marmota-species and to determine the susceptibility of these species to experimental WHV infection. In the present study, 653 sera from three Chinese Marmota-species, Marmota himalayana, Marmota baibacina and Marmota bobak, were screened for WHV-like viruses by serological and molecular assays. The susceptibility to WHV of three species was investigated by experimental infection and monitored by testing of anti-WHc and WHsAg by ELISA, detection of WHV DNA by PCR, and detection of WHV replication intermediates and antigens in liver samples. No evidence for the existence of a genetically closely related virus to WHV in three Chinese Marmota-species was found by serological assays and PCR. M. himalayana was susceptible to WHV infection as inoculated animals became positive for anti-WHc, WHsAg and WHV DNA. Further, WHV replication intermediates and proteins were detected in liver samples. In contrast, M. baibacina remained negative for tested virological parameters. M. bobak species showed a limited susceptibility to WHV. Our data do not support early reports about WHV-like viruses in China. M. himalayana is suitable for the establishment of a model for hepadnaviral infection.

Hypoxic and Cold Adaptation Insights from the Himalayan Marmot Genome.

The Himalayan marmot (Marmota himalayana) is a hibernating mammal that inhabits the high-elevation regions of the Himalayan mountains. Here we present a draft genome of the Himalayan marmot, with a total assembly length of 2.47 Gb. Phylogenetic analyses showed that the Himalayan marmot diverged from the Mongolian marmot approximately 1.98 million years ago. Transcriptional changes during hibernation included genes responsible for fatty acid metabolism in liver and genes involved in complement and coagulation cascades and stem cell pluripotency pathways in brain. Two selective sweep genes, Slc25a14 and ψAamp, showed apparent genotyping differences between low- and high-altitude populations. As a processed pseudogene, ψAamp may be biologically active to influence the stability of Aamp through competitive microRNA binding. These findings shed light on the molecular and genetic basis underlying adaptation to extreme environments in the Himalayan marmot.

Nucleoside analogues alone or combined with vaccination prevent hepadnavirus viremia and induce protective immunity: alternative strategy for hepatitis B virus post-exposure prophylaxis.

OBJECTIVES: The current strategies for hepatitis B virus (HBV) post-exposure prophylaxis (PEP) are not generally available in remote and rural areas of developing countries and/or carry potential risks for infection with blood-borne transmitted pathogens. Nucleotide analogues (NAs) are successfully used for human immunodeficiency virus PEP, and maybe effective for HBV PEP. In this study, we tested the NA-based strategies for HBV PEP using the Chinese woodchuck model. METHODS: Chinese woodchucks were inoculated intravenously with different doses of woodchuck hepatitis virus (WHV). A deoxyguanosine analogue entacavir (ETV), a DNA vaccine pWHcIm, or ETV plus pWHcIm were applied to the infected animals 24h later. Twenty weeks later, the animals were re-challenged with WHV to test for the presence of immunity against WHV. RESULTS: Inoculation with different WHV doses had a strong influence on the course of WHV infection; NA alone or in combination with a DNA vaccine completely prevented viremia after a high dose of WHV inoculation in Chinese woodchucks and induced partial or complete protective immunity, respectively. CONCLUSIONS: NA-based PEP strategies (NA alone or in combination with vaccine) may be an alternative of HBV PEP, especially in those living in the remote and rural areas of the developing countries and the non-responders to the current vaccine, and may be valuable in the PEP of HBV and HIV co-infection after occupational and non-occupational exposure. Further clinical studies are warranted to confirm the valuable of NA-based strategies in HBV PEP.

Molecular characterization of woodchuck CD4 (wCD4) and production of a depletion monoclonal antibody against wCD4.

CD4 T cells play an important role in the immune response against hepatitis B virus (HBV) infection. Woodchucks represent an excellent animal model to study HBV infection. In this study, we characterized the cDNA sequence of woodchuck CD4 (wCD4). The deduced wCD4 protein has four extracellular immunoglobulin-like domains comparable to the other mammalian CD4 molecules. The important extracellular cysteine residues and the intracellular tyrosine protein kinase-binding site of wCD4 are also conserved. The deduced wCD4 protein shows 53-63% identity with the counterparts of other mammalians. Phylogenetic analysis indicates that wCD4 is closely related with the counterparts of primates. Two polyclonal antibodies (pAbs) and four monoclonal Abs (mAbs) against wCD4 were produced. Two pAbs and one mAbs (G2) were found to effectively suppress ConA induced proliferation in vitro. Anti-wCD4 mAb G2 depleted 60% of CD4 cells from healthy woodchucks, while the remaining CD4 cells responded well to ConA stimulation. This work provides a basis for studying CD4 T cell mediated immune responses against HBV infection in the woodchuck model.

Characteristics of Himalayan marmots and their response to an atherogenic diet.

The purpose of the present study was to characterize Himalayan marmot lipoprotein profiles and investigate their response to an atherogenic diet. Sixteen marmots were randomly divided into two groups. The control group was fed with a standard chow diet, and the other group was fed with a chow diet containing 0.3% cholesterol, 6.7% lard, and 3.3% corn oil (designated as HFCD) for 16 weeks. The plasma lipids were measured, and lipoprotein profiles were analyzed. With the chow diet, the major lipoproteins were high density lipoproteins. HFCD feeding increased not only plasma total cholesterol levels but also body weight compared with the control group (P<0.05). Plasma lipoprotein (a) was detected in marmots, and the plasma lipoprotein (a) levels were 4.5-fold higher after being fed HFCD for 16 weeks. However, atherosclerotic lesions were not found in the aorta of HFCD-fed marmots. This study suggested that marmots are HDL-rich mammals and resistant to HFCD-induced atherosclerosis.