Giant panda BAC library construction and assembly of a 650-kb contig spanning major histocompatibility complex class II region

<p>Abstract</p> <p>Background</p> <p>Giant panda is rare and endangered species endemic to China. The low rates of reproductive success and infectious disease resistance have severely hampered the development of captive and wild populations of the giant panda. The major histocompatibility complex (MHC) plays important roles in immune response and reproductive system such as mate choice and mother-fetus bio-compatibility. It is thus essential to understand genetic details of the giant panda MHC. Construction of a bacterial artificial chromosome (BAC) library will provide a new tool for panda genome physical mapping and thus facilitate understanding of panda MHC genes.</p> <p>Results</p> <p>A giant panda BAC library consisting of 205,800 clones has been constructed. The average insert size was calculated to be 97 kb based on the examination of 174 randomly selected clones, indicating that the giant panda library contained 6.8-fold genome equivalents. Screening of the library with 16 giant panda PCR primer pairs revealed 6.4 positive clones per locus, in good agreement with an expected 6.8-fold genomic coverage of the library. Based on this BAC library, we constructed a contig map of the giant panda MHC class II region from <it>BTNL2 </it>to <it>DAXX </it>spanning about 650 kb by a three-step method: (1) PCR-based screening of the BAC library with primers from homologous MHC class II gene loci, end sequences and BAC clone shotgun sequences, (2) DNA sequencing validation of positive clones, and (3) restriction digest fingerprinting verification of inter-clone overlapping.</p> <p>Conclusion</p> <p>The identifications of genes and genomic regions of interest are greatly favored by the availability of this giant panda BAC library. The giant panda BAC library thus provides a useful platform for physical mapping, genome sequencing or complex analysis of targeted genomic regions. The 650 kb sequence-ready BAC contig map of the giant panda MHC class II region from <it>BTNL2 </it>to <it>DAXX</it>, verified by the three-step method, offers a powerful tool for further studies on the giant panda MHC class II genes.</p

Simulation study on giant panda population dynamics model with due consideration for deforestation

AbstractDeforestation has destroyed the home of giant panda and poses a direct threat to their survival. Based on the idea of habitat protection of the trinity of “forest-bamboo-giant panda”, a “forest-bamboo-giant panda” nonlinear dynamics model is established with due consideration for pulse deforestation. Computer numerical simulation is used to study the periodic solutions of this dynamics model and chaos strange attractor, and the ecological significance of the dynamic results. A threshold value in deforestation is thus obtained. That is, when the pulse intensity of deforestation is beyond a given threshold, the giant panda population will be almost extinct even though some forest still remains. When the pulse intensity of deforestation is within a given threshold, an ecological balance among “Forest-bamboo-giant panda” will kept for them to continue to exist

The next widespread bamboo flowering poses a massive risk to the giant panda

The IUCN Red List has downgraded several species from “endangered” to “vulnerable” that still have largely unknown extinction risks. We consider one of those downgraded species, the giant panda, a bamboo specialist. Massive bamboo flowering could be a natural disaster for giant pandas. Using scenario analysis, we explored possible impacts of the next bamboo flowering in the Qinling and Minshan Mountains that are home to most giant pandas. Our results showed that the Qinling Mountains could experience large-scale bamboo flowering leading to a high risk of widespread food shortages for the giant pandas by 2020. The Minshan Mountains could similarly experience a large-scale bamboo flowering with a high risk for giant pandas between 2020 and 2030 without suitable alternative habitat in the surrounding areas. These scenarios highlight thus-far unforeseen dangers of conserving giant pandas in a fragmented habitat. We recommend advance measures to protect giant panda from severe population crashes when flowering happens. This study also suggests the need to anticipate and manage long-term risks to other downgraded species

A MACHINE LEARNING LINEAR REGRESSION MODEL TO PREDICT FUTURE GIANT PANDA POPULATION

Increasingly used as the insignia of China, the zaftig and enchanting Giant Panda lives on mountains of southwest China. The Giant Panda is on the WWF logo and is known as “National Treasure” in China. In this study, we predict the future Giant Panda population by using machine learning algorithms of the simple linear regression model. We take different variables to predict the next 30 years of the Giant Panda population. Focusing on the factors which affect the Giant Panda population. We take several parameters for this research like Bamboo Population, Annual Rainfall in China, Carbon Stock in Bamboo Stems, Deforestation, and Human Influence and Population of Giant Panda. Despite their peak status and relative deficiency of natural predators, pandas are still at risk and multiple intimidations from human influence have left just over 1,800 Pandas in the forest. To be ready for future troubles it is mandatory to have a pre-look of some conditions so that we can be prepared for that. Substantially, Endangered species at the edge of extinction are kept in extra special conservation. The machine learning algorithms developed with a wide-ranging of training datasets that help to find results faster and accurately

Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca)

BACKGROUND: The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda was constructed in this study. RESULTS: This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents of the giant panda haploid genome. Screening the library with 15 genes and 8 microsatellite markers demonstrates that it is representative and has good genome coverage. Furthermore, ten BAC clones harbouring AGXT, GHR, FSHR, IRBP, SOX14, TTR, BDNF, NT-4, LH and ZFX1 were mapped to 8 pairs of giant panda chromosomes by fluorescence in situ hybridization (FISH). CONCLUSION: This is the first large-insert genomic DNA library for the giant panda, and will contribute to understanding this endangered species in the areas of genome sequencing, physical mapping, gene cloning and comparative genomic studies. We also identified the physical locations of ten genes on their relative chromosomes by FISH, providing a preliminary framework for further development of a high resolution cytogenetic map of the giant panda

A Genome-Wide Survey on Basic Helix-Loop-Helix Transcription Factors in Giant Panda

The giant panda (Ailuropoda melanoleuca) is a critically endangered mammalian species. Studies on functions of regulatory proteins involved in developmental processes would facilitate understanding of specific behavior in giant panda. The basic helix-loop-helix (bHLH) proteins play essential roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in over 20 organisms, including fruit fly, zebrafish, mouse and human. Our present study identified 107 bHLH family members being encoded in giant panda genome. Phylogenetic analyses revealed that they belong to 44 bHLH families with 46, 25, 15, 4, 11 and 3 members in group A, B, C, D, E and F, respectively, while the remaining 3 members were assigned into “orphan”. Compared to mouse, the giant panda does not encode seven bHLH proteins namely Beta3a, Mesp2, Sclerax, S-Myc, Hes5 (or Hes6), EBF4 and Orphan 1. These results provide useful background information for future studies on structure and function of bHLH proteins in the regulation of giant panda development

Dominant Components of the Giant Panda Seminal Plasma Metabolome, Characterized by 1H-NMR Spectroscopy

Simple Summary As China's flagship animal, the giant panda (Ailuropoda melanoleuca) attracts much attention due to its small population and low natural reproductive rate. Therefore, artificial insemination has become the leading practical approach in the captive breeding programs of giant pandas worldwide. Seminal plasma acts as a medium between spermatozoa and the external stimuli, and its characteristics have been directly linked to fertility in both artificial insemination and natural fertilization. The current work, for the first time, attempts to characterize, by proton magnetic resonance spectroscopy (H-1-NMR), the metabolome of healthy giant panda seminal plasma. A total of 35 molecules were quantified, with distinct age-related trends highlighted by a multivariate analysis, and the concentrations of 2,3-butanediol were significantly different between individuals younger than 8 years and older than 13 years. In addition, isopropanol's concentration was significantly linked to estrus stages. Besides, the variations in the metabolome's profile with storage time were also evaluated. This study may serve as a reference for research wishing to shed light on the biological mechanisms affecting giant panda sperm's overall quality and may ultimately lead to novel approaches to giant panda artificial insemination. As an assisted breeding technique, artificial insemination has become the main effective practical approach in the captive breeding programs of giant panda worldwide. The composition of seminal plasma plays an important role in the success of breeding. The present work is the first attempt to characterize, by proton magnetic resonance spectroscopy (H-1-NMR), the metabolome of healthy giant panda seminal plasma. A total of 35 molecules were quantified, with the concentration of 2,3-butanediol being significantly different between individuals younger than 8 years and older than 13 years, and other distinct age-related trends were highlighted by a multivariate analysis. Isopropanol's concentration was significantly linked to estrus stages. Besides, the variations in the metabolome's profile during storage were also evaluated. This study may serve as a reference for further research wishing to shed light on the biological mechanisms affecting giant panda sperm's overall quality and may ultimately lead to novel approaches to giant panda artificial insemination

Why Does the Giant Panda Eat Bamboo? A Comparative Analysis of Appetite-Reward-Related Genes among Mammals

Background: The giant panda has an interesting bamboo diet unlike the other species in the order of Carnivora. The umami taste receptor gene T1R1 has been identified as a pseudogene during its genome sequencing project and confirmed using a different giant panda sample. The estimated mutation time for this gene is about 4.2 Myr. Such mutation coincided with the giant panda’s dietary change and also reinforced its herbivorous life style. However, as this gene is preserved in herbivores such as cow and horse, we need to look for other reasons behind the giant panda’s diet switch. Methodology/Principal Findings: Since taste is part of the reward properties of food related to its energy and nutrition contents, we did a systematic analysis on those genes involved in the appetite-reward system for the giant panda. We extracted the giant panda sequence information for those genes and compared with the human sequence first and then with seven other species including chimpanzee, mouse, rat, dog, cat, horse, and cow. Orthologs in panda were further analyzed based on the coding region, Kozak consensus sequence, and potential microRNA binding of those genes. Conclusions/Significance: Our results revealed an interesting dopamine metabolic involvement in the panda’s food choice

The effect of diffusion on giant pandas that live in complex patchy environments

The habitat loss and fragmentation is almost the greatest threat to the survival of the wild giant panda. In this paper, we construct a mathematical model to consider the effect of diffusion on giant pandas that live in complex patchy environments. Our discussion includes the studying of a diffusive n-dimensional single species model, sufficient conditions are derived for the permanence and extinction of the giant panda species. Especially, we also discuss the situations of diffusion of giant pandas between two patches, and numerical simulations are presented to illustrate the results. Furthermore, we consider the existence, uniqueness, and global stability of the positive periodic solution of the n-dimensional single species model. The implications of these results are significant for giant panda conservation

The Panda-Derived Lactobacillus plantarum G201683 Alleviates the Inflammatory Response in DSS-Induced Panda Microbiota-Associated Mice

Intestinal diseases are one of the main causes of captive giant panda death. Their special dietary habits and gastrointestinal tract structure often lead to intestinal epithelium damage and secondary intestinal infection. The captive giant panda is predisposed to suffer from microbiota dysbiosis due to long-term artificial feeding and antibiotic misuse. However, there are few reported probiotics to treat giant panda enteritis and the associated dysbiosis. This study aims to elucidate the mechanism by which Lactobacillus plantarum G201683 (L. plantarum G83), a promising panda-derived probiotic, exerts a protective effect on intestinal inflammation in the dextran sulfate sodium- (DSS) induced panda microbiota-associated (DPMA) mouse model. The DPMA mouse was generated by antibiotic treatment and 5% DSS drinking water administration to assess the effect of L. plantarum G83 on intestinal inflammation and microbiota in vivo. Our results demonstrated the successful generation of a DPMA mouse model with Enterobacteriaceae enrichment, consistent with the giant panda intestinal microbiota. L. plantarum G83 decreased clinical and histological severity of intestinal inflammation, enhanced intestinal tight junction protein expression (ZO-1, Occludin) and alleviated inflammatory cytokine production (TNF-) in the colon of DPMA mice. The administration of L. plantarum G83 altered the microbiota composition by decreasing pathogen associated taxa such as E. coli and increasing abundance of beneficial bacteria including Bifidobacterium spp. These changes in microbiota composition were associated with an increased concentration of short chain fatty acids (SCFA), reduced NF-κB signaling, and an altered balance of T helper cell subsets. Our findings support L. plantarum G83 as a promising probiotic to treat intestinal inflammation in the giant panda