Sox andZfx genes in giant panda

By using PCR cloning techniques, the DNA sequences of the HMG box regions of sixSox genes (pSox) and the zinc finger domains of twoZfz genes (pZfx) in the giant panda were identified. The giant pandaSox genes fell into two subfamilies,SOX-S1 andSOX-S2. ThepSox andpZfx genes of the giant panda were highly homologous to the corresponding genes in mammals and revealed close substitution rates to those in the primates.     

Sequencing,annotation and comparative analysis of nine BACs of giant panda (<Emphasis Type="Italic">Ailuropoda melanoleuca</Emphasis>)

A 10-fold BAC library for giant panda was constructed and nine BACs were selected to generate finish sequences. These BACs could be used as a validation resource for the de novo assembly accuracy of the whole genome shotgun sequencing reads of giant panda newly generated by the Illumina GA sequencing technology. Complete sanger sequencing, assembly, annotation and comparative analysis were carried out on the selected BACs of a joint length 878 kb. Homologue search and de novo prediction methods were used to annotate genes and repeats. Twelve protein coding genes were predicted, seven of which could be functionally annotated. The seven genes have an average gene size of about 41 kb, an average coding size of about 1.2 kb and an average exon number of 6 per gene. Besides, seven tRNA genes were found. About 27 percent of the BAC sequence is composed of repeats. A phylogenetic tree was constructed using neighbor-join algorithm across five species, including giant panda, human, dog, cat and mouse, which reconfirms dog as the most related species to giant panda. Our results provide detailed sequence and structure information for new genes and repeats of giant panda, which will be helpful for further studies on the giant panda.     

HMG-box sequences from microbats homologous to the human SOX30 HMG-box*

SOX genes are a family of genes that encode for proteins which are characterised by the presence of a HMG-domain related to that of the mammalian sex-determining gene (SRY). By definition, the DNA binding domain of SOX genes is at least 50% identical to the 79 amino acid HMG domain of the SRY gene. We report here two HMG-box sequences from two microbat species (R. ferrumequinum and P. Pipistrellus) which were PCR amplified using a primer pair specific to the mouse Sry HMG-box. The high percentage of identity of this sequences with the human and mouse SOX30 HMG-box suggests that they are the SOX30 HMG-box for these two bat species. The sequencing data reported in this paper are available in the EMBL Nucleotide Sequence Database through the following accession numbers: Pipistrellus pipistrellus SOX30 gene: AJ243292; Rhinolophus ferrumequinum SOX30 gene: AJ243293. This revised version was published online in July 2006 with corrections to the Cover Date.     

同域分布的珍稀野生动物对放牧的行为响应策略

保护区内放牧活动对野生动物保护存在负面影响,明确不同物种对放牧干扰的行为响应对制定更有针对性的保护管理政策具有重要意义。使用红外相机研究卧龙自然保护区放牧活动对多种珍稀野生动物的影响,分析放牧激励政策实施前后大熊猫(Ailuropoda melanoleuca)及其同域分布的小熊猫(Ailurus fulgens)、川金丝猴(Rhinopithecus roxellana)、水鹿(Rusa unicolor) 4种珍稀野生动物的照片数、空间分布以及活动模式的变化,探讨这4种动物对放牧的行为响应策略。结果表明:(1)一期(2012—2013),2012年10月实施了禁马政策,同年12月实施放牧(牛羊)激励政策)家畜照片数量很少,4种野生动物照片数相对较多。二期(2014—2015)家畜的照片数显著增加(P0.01),小熊猫(P0.05)与川金丝猴(P0.01)的照片数均显著减少,大熊猫、水鹿的照片数也呈减少趋势;到三期(2016—2017),大熊猫、小熊猫及水鹿3种关注野生动物的照片数基本回升到激励政策实施前的水平,无川金丝猴照片记录。(2)一期,4种野生动物在研究区域有较广的分布;二期,大熊猫、小熊猫的空间分布范围均缩小,无川金丝猴空间分布信息,而家畜、水鹿的空间分布范围有所增加;到三期,大熊猫、小熊猫的空间分布基本恢复到放牧激励政策实施前的区域,无川金丝猴的空间分布信息。(3)放牧激励政策实施前后,大熊猫、小熊猫及川金丝猴活动模式无明显变化,但水鹿的活动更加集中于傍晚,以避开人类与家畜的活动高峰。同域分布的不同的野生动物对人类活动(如放牧)的行为响应策略不同,各保护区在制定相关保护政策时应综合考虑人类干扰对多个物种的影响,增加决策的科学性与合理性。     

Impact of livestock grazing on biodiversity and giant panda habitat

Livestock grazing occurs in many protected areas for wildlife and has become a threat to wildlife worldwide. Livestock grazing within protected areas causes negative effects to rare wildlife (e.g., giant panda [Ailuropoda melanoleuca]) and their habitat. We used the 2,000-km² Wolong National Nature Reserve, Sichuan Province, southwestern China, to document the effects of livestock on the giant panda and its habitat. We monitored arrow bamboo (Bashania fangiana), wildlife sign (i.e., feces and tracks), and characteristics of plant communities in intact habitat (IH; limited livestock grazing) and disturbed habitat (DH; with grazing disturbance) to assess the effects of livestock grazing and the responses of giant pandas and sympatric species across spatial and temporal scales. Bamboo coverage and the height and basal diameter of bamboo in IH were greater than those in DH, whereas the number of herbaceous species and herbaceous coverage in IH were lower than those in DH. Wildlife signs in IH were greater than those in DH; specifically, giant panda and red panda (Ailurus fulgens) signs were greater, whereas signs of sambar (Rusa unicolor) and tufted deer (Elaphodus cephalophus) in IH were similar to those in DH. Livestock grazing reduced bamboo, which may threaten the long-term survival of the giant panda. Our results have implications for understanding and management of livestock grazing in the Wolong National Nature Reserve and elsewhere. © 2019 The Wildlife Society.     

Isolation and sequence analysis of <Emphasis Type="Italic">Sox</Emphasis> genes from lizard <Emphasis Type="Italic">Eremias</Emphasis> multiocellata

The Sox (SRY-related high-mobility-group box) family of genes shares a conserved HMG box and is involved in a diverse range of developmental processes and sex determination in vertebrates. Twenty Sox genes are present in the genomes of humans and mice, but far less is known about the Sox gene family in reptiles. Using two pairs of highly degenerate primers designed from a multiple alignment of Sox amino acid sequences in several species, different positive clones were obtained from male and female Eremias multiocellata, a viviparous lizard which is subject to TSD (temperature-dependent sex determination). These clones were sequenced and identified. They are members of the SoxB (Sox2, Sox14), SoxC (Sox11, Sox12) and SoxE (Sox9a, Sox9b, Sox10) groups. No sex-specific differences were observed. Based on the amino acid sequence similarities, the phylogenetic analysis was carried out and these genes clustered with their orthologues. In addition, we found the gene duplication in E. multiocellata, it may be a mechanism to produce new functional genes.     

Assessing vulnerability of giant pandas to climate change in the Qinling Mountains of China

Climate change might pose an additional threat to the already vulnerable giant panda (Ailuropoda melanoleuca). Effective conservation efforts require projections of vulnerability of the giant panda in facing climate change and proactive strategies to reduce emerging climate‐related threats. We used the maximum entropy model to assess the vulnerability of giant panda to climate change in the Qinling Mountains of China. The results of modeling included the following findings: (1) the area of suitable habitat for giant pandas was projected to decrease by 281 km² from climate change by the 2050s; (2) the mean elevation of suitable habitat of giant panda was predicted to shift 30 m higher due to climate change over this period; (3) the network of nature reserves protect 61.73% of current suitable habitat for the species, and 59.23% of future suitable habitat; (4) current suitable habitat mainly located in Chenggu, Taibai, and Yangxian counties (with a total area of 987 km²) was predicted to be vulnerable. Assessing the vulnerability of giant panda provided adaptive strategies for conservation programs and national park construction. We proposed adaptation strategies to ameliorate the predicted impacts of climate change on giant panda, including establishing and adjusting reserves, establishing habitat corridors, improving adaptive capacity to climate change, and strengthening monitoring of giant panda.     

大熊猫源细菌耐药性研究进展

耐药菌和耐药基因已成为一种新型环境污染物,引发世界公共卫生问题。细菌耐药性尤其是多重耐药菌在人医临床、畜禽养殖以及环境传播等多个方面得到越来越多的关注,而关于大熊猫等野生动物的耐药性研究相对较少。大熊猫(Ailuropoda melanoleuca)是世界公认的珍稀野生动物,其种群数量易受到各种疾病的威胁,尤其是肠道细菌性疾病。随着抗菌药物在疾病预防和控制中的普遍使用,由此带来的耐药性危害日益明显。本文总结了关于大熊猫源细菌耐药的国内外研究报道,对其耐药表型、耐药基因型、耐药机制及水平传播机制等方面内容进行了综述,旨在为大熊猫源细菌耐药性的研究和防控提供依据,为临床科学用药提供理论参考,从而助力大熊猫迁地保护。     

大熊猫精液和包皮菌群组成及潜在致病菌调查

[目的] 大熊猫是我国国家一级保护动物,其种群面临着传染病和栖息地破碎化等持续威胁,其中生殖系统的细菌感染和菌群失衡会影响大熊猫生殖健康,严重者可导致流产,是引起大熊猫繁殖障碍的原因之一。本研究对精液与包皮分泌物样本的菌群组成情况及分离培养潜在致病菌开展研究。[方法] 通过采集13份大熊猫包皮分泌物和12份精液样本,采用16S rRNA扩增子测序技术、细菌培养及PCR鉴定的方法,确定样本中的细菌种类。[结果] 菌群组成分析结果显示,在门水平上,厚壁菌门（Firmicutes）的细菌丰度在大熊猫包皮与精液中均为最高;在属水平上,不同时期的雄性大熊猫包皮的菌群可能会发生改变,棒状杆菌属（Corynebacterium）和Dolosicoccus是Ⅰ期包皮样本中最丰富的微生物菌群,相对丰度分别为15.45%和12.40%;链球菌属（Streptococcus）和埃希氏菌属（Escherichia）是Ⅱ期包皮样本中最丰富的微生物菌群,相对分度分别为37.94%和9.68%;拟杆菌属（Bacteroides）和普雷沃氏菌属（Prevotella）是精液样本中最丰富的微生物菌群,相对丰度分别为14.40%和12.88%。菌群多样性分析结果显示,精液样品高于Ⅰ期包皮样品和Ⅱ期包皮样品,Ⅰ期包皮样品和Ⅱ期包皮样品之间无显著差异。通过细菌分离培养得到肺炎克雷伯菌（Klebsiella pneumonia）在内的多种潜在性致病菌。[结论] 本研究分析了大熊猫精液和不同时期包皮分泌物的菌群组成,其优势菌属存在差异,大熊猫包皮与精液中存在潜在性致病菌,这可能对大熊猫的生殖系统健康带来威胁,其致病性有待进一步研究。     

Does one size fit all? A multispecies approach to regional landscape corridor planning

Aim

The practical value of the single‐species approach to conserve biodiversity could be minimal or negligible when sympatric species are limited by factors that are not relevant to the proposed umbrella species. In this study, we quantitatively evaluated as follows: (1) habitat suitability and potential movement corridors of a single umbrella species, giant panda (Ailuropoda melanoleuca); (2) habitat suitability of sympatric mammals; and (3) the potential effectiveness of the single‐species corridor planning to preserve suitable habitat and its connectivity of other focal species.

Location

Qinling Mountains, central part of China (15,000 km²).

Methods

We collected species distribution, environmental and anthropogenic data and conducted species occupancy modelling for giant panda and six other sympatric species (i.e., takin Budorcas taxicolor, tufted deer Elaphodus cephalophus, Chinese goral Naemorhedus griseus, Reeve's muntjac Muntiacus reevesi, leopard cat Prionailurus bengalensis and yellow‐throated marten Martes flavigula). We then conducted circuit models to identify potential corridors for each species and evaluated the effectiveness of giant panda corridors to restore the habitat connectivity for these sympatric mammals.

Results

Occupancy modelling revealed that each species had a unique set of environmental variables associated with its distribution in the Qinling Mountains. We found that giant panda and all other focal species had some degree of fragmentation to their suitable habitat that required restoring habitat connectivity. Among the eight potential giant panda corridors, conservation efforts to reduce anthropogenic impacts would significantly improve the effectiveness of six corridors, while the other two corridors would require altering the vegetation. Five proposed giant panda corridors had remarkable overlap with corridors proposed for other species. We suggest two giant panda corridors as a priority due to their potential to maximize the benefits to both giant panda and a broader suite of mammals.

Main conclusions

Corridor planning in this region of China will likely continue using the single‐species policy, but our results highlight that not all potential giant panda corridors have equal effectiveness for other wildlife species. When offered multiple alternative actions, conservation planners can prioritize corridor development based on a multispecies perspective without loss of connectivity for the priority species. This approach has strong implications to the conservation of wildlife communities in China, and elsewhere, where conservation plans developed for a single‐species garner most available funding and institutional support.

     

Clonal regeneration of an arrow bamboo, <Emphasis Type="Italic">Fargesia qinlingensis</Emphasis>, following giant panda herbivory

Characteristics of giant panda herbivory sites and clonal regeneration of an arrow bamboo Fargesia qinlingensis following giant panda grazing were studied in the Qinling Mountains of China. Three types of plots were located in a pandas’ summer habitat in 2002: herbivory (naturally grazed by giant pandas), clipped (simulated panda herbivory), and control. Average area of herbivory sites was 2.92 m² and average distance from herbivory sites to the closest tree (dbh > 10 cm) was 1.0 m. Pandas avoided thin bamboo culms with basal diameters <5 mm. Average height of stumps of culms grazed by panda was 0.67 m and average density of grazed culms was 9.0 culms m⁻². Annual culm mortality rate was significantly greater in herbivory and clipped plots than in control plots while annual recruitment rate was not significantly different among the three plot types in 2003. Neither recruitment rate nor mortality rate were significantly different among the three plot types in 2004. Annual recruitment rate was significantly greater than annual mortality rate only in control plots in both 2003 and 2004, suggesting static ramet dynamics in disturbed plots (herbivory and clipped). Density of new shoots was not significantly different, but basal diameter of new shoots was significantly less in herbivory plots compared to control plots in 2002. Differences of annual mortality rate and growth of new shoots found between control plots and herbivory plots suggest that clonal regeneration of F. qinlingensis culms was negatively affected by giant panda grazing. Therefore, no evidence of a clonal integration compensatory response to panda herbivory was found in F. qinlingensis.     

Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs

The giant panda (Ailuropoda melanoleuca) is one of the world’s most beloved endangered mammals. Although the draft genome of this species had been assembled, little was known about the composition of its microRNAs (miRNAs) or their functional profiles. Recent studies demonstrated that changes in the expression of miRNAs are associated with immunity. In this study, miRNAs were extracted from the blood of four healthy giant pandas and sequenced by Illumina next generation sequencing technology. As determined by miRNA screening, a total of 276 conserved miRNAs and 51 novel putative miRNAs candidates were detected. After differential expression analysis, we noticed that the expressions of 7 miRNAs were significantly up-regulated in young giant pandas compared with that of adults. Moreover, 2 miRNAs were up-regulated in female giant pandas and 1 in the male individuals. Target gene prediction suggested that the miRNAs of giant panda might be relevant to the expressions of 4,602 downstream genes. Subseuqently, the predicted target genes were conducted to KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis and we found that these genes were mainly involved in host immunity, including the Ras signaling pathway, the PI3K-Akt signaling pathway, and the MAPK signaling pathway. In conclusion, our results provide the first miRNA profiles of giant panda blood, and the predicted functional analyses may open an avenue for further study of giant panda immunity.     

Sequence variation and genetic diversity in the giant panda

About 336–444 bp mitochondrial D-loop region and tRNA gene were sequenced for 40 individuals of the giant panda which were collected from Mabian, Meigu, Yuexi, Baoxing, Pingwu, Qingchuan, Nanping and Baishuijiang, respectively. 9 haplotypes were found in 21 founders. The results showed that the giant panda has low genetic variations, and that there is no notable genetic isolation among geographical populations. The ancestor of the living giant panda population perhaps appeared in the late Pleistocene, and unfortunately, might have suffered bottleneck attacks. Afterwards, its genetic diversity seemed to recover to some extent. Project supported by the “8.5” Key Project of Chinese Academy of Sciences, the Chairman Foundation of Chinese Academy of Sciences, K. C. Wang Education Foundation, the Applied Basic Research Foundation of Yunnan, the National Natural Science Foundation of China, the Special Foundation for Returned Chinese Scientists, and Zoological Society of San Diego.     

Sox and Zfx genes in giant panda

ＯｎｅｏｆｔｈｅｒｅｃｅｎｔｂｒｅａｋｔｈｒｏｕｇｈｓｏｆｄｅｖｅｌｏｐｍｅｎｔａｌｂｉｏｌｏｇｙｉｓｔｈｅｉｄｅｎｔｉｆｉｃａｔｉｏｎｏｆｔｈｅｔｅｓｔｉｓｄｅｔｅｒｍｉｎｉｎｇｆａｃｔｏｒｇｅｎｅｏｎｔｈｅｍａｍｍａｌｉａｎＹｃｈｒｏｍｏｓｏｍｅ[1],ＳＲＹｇｅｎｅ,ｂｙａｌｏｎｇｈｉｓｔｏｒｙｏｆｓｅａｒｃｈｆｏｒｔｈｅｇｅｎｅ,ｆｒｏｍＢｋｍ,ＨＹａｎｔｉｇｅｎ,ＺＦＸ/ＺＦＹｔｏＳＲＹ/ＳＯＸ(ＳＲＹｂｏｘｇｅｎｅｆａｍｉｌｙ).Ｒｅｃｅｎｔｓｔｕｄｉｅｓｓｈｏｗｔｈａｔａｎｕｍｂｅｒｏｆｃｌｏ…     

Habitat Assessment for Giant Pandas in the Qinling Mountain Region of China

ABSTRACT Because habitat loss and fragmentation threaten giant pandas (Ailuropoda melanoleuca), habitat protection and restoration are important conservation measures for this endangered species. However, distribution and value of potential habitat to giant pandas on a regional scale are not fully known. Therefore, we identified and ranked giant panda habitat in Foping Nature Reserve, Guanyinshan Nature Reserve, and adjacent areas in the Qinling Mountains of China. We used Mahalanobis distance and 11 digital habitat layers to develop a multivariate habitat signature associated with 247 surveyed giant panda locations, which we then applied to the study region. We identified approximately 128 km²of giant panda habitat in Foping Nature Reserve (43.6% of the reserve) and 49 km²in Guanyinshan Nature Reserve (33.6% of the reserve). We defined core habitat areas by incorporating a minimum patch-size criterion (5.5 km²) based on home-range size. Percentage of core habitat area was higher in Foping Nature Reserve (41.8% of the reserve) than Guanyinshan Nature Reserve (26.3% of the reserve). Within the larger analysis region, Foping Nature Reserve contained 32.7% of all core habitat areas we identified, indicating regional importance of the reserve. We observed a negative relationship between distribution of core areas and presence of roads and small villages. Protection of giant panda habitat at lower elevations and improvement of habitat linkages among core habitat areas are important in a regional approach to giant panda conservation.     

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. This finding suggests a new direction for molecular evolution studies behind the panda''s dietary switch.