The giant panda ( Ailuropoda melanoleuca ) somatic nucleus can dedifferentiate in rabbit ooplasm and support early development of the reconstructed egg

The giant panda skeletal muscle cells, uterus epithelial cells and mammary gland cells from an adult individual were cultured and used as nucleus donor for the construction of intenpecies embryos by transferring them into enucleated rabbit eggs. All the three kinds of somatic cells were able to reprogram in rabbit ooplasm and support early embryo development, of which mammary gland cells were proven to be the best, followed by uterus epithelial cells and skeletal muscle cells. The experiments showed that direct injection of mammary gland cell into enucleated rabbit ooplasm, combined within vim development in ligated rabbit oviduct, achieved higher blastocyst development thanin vitro culture after the somatic cell was injected into the perivitelline space and fused with the enucleated egg by electrical stimulation. The chromosome analysis demonstrated that the genetic materials in reconstructed blastocyst cells were the same as that in panda somatic cells. In addition, giant panda mitochondrial DNA (mtDNA) was shown to exist in the intenpecies reconstructed blastocyst. The data suggest that (i) the ability of ooplasm to dedifferentiate somatic cells is not speciesspecific; (ii) there is compatibility between intenpecies somatic nucleus and ooplasm during early development of the reconstructed egg. Project supported by the 1998 Special Fund of the Chinese Academy of Sciences (KY95-J1-318) and a 1999 Special Fund from the Ministry of Science and Technology. Instruments were dominated by Mr. Shum Yam Wa, Heal Force Development Ltd.     

Investigation of various structures of DN A molecules (Ⅲ)—Coil-globe transition of λ-DNA induced by cationic surfactant

The structure transition of λ-DNA induced by cationic surfactant cellar media was investigated by using CD, SEM and AFM. The experimental data of CD revealed that λ-DNA can be induced from B-form to a collapsed structure with the addition of the cationic surfactant CTAB to the system. The condensed process of λ-DNA from coil state to small globular state (diameter about 1.25 μm) and finally big globular state (diameter about 5.4 μm) was observed by using SEM and AFM. Project supported by the Ninth Five-Year Great and Important Project of the Chinese Academy of Sciences and National Postdoctoral Science Foundation of China.     

Effect of DNA binding protein Sshl2 from hyperthermophilic archaeon Sulfolobus shibatae on DNA supercoiling

An 11.5-ku DNA binding protein, designated as Sshl2, was purified from the hyperthermophilic archaeon Sulfolobus shibatae by column chromatography in SP Sepharose, DNA cellulose and phosphocellulose. Sshl2 accounts for about 4 % of the total cellular protein. The protein is capable of binding to both negatively supercoiled and relaxed DNAs. Nick closure analysis revealed that Sshl2 constrains negative supercoils upon binding to DNA. While the ability of the protein to constrain supercoils is weak at 22℃ , it is enhanced substantially at temperatures higher than 37℃ . Both the cellular content and supercoil-constraining ability of Sshl2 suggest that the protein may play an important role in the organization and stabilization of the chromosome of S. shibatae.     

Sox and Zfx 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. Project supported by the Fok Ying Tung Education Foundation, the National Natural Science Foundation of China (Grant No. 39770392) and Wuhan Chenguang Plan.     

圈养大熊猫野化培训期的生境选择特征

大熊猫(Ailuropoda melanoleuca)是我国特有的珍稀物种,也是世界上最濒危的野生动物之一。为了将人工繁育的部分大熊猫个体重引入其历史分布区或复壮野生种群,中国保护大熊猫研究中心从2003年开始进行圈养大熊猫的野外放归工作,通过野化培训以提高圈养大熊猫适应和选择野外环境的能力。对野化培训大熊猫"淘淘"的生境选择研究表明:该野化培训大熊猫幼仔经常活动于新笋密度较大的区域[生境与对照:(2.68±1.14)对(1.58±0.66)],却避开成竹密度过大[(9.91±2.51)对(12.18±4.68)]、竹子较高[(4.57±1.09) m对(4.98±0.66) m]以及枯死竹过多[(2.52±0.86)对(3.39±1.33)]的区域;喜欢活动于离水源[(1.59±0.67)对(2.19±0.87)]和隐蔽场所较近[(5.37±2.14) m对(8.35±7.76)m],以及距离乔木较远[(3.09±0.69) m对(2.70±0.42) m]和郁闭度较低[(1.85±0.57)对(2.10±0.47)]的区域(P < 0.05),新笋密度大小是该栖息地在整个野化培训期间是否被利用的最重要因素。该野化培训大熊猫幼仔保持着与带仔母兽相近的生境选择特征,对竹子环境的选择也与卧龙野生大熊猫相似,野化培训对该大熊猫幼仔产生了积极的作用。野化培训大熊猫幼仔形成的家域和核域面积分别为9.21 hm² 和1.93 hm²,占野化培训圈面积的51.95%和10.89%,其中家域面积仅有卧龙野生大熊猫的1.4%-2.4%,所以在以后的野化培训过程中需要采取增加野化培训圈中环境丰富度等方式,促进野化培训大熊猫形成较大的家域面积。     

Expression of tPA, LH receptor and inhibin a,βA subunits during follicular atresia in rats

By using DNA 3′-end labeling, immunocytochemistry and mRNA insitu hybridization detection techniques, the expression of inhibin subunits and LH receptor in the granulosa cells and tissue-type plasminogen activator (tPA) in the oocytes has been studied in relation to follicular development and atresia. The results demonstrated that: (i) tPA activity in the oocytes of normal developing follicles is undetectable, and increases significantly in the follicle undergoing atresia; (ii) the production of inhibin subunits in granulosa cells is negatively correlated with the expression of oocyte tPA activity, indicating that they may be an important regulator of oocyte tPA production and follicular development; (iii) in atretic follicles, granulosa cells do not express LH receptor and inhibin subunits. It is therefore suggested that tPA may play a role in oocyte self-destruction and clearance in some of atretic follicles, and inhibin of granulosa-origin might be an inhibitory factor for the translation of tPA in the oocyte. Project supported by the National Natural Science Foundation of China (Grant Nos. 39770099 and 39770290), Chinese Academy of Sciences and Rockefeller Foundation/WHO HPR research project.     

Study of tauopathies by comparing <Emphasis Type="Italic">Drosophila</Emphasis> and human <Emphasis Type="Italic">tau</Emphasis> in <Emphasis Type="Italic">Drosophila</Emphasis>

The microtubule-binding protein tau has been investigated for its contribution to various neurodegenerative disorders. However, the findings from transgenic studies, using the same tau transgene, vary widely among different laboratories. Here, we have investigated the potential mechanisms underlying tauopathies by comparing Drosophila (d-tau) and human (h-tau) tau in a Drosophila model. Overexpression of a single copy of either tau isoform in the retina results in a similar rough eye phenotype. However, co-expression of Par-1 with d-tau leads to lethality, whereas co-expression of Par-1 with h-tau has little effect on the rough eye phenotype. We have found analogous results by comparing larval proteomes. Through genetic screening and proteomic analysis, we have identified some important potential modifiers and tau-associated proteins. These results suggest that the two tau genes differ significantly. This comparison between species-specific isoforms may help to clarify whether the homologous tau genes are conserved. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. This study was supported by the National Science Foundation of China (30270341; 30630028), the Multidisciplinary Program (Brain and Mind) of the Chinese Academy of Sciences, the Major State Basic Research Program (“973 program”; G2000077800; G2006CB806600; 2006CB911003), the Precedent Project of Important Intersectional Disciplines in the Knowledge Innovation Engineering of the Chinese Academy of Sciences (KJCX1-09-03).     

Spatial genetic structure and dispersal of giant pandas on a mountain-range scale

Understanding the spatial genetic structure of populations can provide insight into the ecological or evolutionary processes of the species, and enable wise conservation decisions. We examined the spatial genetic structure of a giant panda (Ailuropoda melanoleuca) population in a heterogeneous mountainous landscape using noninvasive genetic sampling and 12 microsatellite loci. Nonrandom genetic structure was detected through spatial autocorrelation analysis, demonstrating a significantly positive autocorrelation over closer distances. Additional spatial analyses showed significantly positive genetic correlation among spatially-proximate males, and no correlation among females and among male–female pairs. These findings suggest a female-biased dispersal pattern and cryptic family grouping among giant pandas on a large mountain-range scale. The spatial extent of genetic structure occurred within 12.5 km, measured by a least-cost path distance model integrating information of habitat quality and habitat preferences of this species. Using the bearing analysis of PASSAGE, we found that directional genetic autocorrelations were in agreement with habitat structure, and habitat heterogeneity may affect the direction of giant panda dispersal. The characterization of spatial genetic structure can provide potentially valuable information for the conservation and management of giant pandas and their habitat.     

“人造精子”介导基因编辑技术的建立与应用

"人造精子",即小鼠孤雄单倍体胚胎干细胞,是一种可在体外长期培养扩增和进行遗传操作的细胞,因其具备胚胎干细胞自我更新和多向分化的特性,并拥有代替精子使卵母细胞"受精",产生半克隆小鼠的能力,而被广泛应用于生命科学研究的各个领域。与CRISPR-Cas9技术相结合,"人造精子"能够同时实现细胞水平和动物水平的复杂基因编辑,因此可作为一个有力的研究工具。本文就"人造精子"技术的建立与改进、在基因编辑方面的应用,以及全基因组标签计划的提出与进展展开综述。     

Reaction of hydroxyl radical with phenylpropanoid glycoside and its derivatives by pulse radiolysis

The reaction of hydroxyl radical with 1 phenylpropanoid glycoside ( PPG), cistanoside C, and its 3 derivatives: 1-O-β-D-2-(p-hydroxyphenyl)-ethanyl-glucose, 6-O-(E)-feruloyl-glucose and 6-O-(E)-p-hydroxy-cinnamoylglucose isolated from folk medicinal herbs was investigated by pulse radiolysis technique respectively. The reaction rate constants were determined by analysis of built-up trace of absorption at λ_(max) of specific transient absorption spectra of PPG and its derivatives upon attacking·OH. All four compounds react with·OH at close to diffusion controlled rate (1.03×10~9—19.139×10~9 L·mol~(-1)·s~(-1)), suggesting that they are effective·OH scavengers. The results demonstrated that the numbers of phenolic hydroxyl groups of PPG and its derivatives are directly related to their scavenging activities. By comparing the reaction rates of·OH with 1-O-β-D-2-(p-hydroxyphenyl)-ethanyl-glucose, 6-O-(E)-feruloyl-glueose or 6-O-(E)-p-hydroxy-cinnomoyl-glucose, it is evident that the phenylethyl g     

Mechanism of regulating the expression of λN gene by ribosomal protein at translational level

In ribosomal protein S12 mutant or L24 mutant the expression of λN gene was depressed at translational level. To study its mechanism the λN gene region of λN -lacZ gene fusion was trimmed from its 5′ end to 3′ end with DNA exonuclease III (DNA cxoIII) in order to alter the TIR (translational initiation region) and the ding region of λN gene. After DNA sequencing 23 species of different λN-lacZ fused genes were obtained. The β-galactosidase activities of these deletants in ribosomal protein mutant were compared with that in wild type strain. The result indicated that (i) S12 mutant could affect 305 subunit’s binding to the TIR of λN gene messenger and cause the difficulty in forming 30s initiation complex and then decrease the efficiency of translational initiation; (ii) in S12 mutant the coding region of λN gene alw affected the expression λN gene; (iii) in L24 mutant the inhibition of λN gene expression was not related to translational initiation and the 5′ end of the coding region of λN gene, but related to the 3′ end of λN gene. Project supported by the National Natural Science Foundation of China (Grant Nos. 39480014, 39570162) and Chinese Academy of Sciences.     

Sixteen novel microsatellite loci developed for the giant panda (Ailuropoda melanoleuca)

Sixteen novel microsatellite DNA loci were developed from the giant panda (Ailuropoda melanoleuca) using a magnetic-bead capture method. A total of 115 alleles were obtained for these markers, ranging from 4 to 12 alleles per locus (average 7.188). These loci exhibited high levels of polymorphic information content and expected heterozygosity, 0.558–0.855 (average 0.729) and 0.628–0.885 (average 0.778), respectively. Therefore, the allelic polymorphism and heterozygosity show that the giant pandas raised in China Research and Conservation Center possess abundant genetic variation. In addition, if the three markers showing null alleles were excluded, the remaining 13 microsatellite loci still presented extremely low non-exclusion probabilities of parentage (0.002), paternity (0.000) and identity (0.000). As a result, this new suit of microsatellite markers would be a very informative tool for the genetic and conservation studies of giant pandas.     

Isolation and properties of an extremely thermophilic xylanolytic bacterium

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An improved,chromosome-level genome of the giant panda (Ailuropoda melanoleuca)

BackgroundThe iconic giant panda (Ailuropoda melanoleuca), as both a flagship and umbrella species endemic to China, is a world famous symbol for wildlife conservation. The giant panda has several specific biological traits and holds a relatively small place in evolution. A high-quality genome of the giant panda is key to understanding the biology of this vulnerable species.FindingsWe generated a 2.48-Gb chromosome-level genome (GPv1) of the giant panda named “Jing Jing” with a contig N50 of 28.56 Mb and scaffold N50 of 134.17 Mb, respectively. The total length of chromosomes (n = 21) was 2.39-Gb, accounting for 96.4% of the whole genome. Compared with the previously published four genomes of the giant panda, our genome is characterized by the highest completeness and the correct sequence orientation. A gap-free and 850 kb length of immunoglobulin heavy-chain gene cluster was manually annotated in close proximity to the telomere of chromosome 14. Additionally, we developed an algorithm to predict the centromere position of each chromosome. We also constructed a complete chromatin structure for “Jing Jing”, which includes inter-chromosome interaction pattern, A/B compartment, topologically associated domain (TAD), TAD-clique and promoter-enhancer interaction (PEI).ConclusionsWe presented an improved chromosome-level genome and complete chromatin structure for the giant panda. This is a valuable resource for the future genetic and genomic studies on giant panda.     

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

Background

The giant panda (Ailuropoda melanoleuca) is a critically endangered species endemic to China. Microsatellites have been preferred as the most popular molecular markers and proven effective in estimating population size, paternity test, genetic diversity for the critically endangered species. The availability of the giant panda complete genome sequences provided the opportunity to carry out genome-wide scans for all types of microsatellites markers, which now opens the way for the analysis and development of microsatellites in giant panda.

Results

By screening the whole genome sequence of giant panda in silico mining, we identified microsatellites in the genome of giant panda and analyzed their frequency and distribution in different genomic regions. Based on our search criteria, a repertoire of 855,058 SSRs was detected, with mono-nucleotides being the most abundant. SSRs were found in all genomic regions and were more abundant in non-coding regions than coding regions. A total of 160 primer pairs were designed to screen for polymorphic microsatellites using the selected tetranucleotide microsatellite sequences. The 51 novel polymorphic tetranucleotide microsatellite loci were discovered based on genotyping blood DNA from 22 captive giant pandas in this study. Finally, a total of 15 markers, which showed good polymorphism, stability, and repetition in faecal samples, were used to establish the novel microsatellite marker system for giant panda. Meanwhile, a genotyping database for Chengdu captive giant pandas (n = 57) were set up using this standardized system. What’s more, a universal individual identification method was established and the genetic diversity were analysed in this study as the applications of this marker system.

Conclusion

The microsatellite abundance and diversity were characterized in giant panda genomes. A total of 154,677 tetranucleotide microsatellites were identified and 15 of them were discovered as the polymorphic and stable loci. The individual identification method and the genetic diversity analysis method in this study provided adequate material for the future study of giant panda.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1268-z) contains supplementary material, which is available to authorized users.     

微卫星标记在大熊猫研究中的应用进展

大熊猫是我国保护最为成功、研究最为深入的珍稀动物之一,可以为其它珍稀濒危物种的保护研究工作提供参考。20世纪70年代末期借助无线电颈圈,大熊猫的生态学研究工作取得了突破性进展,近20年来微卫星标记和非损伤性遗传取样技术的联合使用,将大熊猫的保护研究工作提升到一个崭新的高度。本文在综合所有已发表大熊猫微卫星标记的基础上,梳理了微卫星标记在圈养大熊猫亲子鉴定与遗传管理,野生大熊猫个体识别与种群数量调查、遗传多样性评估、扩散和种群遗传结构研究中的应用情况,并着重介绍了其中29个重要的微卫星标记。同时指出目前微卫星标记的使用存在标记选择不统一、等位基因读数无统一规程等问题,并对应用前景进行了前瞻。     

Non-invasive giant panda paternity exclusion

Giant panda hair samples obtained by noninvasive methods served as a source of DNA for amplification of seven giant panda microsatellite loci utilizing the polymerase chain reaction. Thirteen giant pandas held in Chinese zoos were tested for identification of paternity. Some males listed as sires have been excluded as the biological father of captive-born giant pandas. Because of the death of some potential sires, paternity is still not assigned for some giant pandas, although there is a high likelihood that paternity assignment could be made if postmortem samples are available for genetic analysis. The DNA microsatellite variation assayed by the test we have developed provides a rapid, highly informative, and noninvasive method for paternity identification in giant pandas. © 1994 Wiley-Liss, Inc.     

大熊猫乳汁蛋白组成

测定了2只大熊猫（ailuropoda melanoleuca)乳汁中蛋白含量,乳糖含量,乳蛋白组成,并与成都麻羊（Capra hircus)初乳和中国荷斯坦牛（Bos taurus)乳进行了比较,大熊猫乳蛋白含量平均为41．52g/L,与中国荷斯坦牛乳接近;乳糖平均含量为15．41g/L,极显著低于牛乳和成都麻羊初乳,乳蛋白SDS－PAGE分析表明,大熊猫乳中酪蛋白（CN）含量明显低于羊乳和牛乳;乳中存在3条蛋白含量的区带,而在成都麻羊和中国荷斯坦牛乳电泳图谱的相应位置未见明显的区带,乳中上皮粘蛋白MUC1仅存在1条分子量约为196kDa的区带,未发现多态现象。     

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.     

Immunomodulated signaling in macrophages: Studies on activation of Raf-1, MAPK, cPLA2 and secretion of IL-12

Little is known about the mechanism and signal transduction by LPS-mediated immunomodulation of murine peritoneal macrophages. It is found that the signal molecules of the down-stream of Ras, Raf-1, MAPK p44, and MAPK p42 are phosphorylated, and cPLA₂ is activated with a significant increase of the release of [ H³ ] AA by macrophages in response to LPS and PMA. Compared with the very recent finding that LPS and PMA trigger the activation and translocation of PKC-α and PKC-ε, these findings suggest that there is a connection between PKC signaling pathway and the Raf-1/MAPK pathway and that the activation of these main signaling events may be closely related to the secretion of IL-12 during LPS-induced modulation of macrophages. Project supported by the National Natural Science Foundation of China, Shanghai Joint Laboratory of Life Science, Shanghai Institute of CeIl Biology, and Director’s Foundations of Chinese Academy of Sciences and Shanghai Institute of Cell Biology.