Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species

Background

Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies.

Results

Using high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species.

Conclusions

These findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0557-1) contains supplementary material, which is available to authorized users.     

Identification of the putative staphylococcal AgrB catalytic residues involving the proteolytic cleavage of AgrD to generate autoinducing peptide

The P2 operon of the staphylococcal accessory gene regulator (agr) encodes four genes (agrA, -B, -C, and -D) whose products compose a quorum sensing system: AgrA and AgrC resemble a two-component signal transduction system of which AgrC is a sensor kinase and AgrA is a response regulator; AgrD, a polypeptide that is integrated into the cytoplasmic membrane via an amphipathic alpha-helical motif in its N-terminal region, is the propeptide for an autoinducing peptide that is the ligand for AgrC; and AgrB is a novel membrane protein that involves in the processing of AgrD propeptide and possibly the secretion of the mature autoinducing peptide. In this study, we demonstrated that AgrB had endopeptidase activity, and identified 2 amino acid residues in AgrB (cysteine 84 and histidine 77) that might form a putative cysteine endopeptidase catalytic center in the proteolytic cleavage of AgrD at its C-terminal processing site. Computer analysis revealed that the cysteine and histidine residues were conserved among the potential AgrB homologous proteins, suggesting that the Agr quorum sensing system homologues might also exist in other Gram-positive bacteria.     

风向因素对转基因抗虫棉花基因漂移效率的影响

在转基因作物获准进行环境释放并实行大面积商品化推广的同时,基因漂移所引起的生态环境安全问题不容忽视。本研究以含有双价抗虫基因（Bt/CpTI）的转基因棉花SGK321为花粉供体材料,以常规非转基因棉花品种石远321、中棉35、吉扎1号为花粉受体材料,在温室中人工创造定向风和非定向风条件,应用PCR与蛋白检测相结合的方法,检测外源基因发生基因漂移的效率。结果表明：随着与转基因棉花SGK321距离的增加,外源基因转移至非转基因棉花的基因漂移频率呈现波动性变化。在定向风处理中,基因漂移频率在距离转基因棉花6.4 m处达到峰值33.33%,在测定范围内基因漂移最远距离为25.6 m;而在非定向风处理中,基因漂移频率在距离转基因棉花12.8 m处达到峰值36.67%,在测定范围内基因漂移最远距离为36 m。非定向风可显著提高转移至海岛棉吉扎1号的基因漂移频率。外源基因从SGK321转移至其非转基因亲本石远321的基因漂移频率显著高于转移至陆地棉中棉35和海岛棉吉扎1号的漂移频率。本研究可为转基因棉花的生态安全性分析提供一定的理论参考价值。     

An 11-lncRNA expression could be potential prognostic biomarkers in head and neck squamous cell carcinoma

The aim of our study is to construct the competing endogenous RNA (ceRNA) network of head and neck squamous cell carcinoma (HNSCC) and identify key long noncoding RNAs (lncRNAs) to predict prognosis. The genes whose expression were differentially in HNSCC and normal tissues were explored by the Cancer Genome Atlas database. The ceRNA network was constructed by the Cytoscape software. The lncRNAs which could estimate the overall survival were explored from Cox proportional hazards regression. There are 1997, 589, and 82 mRNAs, lncRNAs, and miRNAs whose expression were statistically significant different, respectively. Then, the network between miRNA and mRNA or miRNA and lncRNA was constructed by miRcode, miRDB, TargetScan, and miRanda. Five mRNAs, 10 lncRNAs, and 3 miRNAs were associated with overall survival. Then, 11-lncRNAs were found to be prognostic factors. Therefore, our research analyzed the potential signature of novel 11-lncRNA as candidate prognostic biomarker from the ceRNA network for patients with HNSCC.     

Construction of conjugative gene transfer system between E. coli and moderately thermophilic, extremely acidophilic Acidithiobacillus caldus MTH-04

A genetic transfer system for introducing foreign genes to biomining microorganisms is urgently needed. Thus, a conjugative gene transfer system was investigated for a moderately thermophilic, extremely acidophilic biomining bacterium, Acidithiobacillus caldus MTH-04. The broad-host-range IncP plasmids RP4 and R68.45 were transferred directly into A. caldus MTH-04 from Escherichia coli by conjugation at relatively high frequencies. Additionally the broad-host-range IncQ plasmids pJRD215, pVLT33, and pVLT35 were also transferred into A. caldus MTH-04 with the help of plasmid RP4 or strains with plasmid RP4 integrated into their chromosome, such as E. coli SM10. The Km(r) and Sm(r) selectable markers from these plasmids were successfully expressed in A. caldus MTH-04. Futhermore, the IncP and IncQ plasmids were transferred back into E. coli cells from A. caldus MTH-04, thereby confirming the initial transfer of these plasmids from E. coli to A. caldus MTH-04. All the IncP and IncQ plasmids studied were stable in A. caldus MTH-04. Consequently, this development of a conjugational system for A. caldus MTH-04 will greatly facilitate its genetic study.     

农作物对Cd毒害的耐性机理探讨

对生长在Ｃｄ污染条件下的８种作物体内Ｃｄ的存在形态分析表明,作物的耐Ｃｄ性与Ｃｄ的形态分布密切相关,在耐性作物体内,蛋白质（多肽）结合Ｃｄ量的比例低于非耐性作物;有机酸盐和一代磷酸盐态Ｃｄ的比例增加;分离得到Ｃｄ诱导蛋白?其中束缚了一定量的Ｃｄ,限制了Ｃｄ以自由态存在,耐性较低的作物本内,大分子量的蛋白质中富Ｃｄ量较高。     

淡水湖泊生态系统退化驱动因子及修复技术研究进展

目前我国多数淡水湖泊污染、退化问题非常严重,诸多修复技术也已初见成效。影响淡水湖泊生态系统退化的驱动因子众多,既有生物因素也有非生物因素,它们之间相互联系,相互作用,且作用机理错综复杂。首先介绍了淡水湖泊生态系统退化的含义及形式;其次,分析、总结了淡水湖泊生态系统退化的驱动因子,从退化的生态学完整性意义和退化修复的技术手段上看,淡水湖泊生态系统主要受物理、化学和生物三大驱动因子影响,且基本遵循"环境变化-驱动力-压力(阈值)-状态-响应"原理;再次,在厘清湖泊生态系统退化驱动原理的基础上,从淡水湖泊生态系统功能模块和湖泊生态系统修复实践经验总结的角度出发,构建了淡水湖泊生态系统修复模块技术体系,并就湖泊富营养化和湖滨湿地生态系统退化修复的技术进行了讨论和对比;最后,对淡水湖泊生态系统修复的环境变化驱动因子的作用机制、作用途径和修复技术的长效机制等方面进行了展望。     

Application of β-glucuronidase (GusA) as an effective reporter for extremely acidophilic Acidithiobacillus ferrooxidans

Applied Microbiology and Biotechnology - Acidithiobacillus ferrooxidans is a model organism for investigating metal sulfide bioleaching. The regulatory mechanism of gene expression by metabolizing...     

Production of d-allose from d-fructose using immobilized l-rhamnose isomerase and d-psicose 3-epimerase

Bioprocess and Biosystems Engineering - d-Allose is a rare sugar, can be used as an ingredient in a range of foods and dietary supplements, has alimentary activities, especially excellent...     

MicroRNA-429 induces tumorigenesis of human non-small cell lung cancer cells and targets multiple tumor suppressor genes

Lung cancer is the major cause of cancer death globally. MicroRNAs are evolutionally conserved small noncoding RNAs that are critical for the regulation of gene expression. Aberrant expression of microRNA (miRNA) has been implicated in cancer initiation and progression. In this study, we demonstrated that the expression of miR-429 are often upregulated in non-small cell lung cancer (NSCLC) compared with normal lung tissues, and its expression level is also increased in NSCLC cell lines compared with normal lung cells. Overexpression of miR-429 in A549 NSCLC cells significantly promoted cell proliferation, migration and invasion, whereas inhibition of miR-429 inhibits these effects. Furthermore, we demonstrated that miR-429 down-regulates PTEN, RASSF8 and TIMP2 expression by directly targeting the 3′-untranslated region of these target genes. Taken together, our results suggest that miR-429 plays an important role in promoting the proliferation and metastasis of NSCLC cells and is a potential target for NSCLC therapy.