Curiously Modern DNA for a ``250 Million-Year-Old' Bacterium

Studies of ancient DNA have attracted considerable attention in scientific journals and the popular press. Several of the more extreme claims for ancient DNA have been questioned on biochemical grounds (i.e., DNA surviving longer than expected) and evolutionary grounds (i.e., nucleotide substitution patterns not matching theoretical expectations for ancient DNA). A recent letter to Nature from Vreeland et al. (2000), however, tops all others with respect to age and condition of the specimen. These researchers extracted and cultured a bacterium from an inclusion body from what they claim is a 250 million-year (Myr)-old salt crystal. If substantiated, this observation could fundamentally alter views about bacterial physiology, ecology and evolution. Here we report on molecular evolutionary analyses of the 16S rDNA from this specimen. We find that 2-9-3 differs from a modern halophile, Salibacillus marismortui, by just 3 unambiguous bp in 16S rDNA, versus the ∼59 bp that would be expected if these bacteria evolved at the same rate as other bacteria. We show, using a Poisson distribution, that unless it can be shown that S. marismortui evolves 5 to 10 times more slowly than other bacteria for which 16S rDNA substitution rates have been established, Vreeland et al.'s claim would be rejected at the 0.05 level. Also, a molecular clock test and a relative rates test fail to substantiate Vreeland et al.'s claim that strain 2-9-3 is a 250-Myr-old bacterium. The report of Vreeland et al. thus falls into a long series of suspect ancient DNA studies. Received: 12 April 2001 / Accepted: 9 June 2001     

Ancient woodland indicators signal the climate change risk for dispersal-limited species

The climate change risk to biodiversity operates alongside a range of anthropogenic pressures. These include habitat loss and fragmentation, which may prevent species from migrating between isolated habitat patches in order to track their suitable climate space. Predictive modelling has advanced in scope and complexity to integrate: (i) projected shifts in climate suitability, with (ii) spatial patterns of landscape habitat quality and rates of dispersal. This improved ecological realism is suited to data-rich model species, though its broader generalisation comes with accumulated uncertainties, e.g. incomplete knowledge of species response to variable habitat quality, parameterisation of dispersal kernels etc. This study adopts ancient woodland indicator species (lichen epiphytes) as a guild that couples relative simplicity with biological rigour. Subjectively-assigned indicator species were statistically tested against a binary habitat map of woodlands of known continuity (>250 yr), and bioclimatic models were used to demonstrate trends in their increased/decreased environmental suitability under conditions of ‘no dispersal’. Given the expectation of rapid climate change on ecological time-scales, no dispersal for ancient woodland indicators becomes a plausible assumption. The risk to ancient woodland indicators is spatially structured (greater in a relative continental compared to an oceanic climatic zone), though regional differences are weakened by significant variation (within regions) in woodland extent. As a corollary, ancient woodland indicators that are sensitive to projected climate change scenarios may be excellent targets for monitoring climate change impacts for biodiversity at a site-scale, including the outcome of strategic habitat management (climate change adaptation) designed to offset risk for dispersal-limited species.     

莲种子蛋白质提取方法比较与双向电泳分析

莲(Nelumbo nucifera Gaertn.)不仅是重要的水生蔬菜作物之一,而且是进行基础研究的好材料。本文采用4种蛋白质提取方法(新型TCA/丙酮法、传统TCA/丙酮法、改良的Tris-HCl法、Tris-饱和酚法)并结合双向电泳技术,对莲子蛋白质提取方法进行筛选与优化。双向电泳实验结果显示,所得蛋白质图谱与莲种子蛋白质组成分布特点一致。通过PDQuest软件分析表明,新型TCA/丙酮法适用于莲子叶和胚芽组织的双向电泳蛋白质提取,而传统TCA/丙酮法则适用于莲胚轴组织双向电泳的蛋白质提取。研究结果为进一步利用质谱进行莲子蛋白质组研究奠定了基础。     

Studies on the Nucleic Acid and Protein Content in the Cotyledon Cells of Lotus Using Fluorescent Imaging System with a Scientific grade Charge Coupled Device

Enzyme dissociated cotyledon cells were obtained from red lotus ( Nelumbo sp. ) on the 5th day and 20th day after fertilization respectively. DNA, RNA and total protein content of individual 5 d and 20 d cell were measured correlatively by microfiuorescent imaging system with a cooled scientific-grade Charge coupled deviced (CCD) camera. The results showed that DNA content of the 20 day cell has become polyploidized from 4C to 8C approximately. The window analysis indicated that relative content of RNA and total protein of the 20 day cell was more than 11 times that of the 5 day cell in the same 4C DNA window respectively. The multiple in-creased of RNA and total protein content was about the same as that of DNA in 2 DNA windows (4C and 8C) of the 20 day cell. These data showed that the enormous accumulation of storage proteins in the cotyledon cells of red lotus depends on both DNA ploidy and selective expression of the subunit genes of the storage proteins during the developmental process.     

The evolution of plant microRNAs: insights from a basal eudicot sacred lotus

microRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre‐eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus. Further analyses of lotus genome revealed that there is an association between loss of miRNA families in descendent plants and in duplicated genomes. Gene dosage balance is crucial in maintaining those preferentially retained MIRNA duplicates by imposing stronger purifying selection. However, these factors and selection influencing miRNA family evolution are not applicable to the putative MIRNA‐likes. Additionally, the MIRNAs participating in lotus pollen–pistil interaction, a conserved process in angiosperms, also have a strong signature of purifying selection. Functionally, sequence divergence in MIRNAs escalates expression divergence of their target genes between temperate and tropical lotus during rhizome and leaf growth. Overall, our study unravels several important factors and selection that determine the miRNA family distribution in plants and duplicated genomes, and provides evidence for functional impact of MIRNA sequence evolution.     

古代DNA研究中污染的控制和识别

现代分子生物学中PCR技术的发展使得直接分析古代动植物和人类材料中的DNA成为可能,这为考古学、人类学和古生物学提供了一种新的研究手段。但由于PCR技术的高度敏感性和古代DNA含量的极其微量性,古代DNA研究也极易受现代DNA污染。如何甄别所获得的DNA是真实的古代DNA而不是污染的现代DNA是所有古代DNA研究工作者都要面临的挑战,污染的控制和识别也因此成为古代DNA研究中一个至关重要的问题。本文将着重讨论在古代DNA研究的各个步骤中应如何进行有效的污染控制和识别。     

应用改良滴冻法超低温保存两种柿属植物的研究

以君迁子（Diospyros lotus L．）和柿（D．kaki Thunb．）组培苗茎尖为试材,对影响超低温保存效果的主要因素,如低温锻炼方式、预培养条件、PVS：（30％甘油＋15％乙二醇＋15％二甲基亚砜＋0．4mol／L蔗糖）处理时间等进行了研究。建立了2种柿属植物的超低温保存程序：（1）切取1cm左右试管苗梢段继代到1／2MS（KNO3和NH4NO3减半）培养基中,交替低温[昼（25±1）℃、夜（4±1）℃]锻炼6周;在含0．5mol／L蔗糖的1／2MS培养基上预培养5d,20℃下装载液（2．0mol／L甘油＋0．4mol／L蔗糖）过渡10min,0℃下PVS2处理1．5h;（2）投入液氮保存;（3）40℃水浴化冻,洗涤5～6次后接种于含1．0mg／LTDZ、0．6g／L可溶性PVP、30g／L蔗糖和7．0g／L琼脂的培养基（作者在优化柿属植物离体培养体系试验中获得）上暗培养1周,转入25℃,1500lx培养室。按照上述程序培养,‘鄂柿1号’、‘湘西甜柿’和君迁子的成活率分别为79．6％、67．4％和60．9％。