广西稀有濒危植物迁地保护评价

从迁地保护的内容、适应性、有效性等方面对桂林植物园迁地保护稀有濒危植物进行评价,结果表明:迁地保护的稀有濒危植物科学性强,96%以上的物种有科学记录,除了银杏等少数几个种属于“保护性收集”外,其它都是“具有保护意义的收集”;75%的种适应或基本适应迁移地的环境,原分布于广西的种明显比分布于广西区外的种适应性更强。按照最小存活种群的标准,该园有73种稀有濒危植物迁地保护有效。     

广西热带稀有濒危植物迁地保护地域探讨

对广西热带稀有濒危植物在广西及邻近省份植物园的引种保育进行对比研究。结果表明:大部分树种在热带和南亚热带可以正常生长,通过适当的保护措施,部分树种在中亚热带的桂林可以保存。低温和霜冻是广西热带稀有濒危树种能否成功保存的主要限制因素,因此,在引种保存过程中要注意防寒和树种的选择,以提高迁地保护的有效性。     

Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage

In bacteria stop codons are recognized by one of two class I release factors (RF1) recognizing TAG, RF2 recognizing TGA, and TAA being recognized by both. Variation across bacteria in the relative abundance of RF1 and RF2 is thus hypothesized to select for different TGA/TAG usage. This has been supported by correlations between TAG:TGA ratios and RF1:RF2 ratios across multiple bacterial species, potentially also explaining why TAG usage is approximately constant despite extensive variation in GC content. It is, however, possible that stop codon trends are determined by other forces and that RF ratios adapt to stop codon usage, rather than vice versa. Here, we determine which direction of the causal arrow is the more parsimonious. Our results support the notion that RF1/RF2 ratios become adapted to stop codon usage as the same trends, notably the anomalous TAG behavior, are seen in contexts where RF1:RF2 ratios cannot be, or are unlikely to be, causative, that is, at 3′untranslated sites never used for translation termination, in intragenomic analyses, and across archaeal species (that possess only one RF1). We conclude that specifics of RF biology are unlikely to fully explain TGA/TAG relative usage. We discuss why the causal relationships for the evolution of synonymous stop codon usage might be different from those affecting synonymous sense codon usage, noting that transitions between TGA and TAG require two-point mutations one of which is likely to be deleterious.     

Homozygosity Haplotype and Whole-Exome Sequencing Analysis to Identify Potentially Functional Rare Variants Involved in Multiple Sclerosis among Sardinian Families

Multiple Sclerosis (MS) is a complex multifactorial autoimmune disease, whose sex- and age-adjusted prevalence in Sardinia (Italy) is among the highest worldwide. To date, 233 loci were associated with MS and almost 20% of risk heritability is attributable to common genetic variants, but many low-frequency and rare variants remain to be discovered. Here, we aimed to contribute to the understanding of the genetic basis of MS by investigating potentially functional rare variants. To this end, we analyzed thirteen multiplex Sardinian families with Immunochip genotyping data. For five families, Whole Exome Sequencing (WES) data were also available. Firstly, we performed a non-parametric Homozygosity Haplotype analysis for identifying the Region from Common Ancestor (RCA). Then, on these potential disease-linked RCA, we searched for the presence of rare variants shared by the affected individuals by analyzing WES data. We found: (i) a variant (43181034 T > G) in the splicing region on exon 27 of CUL9; (ii) a variant (50245517 A > C) in the splicing region on exon 16 of ATP9A; (iii) a non-synonymous variant (43223539 A > C), on exon 9 of TTBK1; (iv) a non-synonymous variant (42976917 A > C) on exon 9 of PPP2R5D; and v) a variant (109859349-109859354) in 3′UTR of MYO16.     

Neosparton darwinii (Verbenaceae), a restricted endemic species. Is it also endangered?

Neosparton darwinii Benth. & Hook. is a ramose, almost leafless shrub, whose growth is restricted to an area on the southwestern coast of Buenos Aires province (Argentina). Its limited distribution could imply risks for its survival. In the present study, we evaluated population characteristics relevant to an assessment of its conservation status and made a preliminary characterization of its habitat. Historical data seem to indicate that the species has undergone a severe reduction in its geographic distribution. We estimated the actual population size to be around 44,000 plants, distributed in a clumped pattern. We found no significant differences between the environments immediately associated with the plants and other similar distant sites, in terms of position on the dune profile, percentage of bare soil and the richness and composition of accompanying plant species. A high proportion of the seeds produced each year is destroyed by parasite bruchid beetles. We have not seen seedlings of N.darwinii in the area. All the laboratory germination essays done to date have produced negative results. The species grows in an area intensively used by tourists. We can foresee quantitative and qualitative reductions in habitat availability. This information points out that N.darwinii is not just a rare species, but its survival is a matter for serious consideration. We suggest certain steps towards effective management to ensure its conservation.     

Cryptic dioecy and leaky dioecy in endemic species of Dombeya (Sterculiaceae) on La Re´union

The high frequency of dioecy on oceanic islands such as Hawaii and New Zealand has attracted a great deal of attention from plant evolutionary biologists. One reason suggested for the high prevalence of dioecy on oceanic islands is that taxa considered truly dioecious may have occasional hermaphrodite flowers, i.e., show leaky dioecy. In this study, we quantified the presence and distribution of leaky dioecy in a group of congeneric endemic species of the genus Dombeya (Sterculiaceae) on La Re´union island (Indian Ocean). All eight species show cryptic dioecy. Five species show strict dioecy and three species show leaky dioecy due to the presence of male trees that set fruit. Species with strict dioecy and large populations tend to occur in mid- to high-altitude moist tropical cloud forest, whereas species in smaller populations at lower altitude and in semidry tropical forest tend to show leaky dioecy. Two reasons for this differential distribution of strict dioecy and leaky dioecy are discussed. First, environmental variation along the altitudinal gradient, biotic and/or abiotic, may influence the breeding system. Second, leaky dioecy may be favored in lowland populations due to the small size and disturbed nature of such populations.     

Intranasal administration of an Escherichia coli-expressed codon-optimized rotavirus VP6 protein induces protection in mice

We are developing rotavirus vaccines based on the VP6 protein of the human G1P[8] [corrected] [J. Virol. 73 (1999) 7574] CJN strain of rotavirus. One prototype candidate consisting of MBP::VP6::His6, a chimeric protein of maltose-binding protein, VP6 and hexahistidine, was expressed mainly as truncated polypeptides in Escherichia coli BL21(DE3) cells. A possible reason for this extensive truncation is the high frequencies of rare bacterial codons within the rotavirus VP6 gene. Expression of truncated recombinant VP6 was found to be reduced, and expression of complete VP6 protein was simultaneously increased, when the protein was expressed in Rosetta(DE3)pLacI E. coli cells that contain increased amounts of transfer RNAs for a selection of rare codons. The same observation was made when a synthetic codon-optimized CJN-VP6 gene was expressed in E. coli BL21 or Rosetta cells. To increase protein recovery, recombinant E. coli cells were treated with 8M urea. Denatured, full-length MBP::VP6::His6 protein was then purified and used for intranasal vaccination of BALB/c mice (2 doses administered with E. coli heat-labile toxin LT(R192G) as adjuvant). Following oral challenge with the G3P[16] [corrected] [J. Virol. 76 (2002) 560] EDIM strain of murine rotavirus, protection levels against fecal rotavirus shedding were comparable (P>0.05) between groups of mice immunized with denatured codon-optimized or native (not codon-optimized) immunogen with values ranging from 87 to 99%. These protection levels were also comparable to those found after immunization with non-denatured CJN VP6. Thus, expression of complete rotavirus VP6 protein was greatly enhanced by codon optimization, and the protection elicited was not affected by denaturation of recombinant VP6.     

Frequency dependence in matings with water-borne sperm

Negative frequency-dependent mating success--the rare male effect--is a potentially powerful evolutionary force, but disagreement exists as to whether previous work, focusing on copulating species, has robustly demonstrated this phenomenon. Noncopulating sessile organisms that release male gametes into the environment but retain their eggs for fertilization may routinely receive unequal mixtures of sperm. Although promiscuity seems unavoidable it does not follow that the resulting paternity obeys 'fair raffle' expectations. This study investigates frequency dependence in the mating of one such species, the colonial ascidian Diplosoma listerianum. In competition with an alternative sperm source males fathered more progeny if previously mated to a particular female than if no mating history existed. This suggests positive frequency-dependent selection, but may simply result from a mate order effect involving sperm storage. With fewer acclimation matings, separated by longer intervals, this pattern was not found. When, in a different experimental design, virgin females were given simultaneous mixtures of gametes at widely divergent concentrations, sperm at the lower frequency consistently achieved a greater than expected share of paternity--a rare male effect. A convincing argument as to why D. listerianum should favour rare sperm has not been identified, as sperm rarity is expected to correlate very poorly with ecological or genetic male characteristics in this pattern of mating. The existence of nongenetic female preferences at the level of colony modules, analogous in effect to fixed female preferences, is proposed. If visible to selection, indirect benefits from increasing the genetic diversity of a sibship appear the only likely explanation of the rare male effect in this system as the life history presents virtually no costs to multiple mating, and a near absence of direct (resource) benefits, whereas less controversial hypotheses of female promiscuity (e.g. trade up, genetic incompatibility) do not seem appropriate.     

A Survey of Codon and Amino Acid Frequency Bias in Microbial Genomes Focusing on Translational Efficiency

Unequal use of synonymous codons has been found in several prokaryotic and eukaryotic genomes. This bias has been associated with translational efficiency. The prevalence of this bias across lineages is currently unknown. Here, a new method (GCB) to measure codon usage bias is presented. It uses an iterative approach for the determination of codon scores and allows the computation of an index of codon bias suitable for interspecies comparison. A server to calculate GCB-values of individual genes as well as a list of compiled results are available at . The method was applied to complete bacterial genomes. The relation of codon usage bias with amino acid composition and the choice of stop codons were determined and discussed.