Defining operational taxonomic units using DNA barcode data

The scale of diversity of life on this planet is a significant challenge for any scientific programme hoping to produce a complete catalogue, whatever means is used. For DNA barcoding studies, this difficulty is compounded by the realization that any chosen barcode sequence is not the gene 'for' speciation and that taxa have evolutionary histories. How are we to disentangle the confounding effects of reticulate population genetic processes? Using the DNA barcode data from meiofaunal surveys, here we discuss the benefits of treating the taxa defined by barcodes without reference to their correspondence to 'species', and suggest that using this non-idealist approach facilitates access to taxon groups that are not accessible to other methods of enumeration and classification. Major issues remain, in particular the methodologies for taxon discrimination in DNA barcode data.     

Immunoproteasome-deficient mice mount largely normal CD8+ T cell responses to lymphocytic choriomeningitis virus infection and DNA vaccination

During viral infection, constitutive proteasomes are largely replaced by immunoproteasomes, which display distinct cleavage specificities, resulting in different populations of potential CD8(+) T cell epitope peptides. Immunoproteasomes are believed to be important for the generation of many viral CD8(+) T cell epitopes and have been implicated in shaping the immunodominance hierarchies of CD8(+) T cell responses to influenza virus infection. However, it remains unclear whether these conclusions are generally applicable. In this study we investigated the CD8(+) T cell responses to lymphocytic choriomeningitis virus infection and DNA immunization in wild-type mice and in mice lacking the immunoproteasome subunits LMP2 or LMP7. Although the total number of virus-specific cells was lower in LMP2 knockout mice, consistent with their having lower numbers of naive cells before infection, the kinetics of virus clearance were similar in all three mouse strains, and LMP-deficient mice mounted strong primary and secondary lymphocytic choriomeningitis virus-specific CD8(+) T cell responses. Furthermore, the immunodominance hierarchy of the four investigated epitopes (nuclear protein 396 (NP(396)) > gp33 > gp276 > NP(205)) was well maintained. We observed a slight reduction in the NP(205)-specific response in LMP2-deficient mice, but this had no demonstrable biological consequence. DNA vaccination of LMP2- and LMP7-deficient mice induced CD8(+) T cell responses that were slightly lower than, although not significantly different from, those induced in wild-type mice. Taken together, our results challenge the notion that immunoproteasomes are generally needed for effective antiviral CD8(+) T cell responses and for the shaping of immunodominance hierarchies. We conclude that the immunoproteasome may affect T cell responses to only a limited number of viral epitopes, and we propose that its main biological function may lie elsewhere.     

The contraction phase of virus-specific CD8+ T cells is unaffected by a pan-caspase inhibitor

The effectiveness of protection conferred by CD8(+) memory T cells is determined by both their quality and their quantity, which suggests that vaccine efficacy might be improved if it were possible to increase the size of the memory pool. Approximately 90% of virus-specific CD8(+) T cells die during the contraction phase and, herein, we have attempted to increase the memory pool by reducing CD8(+) T cell death. CD8(+) T cell contraction has been attributed to apoptosis, or programmed cell death (PCD), which, classically, is dependent on caspases. Caspase-dependent PCD can be prevented by the pan-caspase inhibitor benzyloxycarbonyl-Val-Ala-Asp (OMe)-fluoromethylketone (zVAD), and here we evaluate the effect of this compound on virus-specific T cell responses in mice. zVAD prevented caspase-dependent PCD of freshly isolated virus-specific T cells in tissue culture, and a fluorescent analog, FITC-VAD, entered CD8(+) T cells following in vivo injection. However, despite using 11 different regimens of zVAD administration in vivo, no significant effects on CD8(+) or CD4(+) memory T cell numbers were observed. Furthermore, the CD8(+) memory T cell responses to secondary virus infection were indistinguishable, both qualitatively and quantitatively, in zVAD-treated and normal mice. The absence of effect cannot be attributed to a technical flaw, because identical doses of zVAD were able to rescue mice from hepatocyte apoptosis and lethal intrahepatic hemorrhage, induced by inoculation of anti-Fas Ab. We conclude that the contraction phase of the virus-specific T cell response is unlikely to require caspase-dependent PCD. We propose that contraction can be mediated by an alternative, caspase-independent pathway(s).     

血液磁极化疗法对糖尿病兔胰岛功能的影响

目的观察血液磁极化疗法(简称血磁治疗)对糖尿病(DM)的治疗效果和对胰岛功能的影响。方法制备了四氧嘧啶DM兔模型20只,随机分为两组,即DM模型血磁治疗组及DM模型未治疗组,同时设立正常对照组10只,分别测定治疗前后空腹血糖(FPG)、糖化血红蛋白(HbA1c)、胰岛素(INS)及C-肽(C-P),并于观察期结束后处死动物取胰腺组织常规石蜡包埋切片,行HE及Mallory三色法特殊染色观察3组胰岛形态学变化。结果血磁治疗显著降低DM兔的FPG(P<0.001)。DM治疗组INS及C-P水平较治疗前明显升高(P<0.01),与未治疗组相比差异显著(P<0.05)。胰岛病理改变可见治疗组β细胞数量明显多于DM未治疗组,提示血磁疗法具有促进胰岛修复,改善胰岛功能的作用。结论血磁疗法能够促进DM时受损胰岛组织的修复,改善胰岛β细胞分泌功能,降血糖作用明显。     

Phosphatase activities of cyanobacteria as indicators of nutrient status in a Pyrenees river

There is increasing evidence that fluvial systems are influenced by anthropogenic factors, and disturbance due to pollution and other human interference gives rise to specific problems. It is now imperative that we develop and apply novel and effective ways which allow us to monitor water quality. The present study was planned as part of a programme to develop biological monitoring methods to assess nutrient characteristics of upland calcareous streams and rivers. Phototrophs respond to environmental changes over a period of time, so organisms sampled at one time can potentially provide almost as much information about nutrients in the water as a number of individual chemical measurements. Phosphatase activity is often a good indicator of phosphorus limitation, and field materials could be used to study changes in nutrients dynamics. The calcareous River Muga, north-east Spain, at a site 10 km downstream from its source in the Pyrenees, was therefore chosen for the present study of surface phosphatase activities of the main cyanobacterial communities at different seasons to assess P limitation and establish the suitability of this method for use in monitoring catchment processes. Here we report seasonal changes of phosphatase activity in field populations of Schizothrix coriacea, Rivularia biasolettiana, Tolypothrix distorta var. penicillata and Nostoc verrucosum. All four cyanobacteria showed marked surface phosphomonoesterase and phosphodiesterase activity on each sampling period. Michaelis-Menten kinetic studies showed similar K _m values for the four species suggesting similar affinity for organic P substrates. Light had no effect on phosphatase activities, indicating that there is no need to consider this factor in short-term field assays. However, there was an increase in phosphomonoesterase activity of Rivularia with rise in temperature over the range 10–35°C, which suggests adaptation to the frequent temperature changes in nature. Phosphorus limitation seems the main chemical factor influencing phototrophs in R. Muga. Combined observations on macroscopically visible phototrophs with assays of surface phosphatase activity provide a valuable means of assessing long-term changes in a catchment.     

犬MC1R基因T105A基因座多态性及 与毛色性状相关性的研究The

为了检测犬MC1R基因T105A基因座的多态性,并分析该多态性与犬毛色表型的相关性,抽取111只外科手术学实验用杂种犬血液并提取DNA,记录毛色表型。采用PCR-RFLP技术,对MC1R基因T105A基因座进行基因多态性分析,并对该基因座DNA进行克隆测序;用二元变量相关分析的统计学方法分析基因座多态性与毛色性状之间的相关性。经PCR-RFLP分析结果表明,T105A基因座序列具有多态性,表现为A、B二个等位基因和AA、AB及BB 3种基因型。A、B等位基因频率分别为72.97%和27.03%,基因杂合度（H）为0.39。基因型AA频率为55.86%,BB为9.91%,AB为34.23%。对T105A多态性片段DNA克隆测序后发现,MC1R基因在编码第105位氨基酸的密码子第一个碱基存在由G到A的单碱基突变,该突变导致第105位氨基酸发生由丙氨酸向苏氨酸的改变。统计分析结果表明MC1R基因T105A基因座的多态性与毛色性状不存在显著的相关性,这可能是由于外科手术学实验用犬是杂种犬,其遗传背景不同所致,尚须在纯种犬群体中进一步研究MC1R基因对毛色的影响。 Abstract: In order to detect the polymorphism of T105A in MC1R gene in dogs and to analyze the relationship between the genetic polymorphisms and phenotypes of dog coat color, the blood samples of 111 cross-breed dogs were taken and their genomic DNAs were extracted. The phenotypes of dog coat color were recorded. The T105A locus of MC1R gene in the canine was detected through the technology of PCR-RFLP. Furthermore, the polymorphic fragments at T105A were sequenced. The relationships between the polymorphism of T105A and coat color trait were analyzed by the statistical methods of bivarate correlation analysis. By the method of PCR-RFLP, the T105A polymorphism was found with two alleles A and B and three genotypes AA, AB and BB. The frequencies of two alleles were 72.97% and 27.03%, respectively. The heterozygosity of T105A locus was 0.39. The frequencies of three genotypes were 55.86%, 34.23% and 9.91%, respectively. According to the results of sequencing, one base change from G to A at the position 105 was found at T105A locus and it altered amino acid at the position 105 from alanine to threonine. According to the statistical analysis, no significant association between the polymorphism of MC1R gene and the coat color was found and the result may be due to the differences of genetic background. Further research on MC1R gene should be done in pure breed dogs.     

Microfungi on the Pandanaceae: a revision of the hyphomycete genus Balaniopsis with two new species

During research into microfungi that inhabit decaying parts of the monocotyledonous family Pandanaceae, three species of Balaniopsis were collected. One is Balaniopsis africana as originally described and illustrated by Kiffer as Balanium africanum. The second species is conspecific with the specimen treated as Balaniopsis africana by Kirk, but is introduced here as a new species, Balaniopsis kirkii. The third, Balaniopsis dendroidea, is a new species from Australia. Received: March 21, 2001 / Accepted: October 8, 2001     

Microfungi on the Pandanaceae:Polytretophora macrospora sp. nov.

Polytretophora macrospora is introduced based on specimens from two species ofPandanus in Seychelles. The new species is compared with currently accepted species. A key and a comparative synopsis toPolytetophora species are provided. Numerous specimens ofP. calcarata, collected on members of the Pandanaceae from Australia, Fiji, Hong Kong, Malaysia, New Caledonia, Palau, Philippines, Seychelles and Solomon Islands are also reported, along withP. dendroidea onPandanus sp. from Malaysia.