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Numerous studies revealed high diversity of T4-like bacteriophages in various environments, but so far, little is known about T4-like virus diversity in freshwater bodies, particularly in eutrophic lakes. The present study was aimed at elucidating molecular diversity of T4-like bacteriophages in eutrophic Lake Kotokel located near Lake Baikal by partial sequencing of the major capsid genes (g23) of T4-like bacteriophages. The majority of g23 fragments from Lake Kotokel were most similar to those from freshwater lakes and paddy fields. Despite the proximity and direct water connection between Lake Kotokel and Lake Baikal, g23 sequence assemblages from two lakes were different. UniFrac analysis showed that uncultured T4-like viruses from Lake Kotokel tended to cluster with those from the distant lake of the same trophic status. This fact suggested that the trophic conditions affected the formation of viral populations, particularly of T4-like viruses, in freshwater environments.  相似文献   
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Temperature of leaves or canopies can be used as an indicator of stomatal aperture, which is considered a sensitive response to soil water deficit. In this paper we analyse the robustness and sensitivity of thermal imaging for detecting changes in stomatal conductance and leaf water status in a range of plant species. Thermal imaging successfully distinguished between irrigated and non-irrigated plants of a variety of species under greenhouse or controlled chamber conditions, with strong correlations between thermal indices and stomatal conductance measured by porometry. Our results also highlighted issues that need to be addressed in order to be confident of always detecting drought stress using this technique. These include variability in leaf angles and the limited reliability of 'wet' and 'dry' leaves to represent leaves with stomata fully open or stomata fully closed. These results should assist the design of protocols for application in crop production or ecosystem monitoring.  相似文献   
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The biological role of the protein encoded by the alternative open reading frame (core+1/ARF) of the Hepatitis C virus (HCV) genome remains elusive, as does the significance of the production of corresponding antibodies in HCV infection. We investigated the prevalence of anti-core and anti-core+1/ARFP antibodies in HCV-positive blood donors from Cambodia, using peptide and recombinant protein-based ELISAs. We detected unusual serological profiles in 3 out of 58 HCV positive plasma of genotype 1a. These patients were negative for anti-core antibodies by commercial and peptide-based assays using C-terminal fragments of core but reacted by Western Blot with full-length core protein. All three patients had high levels of anti-core+1/ARFP antibodies. Cloning of the cDNA that corresponds to the core-coding region from these sera resulted in the expression of both core and core+1/ARFP in mammalian cells. The core protein exhibited high amino-acid homology with a consensus HCV1a sequence. However, 10 identical synonymous mutations were found, and 7 were located in the aa(99-124) region of core. All mutations concerned the third base of a codon, and 5/10 represented a T>C mutation. Prediction analyses of the RNA secondary structure revealed conformational changes within the stem-loop region that contains the core+1/ARFP internal AUG initiator at position 85/87. Using the luciferase tagging approach, we showed that core+1/ARFP expression is more efficient from such a sequence than from the prototype HCV1a RNA. We provide additional evidence of the existence of core+1/ARFP in vivo and new data concerning expression of HCV core protein. We show that HCV patients who do not produce normal anti-core antibodies have unusually high levels of anti-core+1/ARFP and harbour several identical synonymous mutations in the core and core+1/ARFP coding region that result in major changes in predicted RNA structure. Such HCV variants may favour core+1/ARFP production during HCV infection.  相似文献   
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Background

The Beijing family is a successful group of M. tuberculosis strains, often associated with drug resistance and widely distributed throughout the world. Polymorphic genetic markers have been used to type particular M. tuberculosis strains. We recently identified a group of polymorphic DNA repair replication and recombination (3R) genes. It was shown that evolution of M. tuberculosis complex strains can be studied using 3R SNPs and a high-resolution tool for strain discrimination was developed. Here we investigated the genetic diversity and propose a phylogeny for Beijing strains by analyzing polymorphisms in 3R genes.

Methodology/Principal Findings

A group of 3R genes was sequenced in a collection of Beijing strains from different geographic origins. Sequence analysis and comparison with the ones of non-Beijing strains identified several SNPs. These SNPs were used to type a larger collection of Beijing strains and allowed identification of 26 different sequence types for which a phylogeny was constructed. Phylogenetic relationships established by sequence types were in agreement with evolutionary pathways suggested by other genetic markers, such as Large Sequence Polymorphisms (LSPs). A recent Beijing genotype (Bmyc10), which included 60% of strains from distinct parts of the world, appeared to be predominant.

Conclusions/Significance

We found SNPs in 3R genes associated with the Beijing family, which enabled discrimination of different groups and the proposal of a phylogeny. The Beijing family can be divided into different groups characterized by particular genetic polymorphisms that may reflect pathogenic features. These SNPs are new, potential genetic markers that may contribute to better understand the success of the Beijing family.  相似文献   
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Aim Species distribution models and geographical information system (GIS) technologies are becoming increasingly important tools in conservation planning and decision‐making. Often the rich data bases of museums and herbaria serve as the primary data for predicting species distributions. Yet key assumptions about the primary data often are untested, and violation of such assumptions may have consequences for model predictions. For example, users of primary data assume that sampling has been random with respect to geography and environmental gradients. Here we evaluate the assumption that plant voucher specimens adequately sample the climatic gradient and test whether violation of this assumption influences model predictions. Location Bolivia and Ecuador. Methods Using 323,711 georeferenced herbarium collections and nine climatic variables, we predicted the distribution of 76 plant species using maximum entropy models (MAXENT) with training points that sampled the climate environments randomly and training points that reflected the climate bias in the herbarium collections. To estimate the distribution of species, MAXENT finds the distribution of maximum entropy (i.e. closest to uniform) subject to the constraint that the expected value for each environmental variable under the estimated distribution matches its empirical average. The experimental design included species that differed in geographical range and elevation; all species were modelled with 20 and 100 training points. We examined the influence of the number of training points and climate bias in training points, elevation and range size on model performance using analysis of variance models. Results We found that significant parts of the climatic gradient were poorly represented in herbarium collections for both countries. For the most part, existing climatic bias in collections did not greatly affect distribution predictions when compared with an unbiased data set. Although the effects of climate bias on prediction accuracy were found to be greater where geographical ranges were characterized by high spatial variation in the degree of climate bias (i.e. ranges where the bias of the various climates sampled by collections deviated considerably from the mean bias), the greatest influence on model performance was the number of presence points used to train the model. Main conclusions These results demonstrate that predictions of species distributions can be quite good despite existing climatic biases in primary data found in natural history collections, if a sufficiently large number of training points is available. Because of consistent overprediction of models, these results also confirm the importance of validating models with independent data or expert opinion. Failure to include independent model validation, especially in cases where training points are limited, may potentially lead to grave errors in conservation decision‐making and planning.  相似文献   
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