Echinostoma revolutum: Freshwater Snails as the Second Intermediate Hosts in Chiang Mai,Thailand

The occurrence of 37-collar spined echinostome metacercariae in freshwater snails was investigated in 6 districts of Chiang Mai Province, Thailand, from October 2011 to April 2012. A total of 2,914 snails that belong to 12 species were examined, and 7 snail species (Clea helena, Eyriesia eyriesi, Bithynia funiculata, Bithynia siamensis siamensis, Filopaludina doliaris, Filopaludina sumatrensis polygramma, and Filopaludina martensi martensi) were found infected with echinostome metacercariae. The prevalence of metacercariae was the highest in Filopaludina spp. (38.5-58.7%) followed by B. funiculata (44.0%), E. eyriesi (12.5%), B. siamensis siamensis (8.2%), and C. helena (5.1%). Metacercariae were experimentally fed to hamsters and domestic chicks, and adult flukes were recovered from both hosts at days 15 and 20 post-infection. The adult flukes were identified based on morphological features, morphometrics, host-parasite relationships, and geographical distribution. They were compatible to Echinostoma revolutum or Echinostoma jurini, with only minor differences. As the adults were recovered from both hamsters and chicks, our specimens were more compatible to E. revolutum rather than E. jurini (reported only from mammals). This is the first report for metacercariae of E. revolutum in the snail host, C. helena, and also confirmed that Filopaludina spp., E. eryresi, and Bithynia spp. act as the second intermediate hosts of E. revolutum under natural conditions, which are indigenously distributed in Chiang Mai province.     

DNA条形码：物种分类和鉴定技术

当前,一项称为“生命的条形码”计划正在欧美等国展开,其目的是实现对地球上现存的约1000万物种进行快速和准确的鉴定。DNA条形码是一种利用短的DNA序列对物种进行鉴定的技术。对DNA条形码的概念和原理进行了介绍,举例说明了其在物种分类、遗传多样性及物种鉴定研究中广泛的利用价值,阐述了当前该领域的研究现状,对未来的发展方向进行了展望。     

Interspecific Interactions Among Larval Trematode Parasites of Freshwater and Marine Snails

Freshwater and marine snails serve as intermediate hosts fornumerous species of larval trematodes. Any particular populationof snails may be infected by several species. It is commonlyobserved that mixed species infections are less frequent thanexpected by change in collections of host snails from naturalpopulations. While several mechanisms might generate such negativeassociations, laboratory studies of freshwater snail-trematodeassociations have demonstrated the presence of strong antagonisticinteractions between intramolluscan larval stages (rediae andsporocysts) of species that infect the same host individual.Both predatory and non-predatory antagonism has been observed,the former taking the form of predation by large, dominant redialforms on the sporocysts and rediae of subordinate species. Theseinteractions are largely hierarchical, although in some systemspriority effects have been observed, and in one case a sporocystspecies replaced a redial species by strong non-predatory antagonism.Several instances of positive association between larval trematodespecies have also been observed. In such cases, interferencewith host defense mechanisms by the first parasite appears toenhance superinfection by the second. My own study of the larvaltrematode guild that infects the salt marsh snail, Cerithideacalifornica, has revealed patterns of association and interactionthat are very similar to those demonstrated by laboratory studiesof freshwater systems. Ultimately, the frequency of interactionsamong larval trematodes depends on the availability, relativeto the numbers of susceptible snails, of infective eggs andmiracidial larvae transmitted from definitive hosts.     

Variation in Desiccation Tolerance in Freshwater Snails and Its Consequences for Invasion Ability

The freshwaters of Martinique (French West Indies) have recently been invaded by snails belonging to the Thiaridae family (Gastropoda; Prosobranchia). Eight distinct Thiarid lines have been successively introduced in Martinique, and are still in the process of sequentially replacing one another within local habitats, revealing a range of increasing invasive abilities. Our aim was to test whether the variation in invasive ability can be partly explained by a specific life-history trait, desiccation tolerance, which might be important in view of the typical instability of tropical freshwater habitats. We therefore tested desiccation tolerance in both juveniles and adults under laboratory conditions. Our data show that, although all Thiarid lines resist desiccation quite well, they exhibit extreme variation in the degree of tolerance. These differences are mostly mediated by individual size, but are definitely of genetic origin given that our individuals were of similar ages and were raised under standardized laboratory conditions. The overall invasive success of a line in Martinique, deduced from field surveys, does not correlate with its desiccation tolerance. However, desiccation tolerance does seem to be a limiting factor for the invasion of the small fraction of habitats that are most exposed to drought. More generally, our study exemplifies the possibility that the invasion differential among habitats, rather than a general invasion ability, be predicted according to a particular life-history trait, within a set of closely related invasive taxa.     

湘江中游江段螺类的种类组成及区系分析

报道了湘江中游江段螺类的调查结果,计有螺类31种(其中5种为湖南省新记录),分别隶属于腹足纲6科11属,其中主要是田螺科的种类.对它们的种类组成、区系、种群大小、分布与栖息环境的关系进行了分析,并讨论了城镇污水未经处理直接排放及修河拦坝对螺类生存环境的影响.     

DNA Barcode ITS Effectively Distinguishes the Medicinal Plant Boerhavia diffusa from Its Adulterants

Boerhavia diffusa (B. diffusa), also known as Punarnava, is an indigenous plant in India and an important component in traditional Indian medicine. The accurate identification and collection of this medicinal herb is vital to enhance the drug’s efficacy and biosafety. In this study, a DNA barcoding technique has been applied to identify and distinguish B. diffusa from its closely-related species. The phylogenetic analysis was carried out for the four species of Boerhavia using barcode candidates including nuclear ribosomal DNA regions ITS, ITS1, ITS2 and the chloroplast plastid gene psbA-trnH. Sequence alignment revealed 26% polymorphic sites in ITS, 30% in ITS1, 16% in ITS2 and 6% in psbA-trnH, respectively. Additionally, a phylogenetic tree was constructed for 15 species using ITS sequences which clearly distinguished B. diffusa from the other species. The ITS1 demonstrates a higher transition/transversion ratio, percentage of variation and pairwise distance which differentiate B. diffusa from other species of Boerhavia. Our study revealed that ITS and ITS1 could be used as potential candidate regions for identifying B. diffusa and for authenticating its herbal products.     

Patterns of DNA Barcode Variation in Canadian Marine Molluscs

Background

Molluscs are the most diverse marine phylum and this high diversity has resulted in considerable taxonomic problems. Because the number of species in Canadian oceans remains uncertain, there is a need to incorporate molecular methods into species identifications. A 648 base pair segment of the cytochrome c oxidase subunit I gene has proven useful for the identification and discovery of species in many animal lineages. While the utility of DNA barcoding in molluscs has been demonstrated in other studies, this is the first effort to construct a DNA barcode registry for marine molluscs across such a large geographic area.

Methodology/Principal Findings

This study examines patterns of DNA barcode variation in 227 species of Canadian marine molluscs. Intraspecific sequence divergences ranged from 0–26.4% and a barcode gap existed for most taxa. Eleven cases of relatively deep (>2%) intraspecific divergence were detected, suggesting the possible presence of overlooked species. Structural variation was detected in COI with indels found in 37 species, mostly bivalves. Some indels were present in divergent lineages, primarily in the region of the first external loop, suggesting certain areas are hotspots for change. Lastly, mean GC content varied substantially among orders (24.5%–46.5%), and showed a significant positive correlation with nearest neighbour distances.

Conclusions/Significance

DNA barcoding is an effective tool for the identification of Canadian marine molluscs and for revealing possible cases of overlooked species. Some species with deep intraspecific divergence showed a biogeographic partition between lineages on the Atlantic, Arctic and Pacific coasts, suggesting the role of Pleistocene glaciations in the subdivision of their populations. Indels were prevalent in the barcode region of the COI gene in bivalves and gastropods. This study highlights the efficacy of DNA barcoding for providing insights into sequence variation across a broad taxonomic group on a large geographic scale.     

Detection of Ehrlichia risticii, the Agent of Potomac Horse Fever, in Freshwater Stream Snails (Pleuroceridae: Juga spp.) from Northern California

Ehrlichia DNA was identified by nested PCR in operculate snails (Pleuroceridae: Juga spp.) collected from stream water in a northern California pasture in which Potomac horse fever (PHF) is enzootic. Sequencing of PCR-amplified DNA from a suite of genes (the 16S rRNA, groESL heat shock operon, 51-kDa major antigen genes) indicated that the source organism closely resembled Ehrlichia risticii, the causative agent of PHF. The minimum percentage of Juga spp. harboring the organism in the population studied was 3.5% (2 of 57 snails). No ehrlichia DNA was found in tissues of 123 lymnaeid, physid, and planorbid snails collected at the same site. These data suggest that pleurocerid stream snails may play a role in the life cycle of E. risticii in northern California.     

Medicinal Plants Recommended by the World Health Organization: DNA Barcode Identification Associated with Chemical Analyses Guarantees Their Quality

Medicinal plants are used throughout the world, and the regulations defining their proper use, such as identification of the correct species and verification of the presence, purity and concentration of the required chemical compounds, are widely recognized. Herbal medicines are made from vegetal drugs, the processed products of medicinal species. These processed materials present a number of challenges in terms of botanical identification, and according to the World Health Organization (WHO), the use of incorrect species is a threat to consumer safety. The samples used in this study consisted of the dried leaves, flowers and roots of 257 samples from 8 distinct species approved by the WHO for the production of medicinal herbs and sold in Brazilian markets. Identification of the samples in this study using DNA barcoding (matK, rbcL and ITS2 regions) revealed that the level of substitutions may be as high as 71%. Using qualitative and quantitative chemical analyses, this study identified situations in which the correct species was being sold, but the chemical compounds were not present. Even more troubling, some samples identified as substitutions using DNA barcoding contained the chemical compounds from the correct species at the minimum required concentration. This last situation may lead to the use of unknown species or species whose safety for human consumption remains unknown. This study concludes that DNA barcoding should be used in a complementary manner for species identification with chemical analyses to detect and quantify the required chemical compounds, thus improving the quality of this class of medicines.     

Identification of a New Motif in Family B DNA Polymerases by Mutational Analyses of the Bacteriophage T4 DNA Polymerase

Structure-based protein sequence alignments of family B DNA polymerases revealed a conserved motif that is formed from interacting residues between loops from the N-terminal and palm domains and between the N-terminal loop and a conserved proline residue. The importance of the motif for function of the bacteriophage T4 DNA polymerase was revealed by suppressor analysis. T4 DNA polymerases that form weak replicating complexes cannot replicate DNA when the dGTP pool is reduced. The conditional lethality provides the means to identify amino acid substitutions that restore replication activity under low-dGTP conditions either by correcting the defect produced by the first amino acid substitution or by generally increasing the stability of polymerase complexes; the second type are global suppressors that can effectively counter the reduced stability caused by a variety of amino acid substitutions. Some amino acid substitutions that increase the stability of polymerase complexes produce a new phenotype—sensitivity to the antiviral drug phosphonoacetic acid. Amino acid substitutions that confer decreased ability to replicate DNA under low-dGTP conditions or drug sensitivity were identified in the new motif, which suggests that the motif functions in regulating the stability of polymerase complexes. Additional suppressor analyses revealed an apparent network of interactions that link the new motif to the fingers domain and to two patches of conserved residues that bind DNA. The collection of mutant T4 DNA polymerases provides a foundation for future biochemical studies to determine how DNA polymerases remain stably associated with DNA while waiting for the next available dNTP, how DNA polymerases translocate, and the biochemical basis for sensitivity to antiviral drugs.     

姜科砂仁属植物DNA条形码序列的筛选

砂仁属（Amomum）隶属于姜科,全属约150种,我国有39种。该属多种植物可作药物或香料,但目前砂仁属的分类还不清楚,准确鉴定物种有很大难度。本研究利用DNA barcoding技术,对砂仁属50种121个个体的matK、rbcL-a、trnH-psbA序列及其不同组合进行比较,用Taxon DNA计算种间、种内bar-coding gap,运用相似法的BLASTn计算条码的正确鉴定率,筛选适合砂仁属的条码片段。结果显示：所有条码的barcoding gap均不存在;matK的正确鉴定率高于trnH-psbA和rbcL-a,联合片段的条码正确鉴定率高于单片段条码,三个片段联合条码的正确鉴定率最高。因此,推荐matK＋rbcL-a＋trnH-psbA作为砂仁属物种鉴定的候选条码。     

Freshwater use analysis of cassava for food feed fuel in the Mun River basin,Thailand

Purpose

This research aims to assess the current freshwater use in the cassava supply chain for food, feed fuel in the Mun basin, and the water scarcity impact and possible options to increase cassava production to meet the future demand following the Renewable and Alternative Energy Development Plan (AEDP) target.

Methods

This research analyzes freshwater use based on ISO 14046 water footprint assessment. The analysis was implemented based on a life cycle perspective that determines the impact on freshwater use from cassava products along their supply chain. Both direct water use and indirect water use that associated are analyzed. Midpoint impact of water use was assessed using water stress index (WSI) to calculate water scarcity footprint.

Results and discussion

The results show that in the current situation, total freshwater use of all cassava-related product in Mun basin in the base case is 1140 million m³/year. When WSI was applied, water scarcity footprint of all cassava-related products in the Mun basin in the base case was only 147 million m³/year. In the scenario 1, increasing irrigation to increase yield in the existing cassava cultivation area in the Mun basin has the largest water use compare to other scenarios. Scenarios 2 and 3, expanding cassava cultivation area in Mun basin and in other regions, have lower water and water scarcity impact than scenario 1. The benefit from transforming paddy rice (in unsuitable areas) to cassava cultivation was also good. However, more resources are required including land, energy, or fertilizer, and other environmental impacts such as greenhouse gas emission or eutrophication could be increased from the increasing resource use. Therefore, the decision-making process needs to consider the trade-off between those factors, and a more complete life cycle assessment (LCA) on the envisioned alternatives should be applied for further analysis.

Conclusions

The increasing demand of biofuels derived from cassava can increase stress on water in the Mun River basin. Increasing irrigation water use in the area as per requirement could possibly increase yield to meet the future feedstock demand but has large water scarcity impact. However, this could be alleviated by using groundwater from additional wells in the farm. Expanding cassava cultivation area could be another option having low water scarcity impact, but it requires more resources and could increase other environmental impacts that need to be further analyzed by a complete LCA.

     

高粱ClC基因家族鉴定、表达与DNA变异分析

氯离子通道蛋白(ClC)是存在于生物体细胞膜上一类分布极其广泛的阴离子通道,在抗盐胁迫等多种生理过程中发挥着非常重要的作用.使用生物信息学方法在高粱基因组中鉴定出10个SbClCs基因,对SbClCs基因家族进行基因组鉴定、启动子、保守基序、系统进化树和基因表达分析.结果显示:SbClCs基因家族主要分布在SBI-01...     

Intraspecific Inversions Pose a Challenge for the trnH-psbA Plant DNA Barcode

Background

The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species.

Methodology/Principal Findings

Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships.

Conclusions/Significance

Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.     

Identification of Major Planktonic Sulfur Oxidizers in Stratified Freshwater Lake

Planktonic sulfur oxidizers are important constituents of ecosystems in stratified water bodies, and contribute to sulfide detoxification. In contrast to marine environments, taxonomic identities of major planktonic sulfur oxidizers in freshwater lakes still remain largely unknown. Bacterioplankton community structure was analyzed in a stratified freshwater lake, Lake Mizugaki in Japan. In the clone libraries of 16S rRNA gene, clones very closely related to a sulfur oxidizer isolated from this lake, Sulfuritalea hydrogenivorans, were detected in deep anoxic water, and occupied up to 12.5% in each library of different water depth. Assemblages of planktonic sulfur oxidizers were specifically analyzed by constructing clone libraries of genes involved in sulfur oxidation, aprA, dsrA, soxB and sqr. In the libraries, clones related to betaproteobacteria were detected with high frequencies, including the close relatives of Sulfuritalea hydrogenivorans.