Miniprimer PCR assay targeting multiple genes: a new rapid and reliable tool for genotyping Pantoea stewartii subsp. stewartii

Aim: Development of a ‘miniprimer’ PCR assay for genotyping Pantoea stewartii subsp. stewartii, the causal agent of the Stewart’s bacterial wilt on maize. Methods and Results: Four 10‐nucleotide (10‐nt) ‘miniprimer’ sets were designed and evaluated in the presence of Titanium Taq DNA polymerase. Under optimal reaction conditions, the miniprimer pair Uni‐BacF‐10/Uni‐BacR‐10 reproducibly generated identical banding patterns among 10 strains of P. stewartii subsp. stewartii, different patterns from strains of P. stewartii subsp. indologenes, other Panteoa species, Clavibacter michiganensis, Pectobacterium spp., Pseudomonas spp. and other bacterial species. The amplicons of Pantoea stewartii subsp. stewartii were cloned and sequenced to identify genes or DNA fragments that are targeted by the miniprimer PCR assay. Of the 14 ‘clone types’ identified, sequences of a 1·23‐kb fragment had a 99·8% similarity to part of the Pantoea stewartii zeaxanthin diglucoside biosynthetic operon ( AY166713 ). Other dominant cloned fragments included a 411‐bp amplicon that exhibited 99·8% similarity to the psaU gene (syn:ysaU; GQ249669 ), a type III protein‐secretion system complex of P. stewartii subsp. stewartii strain DC283, and a 548‐bp fragment showed 63% homology to the Asp/Glu racemase encoding gene in Erwinia tasmaniensis strain ET1/99. Conclusion: The miniprimer PCR assay reported here is highly discriminatory and reproducible in genotyping Pantoea stewartii subsp. stewartii. Significance and Impact of the study: This miniprimer PCR assay could be a new reliable and rapid tool for fingerprinting the Stewart’s wilt pathogen of maize.     

DegePrime,a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571–1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples.     

Identification of New World monkey MHC-DRB alleles using PCR,DGGE and direct sequencing

Identification of New World monkey MHC-DRB alleles has previously relied upon labor-intensive cloning and sequencing techniques. Here we describe a rapid and unambiguous way to distinguish DRB alleles in New World monkeys using the polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and direct sequencing. The highly variable second exon of New World monkey DRB alleles was amplified using generic DRB primers and alleles were separated by DGGE. DNA was then reamplified from plugs removed from the gel and alleles were determined using fluorescent-based sequencing. The validity of this typing procedure was confirmed by the identification of all DRB alleles previously characterized by cloning and sequencing techniques from an individual cotton-top tamarin. Importantly, our analysis revealed DRB alleles not previously identified in this reference animal. Following validation of our technique, the protocol was employed for the characterization of MHC-DRB alleles in four other species of New World monkey: the pygmy marmoset, white-faced saki monkey, long-haired spider monkey and owl monkey. Using this technique, we identified five alleles from the cotton-top tamarin, five alleles from the owl monkey, three alleles from the long-haired spider monkey, three alleles from the white-faced saki monkey and two alleles from the pygmy marmoset. On the basis of phylogenetic tree analyses, 13 new DRB alleles were assigned to eight different MHC-DRB lineages. Whereas traditional DRB typing via cloning and sequencing provides limited information, our new technique provides a simple and relatively rapid way of identifying New World monkey MHC-DRB alleles.Nucleotide sequence data reported are available in the GenBank/EMBL/DDBJ databases under the accession numbers AJ544165–AJ544177     

Lens Crystallins and Their Microbial Homologs: Structure,Stability, and Function

Referee: Franz Schmid, Biochemicshes Laboratorium, Universitaet Bayeuth, D-95440 Bayeuth, Germany

abg-Crystallins are the major protein components in the vertebrate eye lens — a as a molecular chaperone and b and g as structural proteins. Surprisingly, the latter two share some structural characteristics with a number of microbial stress proteins. The common denominator is not only the Greek key topology of their polypeptide chains but also their high intrinsic stability, which, in certain microbial crystallin homologs, is further enhanced by high-affinity Ca²⁺-binding. Recent studies of natural and mutant vertebrate bg-crystallins as well as spherulin 3a from Physarum polycephalum and Protein S from Myxococcus xanthus allowed the correlation of structure and stability of crystallins to be elucidated in some detail. From the thermo-dynamic point of view, stability increments come from (1) local interactions involved in the close packing of the cooperative units, (2) the all-b secondary structure of the Greek-key motif, (3) intramolecular interactions between domains, (4) intermolecular domain interactions, including 3D domain swapping and (v) excluded volume effects due to “molecular crowding” at the high cellular protein concentrations. Apart from these contributions to the Gibbs free energy of stability, significant kinetic stabilization originates from the high activation energy barrier determining the rate of unfolding from the native to the unfolded state. From the functional point of view, the high stability is responsible for the long-term transparency of the eye lens, on the one hand, and the stress resistance of the microorganisms in their dormant state on the other. Local structural perturbations due to chemical modification, wrong protein interactions, or other irreversible processes may lead to protein aggregation. A leading cataract hypothesis is that only after a-crystallin, a member of the small heat-shock protein family, is titrated out does pathological opacity occur. Understanding the structural basis of protein stability in the healthy eye lens is the route to solve the enormous medical and economical problem of cataract.     

Lepidostroma vilgalysii, a new basidiolichen from the New World

The lichenized basidiomycete Lepidostroma vilgalysii from Mexico is described based on morphological analyses. The species is only the second representative of the family Lepidostromataceae documented from the New World, and is one of the few described lichens with an inverted morphology, with the algae in a layer at the base of the thallus. Molecular sequence data from the nuclear ribosomal LSU locus are used to confirm the placement of the holotype in Lepidostroma and to evaluate the molecular distinctiveness of the species from all other described species in the family and genus.     

大学生科学素质教育课程“走进微生物世界”的建设与实践

微生物学的研究和应用在人类社会发展中起着越来越重要的作用。微生物与人类的生产和生活密切相关,开展微生物学方面的素质教育非常必要。因此,我们面向非生物专业本科生开设了"走进微生物世界"素质教育课程。根据学生的知识水平和认知规律,本课程重视知识体系的系统性和关联性,基础理论、生产应用和实践教学等教学内容依次展开,开拓学生视野,培养创新思维。不同的教学内容采用了差别化的教学方法,配合多媒体教学、网络教学和基于云课堂的即时互动教学,提高学生的学习兴趣,学习效果回馈及时,方便师生交流。经过3年的建设,本课程已形成教学方法有特色、教学内容符合学生知识水平和学科发展潮流的素质教育课程。     

Hagenbachia, a misplaced genus of New World Liliaceae

Hagenbachia , which until recently was included in Haemodoraceae, belongs in Asphodeleae in Liliaceae sensu lato or Anthericaceae sensu stricto. Hagenbachia and its putative relatives Echeandia, Anthericum , and Chlorophytum are characterized by anatropous ovules, curved or angled embryos, and nonarillate seeds, which indicate a position in Anthericaceae, as well as a black, colliculose seed coat. Hagenbachia includes five species of Central and South America; one, H. columbiana , is described here. The available data suggest the species are ecologically as well as geographically isolated. There are two broad leaved species. One is endemic to the lowlands of eastern Brazil and the second is found at middle elevations in Costa Rica and Panama and on the eastern slope of the Andes in Ecuador. Of the three narrow leaved species, one is endemic to the Cordillera Central in Columbia, a second is endemic to eastern Paraguay and southeastern Bolivia and the third occurs from eastern Bolivia northeast to east-central Brazil.     

Phylum- and Class-Specific PCR Primers for General Microbial Community Analysis

Amplification of a particular DNA fragment from a mixture of organisms by PCR is a common first step in methods of examining microbial community structure. The use of group-specific primers in community DNA profiling applications can provide enhanced sensitivity and phylogenetic detail compared to domain-specific primers. Other uses for group-specific primers include quantitative PCR and library screening. The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups. Primers specific for the 16S ribosomal sequences of Alphaproteobacteria, Betaproteobacteria, Bacilli, Actinobacteria, and Planctomycetes and for parts of both the 18S ribosomal sequence and the internal transcribed spacer region of Basidiomycota were examined. Primers were tested by comparison to sequences in the ARB 2003 database, and chosen primers were further tested by cloning and sequencing from soil community DNA. Eighty-five to 100% of the sequences obtained from clone libraries were found to be placed with the groups intended as targets, demonstrating the specificity of the primers under field conditions. It will be important to reevaluate primers over time because of the continual growth of sequence databases and revision of microbial taxonomy.     

Isolation of microsatellite markers for Contarinia nasturtii,a European pest invading the New World

Microsatellite markers were developed for epidemiological studies on Contarinia nasturtii (Diptera, Cecidomyiidae), a native European pest that was introduced to the New World in 1996. Nine loci were found to be polymorphic and suitable for the analysis of 56 male individuals that were collected using pheromone traps. These markers all conform to Hardy–Weinberg expectations in at least one of the two tested populations, and carry an average number of 11 alleles among populations and observed levels of heterozygosity ranging from 0.32 to 0.86. Primers for all markers also successfully amplified fragments from Contarinia pisi and Contarinia tritici.     

UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the tree that leads to descendants from either one environment or the other, but not both. UniFrac can be used to determine whether communities are significantly different, to compare many communities simultaneously using clustering and ordination techniques, and to measure the relative contributions of different factors, such as chemistry and geography, to similarities between samples. We demonstrate the utility of UniFrac by applying it to published 16S rRNA gene libraries from cultured isolates and environmental clones of bacteria in marine sediment, water, and ice. Our results reveal that (i) cultured isolates from ice, water, and sediment resemble each other and environmental clone sequences from sea ice, but not environmental clone sequences from sediment and water; (ii) the geographical location does not correlate strongly with bacterial community differences in ice and sediment from the Arctic and Antarctic; and (iii) bacterial communities differ between terrestrially impacted seawater (whether polar or temperate) and warm oligotrophic seawater, whereas those in individual seawater samples are not more similar to each other than to those in sediment or ice samples. These results illustrate that UniFrac provides a new way of characterizing microbial communities, using the wealth of environmental rRNA sequences, and allows quantitative insight into the factors that underlie the distribution of lineages among environments.     

A FRET-Based Real-Time PCR Assay to Identify the Main Causal Agents of New World Tegumentary Leishmaniasis

In South America, various species of Leishmania are endemic and cause New World tegumentary leishmaniasis (NWTL). The correct identification of these species is critical for adequate clinical management and surveillance activities. We developed a real-time polymerase chain reaction (PCR) assay and evaluated its diagnostic performance using 64 archived parasite isolates and 192 prospectively identified samples collected from individuals with suspected leishmaniasis enrolled at two reference clinics in Lima, Peru. The real-time PCR assay was able to detect a single parasite and provided unambiguous melting peaks for five Leishmania species of the Viannia subgenus that are highly prevalent in South America: L. (V.) braziliensis, L. (V.) panamensis, L. (V.) guyanensis, L. (V.) peruviana and L. (V.) lainsoni. Using kinetoplastid DNA-based PCR as a gold standard, the real-time PCR had sensitivity and specificity values of 92% and 77%, respectively, which were significantly higher than those of conventional tests such as microscopy, culture and the leishmanin skin test (LST). In addition, the real-time PCR identified 147 different clinical samples at the species level, providing an overall agreement of 100% when compared to multilocus sequence typing (MLST) data performed on a subset of these samples. Furthermore, the real-time PCR was three times faster and five times less expensive when compared to PCR - MLST for species identification from clinical specimens. In summary, this new assay represents a cost-effective and reliable alternative for the identification of the main species causing NWTL in South America.     

Historical evidence for a pre-Columbian presence of Datura in the Old World and implications for a first millennium transfer from the New World

Datura (Solanaceae)is a small genus of plants that,for long, was thought to occur naturally in both the New and Old Worlds. However, recent studies indicate that all species in the genus originated in the Americas. This finding has prompted the conclusion that no species of Datura could have been present in the Old World prior to its introduction there by Europeans in the early 16th century CE. Further, the textual evidence traditionally cited in support of a pre-Columbian Old World presence of Datura species is suggested to be due to the misreading of classical Greek and Arabic sources. As a result, botanists generally accept the opinion that Datura species were transferred into the Old World in the post-Columbian period. While the taxonomic and geographic evidence for a New World origin for all the Datura species appears to be well supported, the assertion that Datura species were not known in the Old World prior to the 16th century is based on a limited examination of the pre-Columbian non-Anglo sources.We draw on old Arabic and Indic texts and southern Indian iconographic representations to show that there is conclusive evidence for the pre-Columbian presence of at least one species of Datura in the Old World. Given the systematic evidence for a New World origin of the genus, the most plausible explanation for this presence is a relatively recent but pre-Columbian (probably first millennium CE) transfer of at least one Datura species, D. metel, into the Old World. Because D. metel is a domesticated species with a disjunct distribution,this might represent an instance of human-mediated transport from the New World to the Old World, as in the case of the sweet potato (Ipomoea batatas).