玉米与其他六种植物NBS类抗病基因的进化比较分析

具有核苷酸结合位点(nucleotide binding site,NBS)的抗病基因在植物抵抗各种病原菌侵染中起关键作用。对玉米全基因组中具有NBS结构的基因进行鉴定和分析,并结合水稻、高粱、拟南芥、百脉根、苜蓿和杨树的NBS类基因比较其在数量、复制、染色体定位和亲缘关系上的进化差异。发现玉米NBS类基因数量、复制数和成簇基因数均明显少于其他植物。低复制频率可能导致玉米NBS类基因较少,并推测可能导致其功能具有多样性。在基因染色体定位上,除高梁外,玉米与其他五种植物相似,呈不均衡分布。此外,进化树分析表明玉米NBS类基因与高粱的亲缘关系最近,与拟南芥的最远,在物种间表现出较高的保守性。结果对掲示玉米NBS基因的进化特点与发掘有益的NBS类抗病基因提供了重要的理论依据。     

Genetic Diversity and Phylogeny of Rhizobia That Nodulate Acacia spp. in Morocco Assessed by Analysis of rRNA Genes

Forty rhizobia nodulating four Acacia species (A. gummifera, A. raddiana, A. cyanophylla, and A. horrida) were isolated from different sites in Morocco. These rhizobia were compared by analyzing both the 16S rRNA gene (rDNA) and the 16S-23S rRNA spacer by PCR with restriction fragment length polymorphism (RFLP) analysis. Analysis of the length of 16S-23S spacer showed a considerable diversity within these microsymbionts, but RFLP analysis of the amplified spacer revealed no additional heterogeneity. Three clusters were identified when 16S rDNA analysis was carried out. Two of these clusters include some isolates which nodulate, nonspecifically, the four Acacia species. These clusters, A and B, fit within the Sinorhizobium lineage and are closely related to S. meliloti and S. fredii, respectively. The third cluster appeared to belong to the Agrobacterium-Rhizobium galegae phylum and is more closely related to the Agrobacterium tumefaciens species. These relations were confirmed by sequencing a representative strain from each cluster.     

A Well-Resolved Phylogeny of the Trees of Puerto Rico Based on DNA Barcode Sequence Data

Background

The use of phylogenetic information in community ecology and conservation has grown in recent years. Two key issues for community phylogenetics studies, however, are (i) low terminal phylogenetic resolution and (ii) arbitrarily defined species pools.

Methodology/principal findings

We used three DNA barcodes (plastid DNA regions rbcL, matK, and trnH-psbA) to infer a phylogeny for 527 native and naturalized trees of Puerto Rico, representing the vast majority of the entire tree flora of the island (89%). We used a maximum likelihood (ML) approach with and without a constraint tree that enforced monophyly of recognized plant orders. Based on 50% consensus trees, the ML analyses improved phylogenetic resolution relative to a comparable phylogeny generated with Phylomatic (proportion of internal nodes resolved: constrained ML = 74%, unconstrained ML = 68%, Phylomatic = 52%). We quantified the phylogenetic composition of 15 protected forests in Puerto Rico using the constrained ML and Phylomatic phylogenies. We found some evidence that tree communities in areas of high water stress were relatively phylogenetically clustered. Reducing the scale at which the species pool was defined (from island to soil types) changed some of our results depending on which phylogeny (ML vs. Phylomatic) was used. Overall, the increased terminal resolution provided by the ML phylogeny revealed additional patterns that were not observed with a less-resolved phylogeny.

Conclusions/significance

With the DNA barcode phylogeny presented here (based on an island-wide species pool), we show that a more fully resolved phylogeny increases power to detect nonrandom patterns of community composition in several Puerto Rican tree communities. Especially if combined with additional information on species functional traits and geographic distributions, this phylogeny will (i) facilitate stronger inferences about the role of historical processes in governing the assembly and composition of Puerto Rican forests, (ii) provide insight into Caribbean biogeography, and (iii) aid in incorporating evolutionary history into conservation planning.     

A Phylogeny and Timescale for Marsupial Evolution Based on Sequences for Five Nuclear Genes

Even though marsupials are taxonomically less diverse than placentals, they exhibit comparable morphological and ecological diversity. However, much of their fossil record is thought to be missing, particularly for the Australasian groups. The more than 330 living species of marsupials are grouped into three American (Didelphimorphia, Microbiotheria, and Paucituberculata) and four Australasian (Dasyuromorphia, Diprotodontia, Notoryctemorphia, and Peramelemorphia) orders. Interordinal relationships have been investigated using a wide range of methods that have often yielded contradictory results. Much of the controversy has focused on the placement of Dromiciops gliroides (Microbiotheria). Studies either support a sister-taxon relationship to a monophyletic Australasian clade or a nested position within the Australasian radiation. Familial relationships within the Diprotodontia have also proved difficult to resolve. Here, we examine higher-level marsupial relationships using a nuclear multigene molecular data set representing all living orders. Protein-coding portions of ApoB, BRCA1, IRBP, Rag1, and vWF were analyzed using maximum parsimony, maximum likelihood, and Bayesian methods. Two different Bayesian relaxed molecular clock methods were employed to construct a timescale for marsupial evolution and estimate the unrepresented basal branch length (UBBL). Maximum likelihood and Bayesian results suggest that the root of the marsupial tree is between Didelphimorphia and all other marsupials. All methods provide strong support for the monophyly of Australidelphia. Within Australidelphia, Dromiciops is the sister-taxon to a monophyletic Australasian clade. Within the Australasian clade, Diprotodontia is the sister taxon to a Notoryctemorphia + Dasyuromorphia + Peramelemorphia clade. Within the Diprotodontia, Vombatiformes (wombat + koala) is the sister taxon to a paraphyletic possum group (Phalangeriformes) with kangaroos nested inside. Molecular dating analyses suggest Late Cretaceous/Paleocene dates for all interordinal divergences. All intraordinal divergences were placed in the mid to late Cenozoic except for the deepest splits within the Diprotodontia. Our UBBL estimates of the marsupial fossil record indicate that the South American record is approximately as complete as the Australasian record. The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Number of triplets in 16S rRNA gene related with pathogenicity of Bacillus spp. and Clostridium spp

The relation between the number of some trinucleotides in the sequence of 16S rRNA gene and pathogenicity of bacterial species from the genera of Bacillus and Clostridium was revealed. The species of genus Bacillus, which are pathogenic for humans, mammals and insects, have an increased number of AAA and TAT triplets in 16S rRNA gene. Theoretically, these species, B. anthracis and B. cereus for example, may be detected in the specimen by the higher ratio of AAA plus TAT triplets to the number of GGG triplet. Species of genus Clostridium, which are pathogenic for humans and mammals, have a maximum ratio of AAA and TAT triplet numbers. This ratio was higher than 2.6 for pathogenic species and lower than 2.2 for saprophytic ones. These theoretical data may open a new way for detecting pathogenic bacteria through the determination of triplet numbers in the sequences of 16S rRNA or rRNA. However, the mechanism of evolutionary relation between the number of AAA and TAT triplets in the sequence of 16S rRNA gene and the pathogenicity of bacterial species is not known.     

Phylogeny and distribution of nitrate-storing Beggiatoa spp. in coastal marine sediments

Filamentous sulphide-oxidizing Beggiatoa spp. often occur in large numbers in the coastal seabed without forming visible mats on the sediment surface. We studied the diversity, population structure and the nitrate-storing capability of such bacteria in the Danish Limfjorden and the German Wadden Sea. Their distribution was compared to the vertical gradients of O2, NO3- and H2S as measured by microsensors. The main Beggiatoa spp. populations occurred in a 0.5-3 cm thick intermediate zone, below the depth of oxygen and nitrate penetration but above the zone of free sulphide. The Beggiatoa spp. filaments were found to store nitrate, presumably in liquid vacuoles up to a concentration of 370 mM NO3-, similar to the related large marine sulphur bacteria, Thioploca and Thiomargarita. The observations indicate that marine Beggiatoa spp. can live anaerobically and conserve energy by coupling sulphide oxidation with the reduction of nitrate to dinitrogen and/or ammonia. Calculations of the diffusive nitrate flux and the potential sulphide oxidation by Beggiatoa spp. show that the bacteria may play a critical role for the sulphur cycling and the nitrogen balance in these coastal environments. 16S rDNA sequence analysis shows a large diversity of these uncultured, nitrate-storing Beggiatoa spp. Smaller (9-17 micro m wide) and larger (33-40 micro m wide) Beggiatoa spp. represent novel phylogenetic clusters distinct from previously sequenced, large marine Beggiatoa spp. and Thioploca spp. Fluorescence in situ hybridization (FISH) of the natural Beggiatoa spp. populations showed that filament width is a conservative character of each phylogenetic species but a given filament width may represent multiple phylogenetic species in a mixed population.     

PBAD-Based Shuttle Vectors for Functional Analysis of Toxic and Highly Regulated Genes in Pseudomonas and Burkholderia spp. and Other Bacteria

We report the construction of a series of Escherichia-Pseudomonas broad-host-range expression vectors utilizing the P_BAD promoter and the araC regulator for routine cloning, conditional expression, and analysis of tightly controlled and/or toxic genes in pseudomonads.     

Insight into the Evolution of Magnetotaxis in Magnetospirillum spp., Based on mam Gene Phylogeny

Vibrioid- to helical-shaped magnetotactic bacteria phylogenetically related to the genus Magnetospirillum were isolated in axenic cultures from a number of freshwater and brackish environments located in the southwestern United States. Based on 16S rRNA gene sequences, most of the new isolates represent new Magnetospirillum species or new strains of known Magnetospirillum species, while one isolate appears to represent a new genus basal to Magnetospirillum. Partial sequences of conserved mam genes, genes reported to be involved in the magnetosome and magnetosome chain formation, and form II of the ribulose-1,5-bisphosphate carboxylase/oxygenase gene (cbbM) were determined in the new isolates and compared. The cbbM gene was chosen for comparison because it is not involved in magnetosome synthesis; it is highly conserved and is present in all but possibly one of the genomes of the magnetospirilla and the new isolates. Phylogenies based on 16S rRNA, cbbM, and mam gene sequences were reasonably congruent, indicating that the genes involved in magnetotaxis were acquired by a common ancestor of the Magnetospirillum clade. However, in one case, magnetosome genes might have been acquired through horizontal gene transfer. Our results also extend the known diversity of the Magnetospirillum group and show that they are widespread in freshwater environments.     

Phylogeny of Stemphylium spp. based on ITS and glyceraldehyde-3-phosphate dehydrogenase gene sequences

The phylogenetic relationships among 44 isolates representing 16 species of Stemphylium were inferred from ITS and glyceraldehyde-3-phosphate dehydrogenase (gpd) sequence data. The results generally agree with morphological species concepts. There was strong support for monophyly of the genus Stemphylium. Analysis of the gpd fragment in particular was useful for establishing well-supported relationships among the species and isolates of Stemphylium. Species of Stemphylium that appear to have lost the ability to produce a sexual state are scattered among the species with the ability to reproduce sexually (Pleospora spp.). Species that are pathogenic to alfalfa are resolved into two groups. Stemphylium botryosum and two isolates with morphological characters similar to S. globuliferum had identical sequences at both loci. These two loci in S. vesicarium, S. alfalfae and S. herbarum are nearly identical but differ from S. botryosum. The separation of S. vesicarium, S. herbarum and S. alfalfae into separate species by morphometric evidence was not supported by the molecular data. Morphological and developmental characters such as size and shape of conidia, conidiophores, and ascospores, and size and time of maturation of pseudothecia are useful for diagnosing species. However, other morphological characters such as septum development and small variations in conidial wall ornamentation are not as useful.     

基于nrITS、psbA-trnH和DMC1序列中国短柄草族的系统进化和生物地理学研究

短柄草族（Brachypodieae）有短柄草（Brachypodium sylvaticum）和二穗短柄草（Brachypodium distachyum）两种模式植物,具有重要科研价值,与雀麦族（Bromeae）和小麦族（Triticeae）的系统位置关系尚不明确。据此,本文运用最大简约法（MP）、最大似然法（ML）和贝叶斯推断法（BI）对叶绿体基因片段psbA-trnH、核糖体基因转录间隔区ITS、单拷贝核基因片段DMC1以及psbA-trnH+nrITS+DMC1联合序列数据进行分析,来揭示三者的系统学位置关系。研究结果表明,在DMC1、nrITS以及联合基因序列构建的系统进化树中,短柄草族、雀麦族、小麦族各自聚为一支,且具有较高的支持率;在叶绿体基因psbA-trnH构建的系统进化树中,短柄草族聚为一支,雀麦族分散镶嵌在小麦族中,提示小麦族、雀麦族之间发生了多种进化情况。利用BEAST和RASP对psbA-trnH+nrITS+DMC1联合序列分析,结果表明：小麦族起源于西北地区,物种形成时间多集中在13-7 Ma,与青藏高原中新世中晚期（13-7 Ma）的隆起一致;短柄草族起源于西南地区,物种形成时间多集中在3 Ma之后,这与东亚季风的加强和青藏高原上新世以来的剧烈抬升时间一致,中国特有种草地短柄草（Brachypodium pratense）也是在该时间段分化形成。     

Assimilation of sulfur from alkyl- and arylsulfonates by Clostridium spp.

Organisms able to utilize one of several alkyl- and arylsulfonates as sole source of sulfur under anoxic conditions were enriched. Three fermenting bacteria, all putative Clostridium spp., were isolated in pure culture. All three organisms had wide substrate ranges for alkylsulfonates, taurine and arylsulfonates, presumably due to three different enzyme systems. One organism, strain KNNDS (DSM 10612) was selected for further characterization. The organism was possibly a new Clostridium sp., with Clostidium intestinalis as its nearest neighbor (97.6% similarity of rDNA). Strain KNNDS catalyzed complete sulfonate utilization concomitant with growth. Growth yields of approximtely 3 kg protein/mol sulfur were observed, independent of the sulfur source [e.g. sulfate, sulfide, 4-(phenyl)butyl-1-sulfonate, 2,6-naphthyldisulfonate or 4-nitrocatechol sulfate]. We failed to detect significant amounts of either an arylsulfonatase or an arylsulfatase, and we hypothesize different arylsulfatases [EC 3.1.6.1] in aerobes and in Clostridium spp. Received: 15 October / Accepted: 29 November 1996     

Fecal lactoferrin and Clostridium spp. in stools of autistic children

Stools from autistic and healthy children were studied for fecal lactoferrin, Clostridium difficile toxins, Clostridium perfringens enterotoxin and cultured for Clostridium spp. Elevated level of FLA was demonstrated in 24.4% stools, all from boys (31.25%). No toxins were detected. Clostridium spp. was isolated with similar frequency from all samples. C. perfringens were isolated significantly often from the autistic stools, intermediate sensitive strains to penicillin 19%, to clindamycin 11.3%, and to metronidazole 7.5% were detected. Further studies on fecal microflora and inflammatory mediators, with larger groups of patients, are required in order to explain their role in neurological deficits.     

Comparisons of Isozyme Phenotypes in Five Meloidogyne spp. with Isoelectric Focusing

Meloidogyne incognita race 1, M. javanica, M. arenaria race 1, M. hapla, and an undescribed Meloidogyne sp. were analyzed by comparing isozyme phenotypes of esterase, malate dehydrogenase, phosphoglucomutase, isocitrate dehydrogenase, and α-glycerophosphate dehydrogenase. Isozyme phenotypes were obtained from single mature females by isoelectric focusing electrophoresis. Of these five isozymes, only esterase and phosphoglucomutase could be used to separate all five Meloidogyne spp.; however, the single esterase electromorphs were similar for M. incognita and M. hapla. Yet when both nematodes were run on the same gel, differences in their esterase phenotypes were detectable. Isozyme phenotypes from the other three isozymes revealed a great deal of similarity among M. incognita, M. javanica, M. arenaria, and the undescribed Meloidogyne sp.     

肠道梭菌属与2型糖尿病的相关性研究进展

摘要：随着经济社会的发展和人类生活水平的提高,2型糖尿病及其慢性并发症不仅严重影响了患者自身的生活质量,而且也给其家庭和社会带来了沉重的负担,已逐渐成为全球突出的社会问题。如果人体内肠道菌群的结构和功能发生紊乱,则可能引起2型糖尿病的发生,因此肠道菌群成为备受关注的研究对象。相关文献指出肠道菌群中的梭菌属与肠黏膜完整性、内脏脂肪、免疫稳态、能量代谢、肠蠕动有关。本文总结了梭菌属的生物学特性、在机体内的生理功能及与2型糖尿病之间的相关性,旨在为进一步研究肠道梭菌属与2型糖尿病间的关系提供参考。     

Inhibition of Spores of Clostridium spp. by Sodium Nitrite

S ummary . Sodium nitrite heated in a laboratory medium was more inhibitory to spores of Clostridium spp. than nitrite added as a filter-sterilized solution to the same medium. Most spores remained refractile after inhibition for >3 months and some proved viable when inoculated into fresh nitrite-free medium. The inhibitory activity of heated nitrite medium was not stable indefinitely, growth sometimes occurred on re-inoculation with vegetative cells.     

Phylogenetic Diversity and Specificity of Bacteria Closely Associated with Alexandrium spp. and Other Phytoplankton

While several studies have suggested that bacterium-phytoplankton interactions have the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at the species composition level. The objective of the current study was to determine whether there are specific associations between diverse phytoplankton and the bacteria that co-occur with them. We determined the phylogenetic diversity of bacterial assemblages associated with 10 Alexandrium strains and representatives of the major taxonomic groups of phytoplankton in the Gulf of Maine. For this analysis we chose xenic phytoplankton cultures that (i) represented a broad taxonomic range, (ii) represented a broad geographic range for Alexandrium spp. isolates, (iii) grew under similar cultivation conditions, (iv) had a minimal length of time since the original isolation, and (v) had been isolated from a vegetative phytoplankton cell. 16S rRNA gene fragments of most Bacteria were amplified from DNA extracted from cultures and were analyzed by denaturing gradient gel electrophoresis and sequencing. A greater number of bacterial species were shared by different Alexandrium cultures, regardless of the geographic origin, than by Alexandrium species and nontoxic phytoplankton from the Gulf of Maine. In particular, members of the Roseobacter clade showed a higher degree of association with Alexandrium than with other bacterial groups, and many sequences matched sequences reported to be associated with other toxic dinoflagellates. These results provide evidence for specificity in bacterium-phytoplankton associations.     

Histological Comparisons of Parasitism by Schistonchus spp. (Nemata: Aphelenchoididae) in Neotropical Ficus spp.

Syconia (enclosed infructescences) infested with host-specific species of Schistonchus (Aphelenchoididae) were collected from six species of Ficus (Moraceae) native to Florida or Panama. They were sectioned and histologically examined to assess the effects of parasitism. Parasitism by Schistonchus spp. was associated with hypertrophied cells, tissue necrosis, and the presence of an exudate in all species. Occasional hypertrophy of the outer epidermal cells occurred on seed florets, wasp florets, and on the endothecial cells of male florets in F. aurea (subgenus Urostigma) from Florida. Aberrations of the inner mesocarp occurred under the hypertrophied cells on seed florets. In F. laevigata (subgenus Urostigma) from Florida, Schistonchus sp. infested immature male florets and was associated with hypertrophy of endothecial cells, epidermal cells of the anther filaments, and anthers. Schistonchus sp. also caused aberrations of the anther filament, anthers, and pollen. Ficus poponoei (subgenus Urostigma) and F. glabrata (subgenus Pharmacosycea), both from Panama, had hypertrophied outer epidermal cells on seed florets. Ficus poponoei also had Schistonchus sp. within the pedicel of an aborted floret, with hypertrophy of the cortical parenchyma. Ficus trigonata (subgenus Urostigma) from Panama had hypertrophy of the outer epidermis of seed florets. When the outer epidermis on these florets was missing, the inner mesocarp was hypertrophied. Ficus maxima (subgenus Pharmacosycea) from Panama had hypertrophy on the outer epidermis of seed and aborted florets. Schistonchus spp. were not found in wasp larvae or pupae in any of the Ficus spp. examined. Hypertrophy was never observed in the absence of Schistonchus spp.