Dioctophyme renale (Nematoda: Dioctophymatoidea) in the abdominal cavity of Rattus norvegicus in Japan

We collected 24 brown rats, Rattus norvegicus, in Kanagawa Prefecture in Japan and found one rat harboring a dioctophymatid nematode. A single male and a female worm were recovered from the abdominal cavity and were identified as Dioctophyme renale based on morphologic features and a BLAST DNA sequence analysis. We describe the morphological features of the adult worms and eggs from this extremely rare case of D. renale infection in a brown rat.     

Hypertonic Sabouraud Dextrose Agar as a Substrate for Differentiation of Candida dubliniensis

In this study, we aimed to detect the proportion of Candida dubliniensis among yeast strains previously identified as C. albicans by using several phenotypic methods and PCR. For this purpose, we screened 300 strains by using phenotypic tests suggested for the identification of C. dubliniensis in the literature, but we detected high proportion of false-positive reactions. Only two strains (0.6%) were detected as true C. dubliniensis by PCR and API ID 32C methods. Moreover, these two strains gave the expected results with all the phenotypic tests, including modified salt tolerance test for C. dubliniensis. In conclusion, none of the phenotypic methods, except for the modified salt tolerance test, revealed 100% successful results in discrimination of C. albicans and C. dubliniensis species. However, in the tobacco agar test, the rate of false positivity was as low as 0.6%. We suggest that in the case of absence of PCR and other automatized identification systems, these two phenotypic tests can be used in routine laboratories to obtain a presumptive result.     

New mobile genetic elements in <Emphasis Type="Italic">Cupriavidus metallidurans</Emphasis> CH34, their possible roles and occurrence in other bacteria

Cupriavidus metallidurans strain CH34 is a β-Proteobacterium that thrives in low concentrations of heavy metals. The genetic determinants of resistance to heavy metals are located on its two chromosomes, and are particularly abundant in the two megaplasmids, pMOL28 and pMOL30. We explored the involvement of mobile genetic elements in acquiring these and others traits that might be advantageous in this strain using genome comparison of Cupriavidus/Ralstonia strains and related β-Proteobacteria. At least eleven genomic islands were identified on the main replicon, three on pMOL28 and two on pMOL30. Multiple islands contained genes for heavy metal resistance or other genetic determinants putatively responding to harsh environmental conditions. However, cryptic elements also were noted. New mobile genetic elements (or variations of known ones) were identified through synteny analysis, allowing the detection of mobile genetic elements outside the bias of a selectable marker. Tn4371-like conjugative transposons involved in chemolithotrophy and degradation of aromatic compounds were identified in strain CH34, while similar elements involved in heavy metal resistance were found in Delftia acidovorans SPH-1 and Bordetella petrii DSM12804. We defined new transposons, viz., Tn6048 putatively involved in the response to heavy metals and Tn6050 carrying accessory genes not classically associated with transposons. Syntenic analysis also revealed new transposons carrying metal response genes in Burkholderia xenovorans LB400, and other bacteria. Finally, other putative mobile elements, which were previously unnoticed but apparently common in several bacteria, were also revealed. This was the case for triads of tyrosine-based site-specific recombinases and for an int gene paired with a putative repressor and associated with chromate resistance.     

Identification of the MHC class I B locus in cynomolgus monkeys

By determining the nucleotide sequences of more than 700 cDNA clones isolated from 16 cynomolgus monkeys, we identified 26 Mafa-B alleles. In addition, nine sequences with similarity to Mamu-I alleles were identified. Since multiple Mafa-B alleles were found in each individual, it was strongly suggested that the cynomolgus MHC class I B locus might be duplicated and that the Mafa-I locus was derived from the B locus by gene duplication, as in the case of the Mamu-I locus of rhesus monkeys.     

<Emphasis Type="Italic">Astyanax</Emphasis> <Emphasis Type="Italic">bockmanni</Emphasis> Vari and Castro, 2007: an ambiguous karyotype in the <Emphasis Type="Italic">Astyanax</Emphasis> genus

Despite the widespread distribution of Astyanax bockmanni in streams from Upper Paraná River system in central, southeastern, and southern Brazil, just recently, it has been identified as a distinct Astyanax species. Cytogenetic studies were performed in two populations of this species, revealing conservative features. A. bockmanni shows 2n = 50 chromosomes, a karyotypic formula composed of 10 M + 12SM + 12ST + 16A and multiple Ag-NORs. Eight positive signals in subtelocentric/acrocentric chromosomes were identified by fluorescent in situ hybridization (FISH) with 18S rDNA probes. After FISH with 5S rDNA probes, four sites were detected, comprising the interstitial region of a metacentric pair and the terminal region on long arms of another metracentric pair. Little amounts of constitutive heterochromatin were observed, mainly distributed at distal region in two chromosomal pairs. Additionally, heterochromatin was also located close to the centromeres in some chromosomes. No positive signals were detected in the chromosomes of A. bockmanni by FISH with the As-51 satellite DNA probe. The studied species combines a set of characteristics previously identified in two different Astyanax groups. The chromosomal evolution in the genus Astyanax is discussed.     

A classification of subtropical riverine grassland and forest in Chitwan National Park,Nepal

Eight grassland associations with ten phases and two riverine forest associations were identified on the floodplains of Chitwan National Park in lowland Nepal. TwoThemeda arundinacea associations were primarily stable edaphic associations on mollic soils, often with aquic moisture regimes.Themeda associations were floristically similar to adjacent sal forest. Four mixed tall-grass associations primarily ofNarenga porphyrocoma, Saccharum bengalense, andSaccharum spontaneum were identified. These andThemeda arundinacea types were characterized by a very weak component of woody species. Two grass-shrub associations ofSaccharum bengalense andNarenga porphyrocoma with a strong woody species component typical of riverine forest were described.Trewia nudiflora-Bombax ceiba riverine forest and mixed riverine forest types also were identified on the basis of understory composition. Mixed tall-grass and grass-shrub associations appeared to represent early and late phases of grassland succession to riverine forest. Trajectories of succession are controlled primarily by fire and wildlife grazing. The classification refines the general classifications applied to the central Terai of Nepal and India, and should provide insight for classification of other Terai riverine grasslands.Abbreviations DS Dabadghao and Shankarnarayan's 1973 grassland classification for India - IMCY Imperata cylindrica - NAFA Narenga fallax - NAPO Narenga porphyrocoma - PHKA Phragmites karka - SABE Saccharum bengalense - SASP Saccharum spontaneum - THAR Themeda arundinacea     

Phylogenetic relationships among species and genera of Lycoperdaceae based on ITS and LSU sequence data from north European taxa

Phylogenetic relationships, limits of species, and genera within Lycoperdaceae, were inferred by use of ITS and LSU nu-rDNA sequence data. Lycoperdaceae was confirmed as monophyletic, and Mycenastrum corium as a sister taxon to the ingroup. Four major clades were identified and received weak to moderate support and correspond with the genera Lycoperdon, Bovista, Calvatia, and Disciseda. The Lycoperdon clade includes species from Lycoperdon, Vascellum, Morganella, Handkea, Bovistella, and Calvatia. The structure within the Lycoperdon clade is unresolved and several clades are more or less unsupported, which suggests treating the supported Lycoperdon clade as the genus Lycoperdon. L. nigrescens and L. caudatum occur on single branches and their phylogenetic positions could not be resolved. The phylogenetic analyses identified 31 species of Lycoperdon, 11 species of Bovista, six species of Calvatia, and two species of Disciseda. In Lycoperdon three new species were recognized. A new species closely related to B. limosa is identified and discussed. A classification of Lycoperdaceae is proposed based on the results of the phylogenetic analyses. Morphological characters of species within and among identified clades are discussed.     

马齿苋内生菌橘青霉和波兰青霉中抗青枯菌的活性物质

为了挖掘农作物病害生物防治新资源,以药用植物马齿苋(Portulaca oleracea)为材料,通过培养基种植法分离和纯化其根、茎、叶中的内生菌,以青枯菌(Ralstonia solanacearum)的抑菌试验评价其活性,采用菌落形态观察和ITS序列分析鉴定菌种。结果表明,从马齿苋筛选出2种具有抑制青枯菌的内生菌橘青霉(Penicillium citrinum)和波兰青霉(P. polonicum),采用液相与四极杆飞行时间串联质谱(UPLC-QTOF-MS)鉴定2种内生菌的主要活性物质为橘霉素,其对青枯菌的抑制效果比链霉素更好。因此,这为植物青枯病的生物防治提供科学依据。     

An analysis of flavonoid compounds in leaves of Japonolirion (Petrosaviaceae)

Japonolirion, comprising Japonolirion osense Nakai, which occurs on serpentinite at two widely separated localities in Japan, has been considered as an isolated taxon, but more recently has been proved by molecular evidence to be a sister group to an achlorophyllous, mycoheterotrophic genus, Petrosavia. In an effort to research possible characters linking these groups, we analyzed the flavonoid compounds obtained from leaves of Japonolirion using UV spectra, mass spectrometry and ¹H and ¹³C nuclear magnetic resonance, and acid hydrolysis of the original glycosides as well as direct thin layer chromatography and high performance liquid chromatography comparisons with authentic specimens. As a result, we identified seven flavonoids, of which two were major components identified as 6-C-glucosylquercetin 3-O-glucoside and isoorientin. The remaining five were minor components identified as 6-C-glucosylkaempferol 3-O-glucoside, quercetin 3-O-glucoside, quercetin 3-O-arabinoside, vicenin-2 and orientin. Both 6-C-glucosylquercetin 3-O-glucoside and 6-C-glucosylkaempferol 3-O-glucoside were recorded for the first time in nature. Because of their restricted occurrence in angiosperms, both C-glycosylflavonols and 3-O-glycosides of C-glycosylflavonols may be significant chemical markers for assessing relationships of J. osense.     

Proteomic evaluation of gymnosperm pollination drop proteins indicates highly conserved and complex biological functions

The pollination droplet is a highly conservative pollination mechanism that is observed in all major gymnosperm taxa. Proteomics analysis of the pollination drops was carried out on four gymnosperm species: Juniperus communis (common juniper), Juniperus oxycedrus (prickly juniper), Chamaecyparis lawsoniana (Port Orford cedar), and Welwitschia mirabilis. Pollination drop proteins were purified by SDS-PAGE, and the most abundant proteins were analyzed by mass spectrometry and sequenced. Based on BLAST searching of combined amino acid sequences, the following proteins were identified in the following species: an 83-kDa subtilisin-like proteinase, a 62-kDa glycosyl hydrolase, a 47.5-kDa glucan 1,3-β-glucosidase precursor, a 30-kDa chitinase, and a 25-kDa thaumatin-like protein were identified in J. communis; a 30-kDa chitinase, a 25-kDa thaumatin-like protein, and a 32.5-kDa glucanase-like protein were identified in J. oxycedrus; an 83-kDa subtilisin-like proteinase, a 62-kDa β-d-glucan exohydrolase, a 47.5-kDa glucan 1,3-β-glucosidase, and two 25-kDa thaumatin-like proteins were identified in C. lawsoniana, and a 25-kDa chitinase was identified in W. mirabilis. Based on protein identifications, there is strong evidence that the pollination drop functions in both pathogen defense and pollen development. The discovery of similarities in terms of peptide sequence and protein identifications indicates that ovular secretions are functionally conservative, and that they are essential to reproductive success.     

Relationships ofLomatium among other genera ofApiaceae

Lomatium is the largest North American genus ofApiaceae (=Umbelliferae). Relations amongLomatium and other genera have not been well understood. TheApiaceae-Araliaceae lineage and genera of North AmericanApiaceae were analyzed phenetically and cladistically in turn, and seven phenetic alliances of genera are identified. Data on frequencies of character-state combinations were assembled and usingSporne's notions of maximal and minimal co-variation of states, two character-states were identified that are derived among Umbellifer genera. Using cladistic analysis of the alliance consisting ofLomatium and six other genera we identified three sister groups toLomatium:Polytaenia alone;Polytaenia withPseudocymopterus, and a group of four genera. Not all genera in the group of seven withLomatium are supported by autapomorphies impeding phylogenetic reconstructions. Both phenetics and cladistics have helped to suggest and evaluate relationships; to call attention to groups requiring further study, and in particular to identify derived character-states.     

Sexual forms of yeasts in clinical samples

The sexual or teleomorphic state of yeasts has only been described in a few clinically involved species, mainly those of the Saccharomycetaceae family. With the aim of gathering information on their incidence in human pathology, a study has been made of a total of 2,135 strains isolated from clinical samples and cultivated in McClary agar. From these, 8 strains in teleomorphic state were identified: Kluyveromyces marxianus [1], Pichia anomala [2], Pichia farinosa [1], Pichia membranaefaciens [1] and Saccharomyces cerevisiae [3]. The two strains of P. anomala were responsible for fungemia; K. marxianus and the two strains of S. cerevisiae produced vaginitis; the other strains were oral cavity colonizers.     

Cellulose Decomposition under Nitrogen Deficiency by Bacteria Isolated from the Intestines of Phytophagous Vertebrates

A nitrogen-fixing strain identified as Klebsiella pneumonia 402-2 and two endoglucanase-synthesizing Bacillus strains were isolated from the intestines of phytophagous animals. One of the Bacillus strains was identified as Bacillus subtilis GL. Klebsiella pneumoniae 402-2 increased the endoglucanase activity of both Bacillusstrains in mixed cultures.The data on the taxonomic position of strains 402-2 and GL and on the nitrogen-fixing capacity of strain 402-2 were confirmed by sequencing and analyzing their 16S rRNA genes and by amplifying the nitrogenase gene nifH.     

Rodent Diversity in a Highly Degraded Tropical Landscape: Hong Kong, South China

The diverse ecological roles played by different rodent species mean that the loss of some species and superabundance of others could potentially influence a wide range of ecological processes. Hong Kong (22° N, 114° E), with seven million people in a land area of 1100 km², could be considered a `worst case scenario' for the survival of mammalian diversity. Existing information on rodents in Hong Kong was compiled from previous published and unpublished studies, and additional trapping was conducted at 17 non-urban sites. The rodent fauna of modern Hong Kong consists of eight species of rats and mice (Bandicota indica, Mus caroli, M. musculus, Niviventer fulvescens, Rattus norvegicus, R. rattus, R. tanezumi, R. sikkimensis: Muridae), one porcupine (Hystrix brachyura: Hystricidae), and one recently introduced tree squirrel (Callosciurus erythraeus: Sciuridae). Six of the murids are urban or agricultural commensals, so only the porcupine and two murids, N. fulvescens and R. sikkimensis, are likely survivors of Hong Kong's pre-deforestation native rodent fauna. The two murids co-dominate in forest and shrubland, but can also move through grassland, which has probably enabled their survival through repeated cycles of fragmentation and regrowth. Additional forest rodents that may have inhabited Hong Kong in the past are tentatively identified from information on their recent distributions in the region. One possible ecological consequence of Hong Kong's depleted rodent fauna is a shift in the balance between seed predation and seed dispersal, in favor of the former.     

Isolation and identification ofMicrococcus roseus andPlanococcus sp. from schirmacher oasis,antarctica

Five cultures isolated from soil samples collected in Schirmacher oasis, Antarctica, have been identified as members of the familyMicrococcaceae, with 3 belonging to the genusMicrococcus and two toPlanococcus. The 3Micrococcus isolates (37R, 45R and 49R) were red-pigmented and h a d ∼ 75 mol% G + C in their DNA; they were identified asMicrococcus roseus. The twoPlanococcus isolates (30Y and Lz3OR) were yellow and orange in colour, and had 43.5 and 40.9 mol % G + C in their DNA respectively; they were identified asPlanococcus sp.     

Identity, beer spoiling and biofilm forming potential of yeasts from beer bottling plant associated biofilms

Wild yeasts were isolated from process surfaces of two breweries. In total, 41 strains were obtained and differentiated by cultivation on CuSO₄ or crystal violet containing selective media, by fatty acid profiling and by a restriction analysis of the region spanning the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene. The restriction analysis showed the highest differentiating capacity and resulted in eleven groups. These groups were identified by the API ID 32 C kit or by sequencing the D1/D2 region of the 26S rRNA gene. Most of the wild yeasts were identified as Saccharomyces cerevisiae (46% of all isolates) and Candida pelliculosa (anamorph: Pichia anomala) (24%). No obvious differences were detected between the two breweries. While all of the S. cerevisiae isolates were able to grow in beer, only six out of 10 C. pelliculosa strains were able to tolerate this substrate. However, most of the C. pelliculosa strains showed biofilm formation in a microplate assay, but none of the S. cerevisiae isolates. Therefore, it is assumed that the former species is involved in attachment and primary biofilm formation on beer bottling plants, while S. cerevisiae is a late colonizer of a preformed biofilm but increased the beer spoiling potential of the biofilm.     

Molecular Identification of Aeromonas and Coliform Bacteria Isolated on m Endo Media from Lake Erie Waters

Summary Bacteria from recreational waters collected from two Lake Erie beaches in Dunkirk, New York were plated onto m Endo LES media. The 16S rRNA gene was then amplified from coliform and non-coliform bacteria using the polymerase chain reaction. The PCR products were characterized by restriction fragment length polymorphism (RFLP) analysis. A total of 8 RFLP groups were identified from the analysis of 920 samples and selected PCR products from each group were sequenced. The DNA sequence analysis indicated that more than half of the bacteria identified as coliforms on the m Endo plates belonged to the genus Aeromonas from the family Aeromonadaceae. Most of the remaining coliforms were from the Enterobacteriaceae. The data indicate that m Endo agar plates allow the growth of non-coliform bacteria, especially Aeromonas species.     

A putative disease-associated haplotype within the SCN1A gene in Dravet syndrome

Dravet syndrome (DS), previously known as severe myoclonic epilepsy of infancy, is one of the most severe forms of childhood epilepsy. DS is caused by a mutation in the neuronal voltage-gated sodium-channel alpha-subunit gene (SCN1A). However, 25–30% of patients with DS are negative for the SCN1A mutation screening, suggesting that other molecular mechanisms may account for these disorders. Recently, the first case of DS caused by a mutation in the neuronal voltage-gated sodium-channel beta-subunit gene (SCN1B) was also reported. In this report we aim to make the molecular analysis of the SCN1A and SCN1B genes in two Tunisian patients affected with DS. The SCN1A and SCN1B genes were tested for mutations by direct sequencing. No mutation was revealed in the SCN1A and SCN1B genes by sequencing analyses. On the other hand, 11 known single nucleotide polymorphisms were identified in the SCN1A gene and composed a putative disease-associated haplotype in patients with DS phenotype. One of the two patients with putative disease-associated haplotype in SCN1A had also one known single nucleotide polymorphism in the SCN1B gene. The sequencing analyses of the SCN1A gene revealed the presence of a putative disease-associated haplotype in two patients affected with Dravet syndrome.     

A case of chronic necrotizing pulmonary aspergillosis due toAspergillus nidulans

A 55-year old man without immunosuppression clinically showed a coin lesion in the right lower lung on the chest radiographs.Aspergillus nidulans was isolated and identified in both trans-bronchial lung biopsy specimen and resected tissue. The specimens revealed characteristics of chronic necrotizing pulmonary aspergillosis pathologically. Very few reports on cases of pulmonary aspergillosis due toA. nidulans exist, and we were not able to find any reports of similar cases. This case may be the first reported case of chronic necrotizing pulmonary aspergillosis due toA. nidulans.     

采自吉林省敦化市的2个蘑菇目(Agaricales)新记录种

【背景】在中国吉林省延边朝鲜族自治州敦化市寒葱岭红叶谷进行大型真菌资源调查的过程中发现了2个物种。【目的】确定这2个物种的分类地位。【方法】采集大型真菌标本,对其形态进行详细观察和描述,并提取DNA、测定rDNA ITS序列,基于最大似然法和贝叶斯法构建分子系统发育树。【结果】鉴定结果表明,这2个蘑菇目物种分别是径边刺毛鬼伞(Tulosesus callinus)和拉氏红菇(Russula lakhanpalii),在形态上与原始描述高度吻合,系统发育分析也验证了形态学的鉴定结果。【结论】拉氏红菇(R. lakhanpalii)系中国首次报道,径边刺毛鬼伞(T. callinus)为吉林省新记录种。