Taxonomic revision of European Apium L. s.l.: Helosciadium W.D.J.Koch restored

European representatives of Apium sensu lato (Apiaceae), and Apium prostratum and Naufraga balearica, were studied with morphological, fruit anatomical, and palynological methods. Morphometric data were compared with phylogenetic results from previous molecular studies. This confirms that most of the European Apium species belong to a separate group corresponding to the previously named genus Helosciadium. All these species had previously been formally named as Helosciadium species, except for the new combination Helosciadium bermejoi, which is formally described here. Molecular studies place Apium prostratum and Naufraga balearica close to Apium graveolens, the type species of Apium. Our morphometric results show similarities of Naufraga with H. bermejoi, but fruit anatomy distinguishes it both from Helosciadium and from A. graveolens/prostratum. The placement of Cyclospermum leptophyllum in a separate genus is confirmed. Diagnostic keys to the genera and Helosciadium species, and an annotated checklist are given.     

Cryptosporidium apodemi sp. n. and Cryptosporidium ditrichi sp. n. (Apicomplexa: Cryptosporidiidae) in Apodemus spp.

Faecal samples from striped field mice (n = 72) and yellow-necked mice (n = 246) were screened for Cryptosporidium by microscopy and PCR/sequencing. Phylogenetic analysis of small-subunit rRNA, Cryptosporidium oocyst wall protein and actin gene sequences revealed the presence of C. parvum, C. hominis, C. muris and two new species, C. apodemi and C. ditrichi. Oocysts of C. apodemi are smaller than C. ditrichi and both are experimentally infectious for yellow-necked mice but not for common voles. Additionally, infection by C. ditrichi was established in one of three BALB/c mice. The prepatent period was 7–9 and 5–6 days post infection for C. apodemi and C. ditrichi, respectively. The patent period was greater than 30 days for both species. Infection intensity of C. ditrichi ranged from 4000–50,000 oocyst per gram of faeces and developmental stages of C. ditrichi were detected in the jejunum and ileum. In contrast, neither oocysts nor endogenous developmental stages of C. apodemi were detected in faecal or tissue samples, although C. apodemi DNA was detected in contents from the small and large intestine. Morphological, genetic, and biological data support the establishment of C. apodemi and C. ditrichi as a separate species of the genus Cryptosporidium.     

Novelties in the Corticiales: Vuilleminia nilsii sp. nov. and Dendrominia gen. nov. (Basidiomycota)

Vuilleminia nilsii sp. nov. is described based on collections made in Argelès-sur-Mer communal forest, France. It is characterized by a resupinate, smooth, whitish, decorticating basidiocarp, cylindrical cystidia, heavily crystallized matrix, and guttulate, allantoid spores. It can be distinguished from V. coryli by basidiospore size, substrate preferences, abundance of dendrohyphidia, and crystal in the context. Phylogenetic analyses place Vuilleminia ericae, Dendrothele dryina (= V. dryina) and Dendrothele maculata in a distinct, well-defined clade. The new genus Dendrominia is proposed for this clade. The new combinations Dendrominia dryina, D. ericae, and D. maculata are proposed. Dendrothele corticola is regarded as a synonym of D. maculata. A lectotype is selected for V. macrospora. An updated key to the genus Vuilleminia and a key to Dendrominia species are provided.     

Joint Segregation of Biochemical Loci in Salmonidae. II. Linkage Associations from a Hybridized Salvelinus Genome (S. NAMAYCUSHxS. FONTINALIS)

The results of more than 300 pairwise examinations of biochemical loci for joint segregation in brook trout (Salvelinus fontinalis) and in the hybridized genome of lake trout (S. namaycush) x brook trout are summarized. Nineteen loci have been assigned to the following eight linkage groupings on the basis of nonrandom assortment, including cases of both classical linkage and pseudolinkage: ODH with PMI with PGI-3, PGI-2 with SDH, ADA-1 with AGP-2, AAT-(1,2) with AGP-1 with MDH-1, MDH-3 with MDH-4, LDH-3 with LDH-4, IDH-3 with ME-2 and GUS with CPK-1. Pseudolinkage (an excess of nonparental progeny types) was observed only for male testcross parents. The results suggest that this phenomenon involves homeologous chromosome arms as evidenced by the de novo association of presumed duplicate loci in each case. Classical linkage has not been found for the five pairs of duplicate loci examined in Salvelinus, suggesting that not all of the eight metacentrics in the haploid complement involve fusions of homeologous chromosomes. Females consistently showed a greater degree of recombination.     

Parablastocatena tetracerae gen. et sp. nov. and Corynesporella licualae sp. nov. from Hainan, China

Parablastocatena tetracerae gen. et sp. nov. and Corynesporella licualae sp. nov., collected on dead branches of Tetracera asiatica and Licuala fordiana, respectively, in tropical forests of China, are described and illustrated. Parablastocatena tetracerae is the type species for a new monotypic genus in possessing macronematous conidiophores forming distinct synnemata with holoblastic conidiogenesis and euseptate, short-chained conidia ending in a paler brown rostrum, whereas C. licualae is distinguished from described species by the smaller conidia with long appendages. A key to currently accepted species of Corynesporella is provided.     

Morphogenesis of the tail of bacteriophage lambda. III. Morphogenetic pathway.

Precursors of the tail of bacteriophage λ have been detected by measurements of in vitro complementation activities and serum blocking activity in sucrose gradients of lysates defective in tail genes.On the basis of these measurements, a pathway for the assembly of the λ tail is proposed:The morphogenesis of the λ tail starts from the tail fiber (product of gene J) located at the distal end of the tail, and proceeds to the proximal end. Gene J by itself produces a 15 S structure with serum blocking activity but without any detectable in vitro complementation activity, which may be the least advanced precursor of the λ tail or an abortive product. Functions of genes J, I, K, L are required for the formation of a 15 S precursor that has in vitro complementation activities with J⁻, I⁻, K⁻ and L⁻ lysates and serum blocking activity. If the products of genes G and H act on the latter 15 S precursor, a 25 S precursor is made, but this precursor seems either to be in equilibrium with the 15 S precursor or to degrade easily into the 15 S precursor. Gene M has a function of stabilizing the 25 S precursor. After the action of gene M product, the 25 S precursor is ready to serve as a nucleus on which the product of gene V (the major tail protein) assembles. However, gene U product is also necessary at this step for the correct assembly of the major tail protein on the 25 S precursor. Without gene U product the assembly of the major tail protein does not stop at the correct length and a polytail is formed instead of a morphologically normal tail. Finally, gene Z product acts on the morphologically normal tail and makes it a biologically active tail. Without the action of gene Z product, the defective tail binds to a head and forms a phage-like particle which is only very weakly infectious. (The position of gene T in the pathway is not determined, because no sus mutant is available in gene T.)Two abnormal, less efficient pathways are also present in vitro. (1) If gene U product acts on a polytail in an U⁻ lysate, the polytail finally binds to a head and forms a phage particle with an extra long tail which is infectious to a small extent. (2) The function of gene K seems to be bypassed to some extent: K⁻ lysates accumulate particles which sediment as fast as normal phage and which are complemented by other tail⁻ lysates.     

Gilliamella intestini sp. nov., Gilliamella bombicola sp. nov., Gilliamella bombi sp. nov. and Gilliamella mensalis sp. nov.: Four novel Gilliamella species isolated from the bumblebee gut

Spectra of five isolates (LMG 28358^T, LMG 29879^T, LMG 29880^T, LMG 28359^T and R-53705) obtained from gut samples of wild bumblebees of Bombus pascuorum, Bombus lapidarius and Bombus terrestris were grouped into four MALDI-TOF MS clusters. RAPD analysis revealed an identical DNA fingerprint for LMG 28359^T and R-53705 which also grouped in the same MALDI-TOF MS cluster, while different DNA fingerprints were obtained for the other isolates.Comparative 16S rRNA gene sequence analysis of the four different strains identified Gilliamella apicola NCIMB 14804^T as nearest neighbour species. Average nucleotide identity values of draft genome sequences of the four isolates and of G. apicola NCIMB 14804^T were below the 96% threshold value for species delineation and all four strains and G. apicola NCIMB 14804^T were phenotypically distinct. Together, the draft genome sequences and phylogenetic and phenotypic data indicate that the four strains represent four novel Gilliamella species for which we propose the names Gilliamella intestini sp. nov., with LMG 28358^T as the type strain, Gilliamella bombicola sp. nov., with LMG 28359^T as the type strain, Gilliamella bombi sp. nov., with LMG 29879^T as the type strain and Gilliamella mensalis sp. nov., with LMG 29880^T as the type strain.     

Estimation of Fitness Components in DROSOPHILA MELANOGASTER . I. Heterozygote Viability Indices

We examine the assumption of "dominance" with regard to viability of the Cy and Pm marker chromosomes in D. melanogaster . This assumption is often invoked for the extraction of wild-type second chromosomes from natural populations and for the calculation of relative viability indices. Significant genotypic variances for viability are found among both Cy/+_j and Pm/+_i heterozygotes in California and Japanese populations. The magnitude of the Pm/+ _i genotypic variance is substantially less than that of the Cy/+_j heterozygotes (less than one half). Significant reciprocal effects are also found to influence Cy/+_j, Pm/+_i and +_i/+_j viabilities. We conclude that viability indices of heterozygotes based on the Curly method are biased. We suggest that viability indices in the future be expressed relative to the viability of the Cy/Pm genotype (Curly-Plum method) or possibly that of the Pm/+_i genotype (Plum method).     

Fulvifomes hainanensis sp. nov. and F. indicus comb. nov. (Hymenochaetales,Basidiomycota) evidenced by a combination of morphology and phylogeny

Fulvifomes hainanensis sp. nov. is described from tropical China. The new species resembles Fulvifomes rimosus, but differs by uncracked pileal surface, the presence of a black cuticle between tomentum and lower context, and ellipsoid basidiospores. In nuclear large subunit rDNA (nLSU) and internal transcribed spacer (ITS) based phylogenies, F. hainanensis formed a distinct lineage from other sequenced taxa in the Fulvifomes clade. Aurificaria indica, the type of Aurificaria, has typical morphological characters for Fulvifomes, such as lack of setae and production of colored basidiospores. It was transferred to Fulvifomes based on additional evidence from molecular phylogeny, and F. indicus was redescribed according to Chinese collections. Aurificaria, posterior to Fulvifomes, was thus treated as a taxonomic synonym of Fulvifomes, and the concept of Fulvifomes was accordingly emended to include Aurificaria species. Inonotus luteoumbrinus and I. porrectus are similar to F. indicus in morphology, and they were also supported as lineages in the Fulvifomes clade. However, taxonomical adjustments for the two species were not proposed as the specimens yielding their nLSU and ITS sequences were not reexamined in morphology in this study.     

Staphylococcus petrasii sp. nov. including S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov., isolated from human clinical specimens and human ear infections

Thirteen coagulase-negative, oxidase-negative, and novobiocin-susceptible staphylococci were isolated from human clinical specimens. The isolates were differentiated from known staphylococcal species on the basis of 16S rRNA, hsp60, rpoB, dnaJ, tuf, and gap gene sequencing, automated ribotyping, (GTG)₅-PCR fingerprinting, and MALDI-TOF MS analysis. Phylogenetic analysis based on the 16S rRNA gene sequence indicated phylogenetic relatedness of the analyzed strains to Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus devriesei, and Staphylococcus lugdunensis. DNA–DNA hybridization experiments between representative strains CCM 8418^T, CCM 8421^T, and the closest phylogenetic neighbors confirmed that the isolates represent novel Staphylococcus species, for which the name Staphylococcus petrasii sp. nov. is proposed. Genotypic and phenotypic analyses unambiguously split the strains into two closely related subclusters. Based on the results, two novel subspecies S. petrasii subsp. petrasii subsp. nov. and S. petrasii subsp. croceilyticus subsp. nov. are proposed, with type strains CCM 8418^T (=CCUG 62727^T) and CCM 8421^T (=CCUG 62728^T), respectively.     

Burkholderia species in human infections in Mexico: Identification of B. cepacia,B. contaminans,B. multivorans,B. vietnamiensis,B. pseudomallei and a new Burkholderia species

BackgroundBurkholderia sensu stricto is comprised mainly of opportunistic pathogens. This group is widely distributed in the environment but is especially important in clinical settings. In Mexico, few species have been correctly identified among patients, most often B. cepacia is described.Methodology/Principal findingsIn this study, approximately 90 strains identified as B. cepacia with the VITEK2 system were isolated from two medical centers in Mexico City and analyzed by MLSA, BOX-PCR and genome analysis. The initial identification of B. cepacia was confirmed for many strains, but B. contaminans, B. multivorans and B. vietnamiensis were also identified among clinical strains for the first time in hospitals in Mexico. Additionally, the presence of B. pseudomallei was confirmed, and a novel species within the B. cepacia complex was documented. Several strains misidentified as B. cepacia actually belong to the genera Pseudomonas, Stenotrophomonas and Providencia.Conclusions/SignificanceThe presence of different Burkholderia species in Mexico was confirmed. Correct identification of Burkholderia species is important to provide accurate treatment for immunosuppressed patients.     

Copper tolerance in the cuprophyte Haumaniastrum katangense (S. Moore) P.A. Duvign. & Plancke

Cu tolerance and accumulation have been studied in Haumaniastrum katangense, a cuprophyte from Katanga (DR Congo), previously described as a copper hyperaccumulator. Nicotiana plumbaginifolia, a well-known non-tolerant and non-accumulator species, was used as a control. The germination rate of H. katangense was enhanced by copper and fungicide addition, suggesting that fungal pathogens, which restrain germination in normal conditions, are limiting. In hydroponic culture in the Hoagland medium, H. katangense did not grow well, in contrast to N. plumbaginifolia. Better growth was achieved by adding fungicide or higher copper concentrations. The maximal non-effective concentration (NEC) was 12 µM CuSO₄ for H. katangense grown in hydroponics, i.e. 24 times greater than Cu concentration in the Hoagland medium. By comparison, copper concentrations greater than 0.5 µM had a negative effect on the growth of N. plumbaginifolia. EC₅₀ (50% effective concentration) in hydroponics was 40 µM CuSO₄ for H. katangense and 6 µM CuSO₄ for N. plumbaginifolia. EC₁₀₀ (100% effective concentration) was 100 µM CuSO₄ for H. katangense and 15 µM CuSO₄ for N. plumbaginifolia. In soil, growth was also stimulated by Cu addition up to 300 mg kg^-1 CuSO₄. Surplus copper was also required for cultivating H. katangense in sterile conditions, suggesting that Cu excess may be necessary for needs other than pathogen defence. Cu accumulation in the shoot has been measured for N. plumbaginifolia and H. katangense at their respective NEC. Cu allocation in the two species showed a similar response to increasing Cu concentrations, i.e. root/shoot concentration ratio well above 1. In conclusion, H. katangense is highly tolerant to copper and has elevated copper requirement even in the absence of biotic interactions. Its accumulation pattern is typical of an excluder species.     

TRS-based PCR as a potential tool for inter-serovar discrimination of Salmonella Enteritidis,S. Typhimurium,S. Infantis,S. Virchow,S. Hadar,S. Newport and S. Anatum

Salmonella enterica subsp. enterica comprises a number of serovars, many of which pose an epidemiological threat to humans and are a worldwide cause of morbidity and mortality. Most reported food infection outbreaks involve the serovars Salmonella Enteritidis and Salmonella Typhimurium. Rapid identification to determine the primary sources of the bacterial contamination is important to the improvement of public health. In recent years, many DNA-based techniques have been applied to genotype Salmonella. Herein, we report the use of a manual TRS-PCR approach for the differentiation of the Salmonella enterica subspecies enterica serovars in a single-tube assay. One hundred seventy Salmonella strains were examined in this work. These consisted of serovars S. Enteritidis, S. Typhimurium, S. Infantis, S. Virchow, S. Hadar, S. Newport and S. Anatum. Five of the TRS-primers, N₆(GTG)₄, N₆(CAC)₄, N₆(CGG)₄, N₆(CCG)₄ and N₆(CTG)₄, perfectly distinguished the S. Enteritidis and S. Typhimurium serovars, and the N₆(GTG)₄ primer additionally grouped the other five frequently isolated serovars. In our opinion, the TRS-PCR methodology could be recommended for a quick and simple DNA-based test for inter-serovar discrimination of Salmonella strains.     

Detoxification of Benzoxazolinone Allelochemicals from Wheat by Gaeumannomyces graminis var. tritici, G. graminis var. graminis, G. graminis var. avenae, and Fusarium culmorum

The ability of phytopathogenic fungi to overcome the chemical defense barriers of their host plants is of great importance for fungal pathogenicity. We studied the role of cyclic hydroxamic acids and their related benzoxazolinones in plant interactions with pathogenic fungi. We identified species-dependent differences in the abilities of Gaeumannomyces graminis var. tritici, Gaeumannomyces graminis var. graminis, Gaeumannomyces graminis var. avenae, and Fusarium culmorum to detoxify these allelochemicals of gramineous plants. The G. graminis var. graminis isolate degraded benzoxazolin-2(3H)-one (BOA) and 6-methoxy-benzoxazolin-2(3H)-one (MBOA) more efficiently than did G. graminis var. tritici and G. graminis var. avenae. F. culmorum degraded BOA but not MBOA. N-(2-Hydroxyphenyl)-malonamic acid and N-(2-hydroxy-4-methoxyphenyl)-malonamic acid were the primary G. graminis var. graminis and G. graminis var. tritici metabolites of BOA and MBOA, respectively, as well as of the related cyclic hydroxamic acids. 2-Amino-3H-phenoxazin-3-one was identified as an additional G. graminis var. tritici metabolite of BOA. No metabolite accumulation was detected for G. graminis var. avenae and F. culmorum by high-pressure liquid chromatography. The mycelial growth of the pathogenic fungi was inhibited more by BOA and MBOA than by their related fungal metabolites. The tolerance of Gaeumannomyces spp. for benzoxazolinone compounds is correlated with their detoxification ability. The ability of Gaeumannomyces isolates to cause root rot symptoms in wheat (cultivars Rektor and Astron) parallels their potential to degrade wheat allelochemicals to nontoxic compounds.     

Description of three new Alteromonas species Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. isolated from marine environments,and proposal for reclassification of the genus Salinimonas as Alteromonas

In the course of a bioprospective study of marine prokaryotes for cosmetic purposes, four strains, MD_567^T, MD_652^T, MD_674 and PS_109^T, were isolated that 16S rRNA gene affiliation indicated could represent three new species within the family Alteromonadaceae. A thorough phylogenetic, genomic and phenotypic taxonomic study confirmed that the isolates could be classified as three new taxa for which we propose the names Alteromonas antoniana sp. nov., Alteromonas lipotrueae sp. nov. and Alteromonas lipotrueiana sp. nov. In addition, the consistent monophyletic nature of the members of the genera Alteromonas and Salinimonas showed that both taxa should be unified, and therefore we also propose the reclassification of the genus Salinimonas within Alteromonas, as well as new combinations for the species of the former. As the specific epithets profundi and sediminis are already used for Alteromonas species, we created the nomina nova “Alteromonas alteriprofundi” nom. nov. and Alteromonas alterisediminis nom. nov. to accommodate the new names for “Salinimonas profundi” and Salinimonas sediminis. Whole genome comparisons also allowed us to detect the unexpected codification of aromatic hydrocarbon biodegradative compounds, such as benzoate and catechol, whose activity was then demonstrated phenotypically. Finally, the high genomic identity between the type strains of Alteromonas stellipolaris and Alteromonas addita indicated that the latter is a junior heterotypic synonym of Alteromonas stellipolaris.     

Electrotransformation of Lactobacillus delbrueckii subsp. bulgaricus and L. delbrueckii subsp. lactis with Various Plasmids

We describe, for the first time, a detailed electroporation procedure for Lactobacillus delbrueckii. Three L. delbrueckii strains were successfully transformed. Under optimal conditions, the transformation efficiency was 10⁴ transformants per μg of DNA. Using this procedure, we identified several plasmids able to replicate in L. delbrueckii and integrated an integrative vector based on phage integrative elements into the L. delbrueckii subsp. bulgaricus chromosome. These vectors provide a good basis for developing molecular tools for L. delbrueckii and open the field of genetic studies in L. delbrueckii.     

Uridine-cytidine kinase. Kinetic studies and reaction mechanism.

The initial velocity pattern has been determined for uridine-cytidine kinase purified from the murine mast cell neoplasm P815. With either uridine or cytidine as phosphate acceptor, and ATP as phosphate donor, the pattern observed was one of intersecting lines, ruling out a ping-pong reaction mechanism, and suggesting that the reaction probably proceeds by the sequential addition of both substrates to the enzyme to form a ternary complex, followed by the sequential release of the two products. This pattern was obtained whether the reaction was run in 0.01 m potassium phosphate buffer, pH 7.5, or in 0.1 m Tris-HCl, pH 7.2. When analyzed by the Sequen computer program, the data indicated an apparent K_m of the enzyme for uridine of 1.5 × 10^?4m, an apparent K_m for cytidine of 4.5 × 10^?5m, and a K_m for ATP, with uridine or cytidine as phosphate acceptor, of 3.6 × 10^?3m or 2.1 × 10^?3m, respectively. The V was 1.83 μmol phosphorylated/min/mg enzyme protein for the uridine kinase reaction and 0.91 μmol for the cytidine kinase reaction.