Complete genome sequence of Saccharomonospora viridis type strain (P101)

Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified among the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer's lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Methanoculleus marisnigri Romesser et al. 1981 type strain JR1

Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.     

Intracameral bevacizumab and mitomycin C Trabeculectomy for eyes with neovascular glaucoma: a case series

The purpose of this study was to describe the surgical outcomes and safety of intracameral bevacizumab during trabeculectomy in eyes with neovascular glaucoma. Pilot study included four eyes (four patients) with refractory neovascular glaucoma submitted to fornix-based trabeculectomy with adjunctive use of bevacizumab in the anterior chamber during the procedure. Patients were previously treated with panretinal photocoagulation as standard therapy. Variables evaluated were intraocular pressure, bleb appearance, iris neovascularization, intraoperative/postoperative complications, and visual outcomes. No intraoperative complication was observed. The mean follow-up period was 12.75 (range, 12–15 months). All eyes showed significant intraocular pressure control postoperatively. Iris neovascularization reduced significantly within 1 month after surgery. Mild anterior chamber inflammation was observed during follow-up in all eyes. No significant postoperative complication was observed, and no patient presented visual acuity deterioration. Intracameral bevacizumab may be used as an adjunctive therapy during trabeculectomy in eyes with neovascular glaucoma.     

Complete genome sequence of Anaerococcus prevotii type strain (PC1)

Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family 'Peptostreptococcaceae'. A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family 'Peptostreptococcaceae' for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Group size and composition of black-and-gold howler monkeys (<Emphasis Type="Italic">Alouatta caraya</Emphasis>) on the Upper Paraná River,Southern Brazil

In social mammals, group size, sex and age-class composition are important parameters that are required to understand population dynamics and determine conservation strategies. These parameters are known only poorly for the black-and-gold howler monkey (Alouatta caraya). Here, we studied groups of A. caraya on islands and adjacent banks of the Upper Paraná River of southern Brazil, to examine variability in group size and composition. This location is important for this species because of the high density of howlers. Group size was large, varying from 6 to 18 individuals (average = 11.5, standard deviation = 3.3, n = 13). Groups were multi-male, and adult females outnumbered adult males. On average, groups had the following ratios: 1 adult male: 0.5 subadult male: 1.9 adult females: 0.9 juveniles: 0.5 infants. The ratio of 0.2 infant: 1 adult female is less than that in other species, but typical of other studies of the black-and-gold howlers. Here, we discuss environmental and social pressures that may impose structure on large groups of howlers in terms of strategies for living in high densities. We also compare these data with those of the area of sympatry shared between A. caraya and A. clamitans, and suggest that competition may occur between the two species and that reduced fitness may be a consequence of mixed groups. Contribution number 1,746 of the Departamento de Zoologia of Universidade Federal do Paraná (UFPR).     

Imperfect Vertical Transmission of the Endophyte <Emphasis Type="Italic">Neotyphodium</Emphasis> in Exotic Grasses in Grasslands of the Flooding Pampa

Cool-season grasses establish symbioses with vertically transmitted Neotyphodium endophytes widespread in nature. The frequency of endophyte-infected plants in closed populations (i.e., without migrations) depends on both the differential fitness between infected and non-infected plants, and the endophyte-transmission efficiency. Most studies have been focused on the first mechanism ignoring the second. Infection frequency and endophyte transmission from vegetative tissues to seeds were surveyed in two grasses growing in vegetation units that differ in flood and grazing regimes, and soil salinity. Transmission efficiency and infection frequency for tall fescue did not vary significantly and were 0.98 and 1.00, respectively. For Italian ryegrass, transmission efficiency and infection frequency were 0.88 and 0.57 in humid prairies, and 0.96 and 0.96 in the other vegetation units. Only in humid mesophytic meadows, the observed pattern was irrespective of the presence or absence of grazers. Our results suggest that selection forces for endophyte infection are different for both species. Imperfect transmission was only compensated in tall fescue through an increased fitness of infected plants. Interpreting variations of infection frequency only in terms of differential fitness can be misleading, considering that endophyte transmission can be imperfect and variable in nature. Therefore, this study highlights the importance of measuring transmission efficiency.     

Aluminum accumulation and its relationship with mineral plant nutrients in 12 pteridophytes from Venezuela

The purpose of this study was to investigate the aluminum (Al) concentration in Lycopodium clavatum, Dicranopteris flexuosa, Sticherus nudus, Anemia villosa, Cyathea gibbosa, Pteridium arachnoideum, Pteris vittata, Thelypteris dentata, Blechnum occidentale, Elaphoglossum sporadolepis, Nephrolepis cordifolia and Polypodium pseudoaureum, species from 11 families with different phylogenetic position, found on soils with a high concentration of Al (up to 13 g kg^?1 dry mass (DM)). When Al concentration and mineral nutrients in aerial organs were considered, pteridophytes were classified into three groups: group one included pteridophytes with Al concentrations over 1000 mg kg^?1 DM in their aerial organs, a ratio between Al and essential plant nutrients such as Ca, Mg and P higher than one and a K/Al ratio between 0.68 and 2.56 mol mol^?1. In group 1 was the well known Al-accumulator L. clavatum (Lycophyte) as well as the Neotropical ferns D. flexuosa, S. nudus (both basal leptosporangiate ferns), and C. gibbosa (core leptosporangiate tree fern). Group 2, ferns which accumulate Al over 1000 mg kg^?1 DM in their fronds, and had an Al/Ca and Al/Mg ratio <1. Species in this group included E. sporadolepis and N. cordifolia (derived polypod ferns). Group 3, ferns classified as Al-excluders, showing Al concentration <782 mg kg^?1 DM in the fronds, had Al/Ca and Al/Mg ratios <1, Al/P ratio ≤1 and a K/Al ratio between 18.10 and 80.36 mol mol^?1. In group 3, were A. villosa (basal leptosporangiate fern) and the derived polypod ferns P. arachnoideum, P. vittata, T. dentata, B. occidentale and P. pseudoaureum. The translocation factor of Al from subterranean to aerial organs was up to 4 in S. nudus, and subterranean organs from E. sporadolepis showed the highest concentration of Al (12 g kg^?1 DM). We coincide with early literature in that other criteria in addition to the Al concentration should be considered to define the Al accumulation, such as its relationship with macronutrients. For example, we propose the inclusion of K/Al ratio. We conclude that out of six Al-excluders five belonged to the derived polypods while two species from Polypodiales showed high Al concentrations. We reconfirm accumulation of Al in L. clavatum and C. gibbosa and discover two new Al-accumulating species in the more ancient ferns: S. nudus and D. flexuosa.     

Genetic Diversity and Multihost Pathogenicity of Clinical and Environmental Strains of Burkholderia cenocepacia

A collection of 54 clinical and agricultural isolates of Burkholderia cenocepacia was analyzed for genetic relatedness by using multilocus sequence typing (MLST), pathogenicity by using onion and nematode infection models, antifungal activity, and the distribution of three marker genes associated with virulence. The majority of clinical isolates were obtained from cystic fibrosis (CF) patients in Michigan, and the agricultural isolates were predominantly from Michigan onion fields. MLST analysis resolved 23 distinct sequence types (STs), 11 of which were novel. Twenty-six of 27 clinical isolates from Michigan were genotyped as ST-40, previously identified as the Midwest B. cenocepacia lineage. In contrast, the 12 agricultural isolates represented eight STs, including ST-122, that were identical to clinical isolates of the PHDC lineage. In general, pathogenicity to onions and the presence of the pehA endopolygalacturonase gene were detected only in one cluster of related strains consisting of agricultural isolates and the PHDC lineage. Surprisingly, these strains were highly pathogenic in the nematode Caenorhabditis elegans infection model, killing nematodes faster than the CF pathogen Pseudomonas aeruginosa PA14 on slow-kill medium. The other strains displayed a wide range of pathogenicity to C. elegans, notably the Midwest clonal lineage which displayed high, moderate, and low virulence. Most strains displayed moderate antifungal activity, although strains with high and low activities were also detected. We conclude that pathogenicity to multiple hosts may be a key factor contributing to the potential of B. cenocepacia to opportunistically infect humans both by increasing the prevalence of the organism in the environment, thereby increasing exposure to vulnerable hosts, and by the selection of virulence factors that function in multiple hosts.The betaproteobacterium Burkholderia cenocepacia, 1 of now 17 classified species belonging to the Burkholderia cepacia complex (BCC), is ubiquitous and extremely versatile in its metabolic capabilities and interactions with other organisms (38, 40, 57, 58). Strains of B. cenocepacia are pathogens of onion and banana plants, opportunistic pathogens of humans, symbionts of numerous plant rhizospheres, contaminants of pharmaceutical and industrial products, and inhabitants of soil and surface waters (14, 29, 33, 34, 37, 45). Originally described as a pathogen of onions (8), organisms of the BCC emerged in the past 3 decades as serious human pathogens, capable of causing devastating chronic lung infections in persons with cystic fibrosis (CF) or chronic granulomatous disease (21, 24, 28). Infections due to BCC are a serious concern to CF patients due to their inherent antibiotic resistance and high potential for patient-to-patient transmission (23). Although 16 of the BCC species have been recovered from respiratory secretions of CF patients in many countries (46, 58), B. cenocepacia has been the most common species isolated in North America, detected in 50% of 606, 83% of 447, and 45.6% of 1,218 patients in recent studies (35, 46, 52).The epidemiology of infectious disease caused by B. cenocepacia appears to involve patient-to-patient spread of genetically distinct lineages. B. cenocepacia lineages, such as ET12, Midwest, and PHDC, have been identified from large numbers of individuals in disease outbreaks in North America and Europe (11, 32, 54). A recently developed multilocus sequence typing (MLST) scheme has been shown to be a reliable epidemiologic tool for differentiating between the five subgroups (IIIA to IIIE) of B. cenocepacia, and strains representing three of these subgroups (IIIA, IIIB, and IIID) have been recovered from CF patients (2). Outside of the patient-to-patient transmission of clonal lineages, the mode of acquisition of strains causing sporadic cases of B. cenocepacia in CF patients remains unclear, although environmental sources are a logical reservoir for infection. Previously, an isolate of B. cenocepacia indistinguishable from the PHDC epidemic clonal lineage by using standard typing methods (e.g., repetitive-sequence-based PCR, randomly amplified polymorphic DNA, pulsed-field gel electrophoresis) was detected in an agricultural soil sample (34). Similarly, three distinct MLST sequence types containing both clinical and environmental (plant and soil) B. cenocepacia isolates were identified (1). These findings suggest that natural populations of B. cenocepacia in soil or associated with plants are a potential reservoir for the emergence of new human pathogenic lineages.Experimental models for the study of virulence potential and traits of B. cenocepacia include mouse and rat models with genetic defects allowing chronic lung infections to be established (e.g., see reference 48). Nematode (Caenorhabditis elegans), alfalfa (Medicago sativa), and onion (Allium cepa) models have also been routinely utilized for the identification of virulence factors (5, 29, 31). C. elegans has been extensively used to study the pathogenesis and virulence factors of a wide variety of bacterial and fungal pathogens (9, 15, 42, 51, 56). In several pathogens, including Pseudomonas (56) and Burkholderia (20), putative virulence factors important for the pathogenesis in mammalian systems (15, 51) have been identified using the C. elegans model. The C. elegans model might be limited in the detection of host-specific virulence factors; however, several attributes, such as small size and rapid development, make it an excellent whole animal model for pathogenesis research (16, 51).The evidence that individual strains of B. cenocepacia can be pathogenic to both plants and humans and are prevalent in various environmental niches has provoked particular interest in elucidating the clinical pathogenic potential of environmental isolates. The basis of this study was to examine whether genetically related B. cenocepacia strains exhibit shared characteristics that contribute to their pathogenicity in multiple hosts and to examine the potential for circulating environmental isolates to emerge as new clinical pathogens. Here, we tested the degree of virulence in animal (nematode) and plant (onion) infection models, the production of antifungal activity, and the genetic relatedness of clinical and environmental B. cenocepacia subgroup IIIB strains predominantly isolated from Michigan.     

Predation potential and biology of Protogamasellopsis posnaniensis Wisniewski & Hirschmann (Acari: Rhodacaridae)

Rhodacaridae are cosmopolitan mites mentioned as predators, although nothing is known about their potential as biological control agents. One of the objectives of the work reported in this paper was to evaluate the potential of Protogamasellopsis posnaniensis (Acari: Rhodacaridae) as predator of representative species of insects of the families Sciaridae (Bradysia matogrossensis (Lane)) and Thripidae (Frankliniella occidentalis (Pergande)), of mites of the family Acaridae (Tyrophagus putrescentiae (Schrank) and Rhizoglyphus echinopus (Fumouze & Robin) and of nematodes of the family Rhabditidae (Protorhabditis sp.). Another objective was to determine the biological cycle of P. posnaniensis when fed the prey on which it performed best in the preceding predation test. The study was conducted in a laboratory where the experimental units were maintained at 25 ± 1 °C, 97 ± 3% RH and in the dark. Although the predator was able to kill all prey species considered in this study, the most favorable prey were T. putrescentiae, F. occidentalis and Protorhabditis sp. Survivorship of the predator in predation tests was always 98% or higher. Life table biological parameters when the predator was fed T. putrescentiae were: R_o = 109.29; T = 19.06 days; λ = 1.28 e r_m = 0.32 female/female/day. Despite preying upon larvae of B. matogrossensis, eggs of the former can also be killed by the latter. The results indicated that P. posnaniensis is a promising biological control agent, deserving additional studies on its possible use for the control of soil pests.