Characterisation of a novel Emaravirus identified in mosaic-diseased Eurasian aspen (Populus tremula)

Since Emaraviruses have been discovered in 2007 several new species were detected in a range of host plants. Five genome segments of a novel Emaravirus from mosaic-diseased Eurasian aspen (Populus tremula) have been completely determined. The monocistronic, segmented ssRNA genome of the virus shows a genome organisation typical for Emaraviruses encoding the viral RNA-dependent RNA polymerase (RdRP, 268.2 kDa) on RNA1 (7.1 kb), a glycoprotein precursor (GPP, 73.5 kDa) on RNA2 (2.3 kb), the viral nucleocapsid protein (N, 35.6 kDa) on RNA3 (1.6 kb), and a putative movement protein (MP, 41.0 kDa) on RNA4 (1.6 kb). The fifth identified genome segment (RNA5, 1.3 kb) encodes a protein of unknown function (P28, 28.1 kDa). We discovered that it is distantly related to proteins encoded by Emaraviruses, such as P4 of European mountain ash ringspot-associated virus. All proteins from this group contain a central hydrophobic region with a conserved secondary structure and a hydrophobic amino acid stretch, bordered by two highly conserved positions, thus clearly representing a new group of homologues of Emaraviruses. The virus identified in Eurasian aspen is closely associated with observed leaf symptoms, such as mottle, yellow blotching, variegation and chloroses along veins. All five viral RNAs were regularly detectable by RT-PCR in mosaic-diseased P. tremula in Norway, Finland and Sweden (Fennoscandia). Observed symptoms and testing of mosaic-diseased Eurasian aspen by virus-specific RT-PCR targeting RNA3 and RNA4 confirmed a wide geographic distribution of the virus in Fennoscandia. We could demonstrate that the mosaic-disease is graft-transmissible and confirmed that the virus is the causal agent by detection in symptomatic, graft-inoculated seedlings used as rootstocks as well as in the virus-infected scions used for graft-inoculation. Owing to these characteristics, the virus represents a novel species within the genus Emaravirus and was tentatively denominated aspen mosaic-associated virus.     

Evaluation of phylogenetic relationship between three phenotypically different forms of Red date palm weevil Rhynchophorus ferrugineus Oliv. using PCR-based RAPD technique

Abstract

Red date palm weevil Rhynchophorus ferrugineus Oliv. is a widespread major pest of date palm in the Kingdom of Saudi Arabia. Three different forms (black and brown with and without spots on thoracic region) were investigated using PCR-based RAPD technique. Although weevils were collected from the same geographical region of Al-Hassa in Saudi Arabia, the banding profile acquired suggested that black and brown colored morphs are genetically closer compared to the brown with spots. Intra color variation remained minimum in black but brown and brown spotted morphs exhibited more genetic variation. This genetic variation may be either due to the generation of new mutants from the non-spotted or spotted weevil or they may belong to a different race.     

ParA encoded on chromosome II of Deinococcus radiodurans binds to nucleoid and inhibits cell division in Escherichia coli

Bacterial genome segregation and cell division has been studied mostly in bacteria harbouring single circular chromosome and low-copy plasmids. Deinococcus radiodurans, a radiation-resistant bacterium, harbours multipartite genome system. Chromosome I encodes majority of the functions required for normal growth while other replicons encode mostly the proteins involved in secondary functions. Here, we report the characterization of putative P-loop ATPase (ParA2) encoded on chromosome II of D. radiodurans. Recombinant ParA2 was found to be a DNA-binding ATPase. E. coli cells expressing ParA2 showed cell division inhibition and mislocalization of FtsZ-YFP and those expressing ParA2-CFP showed multiple CFP foci formation on the nucleoid. Although, in trans expression of ParA2 failed to complement SlmA loss per se, it could induce unequal cell division in slmAminCDE double mutant. These results suggested that ParA2 is a nucleoid-binding protein, which could inhibits cell division in E. coli by affecting the correct localization of FtsZ and thereby cytokinesis. Helping slmAminCDE mutant to produce minicells, a phenotype associated with mutations in the ‘Min’ proteins, further indicated the possibility of ParA2 regulating cell division by bringing nucleoid compaction at the vicinity of septum growth.     

Liebenberg syndrome is caused by a deletion upstream to the PITX1 gene resulting in transformation of the upper limbs to reflect lower limb characteristics

Liebenberg syndrome (MIM 186550) is a very rare autosomal dominant condition characterized by three main features: dysplasia of all of the bony components of the elbow joint, abnormalities in the shape of carpal bones, and brachydactyly. In this paper, we report a Saudi Arabian family with Liebenberg syndrome. Comparative genomic hybridization (CGH) revealed a 275-kb deletion within the cytogenetic band 5q31.1 which contains the H2AFY gene and 190,428 bp of its downstream region. The deleted region is upstream to the PITX1 gene. The radiological features in the upper limbs of all affected members of the family were almost identical to the phenotype in the mouse model with ectopic expression of Pitx1 in the forelimbs. We therefore re-define the phenotype of Liebenberg syndrome as a transformation of the upper limbs to reflect lower limb characteristics and speculate that the area of deletion contains a regulatory sequence that suppresses the expression of PITX1 in the upper limb buds.     

Microbial maceration and carbonate dissolution on cold‐temperate shelves

Nummulites beaumonti d'Archiac & Haime, 1853, originally described from El Basatin, Gebel Mokattam, Greater Cairo, is redefined from a nummulitic bank at the base of the Maadi Formation from its type locality as neotype. Schaub (1981) described the species from Libya and the type example of this species is still unknown. N. discorbinus Schlotheim (1820) is described as neotype from a nummulitic bank in the Mokattam Formation, which is located in the site of the Citadel tombs, near the Salah El Din Citadel, Gebel Mokattam, Egypt. According to Schaub (1981), the type example of this species is also unknown. For this reason the establishment of the neotypes of these two widespread nummulites species: N. discorbinus (Late Lutetian) and N. beaumonti (Bartonian) is important and tackled in this paper. N. qurnensis n. sp. ( = N. sp. cf. beaumonti in Boukhary et al. 2002) is introduced as a new species from the lower Bartonian part of the Qurn Formation of Helwan. Biometrical studies are carried out on the three species to present up to date information on these Nummulites, with particular attention to their biostratigraphic correlation with the Shallow Benthic Zones (SBZ) of Serra-Kiel et al. 1998. The authors would like to stress the importance of a careful designation of a neotype to avoid the introduction of complicated and unnecessary taxonomic problems.     

Short-term succession of marine microbial fouling communities and the identification of primary and secondary colonizers

Microbial succession during the initial stages of marine biofouling has been rarely studied, especially in the Arabian Gulf. This study was undertaken to follow temporal shifts in biofouling communities in order to identify primary and secondary colonizers. Quantitative analysis revealed a significant increase in total biomass, coverage of macrofoulers, chlorophyll a concentrations, and bacterial counts with time. The relative abundance of the adnate diatoms increased with time, whereas it decreased in the case of the plocon diatoms. Non-metric multidimensional scaling (NMDS) ordination based on MiSeq data placed the bacterial communities in three distinct clusters, depending on the time of sampling. While the relative abundance of Alphaproteobacteria and Flavobacteriia decreased with time, suggesting their role as primary colonizers, the relative abundance of Actinobacteria and Planctomycetia increased with time, suggesting their role as secondary colonizers. Biofouling is a dynamic process that involves temporal quantitative and qualitative shifts in the micro- and macrofouling communities.     

Promoter Analysis for Three Types of EUL-Related Rice Lectins in Transgenic Arabidopsis

In this study, the promoter activity for three types of Euonymus-related lectins (EUL) from rice, further referred to as OrysaEULS2, OrysaEULS3, and OrysaEULD1A was analyzed. In silico promoter analyses showed that the EUL promoters from rice contain next to the typical promoter elements some motifs that are considered to be stress-responsive elements. Furthermore, Arabidopsis thaliana plants were transformed with a promoter::β-glucuronidase (GUS) construct for each of the proteins under study. Subsequently, one-insertion homozygous lines were selected and analyzed for GUS activity. Experiments were performed under normal growth conditions or after application of different stress conditions, in particular treatments with 150 mM NaCl, 100 mM mannitol, and 100 μM abscisic acid (ABA) for 24 h. GUS activity was detected with the OrysaEULS3 and OrysaEULD1A promoters especially in the cotyledons and the young true leaves, respectively, but not with the OrysaEULS2 promoter. The activity of OrysaEULS3 and OrysaEULD1A promoters was increased after ABA and mannitol treatments but decreased after NaCl treatment. We hypothesize that the Euonymus-related rice proteins have a role in sensing and responding to external stresses as well as in the growth of the plant.     

Altitudinal segregation between Ural Owl Strix uralensis and Tawny Owl S. aluco: evidence for competitive exclusion in raptorial birds

Capsule The Owls were significantly segregated in space with the most important factor being altitude.

Aims To establish if the segregation between Ural and Tawny Owl on the level of habitat selection is due to different habitat requirements of the species or a consequence of competitive exclusion.

Methods Seven variables were recorded for habitat of Ural Owls, Tawny Owls that live in sympatry with Ural Owls and Tawny Owls that live in allopatry with Ural Owls. Data were gathered in five mountain areas covered with similar continuous montane forest inside and outside known Ural Owl distribution in Slovenia. Owl territories were surveyed in 2001 using playback method. Evidence for segregation was searched for using discriminant function analysis.

Results The altitudinal distribution of Tawny Owls sympatric to Ural Owls was restricted to low elevations with Ural Owls at high elevations. Where Ural Owls were absent, Tawny Owls widened the altitudinal part of their ecological niche to the mountaintop.

Conclusion Segregation between Tawny and Ural Owls is due to competitive exclusion, with the less competitive Tawny Owl being out-competed by the superior Ural Owl. The forests at foothills are influenced by human presence and therefore avoided by Ural Owls. In areas where both species live in sympatry, these areas act as refugia for Tawny Owls.     

Microbial analysis of cucumbers (Cucumis sativus) produced with tap or treated waste water

There is increasing evidence for a significant role of fruits and vegetables in infectious diseases in humans. Their consumption is increasing and environmental factors such as water availability are impacting their production. In this study, adding fertiliser to tap water (TW) increased the microbial load above that found in treated waste water (TWW); coliforms were also introduced. Low numbers of Bacillus spp. were recovered from inside some healthy cucumber fruits. No visible differences were observed between cucumber plants irrigated with TWW or TW or cucumbers with and without endophytic Bacillus spp. This is noteworthy when considering the use of TWW for crop irrigation.