Evaluation of agar and agarose gels for studying mechanical impedance in rice roots

Agar and agarose gels were evaluated as systems to mechanically impede roots of rice (Oryza sativa L.). Two-layer gels were used so that seedlings established in a layer of weak gel (0.35% weight/volume) and then grew downwards to encounter a treatment gel of up to 5.0% (w/v). Agarose gels were stronger than agar gels of the same concentration, reaching a maximum penetrometer resistance of 1.2 MPa at a concentration of 5.0%, compared to 0.3 MPa with agar. The 5.0% agar gel stimulated elongation of the seminal axis by 40% in seedlings of variety TN1 (compared with elongation in the 0.2% gel), but decreased it by 15% in the variety Lac 23. Although increasing agarose concentration decreased seminal axis elongation in both varieties, the seminal axis did not reach the lower layer of treatment gel when the concentration of the treatment gel was greater than 2.0%. The decreased root elongation was therefore a non-mechanical inhibition. In experiments conducted using a different batch of agarose, these inhibitory effects were not seen and strong agarose gels stimulated seminal axis elongation. It was concluded that the agar and agarose gel systems studied were unsuitable for studying the effect of mechanical impedance on the elongation of rice roots and that great care should be taken in interpreting the results of experiments using gels as a growth medium. This revised version was published online in June 2006 with corrections to the Cover Date.     

Nitrogen uptake by crops,soil distribution and recovery of urea-N in a sorghum—wheat rotation in different soils under Mediterranean conditions

The N uptake by crops, soil distribution and recovery of 15N labelled urea-N (100 kg N ha-1) were investigated in a sorghum-wheat rotation in two silty clay soils (Foggia and Rieti Casabianca) and one silt loam soil (Rieti Piedifiume) under different mediterranean conditions. Non-exchangeable labelled NH4-N represented an important pool at both Rieti sites with higher values (p<0.05) under sorghum (14.0 and 24.6% of the urea N in the 0-20 cm layer at the end of the cropping season) than wheat whereas it was much less important in the Foggia soil (10.0% in the surface soil under sorghum). This is probably related to the clay minerals composition of the three soils; because vermiculite was present in both Rieti sites but not in the Foggia soil. At harvest from 4.4 to 5.3% of the urea N initially applied was present as microbial biomass N in the surface soil layer with no generally significant differences due to location and type of crops. Both sorghum and wheat N yields were higher in the driest site (Foggia) probably due to better light conditions, higher temperatures and irrigation during summer of the sorghum cropping period. The recovery of plant fertilizer N (about 21% for sorghum and 27% for wheat) and the percentage of N in the plant derived from the fertilizer (NDFF) were the lowest at Rieti-Casabianca probably as the result of the protection of immobilized fertilizer N against microbial mineralization by the swelling clays. The fertilizer N unaccounted for was nil or very low (10.8% at Rieti-Casabianca under wheat and 11.8 and 4.9% at Rieti-Piedifiume under sorghum and wheat, respectively). Urea-N losses occurred when Rieti Piedifiume and Rieti Casabianca soils were kept bare. In this case the urea N unaccounted for ranged from 12 to 56% of the urea N with higher losses in Rieti-Piedifiume than in Rieti-Casabianca. The higher recoveries in the latter soil were probably confirmed by the stabilizing effect of clays on the immobilized urea N. This revised version was published online in July 2006 with corrections to the Cover Date.     

Production of the metastatic phenotype by DNA transfection in a rat mammary model.

A syngeneic, immunocompetent rat mammary model has been employed to investigate the molecular basis of the metastatic phenotype. Transfection of the benign rat mammary epithelial cell line Rama 37 with the gene for p9Ka; a small, rat, calcium-binding protein or DNA from metastatic human cell lines derived from a primary breast carcinoma or a pleural effusion yields transfectants with metastatic capabilities. Transfection of DNA from a benign human mammary cell line, a plasmid containing a cDNA for the human basic fibroblast growth factor (bFGF) gene, or the oncogene EJ-ras-1, fails to yield any transfectants expressing the metastatic phenotype.     

Environmental energy and evolutionary rates in flowering plants

The latitudinal gradient in species richness is a pervasive feature of the living world, but its underlying causes remain unclear. We evaluated the hypothesis that environmental energy drives evolutionary rates and thereby diversification in flowering plants. We estimated energy levels across angiosperm family distributions in terms of evapotranspiration, temperature and UV radiation taken from satellite and climate databases. Using the most comprehensive DNA-based phylogenetic tree for angiosperms to date, analysis of 86 sister-family comparisons shows that molecular evolutionary rates have indeed been faster in high-energy regions, but that this is not an intermediate step between energy and diversity. Energy has strong, but independent effects on both species richness and molecular evolutionary rates.     

Recent diversification rates in North American tiger beetles estimated from a dated mtDNA phylogenetic tree

Species-level phylogenies derived from DNA sequence data provide a tool for estimating diversification rates and how these rates change over time, but to date there have been few empirical studies, particularly on insect groups. We use a densely sampled phylogenetic tree based on mitochondrial DNA to investigate diversification rates in the North American tiger beetles (genus Cicindela). Using node ages estimated from sequence data and calibrated by biogeographical evidence, we estimate an average per-lineage diversification rate of at least 0.22 +/- 0.08 species/Myr over the time interval since the most recent colonization that led to a radiation within the continent. In addition, we find evidence for a weak, recent increase in the net diversification rate. This is more consistent with a late Pleistocene increase in the speciation rate than with a constant rate of background extinction, but the results are sensitive to the dating method and taxon sampling. We discuss practical limitations to phylogenetic studies of diversification rates.     

Phylogenetics and speciation

Species-level phylogenies derived from molecular data provide an indirect record of the speciation events that have led to extant species. This offers enormous potential for investigating the general causes and rates of speciation within clades. To make the most of this potential, we should ideally sample all the species in a higher group, such as a genus, ensure that those species reflect evolutionary entities within the group, and rule out the effects of other processes, such as extinction, as explanations for observed patterns. We discuss recent practical and theoretical advances in this area and outline how future work should benefit from incorporating data from genealogical and phylogeographical scales.     

The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species-level phylogenies

Most aquatic beetles in the family Dytiscidae are tightly associated either with running (lotic) or stagnant (lentic) water bodies. The range size of lotic species is known to be, on average, much smaller than that of lentic species, presumably as a result of differences in dispersal strategies in each habitat type. We explored possible effects of these differences on clade evolution and speciation rates by comparing species-level phylogenies based on cytochrome oxidase I (COI) and 16S rRNA mitochondrial genes for two genera, the lentic Ilybius and the lotic Deronectes. The expectation that species turnover is higher in lotic lineages due to their lower dispersal propensity compared to lentic species was not strongly supported. Deronectes displays a higher frequency of recent splits than Ilybius, consistent with the hypothesis, but the difference was not significant compared to expected patterns under a constant speciation rate null model. Similarly, when the degree of sympatry was plotted against relative node age, more allopatric splits were evident in the lentic Deronectes, suggesting a slower rate of range movement since speciation, but the differences were not significant. We discuss two explanations for our failure to detect differences between the two clades. First, current methods for analysing species-level phylogenies may be sensitive to taxonomic and sampling artefacts. Second, lentic and lotic clades may indeed display similar levels of species turnover despite occupying very different habitats at different spatial scales. More work is needed to investigate the effects of population level processes and spatial scale on macroevolutionary dynamics.     

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system

BackgroundIn the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to antibiotic treatment. One example is Singapore, where MRSA ST239, the dominant clone since molecular profiling of MRSA began in the mid-1980s, has been replaced by ST22 isolates belonging to EMRSA-15, a recently emerged pandemic lineage originating from Europe.ResultsWe investigated the population structure of MRSA in Singaporean hospitals spanning three decades, using whole genome sequencing. Applying Bayesian phylogenetic methods we report that prior to the introduction of ST22, the ST239 MRSA population in Singapore originated from multiple introductions from the surrounding region; it was frequently transferred within the healthcare system resulting in a heterogeneous hospital population. Following the introduction of ST22 around the beginning of the millennium, this clone spread rapidly through Singaporean hospitals, supplanting the endemic ST239 population. Coalescent analysis revealed that although the genetic diversity of ST239 initially decreased as ST22 became more dominant, from 2007 onwards the genetic diversity of ST239 began to increase once more, which was not associated with the emergence of a sub-clone of ST239. Comparative genomic analysis of the accessory genome of the extant ST239 population identified that the Arginine Catabolic Mobile Element arose multiple times, thereby introducing genes associated with enhanced skin colonization into this population.ConclusionsOur results clearly demonstrate that, alongside clinical practice and antibiotic usage, competition between clones also has an important role in driving the evolution of nosocomial pathogen populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0643-z) contains supplementary material, which is available to authorized users.     

Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated globally and is increasingly prevalent in India. Here, we present the complete genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors.

Results

Sequencing using single-molecule real-time technology resulted in the assembly of a single continuous chromosomal sequence, which was error-corrected, annotated and compared to nine draft genome assemblies of ST772-MRSA-V from Australia, Malaysia and India. We discovered numerous and redundant resistance genes associated with mobile genetic elements (MGEs) and known core genome mutations that explain the highly antibiotic resistant phenotype of DAR4145. Staphylococcal toxins and superantigens, including the leukotoxin Panton-Valentinin Leukocidin, were predominantly associated with genomic islands and the phage φ-IND772PVL. Some of these mobile resistance and virulence factors were variably present in other strains of the ST772-MRSA-V lineage.

Conclusions

The genomic characteristics presented here emphasize the contribution of MGEs to the emergence of multidrug-resistant and highly virulent strains of community-associated MRSA. Antibiotic resistance was further augmented by chromosomal mutations and redundancy of resistance genes. The complete genome of DAR4145 provides a valuable resource for future investigations into the global dissemination and phylogeography of ST772-MRSA-V.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1599-9) contains supplementary material, which is available to authorized users.