Nutrients Can Enhance the Abundance and Expression of Alkane Hydroxylase CYP153 Gene in the Rhizosphere of Ryegrass Planted in Hydrocarbon-Polluted Soil

Plant-bacteria partnership is a promising strategy for the remediation of soil and water polluted with hydrocarbons. However, the limitation of major nutrients (N, P and K) in soil affects the survival and metabolic activity of plant associated bacteria. The objective of this study was to explore the effects of nutrients on survival and metabolic activity of an alkane degrading rhizo-bacterium. Annual ryegrass (Lolium multiflorum) was grown in diesel-contaminated soil and inoculated with an alkane degrading bacterium, Pantoea sp. strain BTRH79, in greenhouse experiments. Two levels of nutrients were applied and plant growth, hydrocarbon removal, and gene abundance and expression were determined after 100 days of sowing of ryegrass. Results obtained from these experiments showed that the bacterial inoculation improved plant growth and hydrocarbon degradation and these were further enhanced by nutrients application. Maximum plant biomass production and hydrocarbon mineralization was observed by the combined use of inoculum and higher level of nutrients. The presence of nutrients in soil enhanced the colonization and metabolic activity of the inoculated bacterium in the rhizosphere. The abundance and expression of CYP153 gene in the rhizosphere of ryegrass was found to be directly associated with the level of applied nutrients. Enhanced hydrocarbon degradation was associated with the population of the inoculum bacterium, the abundance and expression of CYP153 gene in the rhizosphere of ryegrass. It is thus concluded that the combination between vegetation, inoculation with pollutant-degrading bacteria and nutrients amendment was an efficient approach to reduce hydrocarbon contamination.     

Development of a D genome specific marker resource for diploid and hexaploid wheat

Background

Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome.

Results

In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that can be applied for mapping in modern hexaploid wheat. A NimbleGen array containing both gene-based and repeat junction probe sequences derived from Ae. tauschii was developed and used to map the Chinese Spring nullisomic-tetrasomic lines and deletion bin lines of the D genome chromosomes. Based on these mapping data, we have now anchored 5,171 repeat junction probes and 10,892 gene probes, corresponding to 5,070 gene markers, to the delineated deletion bins of the D genome. The order of the gene-based markers within the deletion bins of the Chinese Spring can be inferred based on their positions on the Ae. tauschii genetic map. Analysis of the probe sequences against the Chinese Spring chromosome sequence assembly database facilitated mapping of the NimbleGen probes to the sequence contigs and allowed assignment or ordering of these sequence contigs within the deletion bins. The accumulated length of anchored sequence contigs is about 155 Mb, representing ~ 3.2 % of the D genome. A specific database was developed to allow user to search or BLAST against the probe sequence information and to directly download PCR primers for mapping specific genetic loci.

Conclusions

In bread wheat, aneuploid stocks have been extensively used to assign markers linked with genes/traits to chromosomes, chromosome arms, and their specific bins. Through this study, we added thousands of markers to the existing wheat chromosome bin map, representing a significant step forward in providing a resource to navigate the wheat genome. The database website (http://probes.pw.usda.gov/ATRJM/) provides easy access and efficient utilization of the data. The resources developed herein can aid map-based cloning of traits of interest and the sequencing of the D genome of hexaploid wheat.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1852-2) contains supplementary material, which is available to authorized users.Keyword: Wheat deletion bins, Molecular markers, Repeat junction markers, NimbleGen array, Recombination, Genetic map     

Solvent Effect on the Photolysis of Riboflavin

The kinetics of photolysis of riboflavin (RF) in water (pH 7.0) and in organic solvents (acetonitrile, methanol, ethanol, 1-propanol, 1-butanol, ethyl acetate) has been studied using a multicomponent spectrometric method for the assay of RF and its major photoproducts, formylmethylflavin and lumichrome. The apparent first-order rate constants (k_obs) for the reaction range from 3.19 (ethyl acetate) to 4.61 × 10⁻³ min⁻¹ (water). The values of k_obs have been found to be a linear function of solvent dielectric constant implying the participation of a dipolar intermediate along the reaction pathway. The degradation of this intermediate is promoted by the polarity of the medium. This indicates a greater stabilization of the excited-triplet states of RF with an increase in solvent polarity to facilitate its reduction. The rate constants for the reaction show a linear relation with the solvent acceptor number indicating the degree of solute–solvent interaction in different solvents. It would depend on the electron-donating capacity of RF molecule in organic solvents. The values of k_obs are inversely proportional to the viscosity of the medium as a result of diffusion-controlled processes.KEY WORDS: dielectric constant, kinetics, photolysis, riboflavin, solvent effect, viscosity     

Foraging activity and population estimation of Microtermes mycophagus Desneux (Isoptera: Termitidae: Macrotermitinae) in Multan,Punjab, Pakistan

The knowledge of the seasonal foraging activity and the numbers of foragers in a colony would be helpful for designing effective termite baiting programs. The current study presents the seasonal activity of Microtermes mycophagus Desneux in a tree plantation in Multan, Punjab, Pakistan, using silk cotton tree wood traps during 2011–2013. The population of M. mycophagus was also estimated using the constant removal method. The number of workers in the underground traps showed a seasonal trend with the highest capture rate occurring during summer and the lowest during winter. The peak in the population (1139 workers/trap) was observed in October after the rainy season. Positive and significant correlation was found between the mean air temperature and the numbers of M. mycophagus workers captured. The constant removal population estimates revealed 16 499–40 265 individuals in the colony of M. mycophagus. Our results suggest that for cost–effective management of the termite species, baiting programs should be started immediately after August when rapid increases in activity of M. mycophagus have been recorded.     

Assessment of circulating biochemical markers and antioxidative status in acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) patients

Various circulating biochemical markers are indicators of pathological state in leukemia and its subtypes. Increased oxidative stress and decreased antioxidant factors portray clear image associated with malignancies during subtypes of leukemia. In this research work we investigated the inter-relationship among the subtypes of leukemia with circulating biochemical markers and oxidative stress in the Pakistani population. This research work was conducted on a total number of 70 subjects in which 20 were control participants and 50 were suffering from leukemia and divided into two subtypes (ALL and AML). Various circulating biomarkers were investigated including hematological, hepatic and renal profiles as well as oxidative stress markers, electrolytes and vitamins C and E. Results show that vitamin E was found to be decreased in diseased sub-types (P < 0.05). Malondialdehyde (MDA) levels were very high in disease sub-types (ALL-B = 8.69 ± 1.59; ALL-T = 8.78 ± 0.97; AML = 8.50 ± 1.29) compared to controls (1.22 ± 0.10; P < 0.05) while the levels of antioxidants [superoxide dismutase (SOD), glutathione peroxidase (GPx), reduced glutathione (GSH), catalase (CAT)], platelets, as well as electrolytes (Ca and Mg) were reduced in patients suffering from leukemia (sub-types). Enhanced levels of oxidative stress (MDA) and decreased levels of enzymatic and non-enzymatic antioxidants reflect the pathological state and impaired cell control in patients suffering from leukemia (subtypes) and show a strong correlation with oxidative stress, indicating that patients’ biological systems are under oxidative stress.     

Living roots magnify the response of soil organic carbon decomposition to temperature in temperate grassland

Increasing atmospheric carbon dioxide (CO₂) concentration is both a strong driver of primary productivity and widely believed to be the principal cause of recent increases in global temperature. Soils are the largest store of the world's terrestrial C. Consequently, many investigations have attempted to mechanistically understand how microbial mineralisation of soil organic carbon (SOC) to CO₂ will be affected by projected increases in temperature. Most have attempted this in the absence of plants as the flux of CO₂ from root and rhizomicrobial respiration in intact plant‐soil systems confounds interpretation of measurements. We compared the effect of a small increase in temperature on respiration from soils without recent plant C with the effect on intact grass swards. We found that for 48 weeks, before acclimation occurred, an experimental 3 °C increase in sward temperature gave rise to a 50% increase in below ground respiration (ca. 0.4 kg C m^?2; Q₁₀ = 3.5), whereas mineralisation of older SOC without plants increased with a Q₁₀ of only 1.7 when subject to increases in ambient soil temperature. Subsequent ¹⁴C dating of respired CO₂ indicated that the presence of plants in swards more than doubled the effect of warming on the rate of mineralisation of SOC with an estimated mean C age of ca. 8 years or older relative to incubated soils without recent plant inputs. These results not only illustrate the formidable complexity of mechanisms controlling C fluxes in soils but also suggest that the dual biological and physical effects of CO₂ on primary productivity and global temperature have the potential to synergistically increase the mineralisation of existing soil C.     

Assessment of Hazardous and Essential Elements in a Food Crop Irrigated with Municipal Sewage Water: Risk Appraisal for Public Health

To assess the impact of sewage water on metal accretion in selected diverse varieties of wheat (i.e., Lasani-2008, ARRI-10, Faisalabad-83, Punjab-85, Aas-2010, and Sehar-2006), their seeds were sown in pots containing soil. The results showed that the concentration of heavy metals in grains from the wheat plants supplied with sewage water was considerably higher than the plants supplied with canal irrigation water (control). In canal water irrigated wheat grains the metal concentrations (mg/kg) ranged from 2.20–3.5 for Cu, 12.50–32.4 for Zn, 22.45–35.22 for Mn, 0.05–0.15 for Pb, 0.012–0.029 for Cd, 2.5–5.3 for Ni, 18.16–29.63 for Fe, and 0.90–3.64 for Cr in different wheat varieties, whereas the wheat grains raised from sewage water, had metal concentrations (mg/kg): 3.8–5.30 for Cu, 29.60–40.50 for Zn, 32.9–50.40 for Mn, 1.14–7.50 for Pb, 0.26–0.42 for Cd, 3.90–7.55 for Ni, 32.21–40.35 for Fe, and 2.88–7.84 for Cr. Since these metals bioaccumulate in wheat grains with unremitting use of metal-enriched wastewater, care has to be taken for irrigating wheat plants with household wastewater for a longer time, particularly in those soils where this crop is grown regularly.     

Proteomic Analysis of Mice Fed Methionine and Choline Deficient Diet Reveals Marker Proteins Associated with Steatohepatitis

The mechanisms underlying the progression of simple steatosis to steatohepatitis are yet to be elucidated. To identify the proteins involved in the development of liver tissue inflammation, we performed comparative proteomic analysis of non-alcoholic steatohepatitis (NASH). Mice fed a methionine and choline deficient diet (MCD) developed hepatic steatosis characterized by increased free fatty acid (FFA) and triglyceride levels as well as alpha-SMA. Two-dimensional proteomic analysis revealed that the change from the normal diet to the MCD diet affected the expressions of 50 proteins. The most-pronounced changes were observed in the expression of proteins involved in Met metabolism and oxidative stress, most of which were significantly downregulated in NASH model animals. Peroxiredoxin (Prx) is the most interesting among the modulated proteins identified in this study. In particular, cross-regulated Prx1 and Prx6 are likely to participate in cellular defense against the development of hepatitis. Thus, these Prx isoforms may be a useful new marker for early stage steatohepatitis. Moreover, curcumin treatment results in alleviation of the severity of hepatic inflammation in steatohepatitis. Notably, curcumin administration in MCD-fed mice dramatically reduced CYP2E1 as well as Prx1 expression, while upregulating Prx6 expression. These findings suggest that curcumin may have a protective role against MCD fed-induced oxidative stress.