Identifying the functional groups and the influence of synthetic chelators on Cd availability and microbial biomass carbon in Cd-contaminated soil

Synthetic chelators play an important role in boosting the microbial biomass carbon (MBC), dissolved organic carbon (DOC), and heavy metal solubility in a contaminated soil toward a sustainability of environment for agricultural crops. Castor plant was grown under different levels of Cd contaminated soil (?Cd and +Cd) following adding three chelating agents, ethylenediaminetetraacetic acid (H₄EDTA), nitriloacetic acid (H₃ NTA), and NH₄ citrate (ammonium citrate) to the soil at rates of 10, 15, and 25 mmol in 5 kg of soil per pot. The highest bioavailable Cd concentrations in soil and castor plant were obtained from NH₄ citrate and H₄EDTA treatments in the contaminated soil. Fourier transform infrared (FTIR) analysis showed that NH₄ citrate was the most effective chelator in Cd-contaminated soil. MBC and DOC contents were significantly increased and reached at 81.98–80.37 and 1.96–1.90 mg kg^?1 respectively, in the (H₃ NTA) and NH₄ citrate treatments in Cd-contaminated soil. Further research is needed to investigate the use of chelators in the phytoextraction of Cd-contaminated soils under field conditions and whether it may be beneficial in accelerating the phytoextraction of Cd through hyperaccumulating plants.     

Sugar beet extract acts as a natural bio-stimulant for physio-biochemical attributes in water stressed wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

The present study investigated the role of sugar beet extract (SBE) as a bio-stimulant to ameliorate the adverse effects of drought on seed germination and growth of wheat (Triticum aestivum L.). Different concentrations of SBE (0, 10, 20, 30, 40 and 50%) were used for priming the wheat seeds. The experiment was conducted in laboratory (PEG-8000 was used to create water stress) as well as under natural environmental conditions (using soil with 100 and 60% field capacity). Significant ameliorating effects of seed priming with SBE were recorded on different germination attributes, i.e., time to 50% emergence (E₅₀), germination index (GI), mean emergence time (MET), germination percentage (G%), coefficient of uniformity of emergence (CUE) and germination energy (GE) under water stress. Without priming, the plants exhibited symptoms of water stress like decreased biomass, reduction in photosynthetic pigments, e.g., chlorophyll, carotenoids. Seed pre-conditioning with SBE improved the plant growth, photosynthetic pigments, antioxidants’ activities and nutrient homeostasis of plants facing water deficit and grown under well-watered conditions. The maximum increase in biomass, content of chlorophyll, carotenoids and activities of superoxide dismutase (SOD) and peroxidase (POD) was 13.4, 8.5, 11.9, 7.6, 13.6, 42.0, 19.8%, respectively, with SBE seed priming under water stress. In conclusion, SBE seed priming effectively reduced the negativities of water stress on seed germination which resulted in better plant growth in terms of enhanced biomass, photosynthetic pigments, antioxidant defense mechanism and better nutrient homeostasis. Overall, the findings suggest that seed pre-conditioning with SBE as a bio-stimulant will be helpful for better crop stand establishment under low field capacity, especially in semi-arid and arid agricultural fields.     

A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA

Salmonella enterica serovar blegdam has a restriction and modification system encoded by genes linked to serB . We have cloned these genes, putative alleles of the hsd locus of Escherichia coli  K-12, and confirmed by the sequence similarities of flanking DNA that the hsd genes of S. enterica serovar blegdam have the same chromosomal location as those of E. coli K-12 and Salmonella enterica serovar typhimurium LT2. There is, however, no obvious similarity in their nucleotide sequences, and while the gene order in S. enterica serovar blegdam is serB hsdM , S and R , that in E. coli K-12 and S. enterica serovar typhimurium LT2 is serB hsdR , M and S . The hsd genes of S. enterica serovar blegdam identify a third family of serB -linked hsd genes (type ID). The polypeptide sequence predicted from the three hsd genes show some similarities (18–50% identity) with the polypeptides of known and putative type I restriction and modification systems; the highest levels of identity are with sequences of Haemophilus influenzae Rd. The HsdM polypeptide has the motifs characteristic of adenine methyltransferases. Comparisons of the HsdR sequence with those for three other families of type I systems and three putative HsdR polypeptides identify two highly conserved regions in addition to the seven proposed DEAD-box motifs.     

Phragmites australis — a helophytic grass — can establish successful partnership with phenol-degrading bacteria in a floating treatment wetland

Helophytic plants contribute significantly in phytoremediation of a variety of pollutants due to their physiological or biochemical mechanisms. Phenol, which is reported to have negative/deleterious effects on plant metabolism at concentrations higher than 500 mg/L, remains hard to be removed from the environmental compartments using conventional phytoremediation procedures. The present study aims to investigate the feasibility of using P. australis (a helophytic grass) in combination with three bacterial strains namely Acinetobacter lwofii ACRH76, Bacillus cereus LORH97, and Pseudomonas sp. LCRH90, in a floating treatment wetland (FTW) for the removal of phenol from contaminated water. The strains were screened based on their phenol degrading and plant growth promoting activities. We found that inoculated bacteria were able to colonize in the roots and shoots of P. australis, suggesting their potential role in the successful removal of phenol from the contaminated water. Pseudomonas sp. LCRH90 dominated the bacterial community structure followed by A. lowfii ACRH76 and B. cereus LORH97. The removal rate was significantly high when compared with the individual partners, i.e., plants and bacteria separately. The plant biomass, which was drastically reduced in the presence of phenol, recovered significantly with the inoculation of bacterial consortia. Likewise, highest reduction in chemical oxygen demand (COD), biochemical oxygen demand (BOD), and total organic carbon (TOC) is achieved when both plants and bacteria were employed. The study, therefore, suggests that P. australis in combination with efficient bacteria can be a suitable choice to FTWs for phenol-degradation in water.     

Investigation of deleterious effects of nsSNPs in the POT1 gene: a structural genomics-based approach to understand the mechanism of cancer development

Protection of telomere 1 (POT1) is one of the key components of shelterin complex, implicated in maintaining the telomere homeostasis, and thus stability of the eukaryotic genome. A large number of non-synonymous single nucleotide polymorphisms (nsSNPs) in the POT1 gene have been reported to cause varieties of human diseases, including cancer. In recent years, a number of mutations in POT1 has been markedly increased, and interpreting the effect of these large numbers of mutations to understand the mechanism of associated diseases seems impossible using experimental approaches. Herein, we employ varieties of computational methods such as PROVEAN, PolyPhen-2, SIFT, PoPMuSiC, SDM2, STRUM, and MAESTRO to identify the effects of 387 nsSNPs on the structure and function of POT1 protein. We have identified about 183 nsSNPs as deleterious and termed them as “high-confidence nsSNPs.” Distribution of these high-confidence nsSNPs demonstrates that the mutation in oligonucleotide binding domain 1 is highly deleterious (one in every three nsSNPs), and high-confidence nsSNPs show a strong correlation with residue conservation. The structure analysis provides a detailed insights into the structural changes occurred in consequence of conserved mutations which lead to the cancer progression. This study, for the first time, offers a newer prospective on the role of POT1 mutations on the structure, function, and their relation to associated diseases.     

Nutrient fluxes via litterfall and leaf litter decomposition vary across a gradient of soil nutrient supply in a lowland tropical rain forest

The extent to which plant communities are determined by resource availability is a central theme in ecosystem science, but patterns of small-scale variation in resource availability are poorly known. Studies of carbon (C) and nutrient cycling provide insights into factors limiting tree growth and forest productivity. To investigate rates of tropical forest litter production and decomposition in relation to nutrient availability and topography in the absence of confounding large-scale variation in climate and altitude we quantified nutrient fluxes via litterfall and leaf litter decomposition within three distinct floristic associations of tropical rain forest growing along a soil fertility gradient at the Sepilok Forest Reserve (SFR), Sabah, Malaysia. The quantity and nutrient content of small litter decreased along a gradient of soil nutrient availability from alluvial forest (most fertile) through sandstone forest to heath forest (least fertile). Temporal variation in litterfall was greatest in the sandstone forest, where the amount of litter was correlated negatively with rainfall in the previous month. Mass loss and N and P release were fastest from alluvial forest litter, and slowest from heath forest litter. All litter types decomposed most rapidly in the alluvial forest. Stand-level N and P use efficiencies (ratios of litter dry mass to nutrient content) were greatest for the heath forest followed by the sandstone ridge, sandstone valley and alluvial forests, respectively. We conclude that nutrient supply limits productivity most in the heath forest and least in the alluvial forest. Nutrient supply limited productivity in sandstone forest, especially on ridge and hill top sites where nutrient limitation may be exacerbated by reduced rates of litter decomposition during dry periods. The fluxes of N and P varied significantly between the different floristic communities at SFR and these differences may contribute to small-scale variation in species composition.     

Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins

The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2‐α_Rα_L (RL nests) or 1,2‐α_Lα_R (LR nests). Many nests form a depression in which an anion or δ‐negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3‐bridging)—which confers a concavity to the nest; one third are of the N2N3 type—which does not. In bridged LR nests N2N3‐bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1β‐bulge loop and an asx‐ or ST‐ motif (N1N3)—remarkably homologous to the N1N3‐bridged Schellman loop—and 3% in a composite structure including a type 2β‐bulge loop and an asx‐motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond. Proteins 2014; 82:3023–3031. © 2014 Wiley Periodicals, Inc.