Analysis of sequence patterns proximal to the stop codons in Oryza sativa

Abstract

A comprehensive analysis of sequence patterns around the stop codons was performed, by using more than 26,000 rice full-length cDNA sequences. Here it is shown that the bias was most outstanding at the position immediately before the stop codons (?1 codon), where the AAC codon was strongly preferred among ANC codons. Compared with other positions, the codon immediately after the stop codons (+1 codon) also displayed an apparent difference, and had a strong consensus for base A at the first, C at the second, and A at the third letters, respectively. Notably, the base biases at the positions directly downstream of the stop codons, such as the +4, +5 and +6 positions, were much stronger than other positions in the 3′-UTR region, suggesting that those base positions might act as an extended stop signal in the process of protein synthesis. Examination of the relationship between sequence pattern and gene expression level, assessed by CAI values and EST counting, revealed a tendency towards bigger base biases for highly expressed genes. It could be inferred that the translation stop signal is possibly involved in many sequence recognition elements other than the stop codons; highly expressed genes should hold strong sequence consensus around the stop codons for efficient translation termination.     

Invasion patterns in riparian habitats: The role of anthropogenic pressure in temperate streams

The riparian flora and the level of invasion in the rivers of the Cantabric watershed in Spain were studied in relation to the ecological status and the anthropogenic pressure. The level of invasion was also analyzed in different riparian habitats: forests, river bars and man-made slopes. For this purpose, 18 sites were sampled and a list of native and alien plant species was made along a 100-m strip at each site. The habitat/s where alien species were found and their abundance per habitat and in the total area were also indicated. Out of 112 alien taxa found, 51 were classified as invasive. Exotic plants native to America were the most common (35%). The level of invasion was significantly higher in the sampling sites subject to high levels of hydrological and morphological disturbances, proxies of the anthropogenic pressure. River bars and man-made slopes supported similar number of alien plant species, higher than forests. We suggest that disturbance in river banks should be minimized as much as possible in order to diminish the risk of invasion.     

Field Evaluation of Willow Under Short Rotation Coppice for Phytomanagement of Metal-Polluted Agricultural Soils

Short rotation coppice (SRC) of willow and poplar might be a promising phytoremediation option since it uses fast growing, high biomass producing tree species with often a sufficient metal uptake. This study evaluates growth, metal uptake and extraction potentials of eight willow clones (Belders, Belgisch Rood, Christina, Inger, Jorr, Loden, Tora and Zwarte Driebast) on a metal-contaminated agricultural soil, with total cadmium (Cd) and zinc (Zn) concentrations of 6.5 ± 0.8 and 377 ± 69 mg kg^?1 soil, respectively. Although, during the first cycle, on average generally low productivity levels (3.7 ton DM (dry matter) ha^?1 y^?1) were obtained on this sandy soil, certain clones exhibited quite acceptable productivity levels (e.g. Zwarte Driebast 12.5 ton DM ha^?1 y^?1). Even at low biomass productivity levels, SRC of willow showed promising removal potentials of 72 g Cd and 2.0 kg Zn ha^?1 y^?1, which is much higher than e.g. energy maize or rapeseed grown on the same soil. Cd and Zn removal can be increased by 40% if leaves are harvested as well. Nevertheless, nowadays the wood price remains the most critical factor in order to implement SRC as an acceptable, economically feasible alternative crop on metal-contaminated agricultural soils.     

Evolution of 1, 3, 5-trisubstituted bipyrazole scaffold based platinum(II) complexes as a biological active agent

Abstract

Square planar mononuclear platinum(II) complexes having general formula [Pt(Lⁿ)Cl₂], (where, Lⁿ?=?L^1–4) were synthesized with neutral bidentate heterocyclic 1,3,5-trisubstituted bipyrazole based ligands. The synthesized compounds were characterized by physicochemical method such as TGA, molar conductance, micro-elemental analysis and magnetic moment, and spectroscopic method such as, FT-IR, UV–vis, ¹H NMR, ¹³C NMR and mass spectrometry. Biological applications of the compounds were carried out using in vitro brine shrimp lethality bioassay, in vitro antimicrobial study against five different pathogens, and cellular level cytotoxicity against Schizosaccharomyces pombe (S. Pombe) cells. Pt(II) complexes were tested for DNA interaction activities using electronic absorption titration, viscosity measurements study, fluorescence quenching technique and molecular docking assay. Binding constants (K_b) of ligands and complexes were observed in the range of 0.23–1.07?×?10⁵?M^?1 and 0.51–3.13?×?10⁵?M^?1, respectively. Pt(II) complexes (I–IV) display an excellent binding tendency to biomolecule (DNA) and possess comparatively high binding constant (K_b) values than the ligands. The DNA binding study indicate partial intercalative mode of binding in complex-DNA. The gel electrophoresis activity was carried out to examine DNA nuclease property of pUC19 plasmid DNA.     

Sowing different mixtures in dry acidic grassland produced priority effects of varying strength

Several longer-term assembly studies on ex-arable land have found that species that arrive first at a disturbed site can play a key role in the further development of the community and that this priority effect influences aboveground productivity, species diversity and stability of the grassland communities that develop. Restoration of nutrient poor, species rich grasslands is often limited by seed dispersal as well as the accessibility of suitable microsites for establishment. Sowing species (i.e. creating priority effects for further assembly) may help overcome such dispersal barriers, but the potential of using priority effects for restoration has not been tested in this type of dry grassland. We tested the hypothesis that sowing two different seed mixtures used for dry acidic grassland restoration onto a sandy substrate (which formed an equivalent to a primary succession) would create priority effects, and that these priority effects would be sustained over a number of years. We followed community assembly and measured aboveground productivity for four years after sowing. We found that priority effects caused by sowing of differently diverse mixtures did also occur in dry acidic grassland habitat, but that how persistent they were over time depended on the response variable considered. Priority effects on species number were not as strong as found in previous ex-arable land studies, whereas priority effects for aboveground productivity were still visible after 4 years. In addition, functional composition of the community still reflected the composition of the seed mixtures 4 years later. Our results suggest that priority effects can occur in nutrient-poor dry acidic grassland but in contrast to more nutrient-rich sites the breadth of responses affected may not be as wide.     

Switching from usual brand cigarettes to a tobacco-heating cigarette or snus: Part 2. Biomarkers of exposure

Abstract

A randomized, multi-center study of adult cigarette smokers switched to tobacco-heating cigarettes, snus or ultra-low machine yield tobacco-burning cigarettes (50/group) was conducted, and subjects’ experience with the products was followed for 24 weeks. Differences in biomarkers of tobacco exposure between smokers and never smokers at baseline and among groups relative to each other and over time were assessed. Results indicated reduced exposure to many potentially harmful constituents found in cigarette smoke following product switching. Findings support differences in exposure from the use of various tobacco products and are relevant to the understanding of a risk continuum among tobacco products.

Trial registration: ClinicalTrials.gov identifier: NCT02061917.     

Circulating cytokine pattern and factors describing rheumatoid arthritis: IL-15 as one of the biomarkers for RA?

The aim of study was to examine relationship among levels of cytokines (IL-6, IL-13, IL-15, TNF-α) and chemokine (IL-8), production of autoantibodies, radiographic progression, and factors describing rheumatoid arthritis (RA). A total of 156 RA patients according to ACR criteria, and 55 control subjects were recruited into study. We observed higher levels of IL-15 within RA patients compared to healthy controls. Correlations among cytokine levels and the measures of rheumatoid factors, anti-CCP, measures of disease activity, and radiographic progression were observed. We conclude that IL-15 level in circulation could serve as one of the biomarkers for RA detection.     

转基因低水平混杂问题——政策与内涵

转基因技术近年来在世界范围内快速发展,但由于不同国家在转基因审批上的不同步,以及各国设立严格的转基因低水平混杂阈值,导致正常的农产品贸易由于无意混入少量转基因成分而发生贸易摩擦,甚至导致贸易中断.从转基因低水平混杂(LLP)的含义出发分析其特殊性,分析了世界主要国家的LLP政策以及严格的LLP政策对贸易产生的负面影响.根据研究结果指出:在当前转基因作物采用率不断提高,以及转基因新品种研发加速背景下,转基因低水平混杂在技术上是不可避免的.因此,有必要在全球范围内建立转基因安全互信机制,各国需要尽量减少审批不同步时滞,设置合理的转基因低水平阈值,降低对正常贸易的负面影响.研究结果对中国转基因LLP政策和有关标准制定有一定借鉴意义.     

ATAC-seq在复杂疾病研究中的应用进展

染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因子结合位点以及核小体的位置。在医学领域,ATAC-seq技术是研究重大疾病发病机制、药物作用机制、新药研发和生物标志物功能等的新一代有力工具。本文对ATAC-seq技术的优势及其在复杂疾病研究中的应用和前景进行了综述,以期为人类复杂疾病基因表达调控机制等相关研究的开展提供借鉴与参考。