Current knowledge of microbial community structures in landfills and its cover soils

Landfills are a vital component of our waste handling processes. Our lack of knowledge on the microbial processes in these systems, however, hampers our ability to design the next generation of landfills that: (1) enhance the rate and extent of waste decomposition, (2) produce byproducts of some value (e.g., methane that can be used for energy generation), and, (3) minimize their overall impact on driving climate change through the emission of greenhouse gases. In this review, the current state of knowledge the microbial community structure and activity in both the refuse and overlying cover soils is discussed, and suggestions provided for future research in this critical aspect of our infrastructure.     

An investigation on the genetic background of <Emphasis Type="Italic">Nostoc flagelliforme</Emphasis> by similarity analysis of its partial genomic DNA and phylogenetic comparison of deduced related species

Nostoc flagelliforme, which is distributed on arid and semi-arid steppes of northwestern parts of China, has attracted increasing interest for its stress tolerance. In order to gain more insight into the genetic background of N. flagelliforme, we sequenced its partial genomic DNA for similarity analyses against current public databases, followed by phylogenetic comparison of N. flagelliforme and the potentially related species deduced from the similarity analyses. Approximately 430 kb genomic sequence (~5% of genome as a rough estimate) was determined from 106 distinct genomic clones. Nucleotide BLAST showed that ~23.1% of the partial genomic sequence was similar to N. punctiforme genomic DNA and ~12.4% to its plasmid DNA. Similar protein search by online FASTA-protein program showed 46.2% of the similar proteins had their corresponding orthologs in N. punctiforme genome. Furthermore, phylogenetic comparison based on 16S rRNA sequences showed N. flagelliforme and N. punctiforme clustered closer among the deduced related species. These results indicated that N. punctiforme might also be potentially close neighbor species of N. flagelliforme, in addition to the formerly regarded close neighbor species N. commune and N. sphaeroids. In general, these data enriched our recognition of the evolutionary relationship between N. flagelliforme and other Nostoc species, especially N. punctiforme.     

Analysis of bacterial communities in rhizosphere soil of continuously cropped healthy and diseased konjac

The bacterial community and diversity in healthy and diseased konjac rhizosphere soils with different ages of continuous cropping were investigated using next-generation sequencing. The results demonstrated that the number of years of continuous cropping significantly altered soil bacterial community and diversity. Soil bacterial Shannon diversity index and Chao 1 index decreased with the increasing cropping years of konjac. After 1 year of cropping, the soil exhibited the highest bacterial relative abundance and diversity. Of the 44 bacterial genera (relative abundance ratio of genera greater than 0.3%), 14 were significantly affected by the duration of continuous cropping and plant status. With increasing continuous cropping, Alicyclobacillus decreased, while Achromobacter, Lactobacillus, Kaistobacter, Rhodoplanes increased after 3 years continuous cropping. Continuous cropping altered the structure and composition of the soil bacterial community, which led to the reduction in the beneficial bacteria and multiplication of harmful bacteria. These results will improve our understanding of soil microbial community regulation and soil health maintenance in konjac farm systems.     

Synthesis and Biological Evaluation of Novel Multi-target-Directed Benzazepines Against Excitotoxicity

Excitotoxicty, a key pathogenic event is characteristic of the onset and development of neurodegeneration. The glutamatergic neurotransmission mediated through different glutamate receptor subtypes plays a pivotal role in the onset of excitotoxicity. The role of NMDA receptor (NMDAR), a glutamate receptor subtype, has been well established in the excitotoxicity pathogenesis. NMDAR overactivation triggers excessive calcium influx resulting in excitotoxic neuronal cell death. In the present study, a series of benzazepine derivatives, with the core structure of 3-methyltetrahydro-3H-benzazepin-2-one, were synthesised in our laboratory and their NMDAR antagonist activity was determined against NMDA-induced excitotoxicity using SH-SY5Y cells. In order to assess the multi-target-directed potential of the synthesised compounds, Aβ_1–42 aggregation inhibitory activity of the most potent benzazepines was evaluated using thioflavin T (ThT) and Congo red (CR) binding assays as Aβ also imparts toxicity, at least in part, through NMDAR overactivation. Furthermore, neuroprotective, free radical scavenging, anti-oxidant and anti-apoptotic activities of the two potential test compounds (7 and 14) were evaluated using primary rat hippocampal neuronal culture against Aβ_1–42-induced toxicity. Finally, in vivo neuroprotective potential of 7 and 14 was assessed using intracerebroventricular (ICV) rat model of Aβ_1–42-induced toxicity. All of the synthesised benzazepines have shown significant neuroprotection against NMDA-induced excitotoxicity. The most potent compound (14) showed relatively higher affinity for the glycine binding site as compared with the glutamate binding site of NMDAR in the molecular docking studies. 7 and 14 have been shown experimentally to abrogate Aβ_1–42 aggregation efficiently. Additionally, 7 and 14 showed significant neuroprotective, free radical scavenging, anti-oxidant and anti-apoptotic properties in different in vitro and in vivo experimental models. Finally, 7 and 14 attenuated Aβ_1–42-induced tau phosphorylation by abrogating activation of tau kinases, i.e. MAPK and GSK-3β. Thus, the results revealed multi-target-directed potential of some of the synthesised novel benzazepines against excitotoxicity.     

Synthetic biology: advancing biological frontiers by building synthetic systems

Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.     

Diel variation of phytoplankton functional groups in a subtropical reservoir in southern Brazil during an autumnal stratification period

A knowledge of diel variation and the vertical distribution of phytoplankton communities may contribute to a better understanding of the driving factors of key species. Applying functional-group classification provides important information on the causes of species selection in the pelagic community. The diel variation of phytoplankton functional groups was analysed during an autumnal stratification period with the aim of understanding their changes in the vertical position related to light, mixing regime and grazing pressure. Phytoplankton and zooplankton communities were sampled every 4 h during a 24-h period in a vertical profile in a subtropical meso-eutrophic reservoir. Strong stratification during a 24-h cycle and a mixed clear epilimnion with partial atelomixis marked the autumn season in the Faxinal reservoir, southern Brazil. The highest phytoplankton densities and biomass were found during the second part of the day, a general pattern reported in the literature, and may be explained by zooplankton dynamics. During the 24-h cycle, phytoplankton functional groups lacking a self-regulating capacity and those able to regulate their vertical position were vertically segregated in the lake. The diel behaviour of both groups was driven by the mixing regime (including atelomixis), light and zooplankton grazing pressure.     

Leaf Chlorophyll Fluorescence: Background and Fundamentals for Plant Biologists

This review on chlorophyll a fluorescence starts with an overview of the primary photochemistry occurring at PSII and a characterization of the so-called “open” and “closed” states of its reaction centers. This provides the theoretical background for understanding the origin of PSII-emitted fluorescence and how its yield varies with the fraction of open reaction centers. The review proceeds to discuss the changes in fluorescence emission following illumination of a dark-adapted leaf and to define the PSII intrinsic quantum yield of photochemistry, which in turn provides an indication of PSII capacity. In light-adapted leaves, it is discussed how the use of modulated fluorometers and the double lighting technique allow an evaluation of photochemical and non-photochemical quenching, two parameters that give useful information about the plant’s photosynthetic performance under field conditions. Finally, it is described how the PSII operational efficiency can be used to calculate the photosynthetic electron transport rate and the conditions under which this is linearly related to the CO₂ assimilation rate. Some requirements for a valid application of the technique as well as some limitations in interpreting its results are discussed.