Study on ecological restoration in near-shore zone of a eutrophic lake, Wuli Bay, Taihu Lake

A two-year restoration period, large-scale ecological restoration demonstration engineering project was carried out in the near-shore zones of Wuli Bay, Taihu Lake. Various methods to restore the aquatic biodiversity and prevent ecological degradation were employed and their effects on water quality and aquatic plants were investigated. The results showed that water quality had been significantly improved in the demonstration zones. The concentrations of TN and TP were about half of those of the reference site in Wuli Bay. The water transparency was 30 cm higher than that in the reference site. The species, cover and biomass of aquatic plants were also significantly increased in the demonstration zones.     

A label-free electrochemical DNA sensor based on exonuclease III-aided target recycling strategy for sequence-specific detection of femtomolar DNA

The present work demonstrates a rapid, single-step and ultrasensitive label-free and signal-off electrochemical sensor for specific DNA detection with excellent discrimination ability for single-nucleotide polymorphisms, taking advantage of Exonuclease III (Exo III)-aided target recycling strategy to achieve signal amplification. Exo III has a specifical exo-deoxyribonuclease activity for duplex DNAs in the direction from 3' to 5' terminus, however its activity on the duplex DNAs with 3'-overhang and single-strand DNA is limited. In response to the specific features of Exo III, the proposed E-DNA sensor is designed such that, in the presence of target DNA, the electrode self-assembled signaling probe hybridizes with the target DNA to form a duplex in the form of a 3'-blunt end at signaling probe and a 3'-overhang end at target DNA. In this way, Exo III specifically recognizes this structure and selectively digests the signaling probe. As a result, the target DNA dissociates from the duplex and recycles to hybridize with a new signaling probe, leading to the digestion of a large amount of signaling probes gradually. A redox mediator, Ru(NH(3))(6)(3+) (RuHex) is employed to electrostatically adsorbed onto signaling probes, which is directly related to the amount and the length of the signaling probes remaining in the electrode, and provides a quantitative measure of sequence-specific DNA with the experimentally measured (not extrapolated) detection limit as low as 20 fM. Moreover, this E-DNA sensor has an excellent differentiation ability for single mismatches with fairly good stability.     

Male gametophyte defective 4 encodes a rhamnogalacturonan II xylosyltransferase and is important for growth of pollen tubes and roots in Arabidopsis

In flowering plants, the growth of pollen tubes is essential for the delivery of sperm to the egg cells. Although many factors (including cell‐wall properties) are involved in this process, little is known about the underlying molecular mechanisms that regulate the growth of pollen tubes. We report here the characterization of an Arabidopsis mutant male gametophyte defective 4 (mgp4) that is severely defective in pollen tube growth. The mgp4 mutation also impairs root growth of pollen‐rescued mgp4 mutant plants generated by expressing MGP4 cDNA under the control of a pollen grain/tube‐specific promoter. The MGP4 gene encodes a putative xylosyltransferase and is expressed in many organs/tissues, including pollen tubes and roots. MGP4 protein expressed in Pichia pastoris exhibited xylosyltransferase activity and transferred d ‐xylose onto l ‐fucose. The pectic polysaccharide rhamnogalacturonan II (RG‐II), isolated from 7‐day‐old pollen‐rescued mutant seedlings, exhibited a 30% reduction in 2‐O‐methyl d ‐xylose residues. Furthermore, an exogenous supply of boric acid enhanced RG‐II dimer formation and partially restored the root growth of the pollen‐rescued mutant seedlings. Taken together, these results suggest that MGP4 plays important roles in pollen tube and root growth by acting as a xylosyltransferase involved in the biosynthesis of pectic RG‐II.     

‘Green tides’ are overwhelming the coastline of our blue planet: taking the world’s largest example

A broad spectrum of events that come under the category of green tide are recognized world-wide as a response to elevated levels of seawater nutrients in coastal areas. Green tides involve a wide diversity of sites, macroalgal species, consequences, and possible causes. Here we review the effect of natural and man-induced environmental fluctuations on the frequency and apparent spread of green tides. This article highlights the need for interdisciplinary research aimed at shedding light on the basic mechanisms governing the occurrence and succession of green algae in coastal seas. This will result in more effective management and mitigation of the effects of green tides, thus safeguarding the intrinsic and commercial value of coastal marine ecosystems.     

Bidirectional regulation of dendritic voltage-gated potassium channels by the fragile X mental retardation protein

How transmitter receptors modulate neuronal signaling by regulating voltage-gated ion channel expression remains an open question. Here we report dendritic localization of mRNA of Kv4.2 voltage-gated potassium channel, which regulates synaptic plasticity, and its local translational regulation by fragile X mental retardation protein (FMRP) linked to fragile X syndrome (FXS), the most common heritable mental retardation. FMRP suppression of Kv4.2 is revealed by elevation of Kv4.2 in neurons from fmr1 knockout (KO) mice and in neurons expressing Kv4.2-3'UTR that binds FMRP. Moreover, treating hippocampal slices from fmr1 KO mice with Kv4 channel blocker restores long-term potentiation induced by moderate stimuli. Surprisingly, recovery of Kv4.2 after N-methyl-D-aspartate receptor (NMDAR)-induced degradation also requires FMRP, likely due to NMDAR-induced FMRP dephosphorylation, which turns off FMRP suppression of Kv4.2. Our study of FMRP regulation of Kv4.2 deepens our knowledge of NMDAR signaling and reveals a FMRP target of potential relevance to FXS.     

Treatment of fresh leachate with high-strength organics and calcium from municipal solid waste incineration plant using UASB reactor

Treatment of a fresh leachate with high-strength organics and calcium from municipal solid waste (MSW) incineration plant by an up-flow anaerobic sludge blanket (UASB) reactor was investigated under mesophilic conditions, emphasizing the influence of organic loading rate (OLR). When the reactor was fed with the raw leachate (COD as high as 70,390-75,480 mg/L) at an OLR of 12.5 kg COD/(m³ d), up to ∼82.4% of COD was removed suggesting the feasibility of UASB process for treating fresh leachates from incineration plants. The ratio of volatile solids/total solids (VS/TS) of the anaerobic sludge in the UASB decreased significantly after a long-term operation due to the precipitation of calcium carbonate in the granules. Scanning electron microscopy (SEM) observation shows that Methanosaeta-like species were in abundance, accompanied by a variety of other species. The result was further confirmed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and sequencing.     

Decoding the genome beyond sequencing: the new phase of genomic research

While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make this transition for the next phase of genomic research, it is essential to acknowledge the importance of new genome-based biological concepts and to establish new technology platforms to decode the genome beyond sequencing.     

Towards better accuracy for missing value estimation of epistatic miniarray profiling data by a novel ensemble approach

Epistatic miniarray profiling (E-MAP) is a powerful tool for analyzing gene functions and their biological relevance. However, E-MAP data suffers from large proportion of missing values, which often results in misleading and biased analysis results. It is urgent to develop effective missing value estimation methods for E-MAP. Although several independent algorithms can be applied to achieve this goal, their performance varies significantly on different datasets, indicating different algorithms having their own advantages and disadvantages. In this paper, we propose a novel ensemble approach EMDI based on the high-level diversity to impute missing values that consists of two global and four local base estimators. Experimental results on five E-MAP datasets show that EMDI outperforms all single base algorithms, demonstrating an appropriate combination providing complementarity among different methods. Comparison results between several fusion strategies also demonstrate that the proposed high-level diversity scheme is superior to others. EMDI is freely available at www.csbio.sjtu.edu.cn/bioinf/EMDI/.