Differential regulation of clathrin and its adaptor proteins during membrane recruitment for endocytosis

In plants, clathrin-mediated endocytosis (CME) is dependent on the function of clathrin and its accessory heterooligomeric adaptor protein complexes, ADAPTOR PROTEIN2 (AP-2) and the TPLATE complex (TPC), and is negatively regulated by the hormones auxin and salicylic acid (SA). The details for how clathrin and its adaptor complexes are recruited to the plasma membrane (PM) to regulate CME, however, are poorly understood. We found that SA and the pharmacological CME inhibitor tyrphostin A23 reduce the membrane association of clathrin and AP-2, but not that of the TPC, whereas auxin solely affected clathrin membrane association, in Arabidopsis (Arabidopsis thaliana). Genetic and pharmacological experiments revealed that loss of AP2 mu or AP2 sigma partially affected the membrane association of other AP-2 subunits and that the AP-2 subunit AP2 sigma, but not AP2 mu, was required for SA-and tyrphostin A23-dependent inhibition of CME. Furthermore, we show that although AP-2 and the TPC are both required for the PM recruitment of clathrin in wild-type cells, the TPC is necessary for clathrin PM association in AP-2-deficient cells. These results indicate that developmental signals may differentially modulate the membrane recruitment of clathrin and its core accessory complexes to regulate the process of CME in plant cells

Regulation of High-Temperature Stress Response by Small RNAs

Temperature extremes constitute one of the most common environmental stresses that adversely affect the growth and development of plants. Transcriptional regulation of temperature stress responses, particularly involving protein-coding gene networks, has been intensively studied in recent years. High-throughput sequencing technologies enabled the detection of a great number of small RNAs that have been found to change during and following temperature stress. The precise molecular action of some of these has been elucidated in detail. In the present chapter, we summarize the current understanding of small RNA-mediated modulation of high- temperature stress-regulatory pathways including basal stress responses, acclimation, and thermo-memory. We gather evidence that suggests that small RNA network changes, involving multiple upregulated and downregulated small RNAs, balance the trade-off between growth/development and stress responses, in order to ensure successful adaptation. We highlight specific characteristics of small RNA-based tem- perature stress regulation in crop plants. Finally, we explore the perspectives of the use of small RNAs in breeding to improve stress tolerance, which may be relevant for agriculture in the near future

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Nucleolar protein nucleolin functions in replication stress–induced DNA damage responses

The nucleolus contains multiple copies of ribosomal (r)DNA, which indicate sites of frequent replication stress and suggest the existence of a mechanism to prevent replication stress–related rDNA instability and the possibility that such a mechanism contributes to the whole genomic stability against replication stress. We have previously reported that nucleolin, a major nucleolar protein, is involved in ionizing radiation–induced DNA damage responses (DDRs) such as ataxia telangiectasia mutated (ATM)-dependent cell cycle checkpoints and homologous recombination (HR) repair. Here, we investigated the role of nucleolin in DDR due to replication stress. The results indicate that following replication stress, nucleolin interacted with the histone γH2AX, proliferating cell nuclear antigen (PCNA), and replication protein A (RPA)32, suggesting that it may be recruited to DNA damage sites on the replication fork. Furthermore, the knockdown of nucleolin by siRNA reduced the activation of ATM and RAD3-related (ATR) kinase and the formation of RAD51 and RPA32 foci after replication stress due to UV or camptothecin exposure, whereas nucleolin overexpression augmented ATR-dependent phosphorylation and RAD51 and RPA accumulation on chromatin. Moreover, these overexpressing cells seemed to increase repair activity and resistance to replication stress. Our results indicate that nucleolin plays an important role in replication stress–induced DDRs such as ATR activation and HR repair. Given that nucleolin overexpression is often observed in many types of cancer cells, our findings suggest that nucleolin is involved in the regulation of resistance to replication stress that may otherwise lead to tumorigenesis and it could be a possible target for chemotherapy and radiotherapy

Spatiotemporal Distribution Characteristics of Nutrients in the Drowned Tidal Inlet under the Influence of Tides: A Case Study of Zhanjiang Bay, China

The tidal dynamics and the characteristics of pollutant migration in the drowned-valley tidal inlet, a typical unit of coastal tidal inlets, are strongly influenced by geomorphological features. Along with the development of society and the economy, the hydrodynamic and water quality environment of the tidal inlet is also becoming more disturbed by human activities, such as reclamation of the sea and the construction of large bridges. In this study, a typical drowned-valley tidal inlet, Zhanjiang Bay (ZJB), was selected for the establishment of a model via coupling of a tidal hydrodynamic model and water quality numerical model. This model can be used to simulate the migration and diffusion of pollutants in ZJB. The spatial and temporal variation processes of water quality factors of the bay under the influence of special geomorphic units was simulated at the tidal-inlet entrance, the flood/ebb tidal delta, and the tidal basin. The results show that ZJB has strong tidal currents that are significantly affected by the terrain. Under the influence of the terrain and tidal currents, the phosphorus and nitrogen concentration at the flood-tide and ebb-tide moments showed obvious temporal and spatial differences in the ebb-tide delta, tidal-inlet entrance, flood-tide delta, and tidal basin. In this study, we analyzed the response mechanism of the water quality environment to the drowned-valley tidal inlet, and this can provide theoretical guidance and a basis for decision-making toward protecting the ecology and water security of ZJB

Spatial and Seasonal Variations of Sedimentary Organic Matter in a Subtropical Bay: Implication for Human Interventions

Elemental (total organic carbon (TOC) and total nitrogen (TN)) and stable carbon and nitrogen isotope compositions (δ13C and δ15N, respectively) in the surface sediment of Zhanjiang Bay (ZJB) in spring and summer were measured to study the spatial and seasonal changes of organic matter (OM) and assess the human-induced and environment-induced changes in the area. The OM in the surface sediment of ZJB was a mixture of terrestrial and marine sources, and was dominated by marine OM (54.9% ± 15.2%). Compared to the central ZJB, the channel and coastal ZJB areas had higher δ13C and δ15N values, higher TOC and TN concentrations, and lower TOC/TN ratios, indicating higher primary productivity and higher percentages of marine OM in the latter two subregions. Mariculture activities, sewage inputs, and dredging were responsible for these phenomena. Clear seasonal variations in OM were observed in ZJB. The average proportions of terrestrial OM in summer increased by 10.2% in the ZJB channel and 26.0% in the coastal ZJB area compared with those in spring. Heavy rainfall brought a large amount of terrestrial OM into the channel and coastal ZJB areas, leading to the increase of the terrestrial OM fraction in these two subregions in summer. In summary, anthropogenic influences had a significant influence on the spatial and seasonal variations of sedimentary OM in ZJB

Development of an allele-specific PCR assay for simultaneous sero-typing of avian pathogenic Escherichia coli predominant O1, O2, O18 and O78 strains.

Systemic infections by avian pathogenic Escherichia coli (APEC) are economically devastating to poultry industries worldwide. E. coli strains belonging to serotypes O1, O2, O18 and O78 are preferentially associated with avian colibacillosis. The rfb gene cluster controlling O antigen synthesis is usually various among different E. coli serotypes. In present study, the rfb gene clusters of E. coli serotypes O1, O2, O18 and O78 were characterized and compared. Based on the serotype-specific genes in rfb gene cluster, an allele-specific polymerase chain reaction (PCR) assay was developed. This PCR assay was highly specific and reliable for sero-typing of APEC O1, O2, O18 and O78 strains. The sensitivity of the assay was determined as 10 pg DNA or 10 colony forming units (CFUs) bacteria for serotypes O2 and O18 strains, and 500 pg DNA or 1,000 CFUs bacteria for serotypes O1 and O78 strains. Using this PCR system, APEC isolates and the infected tissue samples were categorized successfully. Furthermore, it was able to differentiate the serotypes for the samples with multi-agglutination in the traditional serum agglutination assay. Therefore, the allele-specific PCR is more simple, rapid and accurate assay for APEC diagnosis, epidemiologic study and vaccine development

Spatial-Monthly Variations and Influencing Factors of Dissolved Oxygen in Surface Water of Zhanjiang Bay, China

Dissolved oxygen (DO) is one of the most important factors for maintaining a healthy marine ecosystem. The information of DO in large estuaries or bays with large entrances has been widely studied, while it is relatively limited for a bay with a narrow entrance which is vulnerable to human activities. The Zhanjiang Bay, located in the northwestern South China Sea, has a very narrow entrance and suffers from strong anthropogenic activities and obvious seasonal variations in environmental parameters. In this study, we analyzed the spatial and monthly variations of DO, apparent oxygen utilization (AOU), percent oxygen saturation (DO-saturation), and related environmental parameters in the surface water of Zhanjiang Bay to find out the factors controlling the dynamics of DO. Different from many other coastal ecosystems, DO concentrations in the Zhanjiang Bay reached minimum values in late spring and early autumn. The phytoplankton bloom in summer months, which was related to the high concentrations of nutrients brought by rainfall-induced terrestrial inputs, contributed to that phenomenon. Though high chlorophyll a (Chl a) concentrations were observed in both the summer months and December, the DO-saturation values were relatively low and AOU values were relatively high in summer months. Rainfall-induced terrestrial discharge in summer months, which had high concentrations of chemical oxygen demand, contributed much to that phenomenon. The average DO concentrations and DO-saturation values in a hydrological year decreased seaward, and AOU values increased seaward, indicating the anthropogenic influence from terrestrial input. The highest annual average Chl a concentration, relatively high annual average DO-saturation value and relatively low annual AOU value were observed near the Donghai Dam. This indicated that the construction of Donghai Dam has significant influences on the environment of Zhanjiang Bay

Assessing Seasonal Nitrate Contamination by Nitrate Dual Isotopes in a Monsoon-Controlled Bay with Intensive Human Activities in South China

Nitrate (NO3−) dual isotope analysis was performed in Zhanjiang Bay, which is a closed bay with intensive human activities in South China, to investigate seasonal changes in the main NO3− sources and their biogeochemical processes in the monsoon-controlled climate. The relatively low N/P ratios in Zhanjiang Bay suggests that nitrogen (N) is a limiting nutrient, which indicates that the increase of N is favorable for phytoplankton proliferation. However, a sufficient amount of ammonium was found in our study area owing to intensive human activities, which can support biological processes. Thus, less NO3− biological processes were found, indicating that NO3− isotopic characteristics may reveal details of the mixing from various sources. The Bayesian mixing model showed that NO3− in the upper bay originated from manure (43%), soil N (30%), N fertilizer (17%), and N precipitation (10%) during winter, which reflects the local human activities; while NO3- sources during summer were mainly N fertilizer (36%), soil N (32%), and manure (31%), indicating the source as the runoff from the upper river basin. Our results suggest that nitrate dual-isotope was very useful for tracing the main NO3− sources in the condition of the sufficient ammonium, and runoff exerted an important impact on the shift in NO3− sources between both the local source and the source from the upper river basin during the two seasons in this monsoon-controlled bay

Study on Treatment of Low Concentration Oily Wastewater Using Alumina Ceramic Membranes

In this study, alumina ceramic plate microfiltration membranes (ACMs) were used for the treatment of oily wastewater with different concentrations. The permeate oil concentration of the system was basically less than 5 mg·L−1, and the oil rejection rate was up to 97.6%. The effects of raw oil concentration on permeation flux and oil rejection rate of oily wastewater were studied. The results showed that with the increase of raw oil concentration, the oil rejection rate increased slightly due to the existence of oil film on the surface of filtered ACMs. Moreover, the existence of oil film had little effect on the flux change of ceramic membranes. The results showed that the permeability of ACMs mainly depended on their own oleophobic properties. In this system, physical cleaning technology is used to remove oil droplets and particles blocked in membrane pores. The results showed that physical cleaning could significantly recover the permeation flux as well as improve the oil rejection rate. On this basis, a system is proposed as a potential technique for oily wastewater treatment