NaCl胁迫下宁夏枸杞光合作用相关基因差异表达分析

宁夏枸杞是著名的耐盐药用植物,该研究通过室内水培试验,利用高通量测序技术和qRT-PCR技术检测了不同浓度NaCl胁迫(0、100、200、300 mmol/L)下宁夏枸杞叶片光合作用相关基因差异表达,并分析了其叶绿素含量、净光合速率、Rubisco活性的变化,以揭示宁夏枸杞在盐胁迫条件下光合机构及光合作用相关基因差异表达规律,为深入解析宁夏枸杞响应盐胁迫的光合机理奠定基础。结果表明：(1)用100、200、300 mmol/L NaCl胁迫处理7 d时宁夏枸杞分别有14、26、55个光合作用相关基因差异表达,且随着NaCl胁迫程度的增加下调表达基因多于上调表达基因。(2)qRT-PCR结果显示,宁夏枸杞的3个光合作用相关基因ATPε、CLH2、Lhcb3的相对表达量均随着NaCl胁迫程度的加深总体呈显著下降的趋势,qRT-PCR验证结果与RNA-seq测序结果基本一致。(3)随着NaCl胁迫程度的增加,宁夏枸杞叶片中的叶绿素a和叶绿素b含量以及净光合速率和Rubisco活性均呈显著下降的趋势,而类胡萝卜素含量变化不显著。研究认为,宁夏枸杞能通过诱导光合作用相关基因的差异表达来调控叶片...     

Seasonal change and habitat selection of shorebird community at the South Yangtze River Mouth and North Hangzhou Bay, China

Coastal regions are important habitats for migratory shorebirds. The aim of the study is to understand habitat use by migratory shorebirds and to develop a conservation strategy in the sustainable use of wetlands. From March 2004 to January 2005, we conducted a seasonal shorebirds census in ten coastal habitats along the South Yangtze River mouth and North Hangzhou Bay, simultaneously examining the relative seasonal abundance of shorebirds and their spatial distribution. A total of 25 species were identified, the dominant seasonal species were Great Knot (Calidris tenuirostris), Sharp-tailed Sandpiper (Calidris alpine) and Red-necked Stint (Calidris ruficollis) in spring; Kentish Plover (Charadrius alexandrinus), Common Greenshank(Tringa nebularia) and Lesser Sand Plover (Charadrius mongolus) in summer; Kentish Plover, Red-necked Stint and Common Greenshank in autumn; Dunlin(Calidris alpine), Kentish Plover and Marsh Sandpiper (Tringa stagnatilis) in winter. These species accounted for more than 85% of the total shorebirds. The numbers of shorebirds counted was highest in spring and then in autumn, winter and summer respectively. Among the four seasons, there were few significant differences in the number of bird species between the sites outside the seawall (intertidal mudflat) and the sites inside the seawall (artificial wetland), but the average density of shorebirds was obviously different. The habitat-selection analysis of the environmental factors (outside and inside the seawall) impacting on the shorebird community was made in the 10 study sites with Canonical Correspondence Analysis. The study results indicated that: (1) Outside the seawall, the widths of the total intertidal mudflat and bare mudflat were the key factors affecting the shorebirds; the proportion of bulrush (Scirpus×mariquete) covering and supertidal mudflat width had a positive correlation with the abundance of birds, while human disturbance and the proportion of both reed (Phragmites communis) and smooth cord-grass (Spartina alterniflora) covering in total surveyed areas had negative impacts on bird numbers; (2) Inside the seawall, the proportions of areas with shallow water and mudflats occupying the total surveyed area were key factors influencing the number of birds; the size of the bulrush area should have a positive impact on the appearance of shorebirds. Habitats with heavy human disturbance, dense reed and smooth cord-grass or a high water level were not conducive to be inhabited by shorebirds.     

Morphological and Molecular Differences in Two Strains of <Emphasis Type="Italic">Ustilago esculenta</Emphasis>

Ustilago esculenta is a fungal endophyte of Zizania latifolia that plays an important agricultural role in this vegetable crop. The purpose of this study was to characterize sporidial (T) and mycelial (M-T) strains of U. esculenta isolated from sporulating and non-sporulating galls on plants growing in Zhejiang province, China. Morphological comparisons of the T strain and M-T strain were made by optical and scanning electron microscope observation. Genetic differences were examined by sequencing the ITS region of the fungus and examining differential protein expression by two-dimensional gel electrophoresis and MALDI-TOF-MS/MS. The sporidial (T) and mycelial (M-T) strains differed in morphological characteristics of their in vitro single colony formations and in cell shape. Alignment of ITS sequences of the T strain and M-T strain revealed a single mutation between the T strain and M-T strain, but the sequences were the same within strains. A total of 146 proteins were only expressed in the M-T strain, and 242 proteins were only expressed in the T strain isolated from infected plants. A total of 222 proteins were up-regulated or down-regulated in the T strain when compared with the M-T strain. Of these, 18 proteins were identified and eight were associated with processes involving energy metabolism and the cytoskeleton. Two morphology-related proteins, MAP kinase kinase and actin, were differentially expressed. The differences noted in the T strain and M-T strain may lead to a better understanding of the life cycle and morphogenesis in U. esculenta.     

LysGH15B,the SH3b Domain of Staphylococcal Phage Endolysin LysGH15, Retains High Affinity to Staphylococci

LysGH15, a phage endolysin, exhibits a particularly broad lytic spectrum against Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA). Sequence analysis reveals that this endolysin contains a C-terminal cell wall binding domain (SH3b), which causes the endolysin to bind to host strains. In this study, the substrate binding affinity of the SH3b domain (LysGH15B) was evaluated. A fusion protein of LysGH15B and green fluorescent protein (LysGH15B–GFP) were cloned and expressed in Escherichia coli. Laser scanning confocal microscopy was used to detect the fluorescence of the treated cells irradiated at different excitation wavelengths and to determine the binding activity of LysGH15B–GFP and GFP. We found that LysGH15B–GFP not only generated green fluorescence, but, more importantly, also displayed specific affinity to staphylococcal isolates, especially MRSA. In contrast, the single GFP did not display any binding activity. The high affinity was attributed to the portion of LysGH15B and the binding activity of the fusion protein was specific to staphylococci. This study provides an insight into the SH3b domain of LysGH15. The specific binding activity may cause LysGH15B to serve as an anchoring device, and offer an alternative approach for cell surface attachment onto staphylococci.     

Proteomic Analysis of Salt-Responsive Proteins in the Leaves of Mangrove Kandelia candel during Short-Term Stress

Salt stress is a major abiotic stress that limits crop productivity in many regions of the world. A comparative proteomic approach to identify salt stress-responsive proteins and to understand the molecular mechanisms was carried out in the woody halophyte Kandelia candel. Four-leaf-old K. candel seedlings were exposed to 150 (control), 300, 450, and 600 mM NaCl for 3 days. Proteins extracted from the leaves of K. candel seedlings were separated by two-dimensional gel electrophoresis (2-DE). More than 900 protein spots were detected on each gel, and 53 differentially expressed protein spots were located with at least two-fold differences in abundance on 2-DE maps, of which 48 were identified by matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF-TOF/MS). The results showed that K. candel could withstand up to 450 mM NaCl stress by up-regulating proteins that are mainly involved in photosynthesis, respiration and energy metabolism, Na⁺ compartmentalization, protein folding and assembly, and signal transduction. Physiological data, including superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR) activities, hydrogen peroxide (H₂O₂) and superoxide anion radicals (O₂ ⁻) contents, as well as Na⁺ content and K⁺/Na⁺ ratios all correlated well with our proteomic results. This study provides new global insights into woody halophyte salt stress responses. Identification of differentially expressed proteins promotes better understanding of the molecular basis for salt stress reduction in K. candel.     

Exposure Estimation for Risk Assessment of the Phthalate Incident in Taiwan

Background

In May 2011, di(2-ethylhexyl) phthalates (DEHP) and, to a lesser extent, di-iso-nonyl phthalate (DiNP) were found to have been illegally used for many years in Taiwan as clouding agents in foods including sports drinks, juice beverages, tea drinks, fruit jam/nectar/jelly, and health or nutrient supplements.

Objective

To estimate the DEHP exposure for the study participants for the follow-up epidemiological study and health risk assessment.

Methods

A total of 347 individuals possibly highly exposed to phthalate-tainted foods participated in the study. Exposure assessment was performed based on the participants'' responses to a structured questionnaire, self-report of exposure history, urinary metabolite concentrations, and DEHP concentration information in 2449 food records. A Bayesian statistical approach using Markov chain Monte Carlo simulation was employed to deal with the uncertainties in the DEHP concentrations of the contaminated foods and the participants'' likelihood of being exposed.

Results

An estimated 37% and 15% of children younger than 12 years old were exposed to DEHP at medium (20–50 μg / kg_bw / day) and high AvDIs (50–100 μg / kg_bw / day), respectively, prior to the episode (9% and 3% in adults, respectively). Moreover, 11% of children and 1% of adults were highly exposed (> 100 μg / kg_bw / day), with a maximum of 414.1 μg / kg_bw / day and 126.4 μg / kg_bw / day, respectively.

Conclusions

The phthalate exposure-associated adverse health effects for these participants warrant further investigation. The estimation procedure may be applied to other exposure assessment with various sources of uncertainties.     

TMEM106B p.T185S regulates TMEM106B protein levels: implications for frontotemporal dementia

Frontotemporal lobar degeneration (FTLD) is the second leading cause of dementia in individuals under age 65. In many patients, the predominant pathology includes neuronal cytoplasmic or intranuclear inclusions of ubiquitinated TAR DNA binding protein 43 (FTLD‐TDP). Recently, a genome‐wide association study identified the first FTLD‐TDP genetic risk factor, in which variants in and around the TMEM106B gene (top SNP rs1990622) were significantly associated with FTLD‐TDP risk. Intriguingly, the most significant association was in FTLD‐TDP patients carrying progranulin (GRN) mutations. Here, we investigated to what extent the coding variant, rs3173615 (p.T185S) in linkage disequilibrium with rs1990622, affects progranulin protein (PGRN) biology and transmembrane protein 106 B (TMEM106B) regulation. First, we confirmed the association of TMEM106B variants with FTLD‐TDP in a new cohort of GRN mutation carriers. We next generated and characterized a TMEM106B‐specific antibody for investigation of this protein. Enzyme‐linked immunoassay analysis of progranulin protein levels showed similar effects upon T185 and S185 TMEM106B over‐expression. However, over‐expression of T185 consistently led to higher TMEM106B protein levels than S185. Cycloheximide treatment experiments revealed that S185 degrades faster than T185 TMEM106B, potentially due to differences in N‐glycosylation at residue N183. Together, our results provide a potential mechanism by which TMEM106B variants lead to differences in FTLD‐TDP risk.

     

Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli

Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.