Diurnal fluctuations in seawater pH influence the response of a calcifying macroalga to ocean acidification

Coastal ecosystems that are characterized by kelp forests encounter daily pH fluctuations, driven by photosynthesis and respiration, which are larger than pH changes owing to ocean acidification (OA) projected for surface ocean waters by 2100. We investigated whether mimicry of biologically mediated diurnal shifts in pH—based for the first time on pH time-series measurements within a kelp forest—would offset or amplify the negative effects of OA on calcifiers. In a 40-day laboratory experiment, the calcifying coralline macroalga, Arthrocardia corymbosa, was exposed to two mean pH treatments (8.05 or 7.65). For each mean, two experimental pH manipulations were applied. In one treatment, pH was held constant. In the second treatment, pH was manipulated around the mean (as a step-function), 0.4 pH units higher during daylight and 0.4 units lower during darkness to approximate diurnal fluctuations in a kelp forest. In all cases, growth rates were lower at a reduced mean pH, and fluctuations in pH acted additively to further reduce growth. Photosynthesis, recruitment and elemental composition did not change with pH, but δ¹³C increased at lower mean pH. Including environmental heterogeneity in experimental design will assist with a more accurate assessment of the responses of calcifiers to OA.     

广州市风水林群落空间异质性及其对区域物种多样性的贡献

以广州地区村边风水林为研究对象,选取了67个风水林斑块,并在每个斑块内建立了一个20m×20m的样方,调查了其胸径大于1cm的植物组成。首先以种面积关系外推法和非参数法估计了风水林群落对区域生物多样性的贡献;然后以加法准则拆分了gamma多样性,以分析风水林群落物种组成的异质性;最后根据每个风水林群落的物种丰富度、稀有种(在所有群落中只出现一次的物种)数目和谱系多样性分析了在保护中需要优先考虑的区域。结果发现：（1）广州地区风水林群落至少保存了32.74%的区域物种多样性;（2）gamma多样性(184)中绝大部分由beta多样性(163.43)构建,只有很小部分来自于alpha多样性(20.57)。这表明风水林群落在物种组成上具有较高的空间异质性,要想尽可能多地保护风水林内物种多样性,就需要尽可能多地保护风水林群落斑块;（3）相对于平原地区,位于山区的风水林群落具有更高的物种丰富度和谱系多样性以及更多的稀有种数目。在保护资金和土地资源有限的情况下,位于山区的风水林群落应该给予优先考虑。     

The advantage of laser‐capture microdissection over whole tissue analysis in proteomic profiling studies

Laser‐capture microdissection (LCM) offers a reliable cell population enrichment tool and has been successfully coupled to MS analysis. Despite this, most proteomic studies employ whole tissue lysate (WTL) analysis in the discovery of disease biomarkers and in profiling analyses. Furthermore, the influence of tissue heterogeneity in WTL analysis, nor its impact in biomarker discovery studies have been completely elucidated. In order to address this, we compared previously obtained high resolution MS data from a cohort of 38 breast cancer tissues, of which both LCM enriched tumor epithelial cells and WTL samples were analyzed. Label‐free quantification (LFQ) analysis through MaxQuant software showed a significantly higher number of identified and quantified proteins in LCM enriched samples (3404) compared to WTLs (2837). Furthermore, WTL samples displayed a higher amount of missing data compared to LCM both at peptide and protein levels (p‐value < 0.001). 2D analysis on co‐expressed proteins revealed discrepant expression of immune system and lipid metabolisms related proteins between LCM and WTL samples. We hereby show that LCM better dissected the biology of breast tumor epithelial cells, possibly due to lower interference from surrounding tissues and highly abundant proteins. All data have been deposited in the ProteomeXchange with the dataset identifier PXD002381 ( http://proteomecentral.proteomexchange.org/dataset/PXD002381 ).     

Relationships between wild bees,hoverflies and pollination success in apple orchards with different landscape contexts

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Characteristics of a landscape water with high salinity in a coastal city of China and measures for eutrophication control

Eutrophication of landscape waters is drawing public concerns in China but few studies have been conducted on the problem associated with high water salinity as what happens at Sino-Singapore Tianjin Eco-city in Tianjin, a coastal metropolis of northern China. In order to find ways for eutrophication control, a comparative study was conducted on three landscape water bodies, namely Qingjing Lake, Jiyun River and Jiyun River Oxbow, which are under varied conditions of salinity, organic, and nutrients intrusion. The spatial and temporal variations of water quality were revealed by water sampling and analyses, and correlative relationships were obtained between water salinity and other parameters related to eutrophication. By utilizing a trophic level index (TLI), the eutrophication status of the three landscape water bodies in different seasons could further be evaluated. As a result, water temperature, as expected, showed the strongest effect on eutrophication because higher TLI together with higher Chl-a concentrations tended to occur in later spring and summer seasons, while nutrient concentration, especially TP, was also the determinative factor to the eutrophication status. Of the three water bodies, the Jiyun River Oxbow showed a salinity as high as 20 g/L or more in contrast with the other two water bodies with salinity as 4–5 g/L. Although its TP concentration was usually very low (about 0.1 mg/L), it was under a moderate eutrophication status almost in all seasons, indicating that high salinity tends to induce alga growth. Dilution of saline inflow and nutrients reduction could thus be proposed as the main measures for eutrophication control of landscape waters in the study area.     

Distinct cellular states determine calcium signaling response

The heterogeneity in mammalian cells signaling response is largely a result of pre‐existing cell‐to‐cell variability. It is unknown whether cell‐to‐cell variability rises from biochemical stochastic fluctuations or distinct cellular states. Here, we utilize calcium response to adenosine trisphosphate as a model for investigating the structure of heterogeneity within a population of cells and analyze whether distinct cellular response states coexist. We use a functional definition of cellular state that is based on a mechanistic dynamical systems model of calcium signaling. Using Bayesian parameter inference, we obtain high confidence parameter value distributions for several hundred cells, each fitted individually. Clustering the inferred parameter distributions revealed three major distinct cellular states within the population. The existence of distinct cellular states raises the possibility that the observed variability in response is a result of structured heterogeneity between cells. The inferred parameter distribution predicts, and experiments confirm that variability in IP3R response explains the majority of calcium heterogeneity. Our work shows how mechanistic models and single‐cell parameter fitting can uncover hidden population structure and demonstrate the need for parameter inference at the single‐cell level.     

Emerging power of proteomics for delineation of intrinsic tumor subtypes and resistance mechanisms to anti-cancer therapies

Introduction: Despite extreme genetic heterogeneity, tumors often show similar alterations in the expression, stability, and activation of proteins important in oncogenic signaling pathways. Thus, classifying tumor samples according to shared proteomic features may help facilitate the identification of cancer subtypes predictive of therapeutic responses and prognostic for patient outcomes. Meanwhile, understanding mechanisms of intrinsic and acquired resistance to anti-cancer therapies at the protein level may prove crucial to devising reversal strategies.

Areas covered: Herein, we review recent advances in quantitative proteomic technology and their applications in studies to identify intrinsic tumor subtypes of various tumors, to illuminate mechanistic aspects of pharmacological and oncogenic adaptations, and to highlight interaction targets for anti-cancer compounds and cancer-addicted proteins.

Expert commentary: Quantitative proteomic technologies are being successfully employed to classify tumor samples into distinct intrinsic subtypes, to improve existing DNA/RNA based classification methods, and to evaluate the activation status of key signaling pathways.     

Genetic and epigenetic heterogeneity of epithelial ovarian cancer and the clinical implications for molecular targeted therapy

Epithelial ovarian cancer (EOC) is the most lethal gynaecological malignancy, and tumoural heterogeneity (TH) has been blamed for treatment failure. The genomic and epigenomic atlas of EOC varies significantly with tumour histotype, grade, stage, sensitivity to chemotherapy and prognosis. Rapidly accumulating knowledge about the genetic and epigenetic events that control TH in EOC has facilitated the development of molecular‐targeted therapy. Poly (ADP‐ribose) polymerase (PARP) inhibitors, designed to target homologous recombination, are poised to change how breast cancer susceptibility gene (BRCA)‐related ovarian cancer is treated. Epigenetic treatment regimens being tested in clinical or preclinical studies could provide promising novel treatment approaches and hope for improving patient survival.     

Genome Characteristics,Phylogeny and Varying Host Specificity of Polish Kra and Ros Isolates of Tomato torrado virus

The genome sequences of two Polish Kra and Ros isolates of Tomato torrado virus (ToTV) were determined and compared with data of previously described ToTV isolates and other Torradovirus members. Whole‐genome sequence comparisons revealed 97.0–99.6% nucleotide sequence identities and close relatedness, with other known ToTV isolates. The high homology between Kra, Ros and Wal'03 ToTVs is likely responsible for the similar symptoms observed on infected plants. However, the symptoms differed in intensity and various host specificity. We report that Kra ToTV caused a milder expression of symptoms on Solanum tuberosum than Wal'03. We hypothesize this may be a result of the significant variability observed within the 3′‐UTR of RNA1 of Kra as well as of Ros ToTV isolates. In the light of this fact, potato may be considered an indicator plant for distinguishing Kra and Wal'03 ToTV isolates.