Population genomic analyses of protected incense trees Aquilaria sinensis reveal the existence of genetically distinct subpopulations

The incense tree Aquilaria sinensis (Thymelaeaceae) can produce agarwood with commercial values and is now under threat from illegal exploitation in Hong Kong, impairing the local population and biodiversity. Together with other species of Aquilaria, it is listed in the CITES Appendix II, which strictly regulates its international trade. To understand the population structure of A. sinensis and to make relevant conservation measures, we have sequenced 346 individuals collected in Hong Kong and southern mainland China. Population genomic analyses including principal component analysis, neighbor-joining tree construction, ADMIXTURE, and hierarchical pairwise-FST analyses suggested that genetically distinct populations are contained in certain areas. Genomic scan analyses further detected single-nucleotide polymorphism (SNP) outliers related to plant defense, including the CYP71BE gene cluster. In addition to the population analyses, we have developed a modified hexadecyltrimethyl-ammonium bromide (CTAB) DNA extraction protocol for obtaining DNA from agarwood samples in this study, and resequencing of DNA extracted from two agarwood samples using this method allows us to successfully map to the sample corresponding localities in the phylogenetic tree. To sum up, this study suggested that there is a genetically distinct subpopulation of incense tree in Hong Kong that would require special conservation measures and established a foundation for future conservation measures

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Prognostic model to predict postoperative acute kidney injury in patients undergoing major gastrointestinal surgery based on a national prospective observational cohort study.

Background: Acute illness, existing co-morbidities and surgical stress response can all contribute to postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. The aim of this study was prospectively to develop a pragmatic prognostic model to stratify patients according to risk of developing AKI after major gastrointestinal surgery. Methods: This prospective multicentre cohort study included consecutive adults undergoing elective or emergency gastrointestinal resection, liver resection or stoma reversal in 2-week blocks over a continuous 3-month period. The primary outcome was the rate of AKI within 7 days of surgery. Bootstrap stability was used to select clinically plausible risk factors into the model. Internal model validation was carried out by bootstrap validation. Results: A total of 4544 patients were included across 173 centres in the UK and Ireland. The overall rate of AKI was 14·2 per cent (646 of 4544) and the 30-day mortality rate was 1·8 per cent (84 of 4544). Stage 1 AKI was significantly associated with 30-day mortality (unadjusted odds ratio 7·61, 95 per cent c.i. 4·49 to 12·90; P < 0·001), with increasing odds of death with each AKI stage. Six variables were selected for inclusion in the prognostic model: age, sex, ASA grade, preoperative estimated glomerular filtration rate, planned open surgery and preoperative use of either an angiotensin-converting enzyme inhibitor or an angiotensin receptor blocker. Internal validation demonstrated good model discrimination (c-statistic 0·65). Discussion: Following major gastrointestinal surgery, AKI occurred in one in seven patients. This preoperative prognostic model identified patients at high risk of postoperative AKI. Validation in an independent data set is required to ensure generalizability

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Population genomic analyses of protected incense trees Aquilaria sinensis reveal the existence of genetically distinct subpopulations

The incense tree Aquilaria sinensis (Thymelaeaceae) can produce agarwood with commercial values and is now under threat from illegal exploitation in Hong Kong, impairing the local population and biodiversity. Together with other species of Aquilaria, it is listed in the CITES Appendix II, which strictly regulates its international trade. To understand the population structure of A. sinensis and to make relevant conservation measures, we have sequenced 346 individuals collected in Hong Kong and southern mainland China. Population genomic analyses including principal component analysis, neighbor-joining tree construction, ADMIXTURE, and hierarchical pairwise-FST analyses suggested that genetically distinct populations are contained in certain areas. Genomic scan analyses further detected single-nucleotide polymorphism (SNP) outliers related to plant defense, including the CYP71BE gene cluster. In addition to the population analyses, we have developed a modified hexadecyltrimethyl-ammonium bromide (CTAB) DNA extraction protocol for obtaining DNA from agarwood samples in this study, and resequencing of DNA extracted from two agarwood samples using this method allows us to successfully map to the sample corresponding localities in the phylogenetic tree. To sum up, this study suggested that there is a genetically distinct subpopulation of incense tree in Hong Kong that would require special conservation measures and established a foundation for future conservation measures.</p

Table_1_Seasonal drivers of productivity and calcification in the coral Platygyra carnosa in a subtropical reef.docx

Scleractinian corals are increasingly subjected to local stressors combined with global changes. In subtropical areas, corals exhibit metabolic plasticity and resilience in response to variability and extremes in local temperature, salinity, and light; however, the physiological mechanisms by which corals acclimate or adapt to these changing conditions remain disputed. We assessed the physiological status of the coral Platygyra carnosa during a two-year in situ monitoring survey. To obtain metabolic rates (respiration and photosynthesis), photochemical efficiency (Fv / Fm), and biocalcification measurements, non-invasive techniques such as underwater respirometry, Pulse Amplitude Modulated (PAM) fluorometry, total alkalinity measurements, and digital photography were used. Our findings show clear seasonality in water quality parameters, which affected coral health. Elevated temperatures during the summer were below the maximum monthly mean < 31°C) but reduced the energetic productivity of corals (-44% relative to winter). Fluctuations in salinity (25–38 ppt) and pH (7.65–8.44) were linked to rainfall and reduced calcification rates. The conditions during the spring were favorable for coral metabolism and calcification (+20% relative to summer). Overall, our research demonstrates that the metabolic plasticity of P. carnosa in response to shifts in seawater quality allows this species to survive ongoing environmental change. Our in situ observations provide fundamental insights into coral response mechanisms under changing environmental conditions and contribute to projections of coral health under future scenarios of global change.</p