ploidyfrost: Reference-free estimation of ploidy level from whole genome sequencing data based on de Bruijn graphs

Polyploidy is ubiquitous and its consequences are complex and variable. A change of ploidy level generally influences genetic diversity and results in morphological, physiological and ecological differences between cells or organisms with different ploidy levels. To avoid cumbersome experiments and take advantage of the less biased information provided by the vast amounts of genome sequencing data, computational tools for ploidy estimation are urgently needed. Until now, although a few such tools have been developed, many aspects of this estimation, such as the requirement of a reference genome, the lack of informative results and objective inferences, and the influence of false positives from errors and repeats, need further improvement. We have developed ploidyfrost , a de Bruijn graph-based method, to estimate ploidy levels from whole genome sequencing data sets without a reference genome. ploidyfrost provides a visual representation of allele frequency distribution generated using the ggplot2 package as well as quantitative results using the Gaussian mixture model. In addition, it takes advantage of colouring information encoded in coloured de Bruijn graphs to analyse multiple samples simultaneously and to flexibly filter putative false positives. We evaluated the performance of ploidyfrost by analysing highly heterozygous or repetitive samples of Cyclocarya paliurus and a complex allooctoploid sample of Fragaria × ananassa. Moreover, we demonstrated that the accuracy of analysis results can be improved by constraining a threshold such as Cramér's V coefficient on variant features, which may significantly reduce the side effects of sequencing errors and annoying repeats on the graphical structure constructed.     

葫芦茶地上部分化学成分的研究

运用多种色谱法进行分离纯化,并通过理化性质和波谱数据对化合物进行结构鉴定,研究葫芦茶地上部分的化学成分。结果表明:从葫芦茶地上部分分离并鉴定了13个化合物,分别为山柰酚(1)、山柰酚-3-O-α-L-鼠李糖苷(2)、山柰酚-3-O-β-D-葡萄糖苷(3)、山柰酚-3-O-β-D-芸香糖苷(4)、槲皮素-3-O-α-L-鼠李糖苷(5)、山柰酚-3-O-α-L-鼠李糖(1→6)-β-D-半乳糖苷(6)、槲皮素-3-O-β-D-葡萄糖苷(7)、槲皮素-3-O-α-L-鼠李糖(1→6)-β-D-半乳糖苷(8)、芦丁(9)、间苯三酚-O-β-D-葡萄糖苷(10)、对羟基桂皮酸(11)、RoseosideⅡ(12)、儿茶素(13)。其中化合物2、4、5、6、8、9、10、12为首次从该植物中分离得到。     

Relationship between contents of adrenomedullin and distributions of neutral endopeptidase in blood and tissues of rats in septic shock

Adrenomedullin (ADM), a multifunction peptide with important roles in regulating cardiovascular homeostasis, has the vasodilatory properties and is of particular interest in the pathophysiology of sepsis. ADM levels in plasma and tissues are regulated by the proteolysis of neutral endopeptidase (NEP), the major enzyme of ADM degradation. We observed the NEP activity in the plasma, the activity and distribution of NEP and its mRNA expression in the tissues of rats in septic shock to study the possible role of NEP in elevating tissue ADM concentration during sepsis. ADM level increases progressively during sepsis except in the jejunum. Rats in early phase of shock (ES) showed diverse changes in tissue NEP activity. Plasma NEP activity, tissue NEP activity and its protein and mRNA expression in the left ventricle, aorta, jejunum and lung in the late phase of shock (LS) rats were lower than those in ES and the control, but no statistical change of NEP activity in the kidney was observed. The level of ADM was inversely correlated with NEP activity in the plasma, ventricle and aorta and positively correlated with NEP activity in the jejunum. Thus, in sepsis, the local concentration and action of ADM in tissues may be differentially regulated by NEP.     

The Volume Ratio of Ground Glass Opacity in Early Lung CT Predicts Mortality in Acute Paraquat Poisoning

Background

Pulmonary injury is the main cause of death in acute paraquat (PQ) poisoning. However, whether quantitative lung computed tomography (CT) can be useful in predicting the outcome of PQ poisoning remains unknown. We aimed to identify early findings of quantitative lung CT as predictors of outcome in acute PQ poisoning.

Methods

Lung CT scanning (64-slide) and quantitative CT lesions were prospectively measured for patients after PQ intoxication within 5 days. The study outcome was mortality during 90 days follow-up. Survival curves were derived by the Kaplan-Meier method, and mortality risk factors were analyzed by the forward stepwise Cox regression analysis.

Results

Of 97 patients, 41 (42.3%) died. Among the eight different types of lung CT findings which appeared in the first 5-day of PQ intoxication, four ones discriminated between survivors and non-survivors including ground glass opacity (GGO), consolidation, pneumomediastinum and “no obvious lesion”. With a cutoff value of 10.8%, sensitivity of 85.4% and specificity of 89.3%, GGO volume ratio is better than adopted outcome indicators in predicting mortality, such as estimated amount of PQ ingestion, plasma or urine PQ concentration, acute physiology and chronic health evaluation (APACHE) II and sequential organ failure assessment (SOFA) scores. GGO volume ratios above 10.8% were associated with increased mortality (hazard ratio, 5.82; 95% confidence interval, 4.77-7.09; P < 0.001).

Conclusions

The volume ratio of GGO exceeding 10.8% is a novel, reliable and independent predictors of outcome in acute PQ poisoning.     

Intracameral Interleukin 1β, 6, 8, 10, 12p,Tumor Necrosis Factor α and Vascular Endothelial Growth Factor and Axial Length in Patients with Cataract

ObjectiveTo assess associations between the aqueous humour concentration of interleukin IL-1β, IL-6, IL-8, IL-10 and IL-12p, tumor necrosis factor α (TNF-α) and vascular endothelial growth factor (VEGF) and axial length in eyes with cataract.MethodsThe hospital-based investigation included patients who underwent cataract surgery between March 2014 and April 2014. Using aqueous humour collected at the start of cataract surgery, the interleukins IL-1β, IL-6, IL-8, IL-10 and IL-12p, TNF-α and VEGF were examined using a cytometric bead array. Axial length was determined by partial coherence laser interferometry (IOL Master).ResultsThe study included 33 patients with cataract (33 eyes) with a mean age of 69.2±10.8 years (range:50–87 years) and a mean axial length of 24.7±1.9 mm (range:22.6–31.5 mm). Lower aqueous concentration of VEGF was significantly associated with longer axial length (VEGF concentration (pg/mL) = -5.12 x Axial Length (mm) + 163; correlation coefficient r = -0.41; P<0.001) and more myopic refractive error (VEGF concentration (pg/mL) = 1.27xspherical equivalent (diopters)+44.8; r = 0.383; P = 0.002). The aqueous concentrations of all other substances were not significantly (all P>0.10) associated with axial length or refractive error.ConclusionsHigher intravitreal concentrations of VEGF were measured in eyes with a longer axial length, while the intraocular concentrations of IL-1β, IL-6, IL-8, IL-10, IL-12p and TNF-α were not correlated with axial length. The lower concentration of VEGF in axially elongated eyes may be one of the reasons for the lower prevalence of age-related macular degeneration and diabetic retinopathy in myopic eyes.     

中性内肽酶及其抑制剂在心血管疾病过程中的作用

中性内肽酶是一种属于Ⅱ型跨膜蛋白的肽类内切酶,在肽链的氨基端水解疏水氨基酸肽键,灭活心钠素、肾上腺髓质素、血管紧张素、内皮素等心血管活性肽,在高血压病、心力衰竭、动脉粥样硬化和休克等心血管疾病的发病过程中发挥重要作用。     

3种进化类型大豆叶片的某些生理特性比较

半野生、半栽培和栽培大豆叶片可溶性糖和可溶性蛋白含量以及过氧化物酶（POD）和超氧化物歧化酶（SOD）活性均表现为随品种的进化而增加的变化趋势。POD活性在生育期中呈上升变化,SOD活性则随着生育进程逐渐下降。栽培大豆的可溶性糖含量和POD活性以上部叶片最高,半栽培大豆与栽培大豆类似,半野生大豆的变化则不明显。     

三叶草斑潜蝇的入侵、鉴定及在中国适生区分析

介绍了2005年12月首次发现入侵中国大陆的三叶草斑潜蝇Liriomyzatrifolii(Burgess)的形态特征及其与近缘种的形态区别、入侵历史与危害性;利用GARP生态位模型对三叶草斑潜蝇在中国的潜在适生区进行了分析预测,结果表明该虫在中国的潜在适生区涉及范围广,以东部地区的最适宜潜在适生区为主,它的潜在适生区涵盖了热带、亚热带和暖温带等3种气候类型;依据中国大陆目前的发生情况提出对该种入侵害虫的监测方法与防控建议。     

中国尺蛾亚科三新记录属研究（鳞翅目： 尺蛾科）

本文记述中国尺蛾亚科3新记录属及3新记录种： 羚尺蛾Absala dorcada Swinhoe,双弓尺蛾Calleremites subornata Warren,巨尺蛾Pachista superans (Butler)。总结了每个属、种的形态特征;为羚尺蛾 Absala dorcada Swinhoe和巨尺蛾 Pachista superans (Butler) 指定了选模。