Contrasting patterns of morphological variation with dietary preferences in Micropogonias furnieri: insights from stable‐isotope and digestive‐trait analyses

The dietary preferences of populations of whitemouth croaker Micropogonias furnieri, which commonly inhabit estuarine and oceanic environments of the south‐western Atlantic Ocean, were investigated using stable‐isotope analysis and digestive traits, and compared with previous genetic and morphometric surveys of this species. Isotopic and C:N‐derived data suggested that individuals from coastal lagoons are the most differentiated from the remaining localities surveyed. In contrast, the analysis of the digestive traits did not show the same differentiation pattern. The overall correlation between isotopic, molecular and morphological variations suggests that genetic and phenotypic differences among populations are accompanied by differential resource use, supporting the idea that selective forces could be playing an important role in population differentiation.     

Displacement of histamine from liver cells and cell components by ligands for cytochromes P450

Intracellular histamine (HA) and cytochrome P450 monooxygenases (P450) each have been proposed as mediators of cell function, growth, and proliferation. The P450 family of heme enzymes is found in virtually all cells and generates, transforms, or inactivates steroids and other lipids that participate in cell regulation. We previously demonstrated a second messenger role for HA in blood platelets and the formation of a HA-P450 heme complex when exogenous HA was added to microsomes isolated from rat liver cells or to purified human P450 isozymes. Employing a radioimmunoassay, we now demonstrate that rat liver slices, microsomes derived from the livers of adult male rats and mast cell-deficient mice, and hepatoma cells, all contain endogenous HA. HA release from microsomes into the incubation medium, as determined by radioimmunoassay, is enhanced in the presence of carbon monoxide, steroids, and certain drugs, all agents that unite either directly with the iron atom or bind elsewhere within the heme cavity. Rat liver slices preincubated with (3)H-HA release labeled amine into the medium in the presence of those same ligands. These findings provide evidence of an in situ HA-P450 complex and offer further support that the imidazole, HA, is a physiological, intracellular modulator of cytochromes P450 in liver cells, and perhaps of these and other heme proteins in tissues in general.     

国内外心力衰竭治疗质量评价的研究现状

心力衰竭是世界主要的公共卫生问题之一,庞大的心力衰竭患者消耗着大量的医疗资源。近几十年,世界各国专家越来越关注心力衰竭的治疗质量,评价治疗质量已成为医疗体制改革的一项措施。通过总结国内外心力衰竭治疗质量评价的组织机构、评价指标、治疗质量改善项目及有关评价研究,探讨我国心力衰竭治疗质量评价与国外的差距,针对出现的问题,提出相应的建议,为改善我国心力衰竭的治疗质量提供新思路。     

Impacts of the 2014 severe drought on the Microcystis bloom in San Francisco Estuary

The increased frequency and intensity of drought with climate change may cause an increase in the magnitude and toxicity of freshwater cyanobacteria harmful algal blooms (CHABs), including Microcystis blooms, in San Francisco Estuary, California. As the fourth driest year on record in San Francisco Estuary, the 2014 drought provided an opportunity to directly test the impact of severe drought on cyanobacteria blooms in SFE. A field sampling program was conducted between July and December 2014 to sample a suite of physical, chemical, and biological variables at 10 stations in the freshwater and brackish reaches of the estuary. The 2014 Microcystis bloom had the highest biomass and toxin concentration, earliest initiation, and the longest duration, since the blooms began in 1999. Median chlorophyll a concentration increased by 9 and 12 times over previous dry and wet years, respectively. Total microcystin concentration also exceeded that in previous dry and wet years by a factor of 11 and 65, respectively. Cell abundance determined by quantitative PCR indicated the bloom contained multiple potentially toxic cyanobacteria species, toxic Microcystis and relatively high total cyanobacteria abundance. The bloom was associated with extreme nutrient concentrations, including a 20-year high in soluble reactive phosphorus concentration and low to below detection levels of ammonium. Stable isotope analysis suggested the bloom varied with both inorganic and organic nutrient concentration, and used ammonium as the primary nitrogen source. Water temperature was a primary controlling factor for the bloom and was positively correlated with the increase in both total and toxic Microcystis abundance. In addition, the early initiation and persistence of warm water temperature coincided with the increased intensity and duration of the Microcystis bloom from the usual 3 to 4 months to 8 months. Long residence time was also a primary factor controlling the magnitude and persistence of the bloom, and was created by a 66% to 85% reduction in both the water inflow and diversion of water for agriculture during the summer. We concluded that severe drought conditions can lead to a significant increase in the abundance of Microcystis and other cyanobacteria, as well as their associated toxins.     

四川杂谷脑河底栖动物初步调查

于2004年5月对四川杂谷脑河流域9个断面的底栖动物进行了调查。共采集到底栖动物11种,其中水生昆虫8种,软体动物2种和扁形动物1种。应用Beck生物指数对其水质状况进行评价,结果表明杂谷脑河流域除个别断面(红叶减水河段)清洁外,大部分河段有一定程度的污染。     

粤东柘林湾海域富营养化评价与分析

根据2001年7月～2002年7月对拓林湾进行的生态调查所得的数据,运用模糊集理论中的权距离概念结合隶属度的模糊评价方法,以化学耗氧量、总无机氮、活性磷酸盐和叶绿素a为指标,对粤东拓林湾和湾外水域的富营养化状况进行了评价.结果表明,拓林湾的营养状况已达到中营养程度以上,而湾外则处于贫营养状态.     

Histamine enhances cytotrophoblast invasion by inducing intracellular calcium transients through the histamine type-1 receptor

Blastocyst implantation and placentation require molecular and cellular interactions between the uterine endometrium and blastocyst trophectoderm. Previous studies showed that histamine produced in the mouse uterine luminal epithelium interacts with trophoblast histamine type-2 receptors (H2) to initiate blastocyst implantation. However, it is unknown whether similar histamine activity is operative in humans. Using a human cell line (HTR-8/SVneo) derived from first-trimester cytotrophoblasts that expresses both histamine type-1 receptor (H1) and H2, we found that histamine promotes cytotrophoblast invasiveness specifically through activation of H1. Stimulation of H1 in human cytotrophoblasts by histamine induced intracellular Ca2+ (Ca(2+)i) transients by activating phospholipase C and the inositol trisphosphate pathway. The enhanced invasion induced by histamine was blocked by pretreatment with H1 antagonist or by chelation of Ca(2+)i. These findings suggest possible differences between rodents and humans in histamine signaling to the trophoblast.     

Different h2 receptor antihistamines dissimilarly retard the growth of xenografted human melanoma cells in immunodeficient mice

Melanoma cells and tissues contain considerable amounts of histamine and express histamine receptors, suggesting the existence of autocrine and paracrine regulation by histamine. Our previous in vitro results suggested that histamine elevates melanoma cell growth through the H2 receptor. In this work we show that in vivo tumour proliferation in immunodeficient mice xenotransplanted with a human melanoma cell line is diminished by cimetidine, an H2 receptor antagonist, if combined with a tamoxifen derivate acting on cytochrome p450 molecules (DPPE). Ranitidine, another H2 receptor antagonist, has a weaker inhibitory effect, the kinetics and mechanism of which is probably dissimilar to that of the cimetidine/DPPE mixture.     

Measurement of plasma histamine by stable isotope dilution gas chromatography-mass spectrometry: methodology and normal values

A new method for the determination of histamine by stable isotope dilution mass fragmentography is described. The method is specific, sensitive, and accurate, resulting in a within-day coefficient of variation of 4.1% and a day-to-day variation of 7.9%. It was shown that the first blood sample after a venipuncture can contain an artificially elevated plasma histamine concentration. Platelets contain about 7 pmol histamine/10(9) cells. Serum histamine was elevated about four times in comparison with plasma histamine. This phenomenon was mainly ascribed to degranulation of basophilic leukocytes by complement activation during blood clotting. Normal values for plasma histamine were (n = 25) 2.07 +/- 0.75 nmol/liter (mean +/- 1 SD), which is one of the lowest values reported up to now.     

基于NGS的染色质测序在肿瘤研究中的应用

染色质是真核生物细胞核内由核酸和蛋白质组成的复合结构,有着精密且复杂的三维结构。染色质除基本的DNA序列外,内部还存在着不同化学修饰,DNA-蛋白质相互作用,DNA-DNA相互作用和DNA-RNA相互作用,以上这些若发生改变都可能在肿瘤发生发展过程中起到至关重要的作用。通过不同的染色质测序方法,可以解析出这些改变,并进一步加深研究者对肿瘤形成机制的理解,最终应用于肿瘤的治疗。本文对常见的染色质测序技术部分原理和应用进行综述。     

Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA

Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, ‘early detection and rapid response’; (ii) for conserving imperilled native species, ‘protection of biodiversity hotspots’; and (iii) for assessing biosecurity risk, ‘an ounce of prevention equals a pound of cure.’ However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism’s DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next‐generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.     

三种生物质能源植物组织的乙醇提取液对烟粉虱生物活性的影响

为了探讨蓖麻、海滨锦葵等生物质能源植物组织的抽提物作为植物保护剂的可行性,用蓖麻种子、蓖麻叶片、海滨锦葵叶片等生物质能源植物组织的乙醇粗提物处理烟粉虱成虫,4、24、48、72和96 h后测定其体内的谷胱甘肽转移酶和羧酸酯酶活性,并利用Y型嗅觉仪测定烟粉虱对3种生物质能源植物组织的乙醇粗提物的嗅觉反应.结果表明:3种生物质能源植物组织的乙醇粗提物对烟粉虱谷胱甘肽转移酶和羧酸酯酶均有明显影响,随着浓度的提高,其作用增强,其中250倍液的作用与1.8%的阿维菌素3000倍液作用相当.3种提取液的250倍液对烟粉虱成虫具有明显的驱避作用,其中蓖麻种子、蓖麻叶片和海滨锦葵叶片等乙醇粗提物的驱避率分别为100.0%、96.7%和79.4%.表明蓖麻种子、蓖麻叶片和海滨锦葵叶片的乙醇粗抽提物对烟粉虱具有驱避作用和其他生物活性.     

第三脑室注射组胺及其受体激动剂对五肽促胃液素诱导的大鼠胃酸分泌的影响

本文报道第三脑室注射组胺(0.25—2.0μg/5μl)对五肽促胃液素诱导的胃酸分泌的双重影响。雄性Wistar大鼠,重200—300g,戊巴比妥钠腹腔麻醉。用37℃生理盐水通过恒流泵进行连续胃灌流。在静脉恒速灌注五肽促胃液素(7.5μg/kg·h)的基础上,第三脑室注射组胺(0.25μg/5μl)或H_1受体激动剂2-Pyridylethylamine(PEA,10μg/5μl),10min后总酸排出量即开始减少,90min仍未恢复。组胺剂量增至1.0μg或2.0μg时,出现双重效应。部份动物(分别占73％或50％)胃酸分泌减少,另一部分动物(27％或50％)胃酸分泌增多。H_2受体激动剂dimaprit(10μg/5μl)或impromidine(0.1μg/5μl)对胃酸分泌无明显影响。苯海拉明(16μg/0.2ml或32μg/0.2ml,i.m.)预处理可分别取消组胺和PEA的抑胃酸效应。这些结果提示:脑内组胺可能参与胃酸分泌中枢调节。其抑制效应似通过H_1受体介导;双重效应的机制有待进一步研究。     

The ecology and phylogeny of oomycete infections in Asplanchna rotifers

1. Recently, the potential for parasites to influence the ecology and evolution of their zooplankton hosts has been the subject of increasing study. However, most research to date has focussed on Daphnia hosts, and the potential for parasites to influence other zooplankton taxa remains largely unstudied. 2. During routine sampling of zooplankton in a eutrophic lake, we observed that the rotifer Asplanchna girodi was often infected with a parasitic oomycete. Epidemics of this parasite occurred frequently, with three separate events in a single year. Prevalence at peak infection ranged from 29 to 41% and epidemics lasted from 17 to 56 days. Our data indicate that high densities of the host population are required for epidemics to occur. 3. Our morphological and molecular analyses suggest that this parasite is in the genus Pythium. Most Pythium spp. are plant pathogens, but our study supports recent work on Daphnia, suggesting that Pythium spp. are also important parasites of zooplankton. 4. As the parasite in this study was recalcitrant to cultivation, we developed an alternative method to verify its identity. Our approach used quantitative PCR to show that the ribosomal sequences identified increased with increasing density of infected hosts and, thus, were associated with the parasite. This approach should be generally applicable to other plankton parasites that are difficult to cultivate outside their hosts. 5. Infections significantly reduced host fecundity, lifespan and population growth rate. As a result of the virulence of this parasite, it is likely to influence the population ecology and evolution of its Asplanchna host, and may be a useful model system for studies on host–parasite coevolutionary dynamics.     

The Potential Role of Plastome Copy Number as a Quality Biomarker for Plant Products using Real-time Quantitative Polymerase Chain Reaction

Background: Plastids are plant-specific semi-autonomous self-replicating organelles, containing circular DNA molecules called plastomes. Plastids perform crucial functions, including photosynthesis, stress perception and response, synthesis of metabolites, and storage. The plastome and plastid numbers have been shown to be modulated by developmental stage and environmental stimuli and have been used as a biomarker (identification of plant species) and biosensor (an indicator of abiotic and biotic stresses). However, the determination of plastome sequence and plastid number is a laborious process requiring sophisticated equipment.Methods: This study proposes using plastome copy number (PCN), which can be determined rapidly by real-time quantitative polymerase chain reaction (RT-qPCR) as a plant product quality biomarker. This study shows that the PCN log₁₀ and range PCN log₁₀ values calculated from RT-qPCR data, which was obtained for two years from leaves and lint samples of cotton and seed samples of cotton, rice, soybean, maize, and sesame can be used for assessing the quality of the samples.Results: Observation of lower range PCN log₁₀ values for CS (0.31) and CR (0.58) indicated that the PCN showed little variance from the mean PCN log₁₀ values for CS (3.81) and CR (3.85), suggesting that these samples might have encountered ambient environmental conditions during growth and/ or post-harvest storage and processing. This conclusion was further supported by observation of higher range PCN log₁₀ values for RS (3.09) versus RP (0.05), where rice seeds in the RP group had protective hull covering compared to broken hull-less seeds in the RS group. To further support that PCN is affected by external factors, rice seeds treated with high temperatures and pathogens exhibited lower PCN values when compared to untreated seeds. Furthermore, the range PCN log₁₀ values were found to be high for cotton leaf (CL) and lint (Clt) sample groups, 4.11 and 3.63, respectively, where leaf and lint samples were of different sizes, indicating that leaf samples might be of different developmental stage and lint samples might have been processed differently, supporting that the PCN is affected by both internal and external factors, respectively. Moreover, PCN log₁₀ values were found to be plant specific, with oil containing seeds such as SeS (6.49) and MS (5.05) exhibiting high PCN log₁₀ values compared to non-oil seeds such as SS (1.96).Conclusion: In conclusion, it was observed that PCN log₁₀ values calculated from RT-qPCR assays were specific to plant species and the range of PCN log₁₀ values can be directly correlated to the internal and external factors and, therefore might be used as a potential biomarker for assessing the quality of plant products.     

A fault-tolerant method for HLA typing with PacBio data

Background

Human leukocyte antigen (HLA) genes are critical genes involved in important biomedical aspects, including organ transplantation, autoimmune diseases and infectious diseases. The gene family contains the most polymorphic genes in humans and the difference between two alleles is only a single base pair substitution in many cases. The next generation sequencing (NGS) technologies could be used for high throughput HLA typing but in silico methods are still needed to correctly assign the alleles of a sample. Computer scientists have developed such methods for various NGS platforms, such as Illumina, Roche 454 and Ion Torrent, based on the characteristics of the reads they generate. However, the method for PacBio reads was less addressed, probably owing to its high error rates. The PacBio system has the longest read length among available NGS platforms, and therefore is the only platform capable of having exon 2 and exon 3 of HLA genes on the same read to unequivocally solve the ambiguity problem caused by the “phasing” issue.

Results

We proposed a new method BayesTyping1 to assign HLA alleles for PacBio circular consensus sequencing reads using Bayes’ theorem. The method was applied to simulated data of the three loci HLA-A, HLA-B and HLA-DRB1. The experimental results showed its capability to tolerate the disturbance of sequencing errors and external noise reads.

Conclusions

The BayesTyping1 method could overcome the problems of HLA typing using PacBio reads, which mostly arise from sequencing errors of PacBio reads and the divergence of HLA genes, to some extent.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-296) contains supplementary material, which is available to authorized users.