Climate–ecosystem modelling made easy: The Land Sites Platform

Dynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.     

Long-term changes in Noctiluca scintillans blooms along the Chinese coast from 1933 to 2020

Noctiluca scintillans is one of the most common harmful algal species and widely known due to its bioluminescence. In this study, the spatial distribution, seasonal variations, and long-term trends of N. scintillans blooms in China and the related drivers were analyzed and discussed. From 1933 to 2020, a total of 265 events of N. scintillans blooms were recorded in Chinese coastal waters, with a total duration of 1052 days. The first N. scintillans bloom occurred in Zhejiang in 1933, and only three events were recorded before 1980. From 1981 to 2020, N. scintillans caused harmful algal blooms (HABs) almost every year, both the average duration and the proportion of multiphase HABs showed an increasing trend. 1986–1992, 2002–2004, and 2009–2016 were the three peak periods with a frequency of no less than five events of N. scintillans blooms per year. In terms of spatial distribution, N. scintillans blooms spread from the Southeast China Sea to the Bohai Sea after 2000, Guangdong, Fujian, and Hebei were the three provinces with the highest numbers of recorded events of N. scintillans blooms. Moreover, 86.8% of the events of N. scintillans blooms occurred in spring (March, April, and May) and summer (June, July, and August). Among environmental factors, the dissolved inorganic phosphate, dissolved silicate and chemical oxygen demand were significantly correlated with the cell density of N. scintillans during N. scintillans blooms, and most of N. scintillans blooms were recorded in the temperature range of 18.0–25.0°C. Precipitation, hydrodynamics, water temperature, and food availability might be the main factors affecting the spatial–temporal distribution of N. scintillans blooms along the Chinese coast.     

A real-world exploratory study on the feasibility of vonoprazan and tetracycline dual therapy for the treatment of Helicobacter pylori infection in special populations with penicillin allergy or failed in previous amoxicillin-containing therapies

Background

The treatment of Helicobacter pylori (H. pylori) infection is a challenge for those who cannot use amoxicillin.

Objective

To evaluate the eradication rate and adverse effects of vonoprazan and tetracycline dual therapy as first-line and rescue treatment regimens used in special populations with penicillin allergy or failed in previous amoxicillin-containing therapies.

Design

Patients enrolled were those who were H. pylori-positive with selected conditions: (1) allergic to penicillin, either naïve to treatment or had failed before; or (2) failed in previous amoxicillin-containing therapies. All enrolled patients accepted 14-day vonoprazan and tetracycline dual therapy (VT dual therapy) as follows: vonoprazan (20 mg b.i.d.) and tetracycline (500 mg t.i.d. [body weight < 70 kg] or 500 mg q.i.d. [body weight ≥ 70 kg]). H. pylori status was evaluated by ¹³C-urease breath test 6 weeks after treatment. All adverse effects were recorded. Some patients underwent bacterial culture and antibiotic susceptibility testing.

Results

A total of 62 patients were enrolled; 18 of them received VT dual therapy as first-line treatment, 44 patients received VT dual therapy as rescue treatment. Overall, 58 of 62 patients achieved successful eradication (93.5%), while all involved (100%,18/18) succeeded in the first-line treatment group and 40 cases (90.9%, 40/44) succeeded in the rescue treatment group. Sixty-one (61/62, 98.4%) patients completed the whole course of treatment. Adverse events occurred in 6 patients (6/62, 9.7%), while one patient quit because of skin rash. All adverse effects were mild and relieved spontaneously after H. pylori treatment. Five patients achieved successful H. pylori culture, and all strains isolated were sensitive to tetracycline.

Conclusions

For the treatment of H. pylori infection in special populations with penicillin allergy or failed in previous amoxicillin-containing therapies, a 14-day vonoprazan and tetracycline dual therapy was effective and safe as first-line and rescue treatment in our study. Further study is warranted to verify its efficacy, especially for those who cannot use amoxicillin.     

大鼠血小板中的神经肽Y及其对血管收缩的影响

特异性放射免疫分析显示大鼠血小板与富血小板血浆(PRP)分别含NPY免疫活性物质90±16ng/10~7血小板与93±19ng/ml,大大高于普通血浆(1.2±0.1ng/ml)与贫血小板血浆(PPP)(1.7±0.3 ng/ml)中的含量(P<0.001)。血小板样品HPLC各馏分的NPY放免活性峰位与标准NPY的峰位相符。PRP经胶原最大程度聚集后,血小板内的NPY浓度降为34±5 ng/10~7血小板,而PPP中的NPY浓度则升高到26±4 ng/ml。1.6 ml PRP经胶原作用产生最大程度聚集,由此分离所得的PPP引起离体灌流大鼠尾动脉收缩,张力上升380±80 mg;上述PPP经NPY抗血清处理后引起尾动脉收缩的幅度显著减小(190±40 mg,P<0.001)。而1 nmol/L人工合成NPY并不引起血管收缩。结果表明大鼠血小板中含有大量NPY,在不可逆聚集时可以释放,释放的NPY可能参与血小板聚集时释放物质的缩血管效应。     

古菌RecJ蛋白的研究进展

RecJ蛋白属于aspartate-histidine-histidine (DHH)磷酸酯酶超家族,存在于细菌、真核生物和古菌中。细菌RecJ蛋白是一种5′→3′ssDNA外切酶,参与错配修复、同源重组、碱基切除修复等生物学过程。真核生物cell division cycle 45 (Cdc45)蛋白是细菌RecJ核酸酶的同源物,但不具有核酸酶活性。Cdc45蛋白能够与minichromosomemaintenance(MCM)和Go-Ichi-Ni-San(GINS)形成Cdc45-MCM-GINS (CMG)复合物,是真核生物DNA复制的重要组分。在古菌中,几乎所有基因组已测序的古菌均编码一种或多种RecJ蛋白同源物。与细菌RecJ核酸酶不同,古菌RecJ蛋白具有多样化的核酸酶活性,并且能够与MCM和GINS形成类似于真核生物CMG的复合物。因此,古菌RecJ蛋白是参与古菌DNA复制、修复和重组的重要成分。基于目前古菌RecJ蛋白的研究报道,本文综述了古菌RecJ蛋白的活性、结构与功能方面的研究进展,聚焦于不同古菌RecJ蛋白以及它们与细菌RecJ核酸酶和真核生物RecJ同源物的...     

核酸去甲基酶AlkB在毕赤酵母中的表达纯化及在tRNA相关研究中的应用

[目的]核酸的甲基化修饰是一种常见的化学修饰形式,具有重要的生物学功能,却也在一定程度上给一些核酸研究过程带来了技术难度。tRNA上具有的大量甲基化修饰会阻碍逆转录进程,从而降低荧光定量PCR (real-time fluorescence quantitative polymerase chain reaction,RT-qPCR)和高通量测序对其的检测效率。来自大肠杆菌(Escherichia coli)的AlkB蛋白是一种多功能的脱烷基化酶,可以去除DNA和RNA上多种甲基化为代表的修饰,有望解决以上问题。[方法]针对大肠杆菌来源的AlkB,分别尝试在大肠杆菌和毕赤酵母(Pichia pastoris)表达系统中进行诱导表达和纯化,对纯化获得的AlkB进行酶学性质测定。最后以tRNA_UAU^Ile等两种tRNA为代表,研究AlkB的处理对于荧光定量PCR法检测tRNA表达水平的影响。[结果]AlkB在大肠杆菌中表达时多以包涵体形式存在,但是在毕赤酵母中可以成功分泌表达。使用镍柱分离纯化后获得了纯度高于95%的AlkB蛋白,其酶学性质参数如...     

生物淋洗修复钒污染土壤的性能与机理研究

【目的】土壤重金属污染问题日益受到关注,其中钒污染逐渐成为研究热点。淋洗是土壤修复的重要手段,但存在污染大、成本高的缺点。生物淋洗技术因其经济高效且环保的特点能够应用于土壤的修复,但其对钒污染土壤的修复,认识仍非常有限。【方法】本研究采用嗜酸性氧化亚铁硫杆菌对钒污染土壤进行了生物淋洗试验,通过影响因素试验探究了钒的最佳浸出条件,并应用扫描电子显微镜-能量色散X射线谱分析了钒在淋洗过程中的变化,最后对代谢产物进行了解析。【结果】微生物次生代谢产物能促进土壤中钒的溶出。氧化亚铁硫杆菌对土壤钒的浸出效率较高,生物淋洗20 d后土壤中钒的浸出率达到27.4%,进一步的影响因素试验表明,在固体浓度为3%、接种体积为10%、初始pH值为1.8、初始Fe²⁺的浓度为3.0 g/L的条件下,土壤中钒的浸出效果最佳。SEM-EDS分析证实生物淋洗后土壤中钒含量减少,其中以非残渣态形式存在的钒更容易被浸出。代谢组学分析显示氧化亚铁硫杆菌在浸出过程中产生了大量代谢产物来应对重金属胁迫。【结论】生物淋洗技术能够有效地实现土壤钒污染的修复,本研究为钒污染土壤提供了一种环境友好的修复方式。     

内生真菌印度梨形孢诱导小麦抗根腐病作用研究

【目的】明确印度梨形孢(Piriformospora indica)诱导小麦对根腐病产生抗性的作用机制。【方法】用印度梨形孢悬液浸种,以无菌培养液为对照,用病原菌禾谷镰孢菌(Fusarium graminearum)侵染小麦,对其相关生理生化指标及转录组变化进行分析。【结果】禾谷镰孢菌能诱导小麦产生过氧化氢,降低细胞内水含量,破坏细胞膜的稳定性;根部定殖印度梨形孢的小麦细胞内抗氧化酶活性增强,活性氧自由基含量降低,胞内水含量提高,细胞膜稳定性增强;印度梨形孢定殖能改变由于病原菌引起的mRNA转录组变化,抗性相关基因的表达增强。综合表明印度梨形孢定殖能有效地提高小麦对禾谷镰孢菌的抗性。【结论】研究结果为深入理解植物与微生物互作、开发新型高效环保抗根腐病生物制剂提供理论和实验依据。     

硫酸盐对淡水养殖池塘表层底泥微生物的影响

硫酸盐引起的生态学效应已得到了越来越多的关注,但目前关于硫酸盐对养殖池塘底泥微生物的影响还知之甚少。【目的】探究不同浓度硫酸盐对养殖池塘底泥微生物的影响规律及可能的机制。【方法】本研究利用采集自养殖池塘的底泥和表层水构建了试验系统,研究了加入约0 mg/L （对照组）、30 mg/L （T1处理组）、150 mg/L （T2处理组）、500 mg/L （T3处理组） Na₂SO₄后表层底泥微生物的丰度、多样性、组成和共生网络的变化规律,并分析了环境影响因素。【结果】孵育第30天前,各实验组底泥微生物变化不大;但到第50天时,T2和T3处理组微生物丰度和多样性相比对照组均明显下降。相比其他实验组,T1处理组酸杆菌门（Acidobacteriota）、拟杆菌门（Bacteroidota）相对丰度出现显著升高（P<0.05）,T3处理组变形菌门（Proteobacteria）和放线菌门（Actinobacteriota）相对丰度出现显著升高（P<0.05）。与对照组相比,T1处理组增加了较多差异类群（62种）,而T3处理组差异类群大量减少（45种）。共生网络图分析显示硫酸盐浓度的增加引起了底泥微生物网络复杂性的增加,说明微生物群落可能通过自身的调节来响应硫酸盐引起的环境改变。冗余分析（redundant analysis,RDA）和相关性分析揭示底泥总有机碳、总氮和氧化还原电位是影响底泥微生物的主要环境因素,提示底泥微生物可能受到硫酸盐和有机质作用的影响。【结论】较长时间的高浓度硫酸盐会对池塘底泥微生物群落造成重要影响,微生物群落自身的转变和硫酸盐引起的有机质分解改变可能是造成微生物群落变化的关键因素。     

棒状腐败乳杆菌Lc7的生物学特性及益生作用

【目的】对分离自健康成人粪便样本的棒状腐败乳杆菌(Loigolactobacillus coryniformis)Lc7进行分类学鉴定和益生潜力评估。【方法】基于16SrRNA基因和基因组核心基因构建系统发育树,对Lc7进行分类学鉴定;通过耐酸和胆汁酸盐、粘附、抗氧化和抑菌实验,以及溶血、明胶酶活性和抗菌药物敏感性实验,评估Lc7的益生特性。同时,构建小鼠溃疡性结肠炎模型,评估Lc7的体内抗炎潜力。【结果】Lc7鉴定为L. coryniformis,在酸和胆汁酸盐的连续作用下,Lc7的存活率为70.17%。Lc7对HT-29细胞的粘附指数为56.33 CFU/cell,其自聚集和疏水性分别为80%和40%;Lc7对福氏志贺菌和鼠伤寒沙门菌等7个常见致病菌均有较强的抑制能力;对1,1-二苯基-2-苦基肼(1,1-diphenyl-2-picryl-hydrazyl,DPPH)和羟自由基(hydroxyl radicals,·OH)的清除率分别为91.70%和48.53%;Lc7无溶血现象和明胶酶活性,对选取的大多数抗生素均敏感。在小鼠结肠炎实验中,Lc7干预组小鼠结肠长度明显长于模型组(...