Apps can help bridge restoration science and restoration practice

Scientists need to find innovative ways to communicate their findings with restoration practitioners in an era of global change. Apps are a promising bridge between restoration science and practice because they apply broad scientific concepts to specific situations. For example, habitat connectivity promotes ecological function, but practitioners lack ways to incorporate connectivity into decision‐making. We created an app where users calculate how habitat restoration or loss affects connectivity. By providing our app as an example and discussing the benefits and challenges in creating apps for practitioners, we encourage other restoration ecologists to similarly create apps that bridge science with practice.     

Quantifying multiple pressure interactions affecting populations of a recreationally and commercially important freshwater fish

The expanding human global footprint and growing demand for freshwater have placed tremendous stress on inland aquatic ecosystems. Aichi Target 10 of the Convention on Biological Diversity aims to minimize anthropogenic pressures affecting vulnerable ecosystems, and pressure interactions are increasingly being incorporated into environmental management and climate change adaptation strategies. In this study, we explore how climate change, overfishing, forest disturbance, and invasive species pressures interact to affect inland lake walleye (Sander vitreus) populations. Walleye support subsistence, recreational, and commercial fisheries and are one of most sought‐after freshwater fish species in North America. Using data from 444 lakes situated across an area of 475 000 km² in Ontario, Canada, we apply a novel statistical tool, R‐INLA, to determine how walleye biomass deficit (carrying capacity—observed biomass) is impacted by multiple pressures. Individually, angling activity and the presence of invasive zebra mussels (Dreissena polymorpha) were positively related to biomass deficits. In combination, zebra mussel presence interacted negatively and antagonistically with angling activity and percentage decrease in watershed mature forest cover. Velocity of climate change in growing degree days above 5°C and decrease in mature forest cover interacted to negatively affect walleye populations. Our study demonstrates how multiple pressure evaluations can be conducted for hundreds of populations to identify influential pressures and vulnerable ecosystems. Understanding pressure interactions is necessary to guide management and climate change adaptation strategies, and achieve global biodiversity targets.     

pr2-primers: An 18S rRNA primer database for protists

Metabarcoding of microbial eukaryotes (collectively known as protists) has developed tremendously in the last decade, almost solely relying on the 18S rRNA gene. As microbial eukaryotes are extremely diverse, many primers and primer pairs have been developed. To cover a relevant and representative fraction of the protist community in a given study system, an informed primer choice is necessary, as no primer pair can target all protists equally well. As such, a smart primer choice is very difficult even for experts and there are very few online resources available to list existing primers. We built a database listing 285 primers and 83 unique primer pairs that have been used for eukaryotic 18S rRNA gene metabarcoding. In silico performance of primer pairs was tested against two sequence databases: PR² version 4.12.0 for eukaryotes and a subset of silva version 132 for bacteria and archaea. We developed an R -based web application enabling browsing of the database, visualization of the taxonomic distribution of the amplified sequences with the number of mismatches, and testing any user-defined primer or primer set ( https://app.pr2-primers.org ). Taxonomic specificity of primer pairs, amplicon size and location of mismatches can also be determined. We identified universal primer sets that matched the largest number of sequences and analysed the specificity of some primer sets designed to target certain groups. This tool enables guided primer choices that will help a wide range of researchers to include protists as part of their investigations.     

Global research trends and gaps in ecological compensation studies from 1990 to 2020: A scientometric review

Ecosystems are facing severe destruction and threats due to unreasonable human utilization. Repairing damage to nature and protect biodiversity through ecological compensation will be an inevitable measure for achieving sustainable development. To explore the current research hotspots and future research directions of ecological compensation, this paper tries to search the WoS Core Collection and collects 685 ecological compensation papers published between 1990 and 2020. R language and CiteSpace software were applied in this paper. It is found that: (1) The number of articles has gone through the initial explorations, fluctuating growth, and rapid development of the field from 1990 to 2020. Only 7.5% of authors have published more than two papers. (2) Regarding the production of papers, the top 3 countries are the US, China, and the UK. At present, the majority of countries focus on independent research, and international cooperation is gradually strengthening. (3) The current research hotpots mainly invlove biodiversity and sustainable development, ecological compensation for forests and water resources, China's Grain-to-Green Project, poverty reduction, livelihood issues, public participation willingness and equity issues, indicating that ecological compensation is a rapidly emerging interdisciplinary academic field. (4) The results reveal several research directions in the future: strengthening theoretical research, resolving issues pertaining to the complex relationships among stakeholders, encouraging a transformation from qualitative to quantitative research, increasing the focus of ecological compensation models on local conditions, and applying more scientific models and high-tech tools in effect evaluation.     

Selective antibacterial activity of the cationic peptide PaDBS1R6 against Gram-negative bacteria

Infections caused by Gram-negative bacteria, Escherichia coli and Pseudomonas aeruginosa foremost among them, constitute a major worldwide health problem. Bioinformatics methodologies are being used to rationally design new antimicrobial peptides, a potential alternative for treating these infections. One of the algorithms used to develop antimicrobial peptides is the Joker, which was used to design the peptide PaDBS1R6. This study evaluates the antibacterial activities of PaDBS1R6 in vitro and in vivo, characterizes the peptide interaction to target membranes, and investigates the PaDBS1R6 structure in contact with mimetic vesicles. Moreover, we demonstrate that PaDBS1R6 exhibits selective antimicrobial activity against Gram-negative bacteria. In the presence of negatively charged and zwitterionic lipids the structural arrangement of PaDBS1R6 transits from random coil to α-helix, as characterized by circular dichroism. The tertiary structure of PaDBS1R6 was determined by NMR in zwitterionic dodecylphosphocholine (DPC) micelles. In conclusion, PaDBS1R6 is a candidate for the treatment of nosocomial infections caused by Gram-negative bacteria, as template for producing other antimicrobial agents.     

腺苷A_1R在高压氧致中枢神经系统氧中毒发生中的作用研究

目的:探讨腺苷A1受体(A1R)在高压氧(hyperbaric oxygen,HBO)致中枢神经系统氧中毒(central nervous system oxygen toxicity,CNS-OT)发生中的作用。方法:(1)大鼠侧脑室注射A1R选择性激动剂CCPA后观察氧惊厥潜伏期。采用随机数字法将大鼠分为对照组和5μg、10μg以及20μg CCPA给药组。采用侧脑室注射方法分别给予生理盐水和不同剂量CCPA后,进行0.6MPa HBO暴露,记录大鼠的CNS-OT潜伏期。(2)大鼠侧脑室注射A1R选择性抑制剂DPCPX后观察氧惊厥潜伏期。采用随机数字法将大鼠分为对照组和15μg、30μg以及60μg DPCPX给药组。采用脑室注射方法分别给予DMSO和不同剂量DPCPX后,进行0.6 MPa HBO暴露,记录大鼠的CNS-OT潜伏期。结果:脑室注射5μg CCPA组(32.15分±0.8392分)、10μg CCPA组(60.50分±3.150分)和20μg CCPA组(70.91分±2.975分)惊厥潜伏期显著延长,差异有统计学意义(P0.05)。脑室注射30μg DPCPX组(14.09分±1.363分)和60μg DPCPX组(8.564分±0.645分)惊厥潜伏期显著缩短,差异有统计学意义(P0.05)。结论:中枢局部给予腺苷A1R选择性激动剂CCPA可以有效延长CNS-OT的潜伏期;中枢局部给予腺苷A1R选择性抑制剂DPCPX可以有效缩短CNS-OT的潜伏期。     

PTEN regulates IGF‐1R‐mediated therapy resistance in melanoma

Inhibition of the mitogen‐activated protein kinase (MAPK) pathway is a major advance in the treatment of metastatic melanoma. However, its therapeutic success is limited by the rapid emergence of drug resistance. The insulin‐like growth factor‐1 receptor (IGF‐1R) is overexpressed in melanomas developing resistance toward the BRAF^V600 inhibitor vemurafenib. Here, we show that hyperactivation of BRAF enhances IGF‐1R expression. In addition, the phosphatase activity of PTEN as well as heterocellular contact to stromal cells increases IGF‐1R expression in melanoma cells and enhances resistance to vemurafenib. Interestingly, PTEN‐negative melanoma cells escape IGF‐1R blockade by decreased expression of the receptor, implicating that only in melanoma patients with PTEN‐positive tumors treatment with IGF‐1R inhibitors would be a suitable strategy to combat therapy resistance. Our data emphasize the crosstalk and therapeutic relevance of microenvironmental and tumor cell‐autonomous mechanisms in regulating IGF‐1R expression and by this sensitivity toward targeted therapies.     

Association of 25-Hydroxyvitamin D status and genetic variation in the vitamin D metabolic pathway with FEV1 in the Framingham Heart Study

Background

Vitamin D is associated with lung function in cross-sectional studies, and vitamin D inadequacy is hypothesized to play a role in the pathogenesis of chronic obstructive pulmonary disease. Further data are needed to clarify the relation between vitamin D status, genetic variation in vitamin D metabolic genes, and cross-sectional and longitudinal changes in lung function in healthy adults.

Methods

We estimated the association between serum 25-hydroxyvitamin D [25(OH)D] and cross-sectional forced expiratory volume in the first second (FEV₁) in Framingham Heart Study (FHS) Offspring and Third Generation participants and the association between serum 25(OH)D and longitudinal change in FEV₁ in Third Generation participants using linear mixed-effects models. Using a gene-based approach, we investigated the association between 241 SNPs in 6 select vitamin D metabolic genes in relation to longitudinal change in FEV₁ in Offspring participants and pursued replication of these findings in a meta-analyzed set of 4 independent cohorts.

Results

We found a positive cross-sectional association between 25(OH)D and FEV₁ in FHS Offspring and Third Generation participants (P = 0.004). There was little or no association between 25(OH)D and longitudinal change in FEV₁ in Third Generation participants (P = 0.97). In Offspring participants, the CYP2R1 gene, hypothesized to influence usual serum 25(OH)D status, was associated with longitudinal change in FEV₁ (gene-based P < 0.05). The most significantly associated SNP from CYP2R1 had a consistent direction of association with FEV₁ in the meta-analyzed set of replication cohorts, but the association did not reach statistical significance thresholds (P = 0.09).

Conclusions

Serum 25(OH)D status was associated with cross-sectional FEV₁, but not longitudinal change in FEV₁. The inconsistent associations may be driven by differences in the groups studied. CYP2R1 demonstrated a gene-based association with longitudinal change in FEV₁ and is a promising candidate gene for further studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0238-y) contains supplementary material, which is available to authorized users.     

鸭疫里默氏杆菌RecA作为一种内参蛋白的评价

由于缺少适合的内参蛋白,所以用Western blot的方法来研究鸭疫里默氏杆菌蛋白表达的调节尚未见报道。以鸭疫里默氏杆菌基因组为模板,PCR扩增含有组氨酸标签His-tag的rec A基因和截段的rec AP基因,并分别将其克隆于原核表达载体p ET32a。将重组质粒转化到表达菌Rosetta中,经1mmol/L的IPTG诱导进行蛋白质表达。用组氨酸标签亲和试剂镍-琼脂糖进行重组蛋白质的纯化。用纯化的重组蛋白对4周龄的昆明鼠进行免疫,制备多克隆抗体。Western blot实验表明,截段表达的Rec AP的多克隆抗体血清比全长Rec A蛋白的多克隆抗体血清与鸭疫里默氏杆菌总蛋白反应更特异;在铁离子限制性环境和血红素丰富环境中培养的鸭疫里默氏杆菌的Rec A蛋白表达量一致。因此,鸭疫里默氏杆菌的Rec A蛋白可以在铁离子和血红素代谢等研究中作为Western blot的内参蛋白。