Consistent probabilistic outputs for protein function prediction

Background:

The wide availability of genome-scale data for several organisms has stimulated interest in computational approaches to gene function prediction. Diverse machine learning methods have been applied to unicellular organisms with some success, but few have been extensively tested on higher level, multicellular organisms. A recent mouse function prediction project (MouseFunc) brought together nine bioinformatics teams applying a diverse array of methodologies to mount the first large-scale effort to predict gene function in the laboratory mouse.

Results:

In this paper, we describe our contribution to this project, an ensemble framework based on the support vector machine that integrates diverse datasets in the context of the Gene Ontology hierarchy. We carry out a detailed analysis of the performance of our ensemble and provide insights into which methods work best under a variety of prediction scenarios. In addition, we applied our method to Saccharomyces cerevisiae and have experimentally confirmed functions for a novel mitochondrial protein.

Conclusion:

Our method consistently performs among the top methods in the MouseFunc evaluation. Furthermore, it exhibits good classification performance across a variety of cellular processes and functions in both a multicellular organism and a unicellular organism, indicating its ability to discover novel biology in diverse settings.

     

Quantification of manganese and mercury in toenail in vivo using portable X-ray fluorescence (XRF)

Background and objective: Toenail is an advantageous biomarker to assess exposure to metals such as manganese and mercury. Toenail Mn and Hg are in general analyzed by chemical methods such as inductively coupled plasma mass spectrometry and atomic absorption spectrophotometry. In this project, a practical and convenient technology—portable X-ray florescence (XRF)—is studied for the noninvasive in vivo quantification of manganese and mercury in toenail.

Material and methods: The portable XRF method has advantages in that it does not require toenail clipping and it can be done in 3?min, which will greatly benefit human studies involving the assessment of manganese and mercury exposures. This study mainly focused on the methodology development and validation which includes spectral analysis, system calibration, the effect of toenail thickness, and the detection limit of the system. Manganese- and mercury-doped toenail phantoms were made. Calibration lines were established for these measurements.

Results: The results show that the detection limit for manganese is 3.65?μg/g (ppm) and for mercury is 0.55?μg/g (ppm) using 1?mm thick nail phantoms with 10?mm soft tissue underneath.

Discussion and conclusion: We conclude that portable XRF is a valuable and sensitive technology to quantify toenail manganese and mercury in vivo.     

The Poverty of Tourism under Mobilizational Developmentalism in China

ABSTRACT

In China tourism has been promoted not only as a passport to development in general, but also as an effective instrument to help the poor, and to regulate the serious regional disparity between the coastal and inland areas. In practice, tourism has been adopted popularly by local state elites as an important local economic development strategy, especially in poverty-stricken areas. This article studies the pattern of tourism development in China through the historically specific institutional dynamics of mobilizational developmentalism, which is generated from a blending of mobilizational bureaucracy with developmentalism. With the analytical framework of mobilization developmentalism, this article studies a case of “industrialization of tourism” in which the Miao New Year was promoted by a nationally designated poor county as a tourism-led development project. On one hand, this article analyzes how local bureaucrats at various levels of the government responded to the political mobilization of a tourism-led development project. On the other hand, this study explores how local communities respond to tourism projects mobilized from above. This article argues that mobilizational developmentalism shapes a specific set of political, economic and cultural processes among local state elites, tourist operators, and local communities in developing tourism in China.     

我国医师多点执业的现状及政策问题确认

目的 明确我国医师多点执业的现状,并进行政策问题确认。方法 定性研究与定量研究相结合。结果 当前我国医师多点执业尚处于试点推行阶段,各方反响不一;政策的推行面临一系列诸如人事制度、医疗质量保障和医疗争议追究等体制、机制上的政策问题。结论 推行医师多点执业政策是优化资源配置、调动医务人员的积极性、推动公立医院改革的重要举措,但需夯实基础、合理规划、加强监督,逐步深化人事制度改革,促进政策的稳步推行。     

FRET reveals multiple interaction states between two component signalling system proteins of M. tuberculosis

BackgroundTwo component signalling involves interaction between sensor kinase (SK) and response regulator (RR) proteins which depends on their phosphorylation status.MethodsIn this study we report the development of an in vitro FRET assay for studying interaction between fluorescently tagged SK and RR proteins.ResultsUsing TCS proteins of Mycobacterium tuberculosis, we demonstrate that phosphorylation status of SK affects the SK–RR interaction, which varies from one TCS to another. The observation was strengthened by recordings from mutant SK and RR proteins. The assay retained the specificity/crosstalk potential of the participating proteins and reflected the inherent phosphotransfer potentials.ConclusionsSK and RR proteins interact with each other in unphosphorylated state and the phosphorylation affects the interaction between SK and RR, which was reflected as reduction in FRET ratio.General significanceA non-radioactive, in vitro FRET based assay is reported, which can be utilized for studying genome-wide partner screening, identifying crosstalk or specificity in TCSs.     

Applicability of the European Environmental Footprint (EF) methodology in Southern Mediterranean countries—learnings and recommendations for enabling EF-compliant studies in regions outside of Europe

Purpose

The European Commission is thinking about policy options for the European Environmental Footprint (EF) method and aims for a broad support. The SwitchMed initiative is a programme with the overall objective to facilitate the shift towards sustainable consumption and production in the Southern Mediterranean region. One of the objectives of this initiative, carried out in Egypt, Lebanon, Morocco, and Tunisia, is to facilitate access of companies from this region to the outcomes of the EF Rules pilot phase.

Methods

The project was composed of three consecutive phases: (I) awareness raising; (II) local pilots; and (III) dissemination events. The awareness raising and technical workshop activities were meant to expose national stakeholders to the potential impact of the EF system for the national economies. Next, nine environmental footprint studies for selected product categories (so-called PEF pilot studies) were performed to create local capacity and expertise. These were leather and intermediate paper product for Egypt; two studies on wine and one on intermediate paper product in Lebanon; olive oil for Morocco; and pasta, olive oil, and dairy for Tunisia. The learnings from the pilot studies were shared in national dissemination events and used to formulate recommendations for enabling EF-compliant studies in regions outside of Europe.

Results and discussion

There was high attendance to the awareness events in each country. The pilot studies showed many similarities with the European screening studies, but also important differences in the identification of most relevant impact categories, life cycle stages, and processes (‘hotspots analyses’), e.g. related to the local scarcity of water. Based on their pilot study, the local experts made concrete suggestions for shifting towards more sustainable consumption and production. One of the biggest successes of this project is that a couple of these recommendations have already been taken into account by the companies.

Conclusions and recommendations

In Egypt, Lebanon, and Tunisia, a few local experts with a significant level of LCA expertise could be identified and through this project we managed to create local PEF capacity too. In Morocco, more assistance was needed to finish the pilot study. This project made clear that the current ‘PEF and OEF methods’ have serious drawbacks for regions other than Europe. The rules of the EF method need to be reconsidered in order to enable EF-compliant studies in regions outside of Europe. In short, we recommend:

1. 1.

   Developing databases with local inventory data for regions outside of Europe;

2. 2.

   Enlarging access to EF-compliant data by extension of the free access and by facilitation of the availability of conversion tools;

3. 3.

   Taking the local availability of data into account when setting data quality requirements;

4. 4.

   Adapting the rules for data collection and quality to allow for more precise adaptations;

5. 5.

   Including in the PEFCR development, supporting studies for products manufactured outside the EU and/or in a geography with unusual conditions; and

6. 6.

   Updating existing rules specific for certain product categories regularly.

     

When to use what: Methods for weighting and aggregating sustainability indicators

ContextSustainability indices (SIs) have become increasingly important to sustainability research and practice. However, while the validity of SIs is heavily dependent on how their components are weighted and aggregated, the typology and applicability of the existing weighting and aggregation methods remain poorly understood.ObjectivesTo close the knowledge gap regarding when to use which weighting and aggregation methods for constructing SIs, we review the most commonly used methods for weighting and aggregating SIs, discuss their benefits and drawbacks, and suggest a process-oriented approach for choosing appropriate weighting and aggregation methods depending on research objectives.MethodsOur review synthesis was based on peer-reviewed journal articles, books, and reports by international organizations, governmental agencies, and research institutions. After carefully examining their principles, characteristics, and applications, we selected and classified the frequently used methods for indicator weighting and aggregation.ResultsWe systematically discuss the benefits and drawbacks of nine weighting methods and three aggregation methods. We propose a four-step process for choosing the most suitable weighting and aggregation methods based on: research purposes, spatial and temporal scales, and sustainability perspectives.ConclusionsIn this research, we chose the most commonly used methods for weighting and aggregating SIs and analyzed the characteristics, strengths and weaknesses of each method. We found that choosing appropriate weighting and aggregation methods for a specific sustainability assessment project is an extremely important and challenging task. To meet this challenge, we propose a process-oriented approach for properly selecting methods according to the purpose, scale and sustainability concept. This approach can facilitate the proper selection of these methods in sustainability research and practice.     

Vecteurs et instrumentation,pour l’imagerie peroperatoire (V2iP)

ObjectiveThe meaning of this work was to develop a new medical imaging technique aimed to assist the surgical act during the resection of cancerous tumors.MethodThis technique is based on both the specificity of anti-tumor monoclonal antibodies or anti-neovessels peptides and the sensitivity of fluorescent detection. The objective was to develop and offer to surgeons the most effective vector-fluorophore-detection probe association in order to help them to significantly improve the patient's recovery. The development of a fluorescent detection probe fulfils two requirements: avoiding the injection of radioactive molecules which calls for difficult protection procedures and offering such detection to abdominal surgery, for which the background noise caused by the use of radioisotopes makes this technique hardly efficient. The experimental part of the project had the aim of comparing, within animals, the sensitivity and specificity of these techniques. Preclinical study has also been realized for fluorescent markers. Such studies had to show the benefits of the optical method compared to the radioisotopic method for oncology surgeons.ResultsAn industrial prototype of the probe has been developed and tested on animals after injection of the tumor specific molecule conjugated to a fluorescent dye developed within the frame of the project. The digestive tumors could perfectly be visualised.ConclusionThis surgical imaging technique should have a major impact on the practices of oncology surgeons and should lead to less complementary therapies and therefore more comfort for the patients.     

Recent development of advanced biotechnology for wastewater treatment

Abstract

The importance of highly efficient wastewater treatment is evident from aggravated water crises. With the development of green technology, wastewater treatment is required in an eco-friendly manner. Biotechnology is a promising solution to address this problem, including treatment and monitoring processes. The main directions and differences in biotreatment process are related to the surrounding environmental conditions, biological processes, and the type of microorganisms. It is significant to find suitable biotreatment methods to meet the specific requirements for practical situations. In this review, we first provide a comprehensive overview of optimized biotreatment processes for treating wastewater during different conditions. Both the advantages and disadvantages of these biotechnologies are discussed at length, along with their application scope. Then, we elaborated on recent developments of advanced biosensors (i.e. optical, electrochemical, and other biosensors) for monitoring processes. Finally, we discuss the limitations and perspectives of biological methods and biosensors applied in wastewater treatment. Overall, this review aims to project a rapid developmental path showing a broad vision of recent biotechnologies, applications, challenges, and opportunities for scholars in biotechnological fields for “green” wastewater treatment.     

A passive pressure sensor for continuously measuring the intraocular pressure in glaucomatous patients

ObjectiveThe main risk factor for the development of glaucoma, a retinal disease leading to blindness, is an increase in the intraocular pressure (IOP). Reducing this IOP can be obtained by eye drops but unfortunately the disease can still progress because IOP increases are painless, can fluctuate and, thus remain undetected during a visit to an ophthalmologist. The “MATEO” ANR project aims to develop sensors embedded in a contact lens for continuously IOP monitoring.Materials and methodsPressure sensors were produced by MEMS technology and tested with pig eyes obtained at a local slaughterhouse. Solution was injected by 50 μL steps in the eye with a Hamilton syringe while IOP was monitored in parallel with a TonoVET system and an industrial pressure transducer inserted in the injection tubing system.ResultsOur first pressure sensor prototypes were generated and inserted in a lens compatible with eye application. A wireless system was developed to excite the sensor. At same time, it was recorded the data in components inserted into spectacles and a pocket recorder. In parallel, we showed that injecting a solution in the eye anterior chamber triggered an IOP increase smaller and more stable than injections in the posterior chamber. Finally, a direct correlation was observed between IOP measured on the corneal surface with the TonoVET and the pressure transducer placed close to eye injection point.DiscussionOur results indicate that our in vitro model on pig eyes is adequate to test our new lens sensor. Finally, the pressure sensor was successfully inserted in contact lens opening the way for their in vitro and in vivo preclinical validation.     

金针菇信息素信号通路基因在子实体发育过程中的差异表达

【背景】子实体是食用菌的主要商品部位,也是真菌生殖生长的重要结构,其发育受到多种信号途径的调控。【目的】以金针菇(Flammulina filiformis)为材料,对转录组和基因组数据的信息素信号通路基因进行分析获得差异表达的基因,并对其在菌丝生长和子实体发育过程中的表达情况进行分析,以期为研究食用菌子实体发育提供参考。【方法】基于已有的金针菇基因组数据,注释了金针菇信息素信号通路。进一步通过转录组测序鉴定了该通路中参与金针菇子实体发育的关键基因,并对关键基因进行荧光定量PCR验证。【结果】cdc24和ste12基因在子实体发育不同时期的5个样品(原基、伸长期菌柄、伸长期菌盖、成熟期菌柄和成熟期菌盖)中的表达具有显著差异,使用荧光定量PCR技术进行验证与上述结果一致。【结论】cdc24和ste12这2个关键基因可能参与了金针菇子实体发育过程中的组织分化调控机制。     

白念珠菌14-3-3蛋白Bmh1在细胞生长和菌丝发育中的功能解析

【目的】应用Tet-off启动子研究白念珠菌唯一的14-3-3蛋白Bmh1在白念珠菌生长和菌丝发育过程中的功能。【方法】在白念珠菌URA3+菌株SN152中,我们敲除了1个BMH1基因拷贝,并用Tet-off启动子替代另一个BMH1基因拷贝的启动子,得到了可以用强力霉素(Doxycycline)控制Bmh1表达水平的菌株。然后我们通过斑点试验和形态学观察对该菌株的生长和菌丝发育表型进行了分析。通过在ras1、flo8、efg1、cph1、tec1等重要菌丝发育调控因子突变体中过表达Bmh1,我们初步研究了Bmh1在菌丝发育调控网络中的位置。最后,我们构建了一些不同C末端的Bmh1嵌合体并检测了其对白念珠菌生长和菌丝发育的影响。【结果】Doxycycline诱导Bmh1表达水平下调时严重抑制了细胞的生长。非Doxycycline诱导条件下Bmh1高表达强烈促进了细胞的菌丝发育。这一促进作用绕过了ras1、efg1、cph1和tec1等基因缺失的影响,却被flo8基因的缺失阻断。C末端缺失或更换异源C末端的所有Bmh1突变株在Doxycycline诱导时都能够正常生长,但是没有明显促进菌丝发育。【结论】验证了白念珠菌14-3-3蛋白Bmh1是细胞生长所必需的,证明了Tet-off启动子可以严密控制Bmh1的表达水平。Bmh1是一个菌丝发育的正调控因子,位于Ras1、Efg1、Cph1和Tec1的下游,Flo8的上游。Bmh1的保守结构域是细胞生长所必需的,而C末端则是生长非必需的。     

The upcoming new elite among children of immigrants: a cross-country and cross-sector comparison

ABSTRACT

The European-born children of immigrants, often referred to as the second generation, play an important role in the academic debate about integration and assimilation. The successful second generation, defined in terms of possessing a higher education diploma and or professional position, receives increasing attention. In this special issue, we will look at the most successful group: the upcoming “elite” among the descendants of migrants from Turkey, based on data gathered in the ELITES, Pathways to Success project. In this research project we deliberately selected on the dependent variable: being professionally successful in managerial jobs in the corporate business sector, the corporate law sector and the education sector.     

Enhancing hypothiocyanite production by lactoperoxidase – mechanism and chemical properties of promotors

BackgroundThe heme enzyme lactoperoxidase is found in body secretions where it significantly contributes to the humoral immune response against pathogens. After activation the peroxidase oxidizes thiocyanate to hypothiocyanite which is known for its microbicidal properties. Yet several pathologies are accompanied by a disturbed hypothiocyanite production which results in a reduced immune defense.MethodsThe results were obtained by measuring enzyme-kinetic parameters using UV–vis spectroscopy and a standardized enzyme-kinetic test system as well as by the determination of second order rate constants using stopped-flow spectroscopy.ResultsIn this study we systematically tested thirty aromatic substrates for their efficiency to promote the lactoperoxidase-mediated hypothiocyanite production by restoring the native ferric enzyme state. Thereby hydrophobic compounds with a 3,4-dihydroxyphenyl partial structure such as hydroxytyrosol and selected flavonoids emerged as highly efficient promotors of the (pseudo-)halogenating lactoperoxidase activity.ConclusionsThis study discusses important structure-function relationships of efficient aromatic LPO substrates and may contribute to the development of new agents to promote lactoperoxidase activity in secretory fluids of patients.SignificanceThis study may contribute to a better understanding of the (patho-)physiological importance of the (pseudo-)halogenating lactoperoxidase activity. The presented results may in future lead to the development of new therapeutic strategies which, by reactivating lactoperoxidase-derived hypothiocyanite production, promote the immunological activity of this enzyme.     

In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform

Background

In 2018, about 10 million people were found infected by tuberculosis, with approximately 1.2 million deaths worldwide. Despite these numbers have been relatively stable in recent years, tuberculosis is still considered one of the top 10 deadliest diseases worldwide. Over the years, Mycobacterium tuberculosis has developed a form of resistance to first-line tuberculosis treatments, specifically to isoniazid, leading to multi-drug-resistant tuberculosis. In this context, the EU and Indian DBT funded project STriTuVaD—In Silico Trial for Tuberculosis Vaccine Development—is supporting the identification of new interventional strategies against tuberculosis thanks to the use of Universal Immune System Simulator (UISS), a computational framework capable of predicting the immunity induced by specific drugs such as therapeutic vaccines and antibiotics.

Results

Here, we present how UISS accurately simulates tuberculosis dynamics and its interaction within the immune system, and how it predicts the efficacy of the combined action of isoniazid and RUTI vaccine in a specific digital population cohort. Specifically, we simulated two groups of 100 digital patients. The first group was treated with isoniazid only, while the second one was treated with the combination of RUTI vaccine and isoniazid, according to the dosage strategy described in the clinical trial design. UISS-TB shows to be in good agreement with clinical trial results suggesting that RUTI vaccine may favor a partial recover of infected lung tissue.

Conclusions

In silico trials innovations represent a powerful pipeline for the prediction of the effects of specific therapeutic strategies and related clinical outcomes. Here, we present a further step in UISS framework implementation. Specifically, we found that the simulated mechanism of action of RUTI and INH are in good alignment with the results coming from past clinical phase IIa trials.

     

A School Health Project Can Uplift the Health Status of School Children in Nepal

BackgroundSchool health is effective in helping students achieve health literacy, enhance their health-related behaviors, and thereby improve their health status. However, in resource-limited countries, evidence is limited to show the impact of school health. We determined the association of the school health and nutrition (SHN) project activities on students’ a) health knowledge, b) hygiene practices, and c) health outcomes, one year after the project completion.MethodsThis is a cross-sectional study conducted among the schools with the SHN project and without the project in four districts of Nepal. We recruited 604 students from six schools in the project group and 648 students from other six schools in the comparison group. We used a self-administered questionnaire to collect the data, and analyzed them using regression models and a structural equation model (SEM).ResultsStudents from the SHN project group reported the decreased odds of worm infestation (AOR = 0.50, 95% CI: 0.34 to 0.75) and diarrhea/ dysentery infection (AOR = 0.67, 95% CI: 0.47 to 0.97) compared to those in the comparison group. Furthermore, the SEM analysis also showed that the students in the project group were more likely to have better health outcomes (β = 0.03, p< 0.05).ConclusionStudents in the SHN project group were more likely to have better health outcomes compared to those in the comparison group, even after one year of the project completion. As it can bring about sustainable changes for students, it should be scaled up in other parts of the country.     

Botulinum neurotoxin inhibitor binding dynamics and kinetics relevant for drug design

BackgroundA natural product analog, 3-(4-nitrophenyl)-7H-furo[3,2-g]chromen-7-one, which is a nitrophenyl psoralen (NPP) was found to be an effective inhibitor of botulinum neurotoxin type A (BoNT/A).MethodsIn this work, we performed enzyme inhibition kinetics and employed biochemical techniques such as isothermal calorimetry (ITC) and fluorescence spectroscopy as well as molecular modeling to examine the kinetics and binding mechanism of NPP inhibitor with BoNT/A LC.ResultsStudies of inhibition mechanism and binding dynamics of NPP to BoNT/A light chain (BoNT/A LC) showed that NPP is a mixed type inhibitor for the zinc endopeptidase activity, implying that at least part of the inhibitor-enzyme binding site may be different from the substrate-enzyme binding site. By using biochemical techniques, we demonstrated NPP forms a stable complex with BoNT/A LC. These observations were confirmed by Molecular Dynamics (MD) simulation, which demonstrates that NPP binds to the site near the active site.ConclusionThe NPP binding interferes with BoNT/A LC binding to the SNAP-25, hence, inhibits its cleavage. Based on these results, we propose a modified strategy for designing a molecule to enhance the efficiency of the inhibition against the neurotoxic effect of BoNT.General significanceInsights into the interactions of NPP with BoNT/A LC using biochemical and computational approaches will aid in the future development of effective countermeasures and better pharmacological strategies against botulism.     

链霉菌CB02959中四霉素及四烯菌素的鉴定及培养基优化

【背景】四霉素(Tetramycin)和四烯菌素(Tetrin)是具有广谱抗真菌活性的四烯大环内酯类抗生素。链霉菌CB02959是一株雷纳霉素(Leinamycin)类化合物的潜在产生菌株,利用antiSMASH分析其基因组发现该菌株含有一个纳他霉素(Natamycin)类四烯大环内酯化合物的生物合成基因簇。【目的】对Streptomyces sp. CB02959中次级代谢产物进行研究,确定其是否可以产生四烯大环内酯化合物,对其发酵产物进行分离和结构鉴定,并进行初步的发酵优化以提高产量。【方法】基于生物信息学预测和高分辨质谱数据,推测CB02959中多烯化合物的结构;在不同发酵培养基中培养CB02959,确定适合大规模发酵的培养基;敲除tetrA基因以确定目标基因簇和四烯大环内酯化合物产生的相关性;分离和鉴定CB02959产生的主要代谢物的结构;通过改变培养基中葡萄糖、麦芽提取物和胰蛋白胨的含量,提高四烯大环内酯化合物的产量。【结果】通过对CB02959中纳他霉素类化合物生物合成基因簇的分析及16S rRNA基因序列的进化树分析,推测CB02959可能是一株新的四霉素和四烯菌素产生菌;在YEME发酵培养基中对CB02959进行大规模发酵,分离得到4个化合物,鉴定为四霉素A (1)、四霉素B (2)、四烯菌素A (3)、四烯菌素B (4);最后通过培养基的初步优化,将化合物1–4的产量分别提高至208.1、100.0、1 315.6、109.9 mg/L。【结论】通过基因组挖掘策略发现了一株新的四霉素和四烯菌素产生菌链霉菌CB02959,并通过培养基优化提升了其四烯大环内酯化合物的产量,此发现为这类抗真菌天然产物的后续开发奠定了基础。