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Reply to “Beyond microbial carbon use efficiency”

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National Science Review 2024年第4期11卷 35-37页

作者： Feng Tao Johannes Lehmann Ying-Ping Wang Lifen Jiang Bernhard Ahrens Kostiantyn Viatkin Stefano Manzoni Benjamin Z.Houlton Yuanyuan Huang Xiaomeng Huang Yiqi Luo department of Ecology and Evolutionary Biology Cornell University Soil and Crop sciences Section School of Integrative Plant ScienceCornell University CSIRO Environment Max Planck Institute for Biogeochemistry department of Physical Geography and Bolin Centre for Climate Research Stockholm University department of Global Development Cornell University Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences department of Earth System Science Ministry of Education Key Laboratory for Earth System Modelling Institute for Global Change Studies Tsinghua University

In their commentary, Xiao et al.[1]cautioned that the conclusions on the critical role of microbial carbon use efficiency (CUE) in global soil organic carbon (SOC) storage in the paper by Tao et al.[2] might be too simplistic.They claimed that Tao et al.’s study lacked mechanistic consideration of SOC formation and excluded important data sets.Xiao et al. brought up important points,which can be largely reconciled with our findings by understanding the differences in expressing processes in empirical studies and in models.

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Identifying genetic susceptibility to Aspergillus fumigatus infection using collaborative cross mice and RNA-Seq approach

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Animal Models and Experimental Medicine 2024年第1期7卷 36-47页

作者： Roa'a H.S.Yosief Iqbal M.Lone Aharon Nachshon Heinz Himmelbauer Irit Gat-Viks Fuad A.Iraqi department of Clinical Microbiology and Immunology Sackler Faculty of MedicineTel-Aviv UniversityTel-AvivIsrael School of Molecular Cell Biology and Biotechnology George S.Wise Faculty of Life SciencesTel Aviv UniversityTel AvivIsrael Institute of Computational Biology Department of BiotechnologyUniversity of Natural Resources and Life SciencesMuthgasse 181190 ViennaAustria

Background:Aspergillus fumigatus(Af)is one of the most ubiquitous fungi and its infection potency is suggested to be strongly controlled by the host genetic back-ground.The aim of this study was to search for candidate genes associated with host susceptibility to Aspergillus fumigatus(Af)using an RNAseq approach in CC lines and hepatic gene expression.Methods:We studied 31 male mice from 25 CC lines at 8 weeks old;the mice were infected with Af.Liver tissues were extracted from these mice 5 days post-infection,and next-generation RNA-sequencing(RNAseq)was performed.The GENE-E analysis platform was used to generate a clustered heat map matrix.Results:Significant variation in body weight changes between CC lines was ob-served.Hepatic gene expression revealed 12 top prioritized candidate genes differ-entially expressed in resistant versus susceptible mice based on body weight changes.Interestingly,three candidate genes are located within genomic intervals of the previ-ously mapped quantitative trait loci(QTL),including Gm16270 and Stox1 on chromo-some 10 and Gm11033 on chromosome 8.Conclusions:Our findings emphasize the CC mouse model's power in fine mapping the genetic components underlying susceptibility towards Af.As a next step,eQTL analysis will be performed for our RNA-Seq data.Suggested candidate genes from our study will be further assessed with a human cohort with aspergillosis.

关键词： aspergillus fumigatus infection collaborative cross(CC)mice gene expression profile gene-network host susceptibility quantitative trait loci(QTL)mapping RNA-Seq

An oscillation-free Hermite WENO scheme for hyperbolic conservation laws

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Science China Mathematics 2024年第2期67卷 431-454页

作者： Zhuang Zhao Jianxian Qiu School of Mathematical sciences and Institute of natural sciences Shanghai Jiao Tong UniversityShanghai 200240China School of Mathematical sciences and Fujian Provincial Key Laboratory of Mathematical Modeling and High-Performance Scientific Computing Xiamen UniversityXiamen 361005China

In this paper, the sixth-order oscillation-free Hermite weighted essentially non-oscillatory (OFHWENO) scheme is proposed for hyperbolic conservation laws on structured meshes, where the zeroth- andfirst-order moments are the variables for the governing equations. The main difference from other HWENOschemes existing in the literature is that we add high-order numerical damping terms in the first-order momentequations to control spurious oscillations for the OF-HWENO scheme. The OF-HWENO scheme not only canachieve the designed optimal numerical order, but also can be easily implemented as we use only one set ofstencils in the reconstruction procedure and the same reconstructed polynomials are applied for the zeroth- andfirst-order moment equations. In order to obtain the adaptive order resolution when facing discontinuities, atransition polynomial is added in the reconstruction, where the associated linear weights can also be any positivenumbers as long as their summation equals one. In addition, the OF-HWENO scheme still keeps compactnessas only immediate neighbor values are needed in the space discretization. Some benchmark numerical tests areperformed to illustrate the high-order accuracy, high resolution and robustness of the proposed scheme.

关键词： Hermite WENO scheme hyperbolic conservation laws oscillation-free adaptive order discontinuous Galerkin method

Enhancing SAEAs with unevaluated solutions:a case study of relation model for expensive optimization

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Science China(Information sciences) 2024年第2期67卷 41-58页

作者： Hao HAO Xiaoqun ZHANG Aimin ZHOU Institute of natural sciences Shanghai Jiao Tong University Shanghai Frontiers Science Center of Molecule Intelligent Syntheses School of Computer Science and Technology East China Normal University

Surrogate-assisted evolutionary algorithms(SAEAs) hold significant importance in resolving expensive optimization problems. Extensive efforts have been devoted to improving the efficiency of SAEAs through the development of proficient model-assisted solution selection methods, which, however, first requires generating high-quality solutions. The fundamental paradigm of evaluating a limited number of solutions in each generation within SAEAs reduces the variance of adjacent populations, thereby affecting the quality of offspring solutions. This is a frequently encountered issue yet receives little attention. To address the issue, this paper presents a framework using unevaluated solutions to enhance the efficiency of SAEAs.The surrogate model is employed to identify high-quality solutions for the direct generation of new solutions without evaluation. To ensure dependable selection, we have introduced two tailored relation models to select the optimal solution and the unevaluated population. A comprehensive experimental analysis is performed on two test suites, which showcases the superiority of the relation model over regression and classification models in the solution selection phase. Furthermore, the surrogate-selected unevaluated solutions with high potential have been shown to enhance the efficiency of the algorithm significantly.

关键词： expensive optimization unevaluated solutions relation model surrogate-assisted evolutionary algorithm

Visible light cross-linking and bioactive peptides loaded integrated hydrogel with sequential release to accelerate wound healing complicated by bacterial infection

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Nano Research 2024年第3期17卷 1737-1747页

作者： Guiyan Wang Ning Yuan Jun Zhang Man Qin Suwei Dong Yuguang Wang department of Pediatric Dentistry Peking University School and Hospital of StomatologyBeijing 100081China State Key Laboratory of natural and Biomimetic Drugs Chemical Biology Centerand School of Pharmaceutical SciencesPeking UniversityBeijing 100191China department of Prosthodontics Peking University School and Hospital of StomatologyBeijing 100081China

The effective management of bacterial infections that are resistant to multiple drugs remains a substantial clinical challenge.The eradication of drug-resistant bacteria and subsequent promotion of angiogenesis are imperative for the regeneration of the infected wounds.Here,a novel and facile peptide containing injectable hydrogel with sustained antibacterial and angiogenic capabilities is developed.The antibacterial peptide that consists of 11 residues(CM11,WKLFKKILKVL)is loaded onto acrylate-modified gelatin through charge interactions.A vascular endothelial growth factor mimetic peptide KLT(KLTWQELYQLKYKGI)with a GCG(Gly-Cys-Gly)modification at the N-terminal is covalently coupled through a visible light-induced thiol-ene reaction.In this reaction,the acrylate gelatin undergoes cross-linkage within seconds.Based on the physical/chemical double crosslinking strategy,the bioactive peptides achieve sustained and sequential release.The results show that the hydrogel significantly inhibits methicillin-resistant Staphylococcus aureus(MRSA)growth through the rapid release of CM11 peptides at early stage;it forms obvious growth inhibition zones against pathogenic bacterial strains.Moreover,cell counting kit-8 assay and scratch test confirm that the CM11/KLT-functionalized hydrogels promote cell proliferation and migration through the later release of KLT peptides.In a mouse skin wound infected with self-luminous MRSA,the CM11/KLT-functionalized hydrogels enhance wound healing,with rapidly bacterial infection reduction,lower expression of inflammatory factors,and neovascularization promotion.These results suggest that the rationally designed,sustained and sequential release CM11/KLT-functionalized hydrogels have huge potential in promoting the healing of multi-drug resistant bacterial infected wounds.

关键词： antimicrobial peptide vascular endothelial growth factor(VEGF)mimetic peptide sequential release visible-light crosslinking hydrogel wound therapy

MKK4 inhibitor:the hope for liver failure prevention and potential small liver graft transplantation

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Chinese Journal of natural Medicines 2024年第6期22卷 483-485页

作者： ZHANG Yanqiu ZHANG Hao Jiangsu Key Laboratory of Bioactive natural Product Research Department of Natural Medicinal ChemistryChina Pharmaceutical UniversityNanjing 210009China

Liver regeneration represents a fascinating concept that spans from ancient mythology to modern medical science.In Greek mythology,Prometheus,a hero who defied Zeus by stealing fire and giving it to humanity,was subjected to a severe punishment.He was bound to a rock where,each day,an eagle would feast on his liver,which would then miracu-lously regenerate overnight.This myth underscores the liver’s unique regenerative abilities,a feature that is not just le-gendary but also scientifically recognized.

关键词： Liver regeneration Partial hepatectomy MKK4 Drug discovery and development First-in-human phase I trial

Morphological comparison and molecular marker screening of three Skeletonema species found in Changjiang(Yangtze)River Basin

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Journal of Oceanology and Limnology 2024年第3期42卷 923-942页

作者： Jingwen HU Yuxin YI Zhengxin YANG John Patrick KOCIOLEK Pan YU Quanxi WANG Qingmin YOU College of Life sciences Shanghai Normal UniversityShanghai 200235China Museum of natural History University of ColoradoBoulder 80309USA College of Environmental and Geographical sciences Shanghai Normal UniversityShanghai 200235China

In our recent investigations of diatom diversity,we studied three species,namely,Skeletonema costatum,Skeletonema subsalsum,and Skeletonema potamos.Although they have been found frequently in Changjiang(Yangtze)River Basin,their morphological and molecular identification is difficult in taxonomy.Therefore,to integrate morphological and molecular biological approaches,we compared systematically their morphological characters and performed phylogenetic analysis.Twelve strains of Skeletonema were collected and isolated from Shanghai and Jiangsu,China,and their morphological characteristics were examined by light microscopy(LM)and the scanning electron microscopy(SEM).Based on morphological comparison,we determined that S.potamos is easy to distinguish from the other two species.The heavily silicified areolae,undulated or cleft distal ends of terminal fultoportula processes(TFPPs),absence of basal pores of fultoportula processes(FPPs),the rootlike protrusions of FPPs,and no interlocking connection are the stable characteristics that can be used to identify S.potamos.However,there are only two features that can distinguish S.costatum from S.subsalsum,namely the location of terminal rimoportulae(TRPs)and the distal shape of TFPPs.In addition,we amplified and sequenced nine common genetic markers from the strains,from which 101 sequences were obtained,constructed phylogenetic trees based on the nine genes and evaluated that seven genes can be used to identify S.potamos,and revealed that S.subsalsum is the closest known relative of S.costatum,and only ATP synthetase beta-subunit gene(atp B)is able to distinguish them from each other,which strongly support that it is an effective molecular marker for Skeletonema.This work provided a theoretical basis for the taxonomic study of Skeletonema.

关键词： Skeletonema Changjiang River morphological change distinguishing morphological characteristics molecular marker

Peroxisome Proliferator-Activated Receptor-γCoactivator-1αin the Spotlight with Multiple Sclerosis

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Neuroscience Bulletin 2024年第2期40卷 268-272页

作者： Ya-Na Yang Mao-Qing Zhang Feng-Lin Yu Bing Han Ming-Yue Bao Yan He Xing Li Yuan Zhang Key Laboratory of Medicinal Resources and natural Pharmaceutical Chemistry(Shaanxi Normal University) The Ministry of EducationXi’an 710119China College of Life sciences Shaanxi Normal UniversityXi’an 710119China

Multiple sclerosis(MS)is a chronic and incurable autoimmune disease of the central nervous system(CNS)that results in neuro-inflammation and demyelination.Current therapies for MS alleviate symptoms to some extent but fail to realize myelin regeneration.Hence,it is crucial to identify effective targets to promote remyelination.As a widely expressed transcriptional regulator,peroxisome proliferatoractivated receptor-coactivator-1α(PGC-1α)expresses in different cells with high energy consumption,including skeletal muscle cells,brown fat cells,neurons,astrocytes,and oligodendrocyte precursor cell(OPC)[1].Targeting PGC-1αmay be beneficial for CNS development and various neurodegenerative diseases.

关键词： inflammation myelin autoimmune

Groundwater vulnerability assessment using a GIS-based DRASTIC method in the Erbil Dumpsite area (Kani Qirzhala), Central Erbil Basin, North Iraq

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Journal of Groundwater Science and Engineering 2024年第1期12卷 16-33页

作者： Masoud H Hamed Rebwar N Dara Marios C Kirlas department of Earth sciences and Petroleum College of ScienceSalahaddin University-ErbilErbilIraq department of Petroleum Engineering College of EngineeringKnowledge UniversityErbilIraq department of Agriculture Faculty of AgricultureForestry and Natural EnvironmentAristotle University of Thessaloniki

Groundwater vulnerability assessment is a crucial step in the efficient management of groundwater resources,especially in areas with intensive anthropogenic activities and groundwater pollution.In the present study,the DRASTIC method was applied using Geographic Information System(GIS)to delineate groundwater vulnerability zones in the Erbil Dumpsite area,Central Erbil Basin,North Iraq.Results showed that the area was classified into four vulnerability classes:Very low(16.97%),low(27.67%),moderate(36.55%)and high(18.81%).The southern,south-eastern and northern parts of the study area exhibited the highest vulnerability potential,while the central-northern,northern and north-western regions displayed the lowest vulnerability potential.Moreover,results of the single-parameter sensitivity analysis indicated that amongst the seven DRASTIC parameters,the unsaturated zone and the aquifer media were the most influencing parameters.In conclustion,the correlation of 25 nitrate concentration values with the final vulnerability map,assessed using the Pearson correlation coefficient,yielded a satisfactory result of R=0.72.

关键词： DRASTIC Erbil Iraq Groundwater vulnerability assessment Nitrate Pollution Sensitivity analysis