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How the “Folding Funnel” Depends on Size and Structure of Proteins?A View from the Scoring Function Perspective

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Tsinghua Science and Technology 2013年第5期18卷 462-468页

作者： Sheng-You Huang Gordon K. springer the Research Support Computing University of Missouri Bioinformatics Consortium and Department of Computer Science University of Missouri

It has been well accepted that the folding energy landscape may resemble a funnel according to the theory of protein folding. This theory of ＂folding funnel＂ has been extensively studied and thought to play an important role in guiding the sampling process of the protein folding and refinement in protein structure prediction. Here, we have investigated the relationship between the ＂funnel likeness＂ of protein folding and the size/structure of the proteins based on a set of non-homologous proteins we have recently evaluated using a statistical mechanicsbased scoring function ITScorePro. It was found that larger proteins that consist of more helix/sheet structures tend to have a higher score-Root Mean Square Deviation（RMSD） correlation（or a more funnel like energy landscape）.Another measurement in protein folding, Z-score, has also shown some correlation with the size of the *** expected, proteins with a better ＂olding funnel likeness＂（or score-RMSD correlation） tend to have a betterpredicted conformation with a lower RMSD from their native structures. These findings can be extremely valuable for the development and improvement of sampling and scoring algorithms for protein structure prediction.

关键词： energy landscape folding funnel protein structure prediction scoring function protein folding

Role of mitochondria in regulating micro RNA activity and its relevance to the central nervous system

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Neural Regeneration Research 2015年第7期10卷 1026-1028页

作者： Wang-Xia Wang Joe E.springer Sanders-Brown Center on Aging University of Kentucky Physical Medicine and Rehabilitation Spinal Cord and Brain Injury Research Center Anatomy and Neurobiology University of Kentucky

Mitochondria serve as the powerhouse of cells,respond to cellular demands and stressors,and play an essential role in cell signaling,differentiation,and *** mitochondria function has been linked to diverse and complex human diseases such as neurodegenerative diseases,cancers,myopathies,premature aging,and metabolic syndromes（Nunnari and Suomalainen,2012）.

关键词： RNA Role of mitochondria in regulating micro RNA activity and its relevance to the central nervous system gene

GAS TRANSPORT PROPERTIES OF A POLYIMIDE BASED ON 2, 2-BIS (3, 4-DECARBOXYPHENYL) HEXAFLUOROPROPANE AND meta-PHENYLENEDIAMINE

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Chinese Journal of Polymer Science 1998年第1期16卷 86-90页

作者：徐志康徐又一 springer Jürgen Department of Polymer Science & Engineering Zhejiang University Hangzhou 310027 China Institute of Technical Chemistry Technical University of Berlin Berlin 10623 Germany

By means of a vacuum time-lag method, gas transport properties of a polyimide based on 2,2-bis(3,4-decarboxyphenyl) hexafluoropropane dianhydride (6FDA) and meta-phenylenediamine (mPDA) have been measured as a function of upstream pressure and temperature. The results show that no gas-induced plasticization occurs for this polyimide in the upstream pressure range from 1 atm to 20 atm. The temperature dependence of P and D can be described by the Arrhenius equations. The activation energies of permeation and diffusion were obtained for the gas/polymer pair studied and correlated with the size of penetrant gas.

关键词： polyimide membrane gas permeation gas separation

A global analysis of CO_(2)and non-CO_(2)GHG emissions embodied in trade with Belt and Road Initiative countries

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Ecosystem Health and Sustainability 2020年第1期6卷 18-37,17页

作者： Jing Hou Xu Deng Cecilia Han springer Fei Teng Institute of Energy Environment and EconomyTsinghua UniversityBeijingChina Belfer Center for Science and International Affairs Harvard Kennedy SchoolCambridgeMAUSA

Introduction:The Belt and Road Initiative(BRI)is an important cooperative framework that increasingly affects the global economy,trade,and emission ***,most existing studies pay insufficient attention to consumption-based emissions,embodied emissions,and non-CO_(2) greenhouse gases(GHGs).This study constructs a GHG emissions database to study the trends and variations in production-based,consumption-based,and embodied emissions associated with BRI ***:We find that the per capita GHG emissions of BRI countries are lower than the global average but show significant variation within this *** also find that trade-embodied emissions between BRI countries and China are *** a group,BRI countries are anet exporter of GHGs,with a global share of net export emissions of about 20%.In 2011,nearly 80%of GHG export emissions from BRI countries flowed to non-BRI countries,and nearly 15%flowed to China;about 57%of GHG import emissions were from non-BRI countries,and about 38%were from ***:Therefore,this study concludes that the BRI should be used to coordinate climate governance to accelerate and strengthen the dissemination and deployment of low-emissions technologies,strategies,and policies within the BRI so as to avoid a carbon-intensive lock-in effect.

关键词： Belt and Road Initiative(BRI) China consumption-based emissions non-CO_(2)greenhouse gas(NCO2) embodied emissions global multi-regional input-output model(MRIO)

Targeting the mitochondrial permeability transition pore in traumatic central nervous system injury

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Neural Regeneration Research 2018年第8期13卷 1338-1341页

作者： Joe E. springer Pareshkumar Prajapati Patrick G. Sullivan Spinal Lord and Brain Injury Research Center Department of Neuroscience University of Kentucky Lexington KY USA

The mitochondrion serves many functions in the central nervous system （CNS） and other organs beyond the well-recognized role of adenosine triphosphate （ATP） production. This includes calcium-dependent cell signaling, regulation of gene expression, synthesis and release of cytotoxic reactive oxygen species, and the release of cytochrome c and other apoptotic cell death factors. Traumatic injury to the CNS results in a rapid and, in some cases, sustained loss of mitochondrial function. One consequence of compromised mitochondrial function is induction of the mitochondrial permeability transition （mPT） state due to formation of the cyclosporine A sensitive permeability transition pore （mPTP）. In this mini-review, we summarize evidence supporting the involvement of the mPTP as a mediator of mitochondrial and cellular demise following CNS traumatic injury and discuss the beneficial effects and limitations of the current ex- perimental strategies targeting the mPTP.

关键词： mitochondrial permeability transition cyclophilin-D cyclosporine A NIM811 spinal cord injury traumatic brain injury secondary injury functional recovery

Liver fat content determined by magnetic resonance imaging and spectroscopy

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World Journal of Gastroenterology 2010年第13期16卷 1560-1566页

作者： Fabian springer Jürgen Machann Claus D Claussen Fritz Schick Nina F Schwenzer Section on Experimental Radiology Department of Diagnostic and Interventional Radiology University Hospital Tübingen Department of Diagnostic and Intervent ional Radiology University Hospital Tübingen

Hepatic steatosis as the most prevalent liver disorder can either be related to alcoholic liver disease (ALD) or non-alcoholic fatty liver disease (NAFLD). In both conditions, hepatocytes excessively accumulate fatcontaining vacuoles within their cytoplasm, which is the key histological feature. In contrast to ALD, NAFLD is commonly associated with metabolic syndrome, obesity and insulin resistance. To determine increased liver fat content, liver biopsy is currently considered the gold standard. Besides the invasive technique, various other non-invasive techniques have been developed, such as ultrasound, computed tomography (CT), magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) based methods. Among these techniques, ultrasound and CT provide only qualitative information about hepatic steatosis, whereas MRS-or MRI-based methods are able to determine even small amounts of fat accurately. These non-invasive magnetic resonance techniques have already proven their great potential, especially in longitudinal and cross-sectional studies regarding various metabolic conditions and medical treatment regimens. In this review, the most common, non-invasive MRS/MRI techniques for assessment of intrahepatic lipid content are described with their inherent advantages and limitations.

关键词： Hepatic steatosis Magnetic resonance imaging Proton magnetic resonance spectroscopy Lipids

Structural analysis of flagellar axonemes from inner arm dynein knockdown strains of Trypanosoma brucei

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BIOCELL 2012年第3期36卷 133-141页

作者： RANDI ZUKAS ALEX J.CHANG MARIAN RICE AMY L.springer Department of Biology Amherst CollegeAmherstMAUSA Department of Biological Sciences Mount Holyoke CollegeSouth HadleyMAUSA

Trypanosoma brucei is a protozoan flagellate that causes African sleeping *** function in this organism is critical for life cycle progression and pathogenesis,however the regulation of flagellar motility is not well *** flagellar axoneme produces a complex beat through the pre-cisely coordinated firing of many proteins,including multiple dynein *** motors are found in the inner arm and outer arm *** are studying one of the inner arm dynein motors in the *** flagellum:*** knockdown of genes for two components of dynein-f:DNAH10,theαheavy chain,and IC138,an intermediate chain,cause severe motility defects including *** determine if motility defects result from structural disruption of the axoneme,we used two different flagellar preparations to carefully examine axoneme structure in these strains using transmission electron microscopy(TEM).Our analysis showed that inner arm dynein size,axoneme structural integrity and fixed central pair orientation are not significantly different in either knockdown culture when compared to control *** results support the idea that immotility in knockdowns affecting DNAH10 or IC138 results from loss of dynein-f function rather than from obvious structural defects in the axoneme.

关键词： Flagellar motility transmission electron microscopy central pair

Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development

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Molecular Plant 2019年第3期12卷 410-425页

作者： Peng Zhou Candice N.Hirsch Steven P.Briggs Nathan M.springer Department of Plant and Microbial Biology University of MinnesotaSaint PaulMN 55108USA Department of Agronomy and Plant Genetics University of MinnesotaSaint PaulMN 55108USA Division of Biological Sciences University of CaliforniaSanDiegoLaJollaCA92093USA

Gene expression variation is a key component underlying phenotypic variation and heterosis. Transcriptome profiling was performed on 23 different tissues or developmental stages of two maize inbreds, B73 and Mo17, as well as their hybrid. The obtained large-scale datasets provided opportunities to monitor the developmental dynamics of differential expression, additivity for gene expression, and regulatory variation. The transcriptome can be divided into .30 000 genes that are expressed in at least one tissue of one in bred and an additional ~10 000 “silent” genes that are not expressed in any tissue of any genotype, 90% of which are non-syntenic relative to other grasses. Many (.74%) of the expressed genes exhibit differential expression in at least one tissue. However, the majority of genes with differential expression do not exhibit consistent differential expression in different tissues. These genes often exhibit tissue-specific differential expression with equivalent expression in other tissues, and in many cases they switch the directionality of differential expression in different tissues. This suggests widespread variation for tissue-specific regulation of gene expression between the two maize inbreds B73 and Mo17. Nearly 5000 genes are expressed in only one parent in at least one tissue (single parent expression) and 97% of these genes are expressed at mid-parent levels or higher in the hybrid, providing extensive opportunities for hybrid complementation in heterosis. In general, additive expression patterns are much more common than non-additive patterns, and this trend is more pronounced for genes with strong differential expression or single pare nt expressi on. There is relatively little evidence for non-additive expression patterns that are maintained in multiple tissues. The analysis of allele-specific expression allowed classification of cis. and trans-regulatory variation. Genes with c/s-regulatory variation often exhibit additive expression and tend

关键词： maize gene expression heterosis differential expression non-additive expression allele-specific expression

Natural regeneration responses to thinning and burning treatments in ponderosa pine forests and implications for restoration

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Journal of Forestry Research 2022年第3期33卷 741-753页

作者： Tzeidle N.Wasserman Amy E.M.Waltz John Paul Roccaforte Judith D.springer Joseph E.Crouse Ecological Restoration Institute Northern Arizona UniversityP.O.Box 15017FlagstaffAZ86011-5017USA

Understanding naturally occurring pine regeneration dynamics in response to thinning and burning treatments is necessary not only to measure the longevity of the restoration or fuels treatment,but also to assess how well regeneration meets forest sustainability guidelines and whether natural regeneration is sufficient for maintaining a sustainable forest structure and composition.A synthesis review was carried out on the effects of mechanical thinning and prescribed burn treatments on natural pine regeneration response in frequent-fire ponderosa pine forests across the western United *** focus was on site-specific variability in pine regeneration dynamics,temporal trends in regeneration presence and abundance,and response to treatment as described in the current literature using 29 studies that met our evidence-based review *** showed that the effects of thinning and burning treatments on regeneration depended on time since *** thinning,prescribed burning,and thinning plus burn treatments all increased seedling density,but there was high variability among sites and *** were mixed results in the short-term(20 years)concluded that stands can return to pre-treatment densities in terms of total trees per hectare and forest floor duff levels when there are no maintenance treatments *** studies showed the average ponderosa pine seedling presence,survival and growth found in today’s forests to be at a high density;this combined with missed fire cycles could contribute to future fire risk and reduce the efficacy of maintaining fuel reduction goals.

关键词： Regeneration Ponderosa pine Frequent-fire Treatments Thinning Burning