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HRCT quantitative analysis of airway remodeling and airway trapping in the small airway asthma phenotype and its correlation with pulmonary function

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JOURNAL OF ASTHMA 2023年第1期60卷 32-42页

作者： Lu, Dongzhu Yu, Qing Chen, Lichang Liao, Qiannuan Lan, Junkang Chen, Shu-Bing Wang, Cuilan Zeng, Wenyi Wu, Lingling Fan, Chaofan Lu, Peifeng Yu, Huapeng Southern Med Univ Zhujiang Hosp Dept Pulm & Crit Med 253 Ind Ave Guangzhou 510280 Guangdong Peoples R China Southern Med Univ Zhujiang Hosp Dept Radiol Guangzhou Peoples R China Southern Med Univ Shenzhen Hosp Dept Pulm & Crit Med Shenzhen Peoples R China

Objectives We aimed to explore whether large airway remodeling and small airway structural changes exist in subjects with small airway asthma phenotype and to evaluate the relationships between quantitative high-resolution computed tomography (qHRCT) parameters and lung function. Methods We enrolled 15 subjects with small airway asthma phenotype and 18 healthy controls. The two groups were matched by age, sex and body square area (BSA) with propensity score matching (PSM). Pulmonary function and qHRCT parameters [wall thickness (WT), wall area (WA), lumen area (LA), wall area percentage (WA%) of the 4th-6th generations in the right upper lobe apical segmental bronchus (RB1), adjusted by BSA, WT/BSA, WA/BSA, and LA/BSA, relative volume change -860 HU to -950 HU (RVC-860 to -950) and the expiration to inspiration ratio of mean lung density (MLDE/I)) were compared between the groups. Correlation analysis was employed to assess the relationship between qHRCT parameters and pulmonary function. Results The small airway asthma phenotype had significantly higher WA%, RVC-860 to -950 and MLDE/I and lower LA/BSA than the healthy control. Additionally, we found moderate to strong correlations between impulse oscillation (IOS) indices and WA6% and WT6/BSA. No significant correlation was found between bronchial parameters and air trapping parameters (p > 0.05). Conclusions Combining physiological tests with imaging approaches can lead to better evaluation of small airway disfunction (SAD) in asthmatic patients. Additionally, despite nonexistent airflow obstruction in patients with small airway asthma phenotype, large airway remodeling and small airway structural changes may appear simultaneously in the early stage of disease.

关键词： Nonexistent airflow obstruction airway structural changes structure-function relationships early stage propensity score matching

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Recent Advances in Mn,Fe,Co,and Ni-Catalyzed Organic Reactions

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CCS Chemistry 2024年第3期6卷 537-584页

作者： Lu-Jie Li Yuli He Yunhui Yang Jun Guo Zhan Lu Congyang Wang Shaolin Zhu Shou-Fei Zhu College of Chemistry Nankai UniversityTianjin 300071 School of Chemistry and Chemical Engineering Nanjing UniversityNanjingJiangsu Province 210093 Institute of Chemistry Chinese Academy of Sciences and University of Chinese Academy of SciencesBeijing 100190 Department of Chemistry Zhejiang UniversityHangzhouZhejiang Province 310058

This paper reviewed the recent research progress of organic reactions catalyzed by four typical earthabundant and 3d metal catalysts:Mn,Fe,Co,and Ni complexes and mainly focused on the reactions in which these 3d metal catalysts exhibited obvious advantages over other *** mechanism that makes these 3d metal catalysts show unusual properties is another focus of this *** outlook on 3d metal complexes-catalyzed organic reactions was also considered.

关键词： Earth-abundant metal catalysts sustainable organic synthesis structure-function relationships organometallic intermediates hydrocarbon transformations

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Characterizing functional modules in the human thalamus: coactivation-based parcellation and systems-level functional decoding

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BRAIN structure & function 2023年第8期228卷 1811-1834页

作者： Boeken, Ole J. J. Cieslik, Edna C. C. Langner, Robert Markett, Sebastian Humboldt Univ Fac Life Sci Dept Mol Psychol Rudower Chaussee 18 D-12489 Berlin Germany Heinrich Heine Univ Dusseldorf Inst Syst Neurosci Med Fac Dusseldorf Germany Inst Neurosci & Med INM 7 Brain & Behav Res Ctr Julich Julich Germany

The human thalamus relays sensory signals to the cortex and facilitates brain-wide communication. The thalamus is also more directly involved in sensorimotor and various cognitive functions but a full characterization of its functional repertoire, particularly in regard to its internal anatomical structure, is still outstanding. As a putative hub in the human connectome, the thalamus might reveal its functional profile only in conjunction with interconnected brain areas. We therefore developed a novel systems-level Bayesian reverse inference decoding that complements the traditional neuroinformatics approach towards a network account of thalamic function. The systems-level decoding considers the functional repertoire (i.e., the terms associated with a brain region) of all regions showing co-activations with a predefined seed region in a brain-wide fashion. Here, we used task-constrained meta-analytic connectivity-based parcellation (MACM-CBP) to identify thalamic subregions as seed regions and applied the systems-level decoding to these subregions in conjunction with functionally connected cortical regions. Our results confirm thalamic structure-function relationships known from animal and clinical studies and revealed further associations with language, memory, and locomotion that have not been detailed in the cognitive neuroscience literature before. The systems-level decoding further uncovered large systems engaged in autobiographical memory and nociception. We propose this novel decoding approach as a useful tool to detect previously unknown structure-function relationships at the brain network level, and to build viable starting points for future studies.

关键词： Thalamus Systems-level decoding structure-function relationships BrainMap database ALE meta-analysis Neurosynth

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Efficient polyethylene terephthalate degradation at moderate temperature: a protein engineering study of LC-cutinase highlights the key role of residue 243

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FEBS JOURNAL 2023年第12期290卷 3185-3202页

作者： Pirillo, Valentina Orlando, Marco Battaglia, Caren Pollegioni, Loredano Molla, Gianluca Univ Insubria Dept Biotechnol & Life Sci DBSV Varese Italy Univ Insubria Dept Biotechnol & Life Sci DBSV ViaJ H Dunant 3 I-21100 Varese Italy Univ Milano Bicocca Dept Biotechnol & Biosci BtBs Piazza Sci 2 I-20126 Milan Italy

Enzymatic degradation of poly(ethylene terephthalate) (PET) is becoming a reality because of the identification of novel PET-hydrolysing enzymes (PHEs) and the engineering of evolved enzyme variants. Here, improved variants of leaf-branch compost cutinase (LCC), a thermostable enzyme isolated by a metagenomic approach, were generated by a semi-rational protein engineering approach. Starting from a deleted LCC form lacking the secretion signal (Delta LCC), single and double variants possessing a higher activity on PET were isolated. The single-point F243T Delta LCC variant partially (similar to 67%) depolymerized amorphous PET film producing similar to 21.9 mm of products after 27 h of reaction at 72 degrees C. The S101N/F243T Delta LCC double variant reached a further increase in activity on PET. Notably, for both single and double variants the highest conversion yield was obtained at 55 degrees C. Kinetics studies and molecular dynamics simulations support that a slight decreased affinity for PET is responsible for the superior degradation performance of the S101N/F243T variant and that this stems from a slightly higher flexibility of the active site region close to position 243. Furthermore, our findings question the need for a high reaction temperature for PET degradation, at least for LCC: at >= 70 degrees C, the conversion of amorphous PET into a more crystalline polymer, resistant to enzymatic hydrolysis, is favoured. The evolved S101N/F243T Delta LCC variant is able to depolymerize fully 1.3 g of untreated postconsumer PET waste in <= 3 days at 55 degrees C (using 1.25 mg of enzyme only), this making PET enzymatic degradation by engineering LCC a more ecofriendly and sustainable process.

关键词： green technology improved LCC polyethylene terephthalate biodegradation rational design structure-function relationships

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Addressing high excitation conditions in time-resolved X-ray diffraction experiments and issues of biological relevance

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CURRENT OPINION IN STRUCTURAL BIOLOGY 2023年第1期81卷 102624页

作者： Besaw, Jessica E. Miller, R. J. Dwayne Univ Toronto Dept Biochem 1 Kings Coll Circle Toronto ON M5S 1A8 Canada Univ Toronto Dept Chem 80 St George St Toronto ON M5S 3H6 Canada Univ Toronto Dept Phys 80 St George St Toronto ON M5S 3H6 Canada

One of the most important fundamental questions connecting chemistry to biology is how chemistry scales in complexity up to biological systems where there are innumerable possible pathways and competing processes. With the development of ultrabright electron and x-ray sources, it has been possible to literally light up atomic motions to directly observe the reduction in dimensionality in the barrier crossing region to a few key reaction modes. How do these chemical processes further couple to the surrounding protein or macromolecular assembly to drive biological functions? Optical methods to trigger photoactive biological processes are needed to probe this issue on the relevant timescales. However, the excitation conditions have been in the highly nonlinear regime, which questions the biological relevance of the observed structural dynamics.

关键词： Time-resolved crystallography Laser illumination guidelines structure-function relationships

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structure-function-guided design of synthetic peptides with anti-infective activity derived from wasp venom

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CELL REPORTS PHYSICAL SCIENCE 2023年第7期4卷 101459页

作者： Boaro, Andreia Ageitos, Lucia Torres, Marcelo Der Torossian Blasco, Esther Broset Oztekin, Sebahat de la Fuente-Nunez, Cesar Univ Penn Inst Biomed InformatDept Psychiat & Microbiol Inst Translat Med & Therapeut Perelman Sch MedMachine Biol Grp Philadelphia PA 19104 USA Univ Penn Sch Engn & Appl Sci Dept Bioengn & Chem & Biomol Engn Philadelphia PA 19104 USA Univ Penn Penn Inst Computat Sci Philadelphia PA 19104 USA Univ Fed ABC Ctr Ciencias Nat & Humanas BR-09210580 Santo Andre Brazil Univ A Coruna CICA Ctr Interdisciplinar Quim & Biol Dept Quim Fac Ciencias La Coruna 15008 Spain Bayburt Univ Fac Engn Dept Food Engn TR-69000 Bayburt Turkiye

Antimicrobial peptides (AMPs) derived from natural toxins and venoms offer a promising alternative source of antibiotics. Here, through structure-function-guided design, we convert two natural AMPs derived from the venom of the solitary eumenine wasp Eu-menes micado into a-helical AMPs with reduced toxicity that kill Gram-negative bacteria in vitro and in a preclinical mouse model. To identify the sequence determinants conferring antimicrobial ac-tivity, an alanine scan screen and strategic single lysine substitutions are made to the amino acid sequence of these natural peptides. These efforts yield a total of 34 synthetic derivatives, including alanine substituted and lysine-substituted sequences with stabilized a-helical structures and increased net positive charge. The resulting lead synthetic peptides kill the Gram-negative pathogens Escheri-chia coli and Pseudomonas aeruginosa (PAO1 and PA14) by rapidly permeabilizing both their outer and cytoplasmic membranes, exhibit anti-infective efficacy in a mouse model by reducing bacte-rial loads by up to three orders of magnitude, and do not readily select for bacterial resistance.

关键词： venoms antibiotics antimicrobial peptides synthetic peptides structure-function-guided design structure-function relationships bacterial resistance mechanism of action anti-infective activity mouse model

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Unveiling molecular details behind improved activity at neutral to alkaline pH of an engineered DyP-type peroxidase

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COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 2022年 20卷 3899-3910页

作者： Borges, Patricia T. Silva, Diogo Silva, Tomas F. D. Brissos, Vania Canellas, Marina Lucas, Maria Fatima Masgrau, Laura Melo, Eduardo P. Machuqueiro, Miguel Frazao, Carlos Martins, Ligia O. Univ NOVA Lisboa Inst Tecnol Quim & Biol Antonio Xavier Av Republ P-2780157 Oeiras Portugal Univ Lisbon Fac Ciencias BioISI Biosyst & Integrat Sci Inst P-1749016 Lisbon Portugal Zymvol Biomodeling Carrer Roc Boronat 117 Barcelona 08018 Spain Univ Autonoma Barcelona Dept Chem Bellaterra 08193 Spain Univ Algarve Ctr Ciencias Mar P-8005139 Faro Portugal

DyP-type peroxidases (DyPs) are microbial enzymes that catalyze the oxidation of a wide range of substrates, including synthetic dyes, lignin-derived compounds, and metals, such as Mn2+ and Fe2+, and have enormous biotechnological potential in biorefineries. However, many questions on the molecular basis of enzyme function and stability remain unanswered. In this work, high-resolution structures of PpDyP wild-type and two engineered variants (6E10 and 29E4) generated by directed evolution were obtained. The X-ray crystal structures revealed the typical ferredoxin-like folds, with three heme access pathways, two tunnels, and one cavity, limited by three long loops including catalytic residues. Variant 6E10 displays significantly increased loops' flexibility that favors function over stability: despite the considerably higher catalytic efficiency, this variant shows poorer protein stability compared to wild-type and 29E4 variants. Constant-pH MD simulations revealed a more positively charged microenvironment near the heme pocket of variant 6E10, particularly in the neutral to alkaline pH range. This microenvironment affects enzyme activity by modulating the pK(a) of essential residues in the heme vicinity and should account for variant 6E10 improved activity at pH 7-8 compared to the wild-type and 29E4 that show optimal enzymatic activity close to pH 4. Our findings shed light on the structure-function relationships of DyPs at the molecular level, including their pH-dependent conformational plasticity. These are essential for understanding and engineering the catalytic properties of DyPs for future biotechnological applications. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.

关键词： Biorefinery Biocatalysis Directed evolution Protein stability structure-function relationships

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Biochemical and biomechanical characterization of the cervical, thoracic, and lumbar facet joint cartilage in the Yucatan minipig

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JOURNAL OF BIOMECHANICS 2022年 142卷 111238-111238页

作者： Nordberg, Rachel C. Kim, Andrew N. Hight, Justin M. Meka, Rithika S. Elder, Benjamin D. Hu, Jerry C. Athanasiou, Kyriacos A. Univ Calif Irvine Dept Biomed Engn 3131 Engn Hall Irvine CA 92617 USA Mayo Clin Sch Med Dept Neurosurg Orthoped & Biomed Engn 200 1st St SW Rochester MN 55905 USA Univ Calif Irvine Samueli Sch Engn Dept Biomed Engn 3418 Engn Hall Irvine CA 92697 USA

Facet joint arthrosis causes pain in approximately 7 % of the U.S. population, but current treatments are palliative. The objective of this study was to elucidate structure-function relationships and aid in the development of future treatments for the facet joint. This study characterized the articular surfaces of cervical, thoracic, and lumbar facet cartilage from skeletally mature (18-24 mo) Yucatan minipigs. The minipig was selected as the animal model because it is recognized by the U.S. Food and Drug Administration (FDA) and the American Society for Testing and Materials (ASTM) as a translationally relevant model for spine-related indications. It was found that the thoracic facets had a similar to 2 times higher aspect ratio than lumbar and cervical facets. Lumbar facets had 6.9-9.6 times higher % depth than the cervical and thoracic facets. Aggregate modulus values ranged from 135 to 262 kPa, much lower than reported aggregate modulus in the human knee (reported to be 530-701 kPa). The tensile Young's modulus values ranged from 6.7 to 20.3 MPa, with the lumbar superior facet being 304 % and 286 % higher than the cervical inferior and thoracic superior facets, respectively. Moreover, 3D reconstructions of entire vertebral segments were generated. The results of this study imply that structure-function relationships in the facet cartilage are different from other joint cartilages because biochemical properties are analogous to other articular cartilage sources whereas mechanical properties are not. By providing functional properties and a 3D database of minipig facet geometries, this work may supply design criteria for future facet tissue engineering efforts.

关键词： Facet joint Zygapophyseal joint Cartilage Biomechanics structure-function relationships Minipig Characterization

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Recent Advances in the Design of Multi-Substituted Carbazoles for Optoelectronics: Synthesis and structure-Property Outlook

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CHEMPHOTOCHEM 2022年第10期6卷

作者： Konidena, Rajendra Kumar Thomas, K. R. Justin Park, Jong Wook Indian Inst Technol Roorkee Organ Mat Lab Dept Chem Roorkee 247667 Uttar Pradesh India Kyung Hee Univ Dept Chem Engn Suwon 17104 South Korea

Organic synthesis plays a pivotal role in the development of innovative organic functional materials for optoelectronic applications such as organic light emitting diodes (OLEDs), photovoltaics (OPVs), non-linear optics (NLOs), field effect transistors (OFETs) and sensors. Chemical functionalization methods available for polyaromatic hydrocarbons (PAHs) are particularly attractive as they provide opportunities to fine-tune the physicochemical, charge transporting and device parameters. Among the PAHs containing heteroatoms, carbazole is recognized as one of the most promising building blocks for assembling the functional materials for organic electronics, particularly for OLED and OPVs due to its unique features such as good hole transporting ability, excellent thermal and morphological stability, amorphous nature, low cost, high triplet energy and flexibility for functionalization. Until 2011, carbazole-based functional materials were limited to use as a donor in donor-acceptor molecular configurations and as difunctionalized (C3,C6- or C2,C7- or N-) derivatives capable of hole transporting/emitting characteristics. Recently, polyfunctionalization on carbazole at various positions has drawn significant attention as a result of their promising structure-function relationships. Although some reviews have focused on structure-property relationships within difunctionalized carbazoles, recent synthetic advances in the field of polyfunctionalized carbazoles and their resultant structure-property relationships remain unreviewed. To bridge this gap, in this article we review newly emerged synthetic approaches for polyfunctionalization of carbazole and discuss the effects of substitution pattern, chromophore nature and its density on the photophysical and device properties.

关键词： carbazoles optoelectronic devices organic light emitting devices perovskite solar cells structure-function relationships

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Sequentially Regulating the Structural Transformation of Copper Metal-Organic Frameworks (Cu-MOFs) for Controlling Site-Selective Reaction

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ACS APPLIED MATERIALS & INTERFACES 2022年第32期14卷 36845-36854页

作者： Qin, Qi Wang, Di Shao, Zhichao Zhang, Yingying Zhang, Qiang Li, Xinyue Huang, Chao Mi, Liwei Zhongyuan Univ Technol Ctr Adv Mat Res Zhengzhou 450007 Peoples R China Zhongyuan Univ Technol Henan Key Lab Funct Salt Mat Zhengzhou 450007 Peoples R China

Regulating atomically precise sites in catalysts to achieve site-selective reactions is remarkable but challenging. In this work, a convenient and facile solid-gas/ liquid reaction strategy was used to construct controllable active sites in metal-organic frameworks (MOFs) to guide an orientation site-selective reaction. A flexible Cu-I-MOF-1 with dynamics originating from an anionic and tailorable framework could undergo a reversible structural transformation to engineer a topologically equivalent mixed-valent (CuCuII)-Cu-I-MOF-2 via a solid-gas/liquid oxidation/reduction process. More importantly, Cu-I-MOF-1 and (CuCuII)-Cu-I-MOF-2 could further execute the solid-gas/liquid reaction under ammonia vapor/solution to generate Cu-II-MOF-3. Furthermore, the transformation from Cu-I-MOF-1 to (CuCuII)-Cu-I-MOF-2 and Cu-II-MOF-3 served as controllable catalysts to facilitate site-selective reactions to realize direct C-N bond arylations. The results demonstrated that Cu-I-MOF-1 and Cu-II-MOF-3 possessed well-defined platforms with uniformly and accurately active sites to attain a "turn-on/off " process via different reaction routes, providing the desired site-selective ring-opening products.

关键词： metal-organic frameworks structural transformation solid-gas liquid reaction structure-function relationships site-selective reaction

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