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Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering

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Journal of Molecular Cell Biology 2020年第11期12卷 828-856页

作者： Qiang Wu Jia Shou center for Comparative biomedicine MOE Key Lab of Systems BiomedicineState Key Laboratory of Oncogenes and Related GenesInstitute of Systems BiomedicineSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China

Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s,the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology *** particular,the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D *** gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair *** studies revealed,however,that the CRISPR genomeediting system is precise and predictable because of cohesive Cas9 cleavage of targeting ***,we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D ***,we first briefly describe historical genetic studies leading to CRISPR and 3D genome *** then summarize different types of chromosomal rearrangements by DNA fragment ***,we review significant progress from precise ID gene editing toward predictable 3D genome engineering and synthetic *** exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.

关键词： CRISPR,DNA fragment editing 3D genome engineering repair mechanism s chromatin loops precise modifications predictable indels

NECAB family of neuronal calcium-binding proteins in health and disease

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Neural Regeneration Research 2025年第5期20卷 1236-1243页

作者： Diones Bueno Michael K.E.Schafer Sudena Wang Michael J.Schmeisser Axel Methner Institute for Molecular Medicine University Medical Center of the Johannes Gutenberg-UniversityMainzGermany Department of Anesthesiology University Medical Center of the Johannes Gutenberg-UniversityMainzGermany Institute of Anatomy University Medical Center of the Johannes Gutenberg-UniversityMainzGermany

The N-terminal EF-hand calcium-binding proteins 1–3(NECAB1–3) constitute a family of predominantly neuronal proteins characterized by the presence of at least one EF-hand calcium-binding domain and a functionally less well characterized C-terminal antibiotic biosynthesis monooxygenase domain. All three family members were initially discovered due to their interactions with other proteins. NECAB1 associates with synaptotagmin-1, a critical neuronal protein involved in membrane trafficking and synaptic vesicle exocytosis. NECAB2 interacts with predominantly striatal G-protein-coupled receptors, while NECAB3 partners with amyloid-β A4 precursor protein-binding family A members 2 and 3, key regulators of amyloid-β production. This demonstrates the capacity of the family for interactions with various classes of proteins. NECAB proteins exhibit distinct subcellular localizations: NECAB1 is found in the nucleus and cytosol, NECAB2 resides in endosomes and the plasma membrane, and NECAB3 is present in the endoplasmic reticulum and Golgi apparatus. The antibiotic biosynthesis monooxygenase domain, an evolutionarily ancient component, is akin to atypical heme oxygenases in prokaryotes but is not wellcharacterized in vertebrates. Prokaryotic antibiotic biosynthesis monooxygenase domains typically form dimers, suggesting that calcium-mediated conformational changes in NECAB proteins may induce antibiotic biosynthesis monooxygenase domain dimerization, potentially activating some enzymatic properties. However, the substrate for this enzymatic activity remains uncertain. Alternatively, calcium-mediated conformational changes might influence protein interactions or the subcellular localization of NECAB proteins by controlling the availability of protein–protein interaction domains situated between the EF hands and the antibiotic biosynthesis monooxygenase domain. This review summarizes what is known about genomic organization, tissue expression, intracellular localization, interac

关键词： calcium EF hand mitochondria nervous system signal transduction

Microstructure evolution and passivation quality of hydrogenated amorphous silicon oxide(a-SiOx:H) on〈100〉- and 〈111〉-orientated c-Si wafers

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Chinese Physics B 2020年第3期29卷 480-487页

作者： Jun-Fan Chen Sheng-Sheng Zhao Ling-Ling Yan Hui-Zhi Ren Can Han De-Kun Zhang Chang-Chun Wei Guang-Cai Wang Guo-Fu Hou § Ying Zhao Xiao-Dan Zhang Institute of Photoelectronic Thin Film Devices and Technology of Nankai University Tianjin 300350China Key Laboratory of Photoelectronic Thin Film Devices and Technology of Tianjin Tianjin 300350China Engineering center of Thin Film Photoelectronic Technology of Ministry of Education Tianjin 300350China sino-euro Joint Research center for Photovoltaic Power Generation of Tianjin Tianjin 300350China

Hydrogenated amorphous silicon oxide(a-SiOx:H) is an attractive passivation material to suppress epitaxial growth and reduce the parasitic absorption loss in silicon heterojunction(SHJ) solar cells. In this paper, a-SiOx:H layers on different orientated c-Si substrates are fabricated. An optimal effective lifetime(τ(eff)) of 4743 μs and corresponding implied opencircuit voltage(iV(oc)) of 724 mV are obtained on〈100〉-orientated c-Si wafers. While τ(eff) of 2429 μs and iV_(oc) of 699 mV are achieved on 111-orientated substrate. The FTIR and XPS results indicate that the a-SiOx:H network consists of SiOx(Si-rich), Si–OH, Si–O–SiHx, SiO2 ≡ Si–Si, and O3 ≡ Si–Si. A passivation evolution mechanism is proposed to explain the different passivation results on different c-Si wafers. By modulating the a-SiOx:H layer, the planar silicon heterojunction solar cell can achieve an efficiency of 18.15%.

关键词： a-SiO_x:H orientated wafers silicon heterojunction

Epitope Analysis of Anti-SARS-CoV-2 Neutralizing Antibodies

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Current Medical Science 2021年第6期41卷 1065-1074页

作者： Jun-biao XUE Sheng-ce TAO Shanghai center for Systems biomedicine Key Laboratory of Systems Biomedicine(Ministry of Education)Shanghai Jiao Tong UniversityShanghai 200240China

Coronavirus disease 2019 is threatening thousands of millions of people around the *** the absence of specific and highly effective medicines,the treatment of infected persons is still very *** therapeutics,neutralizing antibodies(NAbs)have great *** NAbs have been reported,and most target various regions on the receptor-binding domain of the spike(S)protein,or the N-terminal *** NAbs and NAb cocktails have been authorized for emergency use,and more arc in clinical trials or are under *** this review,considering the angle of binding epitopes on the S protein,we summarize the functions and the underlying mechanisms of a set of well-recognized NAbs and provide guidance for vaccine design and the combinatorial use of these *** addition,we review the NAbs and NAb cocktails that have been approved for emergency use and discuss the effectiveness of these NAbs for combating severe acute respiratory syndrome coronavirus 2 mutants.

关键词： coronavirus disease 2019 severe acute respiratory syndrome coronavirus 2 neutralizing antibody epitope therapeutics vaccine

NONLINEAR LANGEVIN MODEL WITH PRODUCT STOCHASTICITY FOR BIOLOGICAL NETWORKS： THE CASE OF THE SCHNAKENBERG MODEL

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Journal of Systems Science & Complexity 2010年第5期23卷 896-905页

作者： Youfang CAO Jie LIANG Ministry of Education Key Laboratory of Systems biomedicine Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai 200240 China Department of Bioengineering University of Illinois at Chicago Chicago USA

Langevin equation is widely used to study the stochastic effects in molecular networks, as it often approximates well the underlying chemical master equation. However, frequently it is not clear when such an approximation is applicable and when it breaks down. This paper studies the simple Schnakenberg model consisting of three reversible reactions and two molecular species whose concentrations vary. To reduce the residual errors from the conventional formulation of the Langevin equation, the authors propose to explicitly model the effective coupling between macroscopic concentrations of different molecular species. The results show that this formulation is effective in correcting residual errors from the original uncoupled Langevin equation and can approximate the underlying chemical master equation very accurately.

关键词： Langevin equation master equation noise Schnakenberg model.

Temporal dynamics of neonatal hypoxic-ischemic encephalopathy injuries on magnetic resonance imaging

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Neural Regeneration Research 2025年第11期20卷 3144-3150页

作者： Holly Flyger Samantha J.Holdsworth Alistair J.Gunn Laura Bennet Hamid Abbasi Mātai Medical Research Institute Tairāwhiti GisborneNew Zealand Department of Anatomy&Medical Imaging Faculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand center for Brain Research The University of AucklandAucklandNew Zealand Auckland Bioengineering Institute The University of AucklandAucklandNew Zealand

Moderate to severe perinatal hypoxic-ischemic encephalopathy occurs in~1 to 3/1000 live births in high-income countries and is associated with a significant risk of death or neurodevelopmental *** assessment is important to help identify highrisk infants,to help families,and to support appropriate interventions.A wide range of monitoring tools is available to assess changes over time,including urine and blood biomarkers,neurological examination,and *** present,magnetic resonance imaging is unique as although it is expensive and not suited to monitoring the early evolution of hypoxic-ischemic encephalopathy by a week of life it can provide direct insight into the anatomical changes in the brain after hypoxic-ischemic encephalopathy and so offers strong prognostic information on the long-term outcome after hypoxic-ischemic *** review investigated the temporal dynamics of neonatal hypoxic-ischemic encephalopathy injuries,with a particular emphasis on exploring the correlation between the prognostic implications of magnetic resonance imaging scans in the first week of life and their relationship to long-term outcome prediction,particularly for infants treated with therapeutic hypothermia.A comprehensive literature search,from 2016 to 2024,identified 20 pertinent *** review highlights that while the optimal timing of magnetic resonance imaging scans is not clear,overall,it suggests that magnetic resonance imaging within the first week of life provides strong prognostic *** challenges limit the timing consistency,particularly the need for intensive care and clinical ***,although most reports examined the prognostic value of scans taken between 4 and 10 days after birth,there is evidence from small numbers of cases that,at times,brain injury may continue to evolve for weeks after *** suggests that in the future it will be important to explore a wider range of times after hypo

关键词： magnetic resonance imaging neonatal hypoxic-ischemic encephalopathy neurodevelopmental outcomes prognostic biomarkers in neuroimaging scan timing therapeutic hypothermia

Advances in the treatment of autism spectrum disorder:Wharton jelly mesenchymal stem cell transplantation

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World Journal of Methodology 2025年第1期15卷 72-79页

作者： Serdar Kabatas ErdinçCivelek Eyüp Can Savrunlu Umut Karaaslan Özlem Yıldız Erdal Karaöz Department of Neurosurgery University of Health Sciences TurkeyGaziosmanpaşa Training and Research HospitalIstanbul 34255Türkiye Department of Pediatric Allergy-Immunology Institute of Health Sciences Marmara UniversityIstanbul 34865Türkiye center for Stem Cell&Gene Therapy Research and Practice University of Health Sciences TurkeyIstanbul 34255Türkiye Department of Child and Adolescent Psychiatry University of Health SciencesGaziosmanpaşa Training and Research HospitalIstanbul 34255Türkiye Department of Child and Adolescent Psychiatry Kocaeli University Faculty of MedicineKocaeli 41001Türkiye center for Regenerative Medicine and Stem Cell Research&Manufacturing Liv HospitalIstanbul 34340Türkiye Department of Histology and Embryology Istinye UniversityFaculty of MedicineIstanbul 34010Türkiye center for Stem Cell and Tissue Engineering Research and Practice Istinye UniversityIstanbul 34340Türkiye

BACKGROUND Autism spectrum disorder(ASD)is a complex neurodevelopmental disorder with multifaceted *** recent studies,neuroinflammation and immune dysregulation have come to the forefront in its *** are studies suggesting that stem cell therapy may be effective in the treatment of *** To evolve the landscape of ASD treatment,focusing on the potential benefits and safety of stem cell *** A detailed case report is presented,displaying the positive outcomes observed in a child who underwent intrathecal and intravenous Wharton’s jelly-derived mesenchymal stem cells(WJ-MSCs)transplantation combined with *** The study demonstrates a significant improvement in the child’s functional outcomes(Childhood Autism Rating Scale,Denver 2 Developmental Screening Test),especially in language and gross motor *** serious side effects were encountered during the 2-year *** The findings support the safety and effectiveness of WJ-MSC transplantation in managing ASD.

关键词： Autism spectrum disorder Neurorehabilitation Stem cell transplantation Wharton jelly mesenchymal stem cells Inflammation

Co-production of hydrogen, oxygen, and electricity via an integrated solar-driven system with decoupled water electrolyzer and Na-Zn ion battery

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Journal of Energy Chemistry 2025年第1期100卷 621-627页

作者： Fei Lv Longjie Liu Jiazhe Wu Pengfei Wang Lixia Pan Dengwei Jing Yubin Chen International Research center for Renewable Energy State Key Laboratory of Multiphase Flow in Power Engineering Xi'an Jiaotong University

Combining water electrolysis and rechargeable battery technologies into a single system holds great promise for the co-production of hydrogen （H2） and ***,the design and development of such systems is still in its ***,an integrated hydrogen-oxygen （O2）-electricity co-production system featuring a bipolar membrane-assisted decoupled electrolyzer and a Na-Zn ion battery was established with sodium nickelhexacyanoferrate （NaNiHCF） and Zn2+/Zn as dual redox *** decoupled electrolyzer enables to produce H2and O2in different time and space with almost 100%Faradaic efficiency at 100 mA ***,the charged NaNiHCF and Zn electrodes after the electrolysis processes formed a Na-Zn ion battery,which can generate electricity with an average cell voltage of 1.75 V at 10 m A *** connecting Si photovoltaics with the modular electrochemical device,a well-matched solar driven system was built to convert the intermittent solar energy into hydrogen and electric energy with a solar to hydrogen-electricity efficiency of 16.7%,demonstrating the flexible storage and conversion of renewables.

关键词： Hydrogen Electricity Decoupled water electrolyzer Na-Zn ion battery Solar energy

Overcoming mitochondrial dysfunction in neurodegenerative diseases

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Neural Regeneration Research 2023年第7期18卷 1486-1488页

作者： João Pessoa Ana I.Duarte CNC-center for Neuroscience and Cell Biology CIBB-Center for Innovative Biomedicine and BiotechnologyUniversity of CoimbraCoimbraPortugal

Due to their intense electrical activity,neurons have high energy *** requirement makes them particularly sensitive to mitochondrial *** all eukaryotic cells,neurons have intrinsic mechanisms to mitigate the impact of mitochondrial dysfunction and its consequent production of toxic *** such(neuro)protective mechanisms,mitochondrial autophagy(mitophagy)is responsible for the removal of dysfunctional *** inhibition of mitophagy,together with insufficient mitochondrial activity,results in a shortage of adenosine triphosphate(ATP)and the accumulation of reactive oxygen species(ROS)(Simmons et al.,2020).

关键词： protective dysfunction intense