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Red Light Responsive Cre Recombinase for Bacterial Optogenetics. 用于细菌光遗传学的红光响应 Cre 重组酶
IF 3.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-19 DOI: 10.1021/acssynbio.4c00388
Fereshteh Jafarbeglou, Mary J Dunlop

Optogenetic tools have been used in a wide range of microbial engineering applications that benefit from the tunable, spatiotemporal control that light affords. However, the majority of current optogenetic constructs for bacteria respond to blue light, limiting the potential for multichromatic control. In addition, other wavelengths offer potential benefits over blue light, including improved penetration of dense cultures and reduced potential for toxicity. In this study, we introduce OptoCre-REDMAP, a red light inducible Cre recombinase system in Escherichia coli. This system harnesses the plant photoreceptors PhyA and FHY1 and a split version of Cre recombinase to achieve precise control over gene expression and DNA excision. We optimized the design by modifying the start codon of Cre and characterized the impact of different levels of induction to find conditions that produced minimal basal expression in the dark and induced full activation within 4 h of red light exposure. We characterized the system's sensitivity to ambient light, red light intensity, and exposure time, finding OptoCre-REDMAP to be reliable and flexible across a range of conditions. In coculture experiments with OptoCre-REDMAP and the blue light responsive OptoCre-VVD, we found that the systems responded orthogonally to red and blue light inputs. Direct comparisons between red and blue light induction with OptoCre-REDMAP and OptoCre-VVD demonstrated the superior penetration properties of red light. OptoCre-REDMAP's robust and selective response to red light makes it suitable for advanced synthetic biology applications, particularly those requiring precise multichromatic control.

光遗传学工具已被广泛应用于微生物工程领域,这些领域都受益于光所提供的可调时空控制。然而,目前大多数用于细菌的光遗传构造都对蓝光有反应,限制了多色光控制的潜力。此外,与蓝光相比,其他波长的光具有潜在的优势,包括提高了对高密度培养物的穿透力并降低了潜在的毒性。在这项研究中,我们在大肠杆菌中引入了红光诱导 Cre 重组酶系统 OptoCre-REDMAP。该系统利用植物光感受器 PhyA 和 FHY1 以及 Cre 重组酶的分裂版本来实现对基因表达和 DNA 切除的精确控制。我们通过修改 Cre 的起始密码子对设计进行了优化,并对不同诱导水平的影响进行了表征,从而找到了在黑暗中产生最小基础表达并在红光照射 4 小时内诱导完全激活的条件。我们鉴定了该系统对环境光、红光强度和曝光时间的敏感性,发现 OptoCre-REDMAP 在各种条件下都是可靠和灵活的。在 OptoCre-REDMAP 和对蓝光有反应的 OptoCre-VVD 的共培养实验中,我们发现这两个系统对红光和蓝光输入的反应是正交的。用 OptoCre-REDMAP 和 OptoCre-VVD 对红光和蓝光诱导进行直接比较,结果表明红光的穿透性更强。OptoCre-REDMAP 对红光的稳健和选择性响应使其适用于高级合成生物学应用,尤其是那些需要精确多色光控制的应用。
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引用次数: 0
Engineering an αCD206-synNotch Receptor: Insights into the Development of Novel Synthetic Receptors. αCD206-synNotch受体工程学:新型合成受体开发的启示。
IF 3.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-18 DOI: 10.1021/acssynbio.4c00149
Sofija Semeniuk, Bin-Zhi Qian, Elise Cachat

Immune cells play a pivotal role in the establishment, growth, and progression of tumors at primary and metastatic sites. Macrophages, in particular, play a critical role in suppressing immune responses and promoting an anti-inflammatory environment through both direct and indirect cell-cell interactions. However, our understanding of the mechanisms underlying such interactions is limited due to a lack of reliable tools for studying transient interactions between cancer cells and macrophages within the tumor microenvironment. Recent advances in mammalian synthetic biology have introduced a wide range of synthetic receptors that have been used in diverse biosensing applications. One such synthetic receptor is the synNotch receptor, which can be tailored to sense specific ligands displayed on the surface of target cells. With this study, we aimed at developing a novel αCD206-synNotch receptor, targeting CD206+ macrophages, a population of macrophages that play a crucial role in promoting metastatic seeding and persistent growth. Engineered in cancer cells and used in mouse metastasis models, such a tool could help monitor─and provide an understanding of─the effects that cell-cell interactions between macrophages and cancer cells have on metastasis establishment. Here, we report the development of cancer landing-pad cells for versatile applications and the engineering of αCD206-synNotch cancer cells in particular. We report the measurement of their activity and specificity, and discuss unexpected caveats regarding their in vivo applications.

免疫细胞在肿瘤原发和转移部位的建立、生长和恶化过程中发挥着关键作用。尤其是巨噬细胞,通过直接和间接的细胞-细胞相互作用,在抑制免疫反应和促进抗炎环境方面发挥着至关重要的作用。然而,由于缺乏可靠的工具来研究肿瘤微环境中癌细胞与巨噬细胞之间的瞬时相互作用,我们对这种相互作用机制的了解十分有限。哺乳动物合成生物学的最新进展引入了多种合成受体,这些受体已被用于各种生物传感应用中。其中一种合成受体是 synNotch 受体,这种受体可以定制,以感知靶细胞表面显示的特定配体。这项研究旨在开发一种新型 αCD206-synNotch 受体,以 CD206+ 巨噬细胞为靶标。在癌细胞中设计并在小鼠转移模型中使用这种工具,有助于监测--并提供对--巨噬细胞和癌细胞之间的细胞-细胞相互作用对转移建立的影响的理解。在此,我们报告了用于多种应用的癌症着床垫细胞的开发情况,特别是 αCD206-synNotch 癌细胞的工程化。我们报告了对其活性和特异性的测量结果,并讨论了其体内应用中意想不到的注意事项。
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引用次数: 0
Engineering Exopolysaccharide Biosynthesis of Shewanella oneidensis to Promote Electroactive Biofilm Formation for Liquor Wastewater Treatment. 改造一龄雪旺氏菌的多糖生物合成,促进电活性生物膜的形成,用于酒类废水处理。
IF 3.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-18 DOI: 10.1021/acssynbio.4c00417
Zixuan You, Huan Yu, Baocai Zhang, Qijing Liu, Bo Xiong, Chao Li, Chunxiao Qiao, Longhai Dai, Jianxun Li, Wenwei Li, Guosheng Xin, Zhanying Liu, Feng Li, Hao Song

Microbial electrochemical systems (MESs), as a green and sustainable technology, can decompose organics in wastewater to recover bioelectricity. Electroactive biofilms, a microbial community structure encased in a self-produced matrix, play a decisive role in determining the efficiency of MESs. However, as an essential component of the biofilm matrix, the role of exopolysaccharides in electroactive biofilm formation and their influence on extracellular electron transfer (EET) have been rarely studied. Herein, to explore the effects of exopolysaccharides on biofilm formation and EET rate, we first inhibited the key genes responsible for exopolysaccharide biosynthesis (namely, so_3171, so_3172, so_3177, and so_3178) by using antisense RNA in Shewanella oneidensis MR-1. Then, to explore the underlying mechanisms why inhibition of exopolysaccharide synthesis could enhance biofilm formation and promote the EET rate, we characterized cell physiology and electrophysiology. The results showed inhibition of exopolysaccharide biosynthesis not only altered cell surface hydrophobicity and promoted intercellular adhesion and aggregation, but also increased biosynthesis of c-type cytochromes and decreased interfacial resistance, thus promoting electroactive biofilm formation and improving the EET rate of S. oneidensis. Lastly, to evaluate and intensify the capability of exopolysaccharide-reduced strains in harvesting electrical energy from actual liquor wastewater, engineered strain Δ3171-as3177 was further constructed to treat an actual thin stillage. The results showed that the output power density reached 380.98 mW m-2, 11.1-fold higher than that of WT strain, which exhibited excellent capability of harvesting electricity from actual liquor wastewater. This study sheds light on the underlying mechanism of how inhibition of exopolysaccharides impacts electroactive biofilm formation and EET rate, which suggested that regulating exopolysaccharide biosynthesis is a promising avenue for increasing the EET rate.

微生物电化学系统(MES)作为一种绿色可持续技术,可以分解废水中的有机物,从而回收生物电。电活性生物膜是一种包裹在自产基质中的微生物群落结构,对微生物电化学系统的效率起着决定性作用。然而,作为生物膜基质的重要组成部分,外多糖在电活性生物膜形成过程中的作用及其对胞外电子传递(EET)的影响却鲜有研究。在此,为了探索外多糖对生物膜形成和EET速率的影响,我们首先利用反义RNA抑制了Shewanella oneidensis MR-1中负责外多糖生物合成的关键基因(即so_3171、so_3172、so_3177和so_3178)。然后,为了探索抑制外多糖合成可促进生物膜形成和提高EET速率的内在机制,我们对细胞生理和电生理学进行了表征。结果表明,抑制外多糖的生物合成不仅能改变细胞表面的疏水性,促进细胞间的粘附和聚集,还能增加 c 型细胞色素的生物合成,降低界面电阻,从而促进电活性生物膜的形成,提高 S. oneidensis 的 EET 率。最后,为了评估和加强外多糖还原菌株从实际白酒废水中获取电能的能力,进一步构建了工程菌株Δ3171-as3177来处理实际的稀薄蒸馏水。结果表明,其输出功率密度达到 380.98 mW m-2,是 WT 菌株的 11.1 倍,表现出了从实际白酒废水中获取电能的卓越能力。这项研究揭示了抑制外多糖影响电活性生物膜形成和 EET 率的内在机制,表明调节外多糖的生物合成是提高 EET 率的一条可行途径。
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引用次数: 0
Genetic study of intrahepatic cholestasis of pregnancy in Chinese women unveils East Asian etiology linked to historic HBV epidemic 对中国妇女妊娠期肝内胆汁淤积症的基因研究揭示了与历史上 HBV 流行有关的东亚病因
IF 25.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-14 DOI: 10.1016/j.jhep.2024.11.008
Yanhong Liu, Yuandan Wei, Xiaohang Chen, Shujia Huang, Yuqin Gu, Zijing Yang, Xinxin Guo, Hao Zheng, Hanxiao Feng, Mingxi Huang, Shangliang Chen, Tiantian Xiao, Liang Hu, Quanfu Zhang, Yang Zhang, Guo-Bo Chen, Xiu Qiu, Fengxiang Wei, Jianxin Zhen, Siyang Liu

Background & Aims

Intrahepatic cholestasis of pregnancy (ICP) is the most common and high-risk liver disorder during pregnancy, with varying prevalence across populations. Our understanding of the mechanisms underlying ICP and its population difference remains limited. This study delves into the genetic etiology of ICP in East Asians, drawing comparisons with Europeans to comprehend ICP etiology in the context of genetic background and evolution.

Methods

We conducted the hitherto largest-scale genome-wide association studies (GWAS) on fasting total serum bile acids (TBA) and ICP in 98,269 Chinese pregnancies. The findings were replicated in three cohorts and compared with European populations. Additionally, phenome-wide association and spatio-temporal evolution analyses were employed to investigate the function and evolutionary patterns of ICP-associated loci.

Results

We identified eight loci for fasting TBA and four for ICP, including ten novel loci. Notably, we discovered an East-Asian-specific locus within a 0.4Mbp region at 14q24.1, which increases fasting TBA by 6.12 μmol/L and ICP risk by 16.56-fold per risk allele (95% CI: 16.43 to 16.69, P = 7.06×10-381). Phenome-wide association and spatial-temporal evolution analyses revealed that this 14q24.1 ICP risk locus confers resistance to hepatitis B and has become prevalent in East and Southeast Asia within the last 3,000 years.

Conclusions

We uncovered a distinct genetic etiology of ICP in East Asians, likely linked to a historic HBV epidemic in East and Southeast Asia within the last 3,000 years. These findings enhance our understanding of ICP pathophysiology and offer potential for more precise detection, assessment, and treatment of the disorder.

Impact and implications

This study provides novel insights into the genetic basis of intrahepatic cholestasis of pregnancy (ICP) in East Asian populations, where little was previously known. The identification of the East-Asian-specific 14q24.1 locus, associated with both fasting TBA and ICP, and its connection to a historical hepatitis B epidemic emphasize the importance of incorporating population-specific history into disease research. These findings are crucial for researchers studying pregnancy-related liver disorders and clinicians providing care to pregnant women, enabling more accurate screening, risk assessment, and targeted interventions for ICP.
背景& 目的妊娠期肝内胆汁淤积症(ICP)是妊娠期最常见的高危肝脏疾病,在不同人群中的发病率各不相同。我们对 ICP 的发病机制及其人群差异的了解仍然有限。本研究深入探讨了东亚人ICP的遗传病因,并与欧洲人进行了比较,以便在遗传背景和进化的背景下理解ICP的病因。方法我们对98269名中国孕妇的空腹血清总胆汁酸(TBA)和ICP进行了迄今为止最大规模的全基因组关联研究(GWAS)。研究结果在三个队列中得到了重复,并与欧洲人群进行了比较。此外,我们还采用了全表型关联分析和时空进化分析来研究 ICP 相关位点的功能和进化模式。值得注意的是,我们在14q24.1的0.4Mbp区域内发现了一个东亚特异性位点,该位点使空腹TBA增加6.12 μmol/L,使每个风险等位基因的ICP风险增加16.56倍(95% CI:16.43至16.69,P = 7.06×10-381)。全表型关联分析和时空进化分析表明,14q24.1 ICP 风险位点赋予了对乙型肝炎的抵抗力,并在过去 3000 年间在东亚和东南亚流行起来。这些发现加深了我们对 ICP 病理生理学的了解,并为更精确地检测、评估和治疗该疾病提供了可能。 影响和意义这项研究为以前鲜为人知的东亚人群妊娠期肝内胆汁淤积症(ICP)的遗传基础提供了新的见解。东亚特异性 14q24.1 位点的确定与空腹 TBA 和 ICP 都有关联,其与历史上乙型肝炎流行的联系强调了将特定人群的历史纳入疾病研究的重要性。这些发现对于研究妊娠相关肝脏疾病的研究人员和为孕妇提供护理的临床医生来说至关重要,可使ICP的筛查、风险评估和针对性干预更加准确。
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引用次数: 0
Advanced Functional Membranes Based on Amphiphilic Copolymers 基于两性共聚物的先进功能膜
IF 27.1 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-13 DOI: 10.1016/j.progpolymsci.2024.101907
Zhuan Yi, Lijing Zhu, Ruiyan Xiong, Chuanjie Fang, Baoku Zhu, Liping Zhu, Hongbo Zeng
Membranes with advanced and novel functions play important roles in emerging applications ranging from industrial separations, water purification, energy harvesting and storage, health care, biomimetic membranes and more. The performances of membranes in these critical applications are essentially determined by their interfacial interactions with surrounding ions, molecules, particles, emulsions, and bioactive agents. Amphiphilic copolymers containing both hydrophobic and hydrophilic segments will spontaneously assemble into multiphase and hierarchical structures, providing a general solution for regulating the surface physical-chemical properties of membranes used in the aforementioned urgent applications. Controlled synthesis of amphiphilic copolymers and the methods to fabricate copolymers into membranes with predetermined performance are fundamentally important for their applications. In this work, we first summarize the polymerization techniques developed to synthesize amphiphilic copolymers used for membrane materials. We then review the methods to fabricate membranes from amphiphilic copolymers, and summarize urgent applications of advanced functional membranes produced from amphiphilic copolymers. We also discuss some remaining challenges and provide remarks for future perspectives, especially considering that the circular polymer economy and artificial intelligence have already set new requirements for polymer science. This work offers a comprehensive overview of recent advances in functional materials based on amphiphilic polymers, including the working principles and associations between polymer structure, processing strategy, and membrane performances, which can provide new insights into the development of high performance and next generation of polymeric membranes through the precise, function-led synthesis of novel amphiphilic copolymers and controlled membrane fabrication process.
具有先进和新颖功能的膜在工业分离、水净化、能量收集和储存、医疗保健、仿生物膜等新兴应用中发挥着重要作用。膜在这些关键应用中的性能主要取决于其与周围离子、分子、颗粒、乳液和生物活性剂的界面相互作用。含有疏水性和亲水性片段的两亲共聚物会自发组装成多相和分层结构,为调节上述紧急应用中使用的膜的表面物理化学特性提供了一种通用解决方案。两亲共聚物的可控合成以及将共聚物制成具有预定性能的膜的方法对其应用至关重要。在这项工作中,我们首先总结了用于合成膜材料的两亲共聚物的聚合技术。然后,我们回顾了用两亲共聚物制造膜的方法,并总结了用两亲共聚物制造的高级功能膜的迫切应用。我们还讨论了一些尚存的挑战,并对未来前景提出了看法,特别是考虑到循环聚合物经济和人工智能已经对聚合物科学提出了新的要求。本研究全面概述了基于两亲性聚合物的功能材料的最新进展,包括聚合物结构、加工策略和膜性能之间的工作原理和关联,为通过新型两亲性共聚物的精确、功能导向合成和可控膜制造工艺开发高性能和下一代聚合物膜提供了新的见解。
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引用次数: 0
Adipose triglyceride lipase as a target for treatment of metabolic dysfunction-associated steatohepatitis: the role of hepatic and intestinal PPARα 将脂肪甘油三酯脂肪酶作为治疗代谢功能障碍相关性脂肪性肝炎的靶点:肝脏和肠道 PPARα 的作用
IF 25.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-13 DOI: 10.1016/j.jhep.2024.10.046
Frank J. Gonzalez, Yangliu Xia

Section snippets

Financial support

Funded by the National Cancer Institute Intramural Research Program.

Declaration of Competing Interest

The authors declare no conflicts of interest that pertain to this work.Please refer to the accompanying ICMJE disclosure forms for further details.Adipose triglyceride lipase (ATGL), encoded by the PNPLA2 gene in humans, hydrolyzes triacylglycerols to diacylglycerols. PNPLA2 is regulated by insulin, and under conditions of insulin resistance, increased adipocyte ATGL leads to excess production of free fatty acids that are transported to the liver resulting in metabolic dysfunction-associated
部分片段财务支持由美国国家癌症研究所校内研究计划资助。利益冲突声明作者声明没有与本研究相关的利益冲突,详情请参见随附的 ICMJE 披露表。PNPLA2 受胰岛素调节,在胰岛素抵抗的条件下,脂肪细胞 ATGL 的增加会导致游离脂肪酸的过量产生,这些游离脂肪酸被运送到肝脏,从而导致代谢功能障碍相关的疾病。
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引用次数: 0
Activating hepatobiliary water channels for gallstone prevention in complicated gallstone disease 激活肝胆水通道,预防复杂性胆石症中的胆石症
IF 25.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-13 DOI: 10.1016/j.jhep.2024.11.006
Jan G. Hengstler, Nachiket Vartak

Section snippets

Conflict of interest statement

The authors declare no conflict of interest.

Uncited reference

[17]; [18]; [19]; [17]; [18]; [19].

Authors' contributions

JGH and NV developed the ideas presented and wrote the manuscript.

Financial support

No particulars to report
未引用的参考文献[17];[18];[19];[17];[18];[19].作者的贡献JGH和NV提出了自己的观点并撰写了手稿.财务支持无具体细节报告
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引用次数: 0
Non-invasive algorithms could outperform HVPG in selecting candidates for non-selective beta-blockers in cirrhosis 在肝硬化患者非选择性β-受体阻滞剂的候选药物选择方面,无创算法优于 HVPG
IF 25.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-13 DOI: 10.1016/j.jhep.2024.11.011
Emma Vanderschueren

Section snippets

Author contributions

Conceptualization, data curation, formal analysis and writing of the manuscript were performed by EV and WL.

Financial support

None.

Declaration of Competing Interest

WL serves as a consultant for Cook Medical, MRM Health, and CSL Behring, and has received speaker’s fees from Boston Scientific. No other conflicts of interest were withheld.

Acknowledgements

We wish to thank Prof. Antonio Colecchia for his assistance in providing additional data from the validation cohort.
作者贡献构思、数据整理、正式分析和手稿撰写由 EV 和 WL 完成。财务支持无。竞争利益声明WL 担任 Cook Medical、MRM Health 和 CSL Behring 的顾问,并从波士顿科学公司获得演讲费。没有隐瞒其他利益冲突。感谢 Antonio Colecchia 教授协助提供验证队列的其他数据。
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引用次数: 0
Surrender to evidence: the futility of plasma exchange for severe liver disease and liver failure 向证据投降:血浆置换治疗重症肝病和肝衰竭徒劳无益
IF 25.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-13 DOI: 10.1016/j.jhep.2024.11.010
Cyriac Abby Philips, Arif Hussain Theruvath, Aryalakshmi Sreemohan, John Menachery, Rosh Varghese

Section snippets

Authors’ contributions

CAP designed the study and wrote the manuscript, AHT and AL acquired, compiled, and analysed the data, JM and RV finalized the manuscript and made critical revisions, all authors accepted the final version of manuscript for submission.

Financial support

The authors received no financial support to produce this manuscript.

Declaration of Competing Interest

The authors declare no conflicts of interest that pertain to this work.
章节片段作者贡献CAP设计研究并撰写手稿,AHT和AL获取、整理和分析数据,JM和RV对手稿进行定稿和关键性修改,所有作者均接受最终提交的手稿版本。
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引用次数: 0
Unlock AI-Safe-C score's potential at all levels: Improve methods and overcome barriers 释放 AI-Safe-C 评分在各个层面的潜力:改进方法,克服障碍
IF 25.7 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2024-11-13 DOI: 10.1016/j.jhep.2024.11.012
Qin Guo, Hui Li, Chengshan Guo

Section snippets

Authors contributions

Qin Guo: Conceptualization, Writing – original draft; Hui Li: Conceptualization, Funding acquisition, Writing – review & editing; Chengshan Guo: Funding acquisition, Writing – review & editing.

Financial support statement

This work was supported by the Medical and Health Research Project of Baoan District (No. 2023JD250), and the Key Specialties in Clinical Medicine of the People’s Hospital of Baoan Shenzhen(No. 8).

Declaration of Competing Interest

The authors declare no conflicts of interest that pertain to this work.
章节片段作者贡献Qin Guo:构思,撰写-原稿;李慧:构思,经费获取,撰写-审阅和编辑;郭成山:构思,经费获取,撰写-审阅和编辑:财务支持声明本工作得到了宝安区医疗卫生科研项目(编号:2023JD250)和深圳市宝安区人民医院临床医学重点专科(编号:8)的支持。
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引用次数: 0
期刊
ACS Synthetic Biology
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