Liver tissue engineering offers potential in liver transplantation, while the development of hydrogels for scalable scaffolds incorporating natural components and effective functionalities is ongoing. Here, we propose a novel microfluidic 3D printing hydrogel derived from decellularized fish liver extracellular matrix for liver regeneration. By decellularizing fish liver and combining it with gelatin methacryloyl, the hydrogel scaffold retains essential endogenous growth factors such as collagen and glycosaminoglycans. Additionally, microfluidic-assisted 3D printing technology enables precise modulation of the composition and architecture of hydrogels to fulfill clinical requirements. Benefiting from the natural source of materials, the hydrogels exhibit excellent biocompatibility and cellular proliferation capacity for incorporating induced pluripotent stem cell-derived hepatocytes (iPSC-heps). Furthermore, the macroscopic architecture and biomechanical environment of hydrogels foster optimal functional expression of iPSC-heps. Importantly, post-transplantation, the hydrogels significantly enhance survival rates and liver function in mice with acute liver failure, promoting liver regeneration and repair. These findings suggest that microfluidic 3D printed hydrogels represent promising candidates for liver transplantation and functional recovery.
{"title":"Microfluidic 3D printing hydrogels based on fish liver decellularized extracellular matrix for liver regeneration.","authors":"Haozhen Ren, Danqing Huang, Mengdi Qiu, Lingling Xue, Shaoshi Zhu, Jingjing Gan, Cheng Chen, Dayu Chen, Jinglin Wang","doi":"10.1002/SMMD.20240056","DOIUrl":"https://doi.org/10.1002/SMMD.20240056","url":null,"abstract":"<p><p>Liver tissue engineering offers potential in liver transplantation, while the development of hydrogels for scalable scaffolds incorporating natural components and effective functionalities is ongoing. Here, we propose a novel microfluidic 3D printing hydrogel derived from decellularized fish liver extracellular matrix for liver regeneration. By decellularizing fish liver and combining it with gelatin methacryloyl, the hydrogel scaffold retains essential endogenous growth factors such as collagen and glycosaminoglycans. Additionally, microfluidic-assisted 3D printing technology enables precise modulation of the composition and architecture of hydrogels to fulfill clinical requirements. Benefiting from the natural source of materials, the hydrogels exhibit excellent biocompatibility and cellular proliferation capacity for incorporating induced pluripotent stem cell-derived hepatocytes (iPSC-heps). Furthermore, the macroscopic architecture and biomechanical environment of hydrogels foster optimal functional expression of iPSC-heps. Importantly, post-transplantation, the hydrogels significantly enhance survival rates and liver function in mice with acute liver failure, promoting liver regeneration and repair. These findings suggest that microfluidic 3D printed hydrogels represent promising candidates for liver transplantation and functional recovery.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 4","pages":"e20240056"},"PeriodicalIF":0.0,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-22eCollection Date: 2024-12-01DOI: 10.1002/SMMD.20240053
Ding Zhao, Yixiang Zhang, Fan Wang, Rames Kaewmanee, Wenguo Cui, Tianqi Wu, Yawei Du
Phospholipid-based liposomes are among the most successful nanodrug delivery systems in clinical use. However, these conventional liposomes present significant challenges including low drug-loading capacity and issues with drug leakage. Drug-phospholipid conjugates (DPCs) and their assemblies offer a promising strategy for addressing these limitations. In this review, we summarize recent advances in the design, synthesis, and application of DPCs for drug delivery. We begin by discussing the chemical backbone structures and various design strategies such as phosphate head embedding and mono-/bis-embedding in the sn-1/sn-2 positions. Furthermore, we highlight stimulus-responsive designs of DPCs and their applications in treating diseases such as cancer, inflammation, and malaria. Lastly, we explore future directions for DPCs development and their potential applications in drug delivery.
{"title":"Drug-phospholipid conjugate nano-assembly for drug delivery.","authors":"Ding Zhao, Yixiang Zhang, Fan Wang, Rames Kaewmanee, Wenguo Cui, Tianqi Wu, Yawei Du","doi":"10.1002/SMMD.20240053","DOIUrl":"https://doi.org/10.1002/SMMD.20240053","url":null,"abstract":"<p><p>Phospholipid-based liposomes are among the most successful nanodrug delivery systems in clinical use. However, these conventional liposomes present significant challenges including low drug-loading capacity and issues with drug leakage. Drug-phospholipid conjugates (DPCs) and their assemblies offer a promising strategy for addressing these limitations. In this review, we summarize recent advances in the design, synthesis, and application of DPCs for drug delivery. We begin by discussing the chemical backbone structures and various design strategies such as phosphate head embedding and mono-/bis-embedding in the sn-1/sn-2 positions. Furthermore, we highlight stimulus-responsive designs of DPCs and their applications in treating diseases such as cancer, inflammation, and malaria. Lastly, we explore future directions for DPCs development and their potential applications in drug delivery.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 4","pages":"e20240053"},"PeriodicalIF":0.0,"publicationDate":"2024-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-12-03eCollection Date: 2024-12-01DOI: 10.1002/SMMD.20240033
Xin Wang, Dan Mu, Jing Liang, Ruijing Xin, Yukun Zhang, Renyuan Liu, Mei Yao, Bing Zhang
Atherosclerosis (AS) is a major cause of cardiovascular disease. In particular, the unpredictable rupture of vulnerable atherosclerotic plaques (VASPs) can cause serious cardiovascular events such as myocardial infarction, stroke, and even sudden death. Therefore, early evaluation of the vulnerability of atherosclerotic plaques is of great importance. However, clinical imaging techniques are only marginally useful in the presence of severe anatomical structural changes, making it difficult to evaluate plaque vulnerability at an early stage. With the development of molecular imaging and nanotechnology, specific nanoprobes constructed for the pathological features of VASPs have attracted much attention for their ability to visualize VASPs early and noninvasively at the cellular and molecular levels. Here, we outline the pathological features of VASPs, analyze the superiority and limitations of current clinical imaging techniques, introduce the rational design principles of nanoprobes, and systematically summarize the application of nanoprobes to visualize the features of VASPs at the cellular and molecular levels. In addition, we discussed the prospects and urgent challenges in this field, and we believe it will provide new ideas for the early and accurate diagnosis of cardiovascular diseases.
{"title":"Emerging nanoprobes for the features visualization of vulnerable atherosclerotic plaques.","authors":"Xin Wang, Dan Mu, Jing Liang, Ruijing Xin, Yukun Zhang, Renyuan Liu, Mei Yao, Bing Zhang","doi":"10.1002/SMMD.20240033","DOIUrl":"https://doi.org/10.1002/SMMD.20240033","url":null,"abstract":"<p><p>Atherosclerosis (AS) is a major cause of cardiovascular disease. In particular, the unpredictable rupture of vulnerable atherosclerotic plaques (VASPs) can cause serious cardiovascular events such as myocardial infarction, stroke, and even sudden death. Therefore, early evaluation of the vulnerability of atherosclerotic plaques is of great importance. However, clinical imaging techniques are only marginally useful in the presence of severe anatomical structural changes, making it difficult to evaluate plaque vulnerability at an early stage. With the development of molecular imaging and nanotechnology, specific nanoprobes constructed for the pathological features of VASPs have attracted much attention for their ability to visualize VASPs early and noninvasively at the cellular and molecular levels. Here, we outline the pathological features of VASPs, analyze the superiority and limitations of current clinical imaging techniques, introduce the rational design principles of nanoprobes, and systematically summarize the application of nanoprobes to visualize the features of VASPs at the cellular and molecular levels. In addition, we discussed the prospects and urgent challenges in this field, and we believe it will provide new ideas for the early and accurate diagnosis of cardiovascular diseases.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 4","pages":"e20240033"},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-17eCollection Date: 2024-12-01DOI: 10.1002/SMMD.20240026
Yan Zu, Jing Du, Yipu Xu, Mengying Niu, Canlin Hong, Chun Yang
Chondrocytes are commonly applied in regenerative medicine and tissue engineering. Thus, the discovery of optimal culture conditions to obtain cells with good properties and behavior for transplantation is important. In addition to biochemical cues, physical and biomechanical changes can affect the proliferation and protein expression of chondrocytes. Here we investigated the effect of extracellular matrix stiffness on mouse articular chondrocyte phenotype, growth, and subcellular p53 localization. Chondrocytes were seeded on collagen-coated substrates varying in elasticity: 0.5 and 100 kPa. Immunocytochemical staining and immunoblotting showed that a softer substrate significantly increased p53 nuclear localization in chondrocytes. Furthermore, we identified microRNA-532 (miR-532) as a potential p53 target gene to influence cell function, indicating a new target for tissue engineering. These findings provide insight into the influence of physical cues on cell phenotype maintenance and could help improve understanding of cartilage-related pathologies such as osteoarthritis.
{"title":"Change in p53 nuclear localization in response to extracellular matrix stiffness.","authors":"Yan Zu, Jing Du, Yipu Xu, Mengying Niu, Canlin Hong, Chun Yang","doi":"10.1002/SMMD.20240026","DOIUrl":"https://doi.org/10.1002/SMMD.20240026","url":null,"abstract":"<p><p>Chondrocytes are commonly applied in regenerative medicine and tissue engineering. Thus, the discovery of optimal culture conditions to obtain cells with good properties and behavior for transplantation is important. In addition to biochemical cues, physical and biomechanical changes can affect the proliferation and protein expression of chondrocytes. Here we investigated the effect of extracellular matrix stiffness on mouse articular chondrocyte phenotype, growth, and subcellular p53 localization. Chondrocytes were seeded on collagen-coated substrates varying in elasticity: 0.5 and 100 kPa. Immunocytochemical staining and immunoblotting showed that a softer substrate significantly increased p53 nuclear localization in chondrocytes. Furthermore, we identified microRNA-532 (miR-532) as a potential p53 target gene to influence cell function, indicating a new target for tissue engineering. These findings provide insight into the influence of physical cues on cell phenotype maintenance and could help improve understanding of cartilage-related pathologies such as osteoarthritis.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 4","pages":"e20240026"},"PeriodicalIF":0.0,"publicationDate":"2024-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669774/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-11-11eCollection Date: 2024-12-01DOI: 10.1002/SMMD.20240038
Qingfei Zhang, Gaizhen Kuang, Kai Chen, Miaoqing Zhao, Luoran Shang
Bioorthogonal chemistry, recognized as a highly efficient tool in chemical biology, has shown significant value in cancer treatment. The primary objective is to develop efficient delivery strategies to achieve enhanced bioorthogonal drug treatment for tumors. Here, Janus microparticles (JMs) loaded with cyclooctene-modified doxorubicin prodrug (TCO-DOX) and tetrazine-modified indocyanine green (Tz-ICG) triggers are reported. Besides activating TCO-DOX, Tz-ICG is also a photothermal agent used in photothermal therapy (PTT), enabling the simultaneous use of biorthogonal chemotherapy and PTT. Additionally, the DOX could be significantly reduced in systemic toxicity with the modification of cyclooctene. Thus, the developed drug-carrying JMs system exhibits effective tumor cell killing in vitro and effectively inhibits tumor local progress and distant lung metastasis after postoperative treatment with good safety. These results demonstrate that the prepared JMs provide a paradigm for bioorthogonal prodrug activation and localized delivery, and hold great promise for cancer therapy as well as other related applications.
{"title":"Bioorthogonal Janus microparticles for photothermal and chemo-therapy.","authors":"Qingfei Zhang, Gaizhen Kuang, Kai Chen, Miaoqing Zhao, Luoran Shang","doi":"10.1002/SMMD.20240038","DOIUrl":"https://doi.org/10.1002/SMMD.20240038","url":null,"abstract":"<p><p>Bioorthogonal chemistry, recognized as a highly efficient tool in chemical biology, has shown significant value in cancer treatment. The primary objective is to develop efficient delivery strategies to achieve enhanced bioorthogonal drug treatment for tumors. Here, Janus microparticles (JMs) loaded with cyclooctene-modified doxorubicin prodrug (TCO-DOX) and tetrazine-modified indocyanine green (Tz-ICG) triggers are reported. Besides activating TCO-DOX, Tz-ICG is also a photothermal agent used in photothermal therapy (PTT), enabling the simultaneous use of biorthogonal chemotherapy and PTT. Additionally, the DOX could be significantly reduced in systemic toxicity with the modification of cyclooctene. Thus, the developed drug-carrying JMs system exhibits effective tumor cell killing in vitro and effectively inhibits tumor local progress and distant lung metastasis after postoperative treatment with good safety. These results demonstrate that the prepared JMs provide a paradigm for bioorthogonal prodrug activation and localized delivery, and hold great promise for cancer therapy as well as other related applications.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 4","pages":"e20240038"},"PeriodicalIF":0.0,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vertigo is a common symptom of various diseases that affects a large number of people worldwide. Current leading treatments for intractable peripheral vertigo are to intratympanically inject ototoxic drugs such as gentamicin to attenuate the semicircular canal function but inevitably cause hearing injury. Photodynamic therapy (PDT) is a noninvasive therapeutic approach by precisely targeting the diseased tissue. Here, we developed a PDT-based method for treating intractable peripheral vertigo in a mouse model using a polymer-coated photosensitizer chlorin e6 excited by red light. We found that a high dose of PDT attenuated the function of both semicircular canals and otolith organs and damaged their hair cells. Conversely, the PDT exerted no effect on hearing function or cochlear hair-cell viability. These results suggest the therapeutic potential of PDT for treating intractable peripheral vertigo without hurting hearing. Besides, the attenuation level and affected area can be precisely controlled by adjusting the light exposure time. Furthermore, we demonstrated the potential of this therapeutic approach to be minimally invasive with light irradiation through bone results. Thus, our PDT-based approach for attenuating the function of the semicircular canals offers a basis for developing a less-invasive and targeted therapeutic option for treating vertigo.
{"title":"Photodynamic therapy-induced precise attenuation of light-targeted semicircular canals for treating intractable vertigo.","authors":"Yingkun Yang, Tong Zhao, Feixue Mi, Hongzhe Li, Pingbo Huang, Fangyi Chen","doi":"10.1002/SMMD.20230044","DOIUrl":"https://doi.org/10.1002/SMMD.20230044","url":null,"abstract":"<p><p>Vertigo is a common symptom of various diseases that affects a large number of people worldwide. Current leading treatments for intractable peripheral vertigo are to intratympanically inject ototoxic drugs such as gentamicin to attenuate the semicircular canal function but inevitably cause hearing injury. Photodynamic therapy (PDT) is a noninvasive therapeutic approach by precisely targeting the diseased tissue. Here, we developed a PDT-based method for treating intractable peripheral vertigo in a mouse model using a polymer-coated photosensitizer chlorin e6 excited by red light. We found that a high dose of PDT attenuated the function of both semicircular canals and otolith organs and damaged their hair cells. Conversely, the PDT exerted no effect on hearing function or cochlear hair-cell viability. These results suggest the therapeutic potential of PDT for treating intractable peripheral vertigo without hurting hearing. Besides, the attenuation level and affected area can be precisely controlled by adjusting the light exposure time. Furthermore, we demonstrated the potential of this therapeutic approach to be minimally invasive with light irradiation through bone results. Thus, our PDT-based approach for attenuating the function of the semicircular canals offers a basis for developing a less-invasive and targeted therapeutic option for treating vertigo.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 4","pages":"e20230044"},"PeriodicalIF":0.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11669792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142960099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Silk fibroin (SF)-based hydrogels are promising multifunctional adhesive candidates for real-world applications in tissue engineering, implantable bioelectronics, artificial muscles, and artificial skin. However, developing conductive SF-based hydrogels that are suitable for the micro-physiological environment and maintain their physical and chemical properties over long periods of use remains challenging. Herein, we developed an ion-conductive SF hydrogel composed of glycidyl methacrylate silk fibroin (SilMA) and bioionic liquid choline acylate (ChoA) polymer chains, together with the modification of acrylated thymine (ThyA) and adenine (AdeA) functional groups. The resulting polymeric ion-conductive SF composite hydrogel demonstrated high bioactivity, strong adhesion strength, good mechanical compliance, and stretchability. The formed hydrogel network of ChoA chains can coordinate with the ionic strength in the micro-physiological environment while maintaining the adaptive coefficient of expansion and stable mechanical properties. These features help to form a stable ion-conducting channel for the hydrogel. Additionally, the hydrogel network modified with AdeA and ThyA, can provide a strong adhesion to the surface of a variety of substrates, including wet tissue through abundant hydrogen bonding. The biocompatible and ionic conductive SF composite hydrogels can be easily prepared and incorporated into flexible skin or epidermal sensing devices. Therefore, our polymeric SF-based hydrogel has great potential and wide application to be an important component of many flexible electronic devices for personalized healthcare.
丝纤维素(SF)基水凝胶是很有前途的多功能粘合剂,可实际应用于组织工程、植入式生物电子学、人造肌肉和人造皮肤。然而,开发适合微生理环境并能长期保持其物理和化学特性的导电 SF 水凝胶仍具有挑战性。在此,我们开发了一种离子导电 SF 水凝胶,由甲基丙烯酸缩水甘油酯丝纤维素(SilMA)和生物离子液体胆碱酰化物(ChoA)聚合物链组成,并对丙烯化胸腺嘧啶(ThyA)和腺嘌呤(AdeA)官能团进行修饰。由此产生的高分子离子导电 SF 复合水凝胶具有很高的生物活性、很强的粘附强度、良好的机械顺应性和拉伸性。所形成的 ChoA 链水凝胶网络能与微生理环境中的离子强度相协调,同时保持适应性膨胀系数和稳定的机械性能。这些特性有助于为水凝胶形成稳定的离子传导通道。此外,经 AdeA 和 ThyA 修饰的水凝胶网络还能通过丰富的氢键与包括湿组织在内的各种基质表面产生强大的粘附力。这种具有生物相容性和离子传导性的 SF 复合水凝胶可以很容易地制备并整合到柔性皮肤或表皮传感设备中。因此,我们的基于 SF 的聚合物水凝胶具有巨大的潜力和广泛的应用前景,可成为许多用于个性化医疗的柔性电子设备的重要组成部分。
{"title":"Polymeric silk fibroin hydrogel as a conductive and multifunctional adhesive for durable skin and epidermal electronics.","authors":"Fanfan Fu, Changyi Liu, Zhenlin Jiang, Qingyu Zhao, Aining Shen, Yilun Wu, Wenyi Gu","doi":"10.1002/SMMD.20240027","DOIUrl":"https://doi.org/10.1002/SMMD.20240027","url":null,"abstract":"<p><p>Silk fibroin (SF)-based hydrogels are promising multifunctional adhesive candidates for real-world applications in tissue engineering, implantable bioelectronics, artificial muscles, and artificial skin. However, developing conductive SF-based hydrogels that are suitable for the micro-physiological environment and maintain their physical and chemical properties over long periods of use remains challenging. Herein, we developed an ion-conductive SF hydrogel composed of glycidyl methacrylate silk fibroin (SilMA) and bioionic liquid choline acylate (ChoA) polymer chains, together with the modification of acrylated thymine (ThyA) and adenine (AdeA) functional groups. The resulting polymeric ion-conductive SF composite hydrogel demonstrated high bioactivity, strong adhesion strength, good mechanical compliance, and stretchability. The formed hydrogel network of ChoA chains can coordinate with the ionic strength in the micro-physiological environment while maintaining the adaptive coefficient of expansion and stable mechanical properties. These features help to form a stable ion-conducting channel for the hydrogel. Additionally, the hydrogel network modified with AdeA and ThyA, can provide a strong adhesion to the surface of a variety of substrates, including wet tissue through abundant hydrogen bonding. The biocompatible and ionic conductive SF composite hydrogels can be easily prepared and incorporated into flexible skin or epidermal sensing devices. Therefore, our polymeric SF-based hydrogel has great potential and wide application to be an important component of many flexible electronic devices for personalized healthcare.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 3","pages":"e20240027"},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11425052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Peptide spectrum matching is the process of linking mass spectrometry data with peptide sequences. An experimental spectrum can match thousands of candidate peptides with variable modifications leading to an exponential increase in candidates. Completing the search within a limited time is a key challenge. Traditional searches expedite the process by restricting peptide mass errors and variable modifications, but this limits interpretive capability. To address this challenge, we propose Dear-PSM, a peptide search engine that supports full database searching. Dear-PSM does not restrict peptide mass errors, matching each spectrum to all peptides in the database and increasing the number of variable modifications per peptide from the conventional 3-20. Leveraging inverted index technology, Dear-PSM creates a high-performance index table of experimental spectra and utilizes deep learning algorithms for peptide validation. Through these techniques, Dear-PSM achieves a speed breakthrough 7 times faster than mainstream search engines on a regular desktop computer, with a remarkable 240-fold reduction in memory consumption. Benchmark test results demonstrate that Dear-PSM, in full database search mode, can reproduce over 90% of the results obtained by mainstream search engines when handling complex mass spectrometry data collected from different species using various instruments. Furthermore, it uncovers a substantial number of new peptides and proteins. Dear-PSM has been publicly released on the GitHub repository https://github.com/jianweishuai/Dear-PSM.
{"title":"Dear-PSM: A deep learning-based peptide search engine enables full database search for proteomics.","authors":"Qingzu He, Xiang Li, Jinjin Zhong, Gen Yang, Jiahuai Han, Jianwei Shuai","doi":"10.1002/SMMD.20240014","DOIUrl":"https://doi.org/10.1002/SMMD.20240014","url":null,"abstract":"<p><p>Peptide spectrum matching is the process of linking mass spectrometry data with peptide sequences. An experimental spectrum can match thousands of candidate peptides with variable modifications leading to an exponential increase in candidates. Completing the search within a limited time is a key challenge. Traditional searches expedite the process by restricting peptide mass errors and variable modifications, but this limits interpretive capability. To address this challenge, we propose Dear-PSM, a peptide search engine that supports full database searching. Dear-PSM does not restrict peptide mass errors, matching each spectrum to all peptides in the database and increasing the number of variable modifications per peptide from the conventional 3-20. Leveraging inverted index technology, Dear-PSM creates a high-performance index table of experimental spectra and utilizes deep learning algorithms for peptide validation. Through these techniques, Dear-PSM achieves a speed breakthrough 7 times faster than mainstream search engines on a regular desktop computer, with a remarkable 240-fold reduction in memory consumption. Benchmark test results demonstrate that Dear-PSM, in full database search mode, can reproduce over 90% of the results obtained by mainstream search engines when handling complex mass spectrometry data collected from different species using various instruments. Furthermore, it uncovers a substantial number of new peptides and proteins. Dear-PSM has been publicly released on the GitHub repository https://github.com/jianweishuai/Dear-PSM.</p>","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"3 3","pages":"e20240014"},"PeriodicalIF":0.0,"publicationDate":"2024-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11425048/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chuanhui Song, Rui Liu, Yile Fang, Hongcheng Gu, Yu Wang
Oral disease is a severe healthcare challenge that diminishes people's quality of life. Functional hydrogels with suitable biodegradability, biocompatibility, and tunable mechanical properties have attracted remarkable interest and have been developed for treating oral diseases. In this review, we present up‐to‐date research on hydrogels for the management of dental caries, endodontics, periapical periodontitis, and periodontitis, depending on the progression of dental diseases. The strategies of hydrogels for treating oral mucosal diseases and salivary gland diseases are then classified. After that, we focus on the application of hydrogels related to tumor therapy and tissue defects. Finally, the review prospects the restrictions and the perspectives on the utilization of hydrogels in oral disease treatment. We believe this review will promote the advancement of more amicable, functional and personalized approaches for oral diseases.
{"title":"Developing functional hydrogels for treatment of oral diseases","authors":"Chuanhui Song, Rui Liu, Yile Fang, Hongcheng Gu, Yu Wang","doi":"10.1002/smmd.20240020","DOIUrl":"https://doi.org/10.1002/smmd.20240020","url":null,"abstract":"Oral disease is a severe healthcare challenge that diminishes people's quality of life. Functional hydrogels with suitable biodegradability, biocompatibility, and tunable mechanical properties have attracted remarkable interest and have been developed for treating oral diseases. In this review, we present up‐to‐date research on hydrogels for the management of dental caries, endodontics, periapical periodontitis, and periodontitis, depending on the progression of dental diseases. The strategies of hydrogels for treating oral mucosal diseases and salivary gland diseases are then classified. After that, we focus on the application of hydrogels related to tumor therapy and tissue defects. Finally, the review prospects the restrictions and the perspectives on the utilization of hydrogels in oral disease treatment. We believe this review will promote the advancement of more amicable, functional and personalized approaches for oral diseases.","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":"12 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141803678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yuxin Wang, Matthew Chae, Teak-Jung Oh, Kangqiang Qiu, Kritika Mehta, Adrian Tan, Nien‐Pei Tsai, Donglu Shi, Kai Zhang, Jiajie Diao
Bio‐waste is a side product of biomedical research containing carbon, which can be utilized for developing carbon dots (CDs). CDs are known to be useful for a variety of applications because of their unique photoluminescence, low toxicity, and straightforward synthesis. In this paper, we employed a one‐step hydrothermal method to prepare CDs from bio‐waste as the only reactant. The as‐synthesized Cell‐CDs were found to be chemically stable and biocompatible. In addition, the spectra of Cell‐CDs’ emissions covered the visible light, which is ideal for super‐resolution imaging. Particularly, dual‐color imaging can be achieved, for example, by staining the plasma membrane with Cell‐CDs emitting one color and staining cytosolic organelles with Cell‐CDs emitting a different color of fluorescence. Here, we demonstrate such applications by studying the subcellular dynamics of live cells.
{"title":"Sustainable synthesis of carbon dots via bio‐waste recycling for biomedical imaging","authors":"Yuxin Wang, Matthew Chae, Teak-Jung Oh, Kangqiang Qiu, Kritika Mehta, Adrian Tan, Nien‐Pei Tsai, Donglu Shi, Kai Zhang, Jiajie Diao","doi":"10.1002/smmd.20240012","DOIUrl":"https://doi.org/10.1002/smmd.20240012","url":null,"abstract":"Bio‐waste is a side product of biomedical research containing carbon, which can be utilized for developing carbon dots (CDs). CDs are known to be useful for a variety of applications because of their unique photoluminescence, low toxicity, and straightforward synthesis. In this paper, we employed a one‐step hydrothermal method to prepare CDs from bio‐waste as the only reactant. The as‐synthesized Cell‐CDs were found to be chemically stable and biocompatible. In addition, the spectra of Cell‐CDs’ emissions covered the visible light, which is ideal for super‐resolution imaging. Particularly, dual‐color imaging can be achieved, for example, by staining the plasma membrane with Cell‐CDs emitting one color and staining cytosolic organelles with Cell‐CDs emitting a different color of fluorescence. Here, we demonstrate such applications by studying the subcellular dynamics of live cells.","PeriodicalId":74816,"journal":{"name":"Smart medicine","volume":" 46","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141830225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}