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Modernizing histopathological analysis: a fully automated workflow for the digital image analysis of the intestinal microcolony survival assay.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.09.627578
Alexander Baikalov, Ethan Wang, Denae Neill, Nihar Shetty, Trey Waldrop, Kevin Liu, Abagail Delahousessaye, Edgardo Aguilar, Nefetiti Mims, Stefan Bartzsch, Emil Schüler
{"title":"Modernizing histopathological analysis: a fully automated workflow for the digital image analysis of the intestinal microcolony survival assay.","authors":"Alexander Baikalov, Ethan Wang, Denae Neill, Nihar Shetty, Trey Waldrop, Kevin Liu, Abagail Delahousessaye, Edgardo Aguilar, Nefetiti Mims, Stefan Bartzsch, Emil Schüler","doi":"10.1101/2024.12.09.627578","DOIUrl":"10.1101/2024.12.09.627578","url":null,"abstract":"<p><strong>Background: </strong>Manual analysis of histopathological images is often not only time-consuming and painstaking but also prone to error from subjective evaluation criteria and human error. To address these issues, we created a fully automated workflow to enumerate jejunal crypts in a microcolony survival assay to quantify gastrointestinal damage from radiation.</p><p><strong>Methods and materials: </strong>After abdominal irradiation of mice, jejuna were obtained and prepared on histopathologic slides, and crypts were counted manually by trained individuals. The automated workflow (AW) involved obtaining images of jejunal slices from the irradiated mice, followed by cropping and normalizing the individual slice images for resolution and color; using deep learning-based semantic image segmentation to detect crypts on each slice; using a tailored algorithm to enumerate the crypts; and tabulating and saving the results. A graphical user interface (GUI) was developed to allow users to review and correct the automated results.</p><p><strong>Results: </strong>Crypts counted manually exhibited a mean absolute percent deviation of (34 ± 26)% between individuals vs the group mean across counters, which was reduced to (11 ± 6)% across the 3 most-experienced counters. The AW processed a sample image dataset from 60 mice in a few hours and required only a few minutes of active user effort. AW counts deviated from experts' mean counts by (10 ± 8)%. The AW thereby allowed rapid, automated evaluation of the microcolony survival assay with accuracy comparable to that of trained experts and without subjective inter-observer variation.</p><p><strong>Highlights: </strong>We fully automated the digital image analysis of a microcolony survival assayAnalyzing 540 images takes a few hours with only minutes of active user effortThe automated workflow (AW) is just as accurate as trained expertsThe AW eliminates subjective inter-observer variation and human errorHuman review possible with built-in graphical user interface.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661163/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878379","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}
引用次数: 0
A generalized theoretical framework to investigate multicomponent actin dynamics.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.10.627743
Mintu Nandi, Shashank Shekhar, Sandeep Choubey
{"title":"A generalized theoretical framework to investigate multicomponent actin dynamics.","authors":"Mintu Nandi, Shashank Shekhar, Sandeep Choubey","doi":"10.1101/2024.12.10.627743","DOIUrl":"10.1101/2024.12.10.627743","url":null,"abstract":"<p><p>The length of actin filaments is regulated by the combined action of hundreds of actin-binding proteins. While the roles of individual proteins are well understood, how they combine to regulate actin dynamics in vivo remains unclear. Recent advances in microscopy have enabled precise, high-throughput measurements of filament lengths over time. However, the absence of a unified theoretical framework has hindered a mechanistic understanding of the multicomponent regulation of actin dynamics. To address this, we propose a general kinetic model that captures the combined effects of multiple regulatory proteins on actin dynamics. We provide closed-form expressions for both time-dependent and steady-state moments of the filament length distribution. Our framework not only differentiates between various regulatory mechanisms but also serves as a powerful tool for interpreting current data and driving future experiments.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879405","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}
引用次数: 0
Sir2 is required for the quiescence-specific condensed three-dimensional chromatin structure of rDNA.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.12.628092
Christine Cucinotta, Rachel Dell, Kris Alavattam, Toshio Tsukiyama
{"title":"Sir2 is required for the quiescence-specific condensed three-dimensional chromatin structure of rDNA.","authors":"Christine Cucinotta, Rachel Dell, Kris Alavattam, Toshio Tsukiyama","doi":"10.1101/2024.12.12.628092","DOIUrl":"10.1101/2024.12.12.628092","url":null,"abstract":"<p><p>Quiescence in <i>Saccharomyces cerevisiae</i> is a reversible G<sub>0</sub> crucial for long-term survival under nutrient-deprived conditions. During quiescence, the genome is hypoacetylated and chromatin undergoes significant compaction. However, the 3D structure of the ribosomal DNA (rDNA) locus in this state is not well understood. Here, we report that the rDNA locus in quiescent cells forms a distinct condensed loop-like structure, different from structures observed during the mitotic cell cycle. Deletion of <i>SIR2</i> disrupts this structure, causing it to collapse into a small dot and resulting in quiescence entry and exit defects. In contrast, Sir2 affects rDNA structure only modestly in G2/M phase. In the absence of Sir2, occupancy of both RNA Polymerase II and histone H3 increase at the rDNA locus during quiescence and through quiescence exit, further indicating gross defects in chromatin structure. Together, these results uncover a previously undescribed rDNA chromatin structure specific to quiescent cells and underscore the importance of Sir2 in facilitating the transition between cellular states.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661206/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878813","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}
引用次数: 0
Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.11.628030
Sandhya Bangaru, Abigail M Jackson, Jeffrey Copps, Monica L Fernández-Quintero, Jonathan L Torres, Sara T Richey, Bartek Nogal, Leigh M Sewall, Alba Torrents de la Peña, Asma Rehman, Mimi Guebre-Xabier, Bethany Girard, Rituparna Das, Kizzmekia S Corbett-Helaire, Robert A Seder, Barney S Graham, Darin K Edwards, Nita Patel, Gale Smith, Andrew B Ward
{"title":"Structural serology of polyclonal antibody responses to mRNA-1273 and NVX-CoV2373 COVID-19 vaccines.","authors":"Sandhya Bangaru, Abigail M Jackson, Jeffrey Copps, Monica L Fernández-Quintero, Jonathan L Torres, Sara T Richey, Bartek Nogal, Leigh M Sewall, Alba Torrents de la Peña, Asma Rehman, Mimi Guebre-Xabier, Bethany Girard, Rituparna Das, Kizzmekia S Corbett-Helaire, Robert A Seder, Barney S Graham, Darin K Edwards, Nita Patel, Gale Smith, Andrew B Ward","doi":"10.1101/2024.12.11.628030","DOIUrl":"10.1101/2024.12.11.628030","url":null,"abstract":"<p><p>Current COVID-19 vaccines are largely limited in their ability to induce broad, durable immunity against emerging viral variants. Design and development of improved vaccines utilizing existing platforms requires an in-depth understanding of the antigenic and immunogenic properties of available vaccines. Here we examined the antigenicity of two of the original COVID-19 vaccines, mRNA-1273 and NVX-CoV2373, by electron microscopy-based polyclonal epitope mapping (EMPEM) of serum from immunized non-human primates (NHPs) and clinical trial donors. Both vaccines induce diverse polyclonal antibody (pAb) responses to the N-terminal domain (NTD) in addition to the receptor-binding domain (RBD) of the Spike protein, with the NTD supersite being an immunodominant epitope. High-resolution cryo-EMPEM studies revealed extensive pAb responses to and around the supersite with unique angles of approach and engagement. NTD supersite pAbs were also the most susceptible to variant mutations compared to other specificities, indicating that ongoing Spike ectodomain-based vaccine design strategies should consider immuno-masking this site to prevent induction of these strain-specific responses.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879450","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}
引用次数: 0
Vitrification and rapid rewarming of precision-cut liver slices for pharmacological and biomedical research.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.08.627273
Srivasupradha Ramesh, Joseph Sushil Rao, Bat-Erdene Namsrai, Benjamin Fisher, Diane K Tobolt, Michael Megaly, Michael L Etheridge, Timothy L Pruett, Davis Seelig, Paari Murugan, Bashar Aldaraiseh, Erik B Finger, John C Bischof
{"title":"Vitrification and rapid rewarming of precision-cut liver slices for pharmacological and biomedical research.","authors":"Srivasupradha Ramesh, Joseph Sushil Rao, Bat-Erdene Namsrai, Benjamin Fisher, Diane K Tobolt, Michael Megaly, Michael L Etheridge, Timothy L Pruett, Davis Seelig, Paari Murugan, Bashar Aldaraiseh, Erik B Finger, John C Bischof","doi":"10.1101/2024.12.08.627273","DOIUrl":"10.1101/2024.12.08.627273","url":null,"abstract":"<p><strong>Background and aims: </strong>High-throughput in vitro pharmacological toxicity testing is essential for drug discovery. Precision-cut liver slices (PCLS) provide a robust system for screening that is more representative of the complex 3D structure of the whole liver than isolated hepatocytes. However, PCLS are not available as off-the-shelf products, significantly limiting their translational potential. Cryopreservation could solve this bottleneck by effectively preserving PCLS indefinitely until their time of use. Conventional cryopreservation (slow cooling in DMSO-forming ice) results in poor PCLS viability and function and, therefore, has proven unsuitable. Here, we explore an \"ice-free\" cryopreservation approach called vitrification and focus on culturing and assessing PCLS for 3 days post-vitrification and rewarming, given that most acute drug toxicity tests are conducted over 24h.</p><p><strong>Methods: </strong>Rat liver slices were diffusively loaded with a cryoprotective agent (CPA) cocktail consisting of EG and Sucrose. The CPA-loaded PCLS were placed on a polymer cryomesh, vitrified in liquid nitrogen (LN2), and rapidly rewarmed in CPA. The vitrified and rewarmed PCLS were subsequently cultured in a controlled volume of serum-free, chemically defined media for 3 days.</p><p><strong>Results: </strong>The cryopreserved PCLS maintained high viability, morphology, function, enzymatic activity, and drug toxicity response. Results show that the vitrified PCLS perform comparably to untreated controls and significantly outperform conventionally cryopreserved PCLS in all assessments (<i>p</i> < 0.05).</p><p><strong>Conclusions: </strong>Rapid vitrification and rewarming of PCLS using cryomesh enabled successful preservation and culture. This approach maintained high viability, function, enzymatic activity, and drug response for 3 days in culture, similar to controls.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879572","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}
引用次数: 0
Single-cell multi-omic analysis of fibrolamellar carcinoma reveals rewired cell-to-cell communication patterns and unique vulnerabilities.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.11.627911
Alaa R Farghli, Marina Chan, Marc S Sherman, Lindsay K Dickerson, Bo Shui, Manabu Nukaya, Andreas Stephanou, Rosanna K Ma, Brian J Pepe-Mooney, Colton J Smith, Donald Long, Paul R Munn, Adrian McNairn, Jennifer K Grenier, Michael Karski, Sean M Ronnekleiv-Kelly, Venu G Pillarisetty, Wolfram Goessling, Taranjit S Gujral, Khashayar Vakili, Praveen Sethupathy
{"title":"Single-cell multi-omic analysis of fibrolamellar carcinoma reveals rewired cell-to-cell communication patterns and unique vulnerabilities.","authors":"Alaa R Farghli, Marina Chan, Marc S Sherman, Lindsay K Dickerson, Bo Shui, Manabu Nukaya, Andreas Stephanou, Rosanna K Ma, Brian J Pepe-Mooney, Colton J Smith, Donald Long, Paul R Munn, Adrian McNairn, Jennifer K Grenier, Michael Karski, Sean M Ronnekleiv-Kelly, Venu G Pillarisetty, Wolfram Goessling, Taranjit S Gujral, Khashayar Vakili, Praveen Sethupathy","doi":"10.1101/2024.12.11.627911","DOIUrl":"10.1101/2024.12.11.627911","url":null,"abstract":"<p><p>Fibrolamellar carcinoma (FLC) is a rare malignancy disproportionately affecting adolescents and young adults with no standard of care. FLC is characterized by thick stroma, which has long suggested an important role of the tumor microenvironment. Over the past decade, several studies have revealed aberrant markers and pathways in FLC. However, a significant drawback of these efforts is that they were conducted on bulk tumor samples. Consequently, identities and roles of distinct cell types within the tumor milieu, and the patterns of intercellular communication, have yet to be explored. In this study we unveil cell-type specific gene signatures, transcription factor networks, and super-enhancers in FLC using a multi-omics strategy that leverages both single-nucleus ATAC-seq and single-nucleus RNA-seq. We also infer completely rewired cell-to-cell communication patterns in FLC including signaling mediated by SPP1-CD44, MIF-ACKR3, GDF15-TGFBR2, and FGF7-FGFR. Finally, we validate findings with loss-of-function studies in several models including patient tissue slices, identifying vulnerabilities that merit further investigation as candidate therapeutic targets in FLC.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661214/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878677","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}
引用次数: 0
Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.12.628180
Maria Blumenkrantz, Felicia Woron, Ernesto Gagarin, Everett Weinstein, Maryam H Kamel, Leonardo Campos, Agnieszka Geras, Troy Anderson, Julia Mo, Desmarie Sherwood, Maya Gwin, Bianca Dumitrascu, Nadeen O Chahine, Joanna Smeeton
{"title":"Dynamic cell fate plasticity and tissue integration drive functional synovial joint regeneration.","authors":"Maria Blumenkrantz, Felicia Woron, Ernesto Gagarin, Everett Weinstein, Maryam H Kamel, Leonardo Campos, Agnieszka Geras, Troy Anderson, Julia Mo, Desmarie Sherwood, Maya Gwin, Bianca Dumitrascu, Nadeen O Chahine, Joanna Smeeton","doi":"10.1101/2024.12.12.628180","DOIUrl":"10.1101/2024.12.12.628180","url":null,"abstract":"<p><p>Adult mammalian synovial joints have limited regenerative capacity, where injuries heal with mechanically inferior fibrotic tissues. Here we developed a unilateral whole-joint resection model in adult zebrafish to advance our understanding of how to stimulate regrowth of native synovial joint tissues. Using a combination of microCT, histological, live imaging, and single-cell RNA sequencing (scRNAseq) approaches after complete removal of all joint tissues, we find de novo regeneration of articular cartilage, ligament, and synovium into a functional joint. Clonal lineage tracing and scRNAseq implicate a multipotent, neural crest-derived population in the adult skeleton as a cell source for these regenerating tissues. Together, our findings reveal latent molecular and cellular programs within the adult skeleton that are deployed to regenerate a complex joint with lubricated articular cartilage.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879277","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}
引用次数: 0
Engineering a Biosynthetic Pathway for the Production of (+)-Brevianamides A and B in Escherichia coli.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.10.627567
Casandra P Sandoval Hurtado, Samantha P Kelly, Vikram Shende, Makayla Perez, Brian J Curtis, Sean A Newmister, Kaleb Ott, Filipa Pereira, David H Sherman
{"title":"Engineering a Biosynthetic Pathway for the Production of (+)-Brevianamides A and B in <i>Escherichia coli</i>.","authors":"Casandra P Sandoval Hurtado, Samantha P Kelly, Vikram Shende, Makayla Perez, Brian J Curtis, Sean A Newmister, Kaleb Ott, Filipa Pereira, David H Sherman","doi":"10.1101/2024.12.10.627567","DOIUrl":"10.1101/2024.12.10.627567","url":null,"abstract":"<p><p>The privileged fused-ring system comprising the bicyclo[2.2.2]diazaoctane (BDO) core is prevalent in diketopiperazine (DKP) natural products with potent and diverse biological activities, with some being explored as drug candidates. Typically, only low yields of these compounds can be extracted from native fungal producing strains and the available synthetic routes remain challenging due to their structural complexity. BDO-containing DKPs including (+)-brevianamides A and B are assembled via multi-component biosynthetic pathways incorporating non-ribosomal peptide synthetases, prenyltransferases, flavin monooxygenases, cytochrome P450s and semi-pinacolases. To simplify access to this class of alkaloids, we designed an engineered biosynthetic pathway in <i>Escherichia coli</i> , composed of six enzymes sourced from different kingdoms of life. The pathway includes a cyclodipeptide synthase (NascA), a cyclodipeptide oxidase (DmtD2/DmtE2), a prenyltransferase (NotF), a flavin-dependent monooxygenase (BvnB), and kinases (PhoN and IPK). Cultivated in glycerol supplemented with prenol, the engineered <i>E. coli</i> strain produces 5.3 mg/L of (-)-dehydrobrevianamide E ( <b>4</b> ), which undergoes a terminal, <i>ex vivo</i> lithium hydroxide catalyzed rearrangement reaction to yield (+)-brevianamides A and B with a 46% yield and a 92:8 diastereomeric ratio. Additionally, titers of <b>4</b> were increased eight-fold by enhancing NADPH pools in the engineered <i>E. coli</i> strain. Our study combines synthetic biology, biocatalysis and synthetic chemistry approaches to provide a five-step engineered biosynthetic pathway for producing complex indole alkaloids in <i>E. coli</i> .</p><p><strong>Abstract figure: </strong></p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661150/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879321","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}
引用次数: 0
Survivin modulates stiffness-induced vascular smooth muscle cell motility.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.11.628062
Thomas Mousso, Kalina Rice, Bat-Ider Tumenbayar, Khanh Pham, Yuna Heo, Su Chin Heo, Kwonmoo Lee, Andrew T Lombardo, Yongho Bae
{"title":"Survivin modulates stiffness-induced vascular smooth muscle cell motility.","authors":"Thomas Mousso, Kalina Rice, Bat-Ider Tumenbayar, Khanh Pham, Yuna Heo, Su Chin Heo, Kwonmoo Lee, Andrew T Lombardo, Yongho Bae","doi":"10.1101/2024.12.11.628062","DOIUrl":"10.1101/2024.12.11.628062","url":null,"abstract":"<p><p>Arterial stiffness is a key contributor to cardiovascular diseases, including atherosclerosis, restenosis, and coronary artery disease, it has been characterized to be associated with the aberrant migration of vascular smooth muscle cells (VSMCs). However, the underlying molecular mechanisms driving VSMC migration in stiff environments remain incompletely understood. We recently demonstrated that survivin, a member of the inhibitor of apoptosis protein family, is highly expressed in both mouse and human VSMCs cultured on stiff polyacrylamide hydrogels, where it modulates stiffness-mediated cell cycle progression and proliferation. However, its role in stiffness-dependent VSMC migration remains unknown. To assess its impact on migration, we performed time-lapse video microscopy on VSMCs seeded on fibronectin-coated soft and stiff polyacrylamide hydrogels, mimicking the physiological stiffness of normal and diseased arteries, with either survivin inhibition or overexpression. We observed that VSMC motility increased under stiff conditions, while pharmacologic or siRNA-mediated inhibition of survivin reduced stiffness-stimulated migration to rates similar to those observed under soft conditions. Further investigation revealed that cells on stiff hydrogels exhibited greater directional movement and robust lamellipodial protrusion compared to those on soft hydrogels. Interestingly, survivin-inhibited cells on stiff hydrogels showed reduced directional persistence and lamellipodial protrusion compared to control cells. We also examined whether survivin overexpression alone is sufficient to induce cell migration on soft hydrogels, and found that survivin overexpression modestly increased cell motility and partially rescued the lack of directional persistence compared to GFP-expressing control VSMCs on soft hydrogels. In conclusion, our findings demonstrate that survivin plays a key role in regulating stiffness-induced VSMC migration, suggesting that targeting survivin and its signaling pathways could offer therapeutic strategies for addressing arterial stiffness in cardiovascular diseases.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879521","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}
引用次数: 0
Jan and mini-Jan, a model system for potato functional genomics.
bioRxiv : the preprint server for biology Pub Date : 2024-12-12 DOI: 10.1101/2024.12.10.627817
Haoyang Xin, Luke W Strickland, John P Hamilton, Jacob K Trusky, Chao Fang, Nathaniel M Butler, David S Douches, C Robin Buell, Jiming Jiang
{"title":"Jan and mini-Jan, a model system for potato functional genomics.","authors":"Haoyang Xin, Luke W Strickland, John P Hamilton, Jacob K Trusky, Chao Fang, Nathaniel M Butler, David S Douches, C Robin Buell, Jiming Jiang","doi":"10.1101/2024.12.10.627817","DOIUrl":"10.1101/2024.12.10.627817","url":null,"abstract":"<p><p>Potato (<i>Solanum tuberosum</i>) is the third most important food crop in the world. Although the potato genome has been fully sequenced, functional genomics research of potato lags relative to other major food crops due primarily to the lack of a model experimental potato line. Here, we present a diploid potato line, 'Jan', which possesses all essential characteristics for facile functional genomics studies. Jan has a high level of homozygosity after seven generations of self-pollination. Jan is vigorous and highly fertile with outstanding tuber traits, high regeneration rates, and excellent transformation efficiencies. We generated a chromosome-scale genome assembly for Jan, annotated genes, and identified syntelogs relative to the potato reference genome assembly DMv6.1 to facilitate functional genomics. To miniaturize plant architecture, we developed two \"mini-Jan\" lines with compact and dwarf plant stature using CRISPR/Cas9-mediated mutagenesis targeting the <i>Dwarf</i> and <i>Erecta</i> genes related to growth. Mini-Jan mutants are fully fertile and will permit higher-throughput studies in limited growth chamber and greenhouse space. Thus, Jan and mini-Jan provide an outstanding model system that can be leveraged for gene editing and functional genomics research in potato.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661178/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879455","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}
引用次数: 0
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