bioRxiv最新文献

{"title":"Single-egg Comet Assay: a protocol to quantify DNA damage in aquatic dormant stages","authors":"Rejin Salimraj, Alessio Perotti, M. Wojewodzic, Dagmar Frisch","doi":"10.1101/2024.08.06.606806","DOIUrl":"https://doi.org/10.1101/2024.08.06.606806","url":null,"abstract":"The comet assay (CA) was originally developed as toxicity test and quantifies DNA integrity from the distribution of DNA across an electric field. Compromised DNA moves across electric fields faster than intact DNA strands, leaving a quantifiable signature that resembles a comet tail. The dimensions of this comet tail reflect relative DNA damage. We optimized the CA protocol for individual dormant propagules (Single-egg Comet Assay or SE-CA) to inform downstream analyses such as DNA sequencing, of the DNA quality contained in natural genetic archives of past populations. As a model we used dormant eggs of the microcrustacean Daphnia. We tested the SE-CA protocol on impact of processing and storage conditions for dormant eggs and used it to assess DNA damage related to aging of eggs retrieved from recently deposited to centuries-old lake sediment. The SE-CA successfully determined the degree of DNA damage in individual eggs frozen in liquid nitrogen, or at -80°C as well as damage caused by bleaching and historical egg age. In conclusion, our protocol provides a cost-effective method of assessing DNA damage in sedimentary propagules such as dormant Daphnia eggs. More generally, the SE-CA can be applied to test DNA integrity in individual propagules prior to genome sequencing or to quantify environmental impacts on natural sedimentary biobanks.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"66 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926548","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}

{"title":"Two TAL effectors of Xanthomonas citri pv. malvacearum target GhSWEET15 as the susceptibility genes for bacterial blight of cotton","authors":"Syed Mashab Ali Shah, Fazal Haq, Kunxuan Huang, Qi Wang, Linlin Liu, Ying Li, Yong Wang, Asaf Khan, Ruihuan Yang, M. Khojasteh, Xiameng Xu, Zhengyin Xu, Gongyou Chen","doi":"10.1101/2024.08.06.606744","DOIUrl":"https://doi.org/10.1101/2024.08.06.606744","url":null,"abstract":"Bacterial Blight of Cotton (BBC) caused by Xanthomonas citri pv. malvacearum (Xcm) is an important and destructive disease affecting cotton plants. Transcription activator-like effectors (TALEs) released by the pathogen regulate cotton resistance to the susceptibility. In this study, we sequenced the whole genome of Xcm Xss-V2-18 and identified eight tal genes; seven on the plasmids and one on the chromosome. Deletion and complementation experiments of Xss-V2-18 tal genes demonstrated that Tal1b is required for full virulence on cotton. Transcriptome profiling coupled with TALE-binding element prediction revealed that Tal1b targets GhSWEET15A04/D04 and GhSWEET15D02 simultaneously. Expression analysis confirmed the independent inducibility of GhSWEET15A04/D04 and GhSWEET15D02 by Tal1b, whereas GhSWEET15A04/D04 is additionally targeted by Tal1. Moreover, GUS (β-glucuronidase) and Xa10-mediated HR (hypersensitive response) assays indicated that the EBEs are required for the direct and specific activation of the candidate targets by Tal1 and Ta1b. These findings may advance our understanding of the dynamics between TALEs and EBEs, and decipher a simple and effective DNA-binding mechanism that could lead to the development of more efficient methods for gene editing and transgenic research.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"7 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925623","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}

{"title":"Optics-free reconstruction of 2D images via DNA barcode proximity graphs","authors":"Hanna Liao, Sanjay Kottapalli, Yuqi Huang, Matthew Chaw, Jase Gehring, Olivia Waltner, Melissa Phung-Rojas, R. Daza, Frederick A. Matsen, C. Trapnell, Jay Shendure, Sanjay R Srivatsan","doi":"10.1101/2024.08.06.606834","DOIUrl":"https://doi.org/10.1101/2024.08.06.606834","url":null,"abstract":"Spatial genomic technologies include imaging- and sequencing-based methods (1–3). An emerging subcategory of sequencing-based methods relies on a surface coated with coordinate-associated DNA barcodes, which are leveraged to tag endogenous nucleic acids or cells in an overlaid tissue section (4–7). However, the physical registration of DNA barcodes to spatial coordinates is challenging, necessitating either high density printing of coordinate-specific oligonucleotides or in situ sequencing/probing of randomly deposited, oligonucleotide-bearing beads. As a consequence, the surface areas available to sequencing-based spatial genomic methods are constrained by the time, labor, cost, and instrumentation required to either print, synthesize or decode a coordinate-tagged surface. To address this challenge, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free, DNA microscopy (8) inspired method. With SCOPE, the relative positions of randomly deposited beads on a 2D surface are inferred from the ex situ sequencing of chimeric molecules formed from diffusing “sender” and tethered “receiver” oligonucleotides. As a first proof-of-concept, we apply SCOPE to reconstruct an asymmetric “swoosh” shape resembling the Nike logo (16.75 × 9.25 mm). Next, we use a microarray printer to encode a “color” version of the Snellen eye chart for visual acuity (17.18 × 40.97 mm), and apply SCOPE to achieve optics-free reconstruction of individual letters. Although these are early demonstrations of the concept and much work remains to be done, we envision that the optics-free, sequencing-based quantitation of the molecular proximities of DNA barcodes will enable spatial genomics in constant experimental time, across fields of view and at resolutions that are determined by sequencing depth, bead size, and diffusion kinetics, rather than the limitations of optical instruments or microarray printers.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"32 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141926950","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}

{"title":"Differential Contributions of CA3 and Entorhinal Cortex Inputs to Ripple Patterns in the Hippocampus Under Cannabidiol","authors":"Adrian Aleman-Zapata, Melisa Maidana Capitan, Anumita Samanta, Pelin Özsezer, K. Agarwal, Tugdual Adam, Abdelrahman Rayan, Lisa Genzel","doi":"10.1101/2024.08.06.606645","DOIUrl":"https://doi.org/10.1101/2024.08.06.606645","url":null,"abstract":"Cannabidiol (CBD), increasingly recognized for its potential to treat insomnia, notably extends NonREM sleep phases and modifies sleep-associated ripple dynamics. Utilizing a threshold-based approach, our study differentiated distinct ripple types in rats, clarifying the contributions of intra-hippocampal (CA3) and cortical (mEC) regions to these events. The findings reveal that CBD primarily influences the CA3’s input to the CA1, resulting in an increased occurrence of short ripples predominantly induced by cortical (mEC) activity and a corresponding decrease in long, intra-hippocampal sharp-wave-ripples. This study highlights the critical interplay between the CA3 and entorhinal cortex dynamics in shaping the characteristics of hippocampal ripples under the influence of CBD.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927715","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}

{"title":"Therapeutic potential of red blood cell-derived extracellular vesicles in reducing neuroinflammation and protecting against retinal degeneration","authors":"Rakshanya Sekar, Adrian V. Cioanca, Yilei (Evelyn) Yang, K. S. Kamath, Luke Carroll, Riccardo Natoli, Yvette Wooff","doi":"10.1101/2024.08.06.606930","DOIUrl":"https://doi.org/10.1101/2024.08.06.606930","url":null,"abstract":"Neuroinflammation is a pathological process mediated through immune cell activation and pro-inflammatory cytokine release, resulting in neuronal cell death. In the central nervous system (CNS), neuroinflammation is a characteristic feature underlying the onset and progression of retinal and neurodegenerative diseases. Targeting neuroinflammation to reduce neuronal cell death and protect against visual and cognitive declines is therefore a key therapeutic strategy. However, due to the complex and multi-faceted nature of these diseases, to date there has been little therapeutic success with single target approaches insufficient to tackle widespread and multi-pathway inflammatory cascades. Furthermore, as the retina and brain reside within immune-privileged environments, a major challenge in treating these diseases is producing and delivering a therapeutic that, in itself, does not exacerbate inflammation. Extracellular vesicles (EV), derived from red blood cells (RBC EV), present a promising solution to overcome these hurdles, due to their innate ability to cross blood-tissue barriers, biocompatible nature, and their broad anti-inflammatory properties to modulate complex neuroinflammatory pathways. This study therefore investigated the therapeutic potential of RBC EV in mediating neuroinflammation using an in-vivo photo-oxidative damage model of retinal degeneration as a model for CNS neuroinflammation. In this work, we developed a novel incubation pipeline using N1 medium supplement and superoxide dismutase (SOD) supplementation to promote the production of safe, neuroprotective, and anti-inflammatory RBC EV. Delivery of RBC EV in vivo, was shown to be safe with strong penetration across all retinal layers. Further, therapeutic administration of RBC EV via local intravitreal injection significantly reduced inflammation and cell death and preserved retinal function. Notably, strong safety and therapeutic efficacy was also demonstrated in the retina following systemic (intraperitoneal) administration, highlighting a potential game-changing approach for less-invasive therapeutic delivery to the CNS. Finally, multi-omic analyses and in vitro findings supported an anti-inflammatory mechanism-of-action, with RBC EV modulating pro-inflammatory cytokine release, including those known to be involved in the pathogenesis of retinal and neurodegenerative diseases. Taken together, these findings highlight the broad applicability of RBC EV in treating neuroinflammation in the CNS, presenting a scalable and effective treatment approach for these currently untreatable diseases.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"7 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927733","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}

{"title":"Genomic sequencing to detect cross-breeding quality in dogs: an example studying disorders in sexual development","authors":"Luciana de Gennaro, Matteo Burgio, G. Lacalandra, Francesco Petronella, Alberto L’Abbate, Francesco Ravasini, B. Trombetta, Annalisa Rizzo, Mario Ventura, Vincenzo Cicirelli","doi":"10.1101/2024.08.07.606952","DOIUrl":"https://doi.org/10.1101/2024.08.07.606952","url":null,"abstract":"Background Disorders of Sexual Development (DSD) in dogs, similar to humans, arise from irregularities in genetic determinants, gonadal differentiation, or phenotypic sex development. The French Bulldog, a breed that has seen a surge in popularity and demand, has also shown a marked increase in DSD incidence. This study aims to characterize the genetic underpinnings of DSD in a French Bulldog named Brutus, exhibiting ambiguous genitalia and internal sexual anatomy, and to explore the impact of breeding practices on genetic diversity within the breed. Methods We utilized a comprehensive approach combining conventional cytogenetics, molecular techniques, and deep sequencing to investigate the genetic profile of Brutus. The sequence data were compared to three other male French Bulldogs genome sequences with typical reproductive anatomy, including Brutus’s father, and the canine reference genome (CanFam6). Findings Our findings revealed a 22% mosaicism (78, XX/77, XX), the absence of the SRY gene, and the presence of 43 unique Single Nucleotide Variants (SNVs) not inherited from the father. Notably, the Run of Homozygosity (ROH) analysis showed Brutus has a significantly higher number of homozygous segments compared to other Bulldogs, with a total length of these fragments 50% greater than the average, strongly suggesting this dog is the product of the mating between siblings. While no direct causative genes for the DSD phenotype were identified four candidate loci warranting further investigation were highlighted. Conclusions Our study highlighted the need for a better annotated and curated reference dog genome to define genes causative of any specific phenotype, suggests a potential genetic basis for the DSD phenotype in dogs, and underscores the consequences of uncontrolled breeding practices in French Bulldogs. These findings highlight the importance of implementing strategic genetic management to preserve genetic health and diversity in canine populations.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"41 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929692","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}

{"title":"Engineering synthetic agonists for targeted activation of Notch signaling","authors":"David H. Perez, Daniel Antfolk, Elliot Medina, David Gonzalez-Perez, Vincent C. Luca","doi":"10.1101/2024.08.06.606897","DOIUrl":"https://doi.org/10.1101/2024.08.06.606897","url":null,"abstract":"Notch signaling regulates cell fate decisions and has context-dependent tumorigenic or tumor suppressor functions. Although several Notch inhibitors are under development as cancer therapies, the mechanical force requirement for Notch receptor activation has hindered attempts to generate soluble agonists. To address this problem, we engineered synthetic Notch agonist (SNAG) proteins that mimic the tension-generating mechanism of endogenous ligands. SNAGs were designed by fusing a high-affinity variant of the Notch ligand Delta-like 4 (DLL4) to antibody fragments that induce target internalization. This bispecific format enables the SNAG-bound biomarkers to “pull” on Notch receptors, triggering Notch activation in mixed populations of biomarker-expressing and non-expressing cells. SNAGs targeting the immune checkpoint PDL1 potently activated Notch in co-cultures of Notch1-and PDL1-expressing cells, but not in monocultures of Notch1-expressing cells alone. Additional SNAGs targeting the tumor antigens CD19 and HER2 also activated Notch in mixed cell populations, indicating that the SNAG design concept is adaptable to multiple biomarkers. SNAG-mediated Notch activation was blocked by a dynamin inhibitor, and efficacy increased dramatically when SNAGs were dimerized via fusion to antibody Fc domains, suggesting that endocytosis and multimerization are important for optimal SNAG function. These insights will greatly expand our ability to modulate Notch signaling for applications in immunotherapy and regenerative medicine.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"33 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927535","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}

{"title":"A sticky Poisson Hidden Markov Model for spike data","authors":"Tianshu Li, Giancarlo La Camera","doi":"10.1101/2024.08.07.606969","DOIUrl":"https://doi.org/10.1101/2024.08.07.606969","url":null,"abstract":"Fitting a hidden Markov Model (HMM) to neural data is a powerful method to segment a spatiotemporal stream of neural activity into sequences of discrete hidden states. Application of HMM has allowed to uncover hidden states and signatures of neural dynamics that seem relevant for sensory and cognitive processes. This has been accomplished especially in datasets comprising ensembles of simultaneously recorded cortical spike trains. However, the HMM analysis of spike data is involved and requires a careful handling of model selection. Two main issues are: (i) the cross-validated likelihood function typically increases with the number of hidden states; (ii) decoding the data with an HMM can lead to very rapid state switching due to fast oscillations in state probabilities. The first problem is related to the phenomenon of over-segmentation and leads to overfitting. The second problem is at odds with the empirical fact that hidden states in cortex tend to last from hundred of milliseconds to seconds. Here, we show that we can alleviate both problems by regularizing a Poisson-HMM during training so as to enforce large self-transition probabilities. We call this algorithm the ‘sticky Poisson-HMM’ (sPHMM). When used to-gether with the Bayesian Information Criterion for model selection, the sPHMM successfully eliminates rapid state switching, outperforming an alternative strategy based on an HMM with a large prior on the self-transition probabilities. The sPHMM also captures the ground truth in surrogate datasets built to resemble the statistical properties of the experimental data.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"15 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925917","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}

{"title":"Genomic data reveal a north-south split and introgression history of blood fluke (Schistosoma haematobium) populations from across Africa","authors":"R. N. Platt, Egie E. Enabulele, Ehizogie Adeyemi, Marian O Agbugui, OG Ajakaye, E. C. Amaechi, Chika E Ejikeugwu, Christopher Igbeneghu, V. Njom, Precious Dlamini, Grace-Ann Arya, Robbie Diaz, M. Rabone, F. Allan, Bonnie Webster, A. Emery, David Rollinson, Timothy J.C. Anderson","doi":"10.1101/2024.08.06.606828","DOIUrl":"https://doi.org/10.1101/2024.08.06.606828","url":null,"abstract":"The human parasitic fluke, Schistosoma haematobium hybridizes with the livestock parasite S. bovis in the laboratory, but the extent of hybridization in nature is unclear. We analyzed 34.6 million single nucleotide variants in 162 samples from 18 African countries, revealing a sharp genetic discontinuity between northern and southern S. haematobium. We found no evidence for recent hybridization. Instead the data reveal admixture events that occurred 257-879 generations ago in northern S. haematobium populations. Fifteen introgressed S. bovis genes are approaching fixation in northern S. haematobium with four genes potentially driving adaptation. We identified 19 regions that were resistant to introgression; these were enriched on the sex chromosomes. These results (i) demonstrate strong barriers to gene flow between these species, (ii) indicate that hybridization may be less common than currently envisaged, but (iii) reveal profound genomic consequences of interspecific hybridization between schistosomes of medical and veterinary importance.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"11 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141927497","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}

{"title":"Phlorotannin rich Ascophyllum nodosum seaweed extract inhibits influenza infection","authors":"D. F. Mega, Parul Sharma, Anja Kipar, U. Hetzel, Chloe Bramwell, Alan Merritt, Samuel Wright, Chris Plummer, R. Urbanowicz, James P. Stewart","doi":"10.1101/2024.08.08.606782","DOIUrl":"https://doi.org/10.1101/2024.08.08.606782","url":null,"abstract":"Seaweed derived compounds are a renewable resource utilised in the manufacturing and food industry. This study focuses on an Enriched seaweed extract (ESE) isolated from Ascophyllum nodosum. ESE was screened for antiviral activity by plaque reduction assays against influenza A viruses (IAV) H1N1 and H3N2 subtypes. Time of addition assays and FACS analysis were used to help determine the modes of action. The therapeutic potential of ESE was then explored using differentiated human bronchiole epithelial cells at the air liquid interphase and a murine model challenged with IAV. The data indicates ESE primarily interacts directly with virions, preventing virus cell binding. Interestingly, ESE also inhibits early and late stage of the influenza A lifecycle when treatment occurs after cell binding. This inhibitory effect appears to prevent internalisation of virus and release of progeny virus by targeting neuraminidase activity. Intranasal administration of ESE in mice infected with IAV reduced viral load in lung tissue. ESE may be a promising broad acting antiviral agent in the treatment of influenza infections.","PeriodicalId":505198,"journal":{"name":"bioRxiv","volume":"52 51","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141929318","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}