bioRxiv (Cold Spring Harbor Laboratory)最新文献

{"title":"Electronic Polarizability Tunes the Function of the Human Bestrophin 1 Cl⁻Channel","authors":"Linda X Phan, Aaron P Owji, Tingting Yang, Jason Crain, Mark Sansom, Stephen J Tucker","doi":"10.1101/2023.11.14.567055","DOIUrl":"https://doi.org/10.1101/2023.11.14.567055","url":null,"abstract":"Mechanisms of anion permeation within ion channels and nanopores remain poorly understood. Recent cryo-electron microscopy structures of the human bestrophin 1 chloride channel (hBest1) provide an opportunity to evaluate ion interactions predicted by molecular dynamics (MD) simulations against experimental observations. We implement the fully polarizable forcefield AMOEBA in MD simulations of open and partially-open states of the hBest1. The AMOEBA forcefield models multipole moments up to the quadrupole; therefore, it captures induced dipole and anion-π interactions. By including polarization we demonstrate the key role that aromatic residues play in ion permeation and the functional advantages of pore asymmetry within the highly conserved hydrophobic neck of the pore. We establish that these only arise when electronic polarization is included in the molecular models. We also show that Cl − permeation in this region can be achieved through hydrophobic solvation concomitant with partial ion dehydration, which is compensated for by the formation of contacts with the edge of the phenylalanine ring. Furthermore, we demonstrate how polarizable simulations can help determine the identity of ion-like densities within high-resolution cryo-EM structures. Crucially, neglecting polarization in simulation of these systems results in the localization of Cl − at positions that do not correspond with their experimentally resolved location. Overall, our results demonstrate the importance of including electronic polarization in realistic and physically accurate models of biological systems.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"40 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992526","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 multiscale approach to investigate fluorescence and NDVI imaging as proxy of photosynthetic traits in wheat","authors":"Nicolas Virlet, João Paulo Pennacchi, Pouria Sadeghi-Tehran, Tom Ashfield, Douglas Orr, Elizabete Carmo-Silva, Malcolm Hawkesford","doi":"10.1101/2023.11.10.566533","DOIUrl":"https://doi.org/10.1101/2023.11.10.566533","url":null,"abstract":"With the development of the digital phenotyping, repeated measurements of agronomic traits over time are easily accessible, notably for morphological and phenological traits. However high throughput methods for estimating physiological traits such as photosynthesis are lacking. This study demonstrates the links of fluorescence and reflectance imaging with photosynthetic traits. Two wheat cultivars were grown in pots in a controlled environment. Photosynthesis was characterised by gas-exchange and biochemical analysis at five time points, from booting to 21 days post anthesis. On the same days imaging was performed on the same pots, at leaf and plant scale, using indoor and outdoor phenotyping platforms, respectively. Five image variables (Fv/Fm and NDVI at the whole plant level and Fv/Fm, Φ(II)532 and Φ(NPQ)1077 at the leaf scale) were compared to variables from A-Ci and A-Par curves, biochemical analysis, and fluorescence instruments. The results suggested that the image variables are robust estimators of photosynthetic traits, as long as senescence is driving the variability. Despite contrasting cultivar behaviour, linear regression models which account for the cultivar and the interaction effects, further improved the modelling of photosynthesis indicators. Finally, the results highlight the challenge of discriminating functional to cosmetic stay green genotypes using digital imaging.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"37 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992985","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":"Sleep Disruption in a Mouse Model of Chronic Traumatic Brain Injury","authors":"Andrew R Morris, Erwin K Gudenschwager Basso, Miguel A Gutierrez-Monreal, Rawad Daniel Arja, Firas H Kobeissy, Christopher G Janus, Kevin KW Wang, Jiepei Zhu, Andrew C Liu","doi":"10.1101/2023.11.10.566553","DOIUrl":"https://doi.org/10.1101/2023.11.10.566553","url":null,"abstract":"Chronic sleep/wake disturbances are strongly associated with traumatic brain injury (TBI) in patients and are being increasingly recognized. However, the underlying mechanisms are largely understudied and there is an urgent need for animal models of lifelong sleep/wake disturbances. The objective of this study was to develop a chronic TBI rodent model and investigate the lifelong chronic effect of TBI on sleep/wake behavior. We performed repetitive midline fluid percussion injury (rmFPI) in four months old mice and monitored their sleep/wake behavior using the non-invasive PiezoSleep system. The sleep/wake states were recorded before injury (baseline) and then monthly thereafter. We found that TBI mice displayed a significant decrease in sleep duration in both the light and dark phases, beginning at three months post-TBI and continuing throughout the study. Consistent with the sleep phenotype, these TBI mice showed circadian locomotor activity phenotypes and exhibited reduced anxiety-like behavior. TBI mice also gained less weight, and had less lean mass and total body water content, compared to sham controls. Furthermore, TBI mice showed extensive brain tissue loss and increased GFAP and IBA1 levels in the hypothalamus and the vicinity of the injury, indicative of chronic neuropathology. In summary, our study identified a critical time window of TBI pathology and associated circadian and sleep/wake phenotypes. Future studies should leverage this mouse model to investigate the molecular mechanisms underlying the chronic sleep/wake phenotypes following TBI early in life.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"33 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134993584","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":"Does stomatal patterning in amphistomatous leaves minimize the CO2 diffusion path length within leaves?","authors":"Jacob Lewis Watts, Graham J Dow, Thomas N Buckley, Chris D Muir","doi":"10.1101/2023.11.13.566960","DOIUrl":"https://doi.org/10.1101/2023.11.13.566960","url":null,"abstract":"Photosynthesis is co-limited by multiple factors depending on the plant and its environment. These include biochemical rate limitations, internal and external water potentials, temperature, irradiance, and carbon dioxide (CO2). Amphistomatous leaves have stomata on both abaxial and adaxial leaf surfaces. This feature is considered an adaptation to alleviate CO2 diffusion limitations in productive environments where other factors are not limiting as the diffusion path length from stomate to chloroplast is effectively halved. Plants can also reduce CO2 limitations through other aspects of optimal stomatal anatomy: stomatal density, distribution, patterning, and size. A number of studies have demonstrated that stomata are overdispersed on a single leaf surface; however, much less is known about stomatal anatomy in amphistomatous leaves, especially the coordination between leaf surfaces, despite their prevelance in nature and near ubiquity among crop species. Here we use novel spatial statistics based on simulations and photosynthesis modeling to test hypotheses about how amphistomatous plants may optimize CO2 limitations in the model angiosperm Arabidopsis thaliana grown in different light environments. We find that 1) stomata are overdispersed, but not ideally dispersed, on both leaf surfaces across all light treatments; 2) abaxial and adaxial leaf surface patterning are independent; and 3) the theoretical improvements to photosynthesis from abaxial-adaxial stomatal coordination are miniscule (≪ 1%) across the range of feasible parameter space. However, we also find that 4) stomatal size is correlated with the mesophyll volume that it supplies with CO2, suggesting that plants may optimize CO2 diffusion limitations through alternative pathways other than ideal, uniform stomatal spacing. We discuss the developmental, physical, and evolutionary constraits which may prohibit plants from reaching the theoretical adaptive peak of uniform stomatal spacing and inter surface stomatal coordination. These findings contribute to our understanding of variation in the anatomy of amphistomatous leaves.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"33 18","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134993736","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":"Impaired migration and metastatic spread of human melanoma by a novel small molecule targeting the transmembrane domain of death receptor p75NTR","authors":"Vanessa Lopes-Rodrigues, Samuel A. Nyantakyi, Xueqing Lun, Jianbo Zhang, Ajeena Ramanujuan, Shuhailah Salim, Michael Saleeb, Donna L. Senger, Carlos F. Ibanez","doi":"10.1101/2023.11.13.566904","DOIUrl":"https://doi.org/10.1101/2023.11.13.566904","url":null,"abstract":"Receptor transmembrane domains (TMDs) are crucially involved in relaying ligand information from extracellular to intracellular spaces and represent attractive targets for small molecule manipulation of receptor function. Screening a library of over 8,000 drug-like compounds with an assay based on the TMD of death receptor p75NTR, we identified a novel small molecule capable of inhibiting p75NTR-mediated migration of human melanoma cells. Employing medicinal chemistry, a more potent derivative termed Np75-4A22 was identified that blocks nerve growth factor (NGF)-mediated melanoma invasion at submicromolar concentrations. Mechanistically, Np75-4A22 was found, at least in part, to function by antagonizing NGF-mediated recruitment of the actin-bundling protein fascin to p75NTR and its association with the actin cytoskeleton. Importantly, preclinical assessment of Np75-4A22 showed high oral bioavailability, low toxicity, and significant inhibition of melanoma lung metastases in a highly metastatic mouse model. These results support further development of this approach as an alternative or complementary strategy for patients that do not respond to conventional chemotherapy or immune checkpoint inhibitors.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"56 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134901678","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":"Genetic factors acting prior to dormancy in sour cherry influence bloom time the following spring","authors":"Charity Z Goeckeritz, Chloe Grabb, Rebecca Grumet, Amy F Iezzoni, Courtney A Hollender","doi":"10.1101/2023.11.09.566501","DOIUrl":"https://doi.org/10.1101/2023.11.09.566501","url":null,"abstract":"Bloom time is central to tree fruit production, and for Prunus species floral development leading up to bloom spans four seasons. Understanding this entire process is crucial for developing strategies to manipulate bloom time to prevent crop loss due to climate change. Here, we present a detailed examination of flower development from initiation until bloom for early- and late-blooming sour cherries ( Prunus cerasus ) from a population segregating for a major bloom time QTL on chromosome 4. Using a new staging system, we identified floral buds from early-blooming trees were persistently more advanced than those from late-blooming siblings. A gDNA coverage analysis revealed the late-blooming haplotype of this QTL, k, is located on a subgenome originating from the late-blooming P. fruticosa progenitor. Transcriptome analyses identified a large number of genes within this QTL as differentially expressed between early- and late-blooming trees during the vegetative-to-floral transition. From these, we identified candidate genes for the late bloom phenotype, including multiple transcription factors homologous to REproductive Meristem (REM) B3 domain-containing proteins. Additionally, we determined the basis of k in sour cherry is likely separate from candidate genes found in sweet cherry–suggesting several major regulators of bloom time are located on Prunus chromosome 4.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"17 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134955775","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":"Serotonin transporter-dependent histone serotonylation in placenta contributes to the neurodevelopmental transcriptome","authors":"Jennifer C Chan, Natalia Alenina, Ashley M Cunningham, Aarthi Ramakrishnan, Li Shen, Michael Bader, Ian Maze","doi":"10.1101/2023.11.14.567020","DOIUrl":"https://doi.org/10.1101/2023.11.14.567020","url":null,"abstract":"Brain development requires appropriate regulation of serotonin (5-HT) signaling from distinct tissue sources across embryogenesis. At the maternal-fetal interface, the placenta is thought to be an important contributor of offspring brain 5-HT and is critical to overall fetal health. Yet, how placental 5-HT is acquired, and the mechanisms through which 5-HT influences placental functions, are not well understood. Recently, our group identified a novel epigenetic role for 5-HT, in which 5-HT can be added to histone proteins to regulate transcription, a process called H3 serotonylation. Here, we show that H3 serotonylation undergoes dynamic regulation during placental development, corresponding to gene expression changes that are known to influence key metabolic processes. Using transgenic mice, we demonstrate that placental H3 serotonylation largely depends on 5-HT uptake by the serotonin transporter (SERT/SLC6A4). SERT deletion robustly reduces enrichment of H3 serotonylation across the placental genome, and disrupts neurodevelopmental gene networks in early embryonic brain tissues. Thus, these findings suggest a novel role for H3 serotonylation in coordinating placental transcription at the intersection of maternal physiology and offspring brain development.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"49 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991305","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":"Strong sequence dependence in RNA/DNA hybrid strand displacement kinetics","authors":"Francesca G Smith, John P Goertz, Molly M Stevens, Thomas E Ouldridge","doi":"10.1101/2023.11.14.567030","DOIUrl":"https://doi.org/10.1101/2023.11.14.567030","url":null,"abstract":"Strand displacement reactions underlie dynamic nucleic acid nanotechnology. The kinetic and thermodynamic features of DNA-based displacement reactions are well understood and well predicted by current computational models. By contrast, understanding of RNA/DNA hybrid strand displacement kinetics is limited, restricting the design of increasingly complex RNA/DNA hybrid reaction networks with more tightly regulated dynamics. Given the importance of RNA as a diagnostic biomarker, and its critical role in intracellular processes, this shortfall is particularly limiting for the development of strand displacement-based therapeutics and diagnostics. Herein, we characterise 22 RNA/DNA hybrid strand displacement systems, systematically varying several common design parameters including toehold length and branch migration domain length. We observe the differences in stability between RNA-DNA hybrids and DNA-DNA duplexes have large effects on strand displacement rates, with rates for equivalent sequences differing by up to 3 orders of magnitude. Crucially, however, this effect is strongly sequence-dependent, with RNA invaders strongly favoured in a system with RNA strands of high purine content, and disfavoured in a system when the RNA strands have low purine content. These results lay the groundwork for more general design principles, allowing for creation of de novo reaction networks with novel complexity while maintaining predictable reaction kinetics.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"48 14","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992190","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":"Gene flow from Fraxinus cultivars into natural stands of Fraxinus pennsylvanica occurs range-wide, is regionally extensive, and is associated with a loss of allele richness","authors":"Everett A Abhainn, Devin L Shirley, Robert K Stanley, Tatum Scarpato, Jennifer L Koch, Jeanne Romero-Severson","doi":"10.1101/2023.11.10.566611","DOIUrl":"https://doi.org/10.1101/2023.11.10.566611","url":null,"abstract":"In North America, the ubiquitous planting of a comparatively small number of Fraxinus (ash) cultivars in both urban and rural environments over the last 70-80 years may have permitted extensive gene flow into naturally regenerated stands. In the light of multiple biotic threats to the North American Fraxinus, an assessment of the extent of gene flow from ash cultivars and the current state of genetic diversity in F. pennsylvanica (green ash), one of the most widely distributed species, is needed to inform seed collection strategies for the preservation of genetic diversity range-wide. We used 16 EST-SSR markers to genotype 1291 trees from 48 naturally regenerated populations of green ash across the native range, 19 F. pennsylvanica cultivars and one F. americana (white ash) cultivar. We detected first generation cultivar parentage with high confidence in 172 individuals in 34 of the 48 populations and extensive cultivar parentage (23-50%) in eight populations. The incidence of cultivar parentage was negatively associated with allele richness (R2 = 0.151, p = 0.006). The high frequency of cultivar propagule dispersal in our study suggests that a significant proportion of the standing genetic variation in local populations may not be of local origin, a result that has serious implications for the study of adaptive variation and the conservation of the Fraxinus gene pool.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"34 15","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134992677","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":"Liver sinusoidal endothelial cells constitute a major route for hemoglobin clearance","authors":"Gabriela Zurawska, Zuzanna Sas, Aneta Jonczy, Patryk Slusarczyk, Raghunandan Mahadeva, Marta Chwalek, Maria Kulecka, Izabela Rumienczyk, Morgane Moulin, Kamil Jastrzebski, Michal Mikula, Anders Etzerodt, Marta Miaczynska, Tomasz P. Rygiel, Katarzyna Mleczko-Sanecka","doi":"10.1101/2023.11.14.566925","DOIUrl":"https://doi.org/10.1101/2023.11.14.566925","url":null,"abstract":"Mild hemolysis of senescent erythrocytes occurs physiologically in the spleen, resulting in hemoglobin (Hb) release, whereas pathologic erythrocyte rupture characterizes several diseases. Iron recycling from Hb and Hb detoxification have been attributed to the sequestration of Hb-haptoglobin complexes by macrophages. However, we found the existence of additional efficient Hb clearance routes in mice. We identified liver sinusoidal endothelial cells (LSECs) as the primary cells responsible for Hb sequestration, a process that involves macropinocytosis and operates independently of the Hb-haptoglobin receptor CD163. LSECs expressed heme oxygenase 1 and hepcidin-controlled ferroportin and were the most efficient cellular scavengers of Hb at doses below and above the haptoglobin binding capacity. Erythrocyte transfusion assays further demonstrated that while splenic red pulp macrophages are adept at erytrophagocytosis, liver Kupffer cells and LSECs mainly clear erythrocyte ghosts and Hb, respectively, transported from the spleen via the portal circulation. High-dose Hb injections in mice resulted in transient hepatic iron retention and early activation of the gene encoding heme oxygenase 1 (Hmox1) in LSECs. This response was associated with the transcriptional induction of the iron-sensing angiokine Bmp6, culminating in hepcidin-mediated transient serum hypoferremia. Injection of Hb and iron citrate elicited distinct transcriptional signatures in LSECs, and the Bmp6 induction was phenocopied by erythrocyte lysis upon phenylhydrazine. Collectively, we propose that LSECs provide a key mechanism for Hb clearance, a function that establishes the spleen-liver axis for physiological iron recycling from Hb and contributes to heme detoxification during hemolysis, coupled with the induction of the BMP6-hepcidin axis, ultimately restoring iron homeostasis.","PeriodicalId":486943,"journal":{"name":"bioRxiv (Cold Spring Harbor Laboratory)","volume":"29 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134954549","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}