bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.10.602956

Mark A. Buckner, Steven T. Hoge, B. Danforth

{"title":"Forecasting the Effects of Global Change on a Bee Biodiversity Hotspot","authors":"Mark A. Buckner, Steven T. Hoge, B. Danforth","doi":"10.1101/2024.07.10.602956","DOIUrl":"https://doi.org/10.1101/2024.07.10.602956","url":null,"abstract":"The Mojave and Sonoran Deserts, recognized as a global hotspot for bee biodiversity, are experiencing habitat degradation from urbanization, utility-scale solar energy (USSE) development, and climate change. In this study, we evaluated the current and future distribution of bee diversity in the region, assessed how protected areas safeguard bee species richness, and predicted how global change may affect bees across the region. Using Joint Species Distribution Models (JSDMs) of 148 bee species, we project changes in species distributions, occurrence area, and richness across the region under four global change scenarios between 1971 and 2050. We evaluated the threat posed by USSE development and predicted how climate change will affect the suitability of protected areas for conservation. Our findings indicate that changes in temperature and precipitation do not uniformly affect bee richness across the region. Protected areas in the Sonoran and Mojave Deserts are projected to experience mean losses of up to 5.8 species, whereas protected areas at higher elevations and transition zones may gain up to 7.8 species. Outside protected areas, bee diversity is threatened by urbanization and USSE development. Areas prioritized for future USSE development have an average species richness of 4.2 species higher than the study area average, and lower priority areas have 8.2 more species. USSE zones are expected to experience declines of 2.7 to 8.0 species by 2050 due to climate change alone. Despite the importance of solitary bees for pollination, their diversity is often overlooked in land management decisions. Our results show the utility of JSDMs for extending the usability of existing data-limited bee species records, easing the inclusion of these species in conservation and land management decision-making. The multiple threats from global change drivers underscore the importance of including ecologically vital, though often data-limited, species in land-use decisions.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"38 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141643611","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}

引用次数: 0

Two for tau: Automated model discovery reveals two-stage tau aggregation dynamics in Alzheimer’s disease 两个 tau：自动模型发现揭示了阿尔茨海默病中两个阶段的 tau 聚集动力学

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.15.603581

Charles A. Stockman, Alain Goriely, E. Kuhl

{"title":"Two for tau: Automated model discovery reveals two-stage tau aggregation dynamics in Alzheimer’s disease","authors":"Charles A. Stockman, Alain Goriely, E. Kuhl","doi":"10.1101/2024.07.15.603581","DOIUrl":"https://doi.org/10.1101/2024.07.15.603581","url":null,"abstract":"Alzheimer’s disease is a neurodegenerative disorder characterized by the presence of amyloid-β plaques and the accumulation of misfolded tau proteins and neurofibrillary tangles in the brain. A thorough understanding of the local accumulation of tau is critical to develop effective therapeutic strategies. Tau pathology has traditionally been described using reaction-diffusion models, which succeed in capturing the global spread, but fail to accurately describe the local aggregation dynamics. Current mathematical models enforce a single-peak behavior in tau aggregation, which does not align well with clinical observations. Here we identify a more accurate description of tau aggregation that reflects the complex patterns observed in patients. We propose an innovative approach that uses constitutive neural networks to autonomously discover bell-shaped aggregation functions with multiple peaks from clinical positron emission tomography (PET) data of misfolded tau protein. Our method reveals previously overlooked two-stage aggregation dynamics by uncovering a twoterm ordinary differential equation that links the local accumulation rate to the tau concentration. When trained on data from amyloid-β positive and negative subjects, the neural network clearly distinguishes between both groups and uncovers a more subtle relationship between amyloid-β and tau than previously postulated. In line with the amyloid-tau dual pathway hypothesis, our results show that the presence of toxic amyloid-β influences the accumulation of tau, particularly in the earlier disease stages. We expect that our approach to autonomously discover the accumulation dynamics of pathological proteins will improve simulations of tau dynamics in Alzheimer’s disease and provide new insights into disease progression.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"60 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141643949","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}

引用次数: 0

Nitrogen sharing strategies in six clonal species 六种克隆物种的分氮策略

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.12.603230

J. Duchoslavová

{"title":"Nitrogen sharing strategies in six clonal species","authors":"J. Duchoslavová","doi":"10.1101/2024.07.12.603230","DOIUrl":"https://doi.org/10.1101/2024.07.12.603230","url":null,"abstract":"Nitrogen is often a limiting factor for plant growth, and its availability is a major determinant of level of competition. In clonal plants, patterns of nitrogen translocation between ramets may be part of plant nitrogen economics, and, as such, may also be related to the typical availability of nitrogen. In nutrient-poor habitats, extensive nutrient sharing balancing resource availability may be important, whereas nutrient sharing between established ramets may not be beneficial in productive habitats. I tested the proposed nutrient sharing strategies on nitrogen translocation in six stoloniferous species that occur in habitats of varying productivity. Mother and daughter ramets of each species were grown either in a homogeneous nutrient-poor treatment or in a “nutrient-poor to nutrient-rich” treatment. I traced the translocation of nitrogen in both directions using stable isotope labelling when the daughter ramets were one month old. Surprisingly, I found no effect of nutrient treatment on nitrogen translocation. Instead, each species translocated nitrogen either acropetally, basipetally, or equally in both directions. There was no relationship between the direction of translocation and the productivity of the species’ habitats. However, net translocation seemed to be related to the relative size of daughters across species, and within Veronica officinalis. The results suggest that the relative size of plant parts is an important determinant of the strength of the sink for nitrogen they form, and that the growth habit of a species can affect its nitrogen translocation. Under certain conditions, such internally induced source-sink relationships may dominate over external nitrogen heterogeneity. I speculate that growth habit, together with nitrogen translocation patterns, may be part of adaptive growth strategies.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"8 14","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141640437","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}

引用次数: 0

Emergence of cellular nematic order is a conserved feature of gastrulation in animal embryos 细胞线序的出现是动物胚胎胃形成的一个保守特征

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.11.603175

Xin Li, Robert J. Huebner, Margot Kossmann Williams, Jessica Sawyer, M. Peifer, John B. Wallingford, D. Thirumalai

引用次数: 0

The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multi-part RNA regulatory modules Rbfox1/LASR 复合物通过识别多部分 RNA 调控模块来控制替代性前 mRNA 剪接

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.12.603345

Parham Peyda, Chia-Ho Lin, Kelechi Onwuzurike, Douglas L. Black

{"title":"The Rbfox1/LASR complex controls alternative pre-mRNA splicing by recognition of multi-part RNA regulatory modules","authors":"Parham Peyda, Chia-Ho Lin, Kelechi Onwuzurike, Douglas L. Black","doi":"10.1101/2024.07.12.603345","DOIUrl":"https://doi.org/10.1101/2024.07.12.603345","url":null,"abstract":"The Rbfox proteins regulate alternative pre-mRNA splicing by binding to the RNA element GCAUG. In the nucleus, most of Rbfox is bound to LASR, a complex of RNA-binding proteins that recognize additional RNA motifs. However, it remains unclear how the different subunits of the Rbfox/LASR complex act together to bind RNA and regulate splicing. We used a nuclease-protection assay to map the transcriptome-wide footprints of Rbfox1/LASR on nascent cellular RNA. In addition to GCAUG, Rbfox1/LASR binds RNA containing motifs for LASR subunits hnRNPs M, H/F, C, and Matrin3. These elements are often arranged in tandem, forming multi-part modules of RNA motifs. To distinguish contact sites of Rbfox1 from the LASR subunits, we analyzed a mutant Rbfox1(F125A) that has lost RNA binding but remains associated with LASR. Rbfox1(F125A)/LASR complexes no longer interact with GCAUG but retain binding to RNA elements for LASR. Splicing analyses reveal that in addition to activating exons through adjacent GCAUG elements, Rbfox can also stimulate exons near binding sites for LASR subunits. Mini-gene experiments demonstrate that these diverse elements produce a combined regulatory effect on a target exon. These findings illuminate how a complex of RNA-binding proteins can decode combinatorial splicing regulatory signals by recognizing groups of tandem RNA elements.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"1 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141640236","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}

引用次数: 0

Neural specialisation for concrete and abstract concepts revealed through meta-analysis 通过元分析揭示具体概念和抽象概念的神经特异性

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.11.603079

Paul Hoffman, Matthew Bair

引用次数: 0

Estimating cis and trans contributions to differences in gene regulation 估计顺式和反式对基因调控差异的贡献

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.13.603403

Ingileif B. Hallgrímsdóttir, M. Carilli, L. Pachter

引用次数: 0

Protrudin acts at ER-endosome contacts to promote KIF5-mediated endosomal fission and endosome-to-Golgi transport Protrudin在ER-内质体接触处发挥作用，促进KIF5介导的内质体裂变和内质体到高尔基体的转运

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.15.602703

Julia Kleniuk, A. G. Nadadhur, Emily Wolfenden, Catherine Rodger, Eliska Zlamalova, Evan Reid

{"title":"Protrudin acts at ER-endosome contacts to promote KIF5-mediated endosomal fission and endosome-to-Golgi transport","authors":"Julia Kleniuk, A. G. Nadadhur, Emily Wolfenden, Catherine Rodger, Eliska Zlamalova, Evan Reid","doi":"10.1101/2024.07.15.602703","DOIUrl":"https://doi.org/10.1101/2024.07.15.602703","url":null,"abstract":"Protrudin binds ER-localised VAPs and endosomal phosphoinositides to form ER-endosome contacts that promote endosomal tubule fission and endosome-to-Golgi traffic. Protrudin recruits KIF5 to provide a FYCO1-independent force to fission endosomal tubules in neurons and non-polarised cells. Abstract Fission of transport tubules from early endosomes is required for endosomal sorting, but mechanisms of endosomal tubule fission (ETF) are incompletely understood. We show protrudin acts at ER-endosome contacts to promote ETF and endosome-to-Golgi traffic. Protrudin-mediated ETF required its ability to interact with ER-localised VAP proteins, endosomal phosphoinositides and KIF5. These properties also regulated the distance between protrudin and endosomal tubules. The defective ETF phenotype of increased endosomal tubulation in cells lacking protrudin was phenocopied by depletion of KIF5, but not FYCO1, a motor protein adaptor implicated in protrudin-dependent late endosome motility. It also required intact microtubules and dynein, consistent with a model where protrudin facilitates a tug-of-war between KIF5 and dynein to fission tubules. In addition to its direct role, protrudin links many other machineries involved in ETF, thus our findings elucidate how ETF is co-ordinated. These machineries are enriched for proteins implicated in hereditary motor neuron disorders, and protrudin or KIF5 depletion caused defective ETF in human neurons.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"5 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141641858","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}

引用次数: 0

MAGE-A4-Responsive Plasma Cells Promote Non-Small Cell Lung Cancer MAGE-A4反应性浆细胞促进非小细胞肺癌的发生

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.10.602985

Dominique Armstrong, Cheng-Yen Chang, Monica J. Hong, Linda Green, William Hudson, Yichao Shen, Li-Zhen Song, Sheetal Jammi, Benjamin Casal, Chad J. Creighton, Alexandre Carisey, X. Zhang, Neil J. McKenna, Sung Wook Kang, Hyun-Sung Lee, D. Corry, F. Kheradmand

{"title":"MAGE-A4-Responsive Plasma Cells Promote Non-Small Cell Lung Cancer","authors":"Dominique Armstrong, Cheng-Yen Chang, Monica J. Hong, Linda Green, William Hudson, Yichao Shen, Li-Zhen Song, Sheetal Jammi, Benjamin Casal, Chad J. Creighton, Alexandre Carisey, X. Zhang, Neil J. McKenna, Sung Wook Kang, Hyun-Sung Lee, D. Corry, F. Kheradmand","doi":"10.1101/2024.07.10.602985","DOIUrl":"https://doi.org/10.1101/2024.07.10.602985","url":null,"abstract":"Adaptive immunity is critical to eliminate malignant cells, while multiple tumor-intrinsic factors can alter this protective function. Melanoma antigen-A4 (MAGE-A4), a cancer-testis antigen, is expressed in several solid tumors and correlates with poor survival in non-small cell lung cancer (NSCLC), but its role in altering antitumor immunity remains unclear. We found that expression of MAGE-A4 was highly associated with the loss of PTEN, a tumor suppressor, in human NSCLC. Here we show that constitutive expression of human MAGE-A4 combined with the loss of Pten in mouse airway epithelial cells results in metastatic adenocarcinoma enriched in CD138+ CXCR4+ plasma cells, predominantly expressing IgA. Consistently, human NSCLC expressing MAGE-A4 showed increased CD138+ IgA+ plasma cell density surrounding tumors. The abrogation of MAGE-A4-responsive plasma cells (MARPs) decreased tumor burden, increased T cell infiltration and activation, and reduced CD163+CD206+ macrophages in mouse lungs. These findings suggest MAGE-A4 promotes NSCLC tumorigenesis, in part, through the recruitment and retention of IgA+ MARPs in the lungs.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"60 15","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141643954","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}

引用次数: 0

Investigating the effects of transcutaneous Vagus Nerve Stimulation on motor cortex excitability and inhibition through paired-pulse Transcranial Magnetic Stimulation 通过成对脉冲经颅磁刺激研究经皮迷走神经刺激对运动皮层兴奋性和抑制性的影响

bioRxiv Pub Date : 2024-07-16 DOI: 10.1101/2024.07.12.603338

Boscarol Sara, Turchi Letizia, Oldrati Viola, Urgesi Cosimo, Finisguerra Alessandra

{"title":"Investigating the effects of transcutaneous Vagus Nerve Stimulation on motor cortex excitability and inhibition through paired-pulse Transcranial Magnetic Stimulation","authors":"Boscarol Sara, Turchi Letizia, Oldrati Viola, Urgesi Cosimo, Finisguerra Alessandra","doi":"10.1101/2024.07.12.603338","DOIUrl":"https://doi.org/10.1101/2024.07.12.603338","url":null,"abstract":"Transcutaneous Vagus Nerve stimulation (tVNS) has been proposed as a prospective treatment for clinical conditions with altered GABAergic transmission. While possible effects of tVNS on behavioral performance in inhibitory control tasks have been previously reported, neurophysiological evidence showing its effects on GABA-mediated inhibition in the motor cortex is limited. Concurrently, the possible influence of participant’s gender and state conditions remains unexplored. Here, we applied, single- and paired-pulse TMS to the right or the left primary motor in two different groups of participants. We measured corticospinal excitability (CSE), short and long intracortical inhibition (SICI and LICI), cortical silent period (cSP) and intracortical facilitation (ICF) indexes. The measures were taken, in separated sessions of a within-subject design, at baseline prior to tVNS and after delivering active and sham tVNS in the Cymba conchae of the left ear. To exploit state dependent effects and assess the role of tVNS in motor learning, tVNS was applied, during the execution of a computerized visuomotor task. In the left TMS group, we observed better visuomotor performance during active than sham tVNS, regardless of participant’s gender. Interestingly, in both groups, we found a specific increase of SICI, which is mediated by GABAa activity, after active compared to sham-tVNS and baseline evaluations, which was specifically limited to female participants. No effects on CSE, ICF or GABAb-mediated intracortical inhibition indexes were observed. The results show specific effects of tVNS on motor learning and GABAa-mediated motor inhibition, providing supportive evidence for the application of tVNS as an alternative and coadjuvant treatment for disorders featured by altered inhibition mechanisms.","PeriodicalId":9124,"journal":{"name":"bioRxiv","volume":"6 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141641127","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}

引用次数: 0

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