Pub Date : 2024-08-06eCollection Date: 2024-08-01DOI: 10.1093/pnasnexus/pgae284
Behrouz G Esfahani, Peter S Randolph, Ruizhi Peng, Timothy Grant, M Elizabeth Stroupe, Scott M Stagg
In cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result in issues like aggregation and preferred orientations at the air/water interface. Many alternative methods have been proposed, but there remains a lack a universal solution, and multiple techniques are often required for challenging samples. Here, we demonstrate the use of lipid nanotubes with nickel NTA headgroups as a platform for cryo-EM sample preparation. His-tagged specimens of interest are added to the tubules, and they can be frozen by conventional plunge freezing. We show that the nanotubes protect samples from the air/water interface and promote a wider range of orientations. The reconstruction of average subtracted tubular regions (RASTR) method allows for the removal of the nanotubule signal from the cryo-EM images resulting in isolated images of specimens of interest. Testing with β-galactosidase validates the method's ability to capture particles at lower concentrations, overcome preferred orientations, and achieve near-atomic resolution reconstructions. Since the nanotubules can be identified and targeted automatically at low magnification, the method enables fully automated data collection. Furthermore, the particles on the tubes can be automatically identified and centered using 2D classification enabling particle picking without requiring prior information. Altogether, our approach that we call specimen preparation on a tube RASTR holds promise for overcoming air-water interface and preferred orientation challenges and offers the potential for fully automated cryo-EM data collection and structure determination.
在低温电子显微镜(cryo-EM)中,尽管近年来取得了进步,但试样制备仍然是一个瓶颈。传统的切入式冷冻方法通常会导致空气/水界面的聚集和优先取向等问题。人们已经提出了许多替代方法,但仍然缺乏通用的解决方案,而且对于具有挑战性的样品往往需要多种技术。在这里,我们展示了使用带有 NTA 镍头基的脂质纳米管作为冷冻电镜样品制备平台的方法。将 His 标记的相关样本添加到纳米管中,然后用传统的冷冻方法对其进行冷冻。我们的研究表明,纳米管能保护样品不受空气/水界面的影响,并能促进更广泛的取向。通过平均减去管状区域重建(RASTR)方法,可以从低温电子显微镜图像中去除纳米管信号,从而得到相关标本的孤立图像。使用 β-半乳糖苷酶进行的测试验证了该方法能够捕获低浓度颗粒、克服优先取向并实现近原子分辨率重建。由于纳米管可在低倍放大镜下自动识别和锁定,该方法可实现全自动数据采集。此外,纳米管上的颗粒可以通过二维分类自动识别和对中,从而实现颗粒拾取,而无需事先了解相关信息。总之,我们称之为在管子 RASTR 上制备试样的方法有望克服空气-水界面和优先定向难题,并为全自动冷冻电镜数据收集和结构确定提供了潜力。
{"title":"SPOT-RASTR-A cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface.","authors":"Behrouz G Esfahani, Peter S Randolph, Ruizhi Peng, Timothy Grant, M Elizabeth Stroupe, Scott M Stagg","doi":"10.1093/pnasnexus/pgae284","DOIUrl":"10.1093/pnasnexus/pgae284","url":null,"abstract":"<p><p>In cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result in issues like aggregation and preferred orientations at the air/water interface. Many alternative methods have been proposed, but there remains a lack a universal solution, and multiple techniques are often required for challenging samples. Here, we demonstrate the use of lipid nanotubes with nickel NTA headgroups as a platform for cryo-EM sample preparation. His-tagged specimens of interest are added to the tubules, and they can be frozen by conventional plunge freezing. We show that the nanotubes protect samples from the air/water interface and promote a wider range of orientations. The reconstruction of average subtracted tubular regions (RASTR) method allows for the removal of the nanotubule signal from the cryo-EM images resulting in isolated images of specimens of interest. Testing with β-galactosidase validates the method's ability to capture particles at lower concentrations, overcome preferred orientations, and achieve near-atomic resolution reconstructions. Since the nanotubules can be identified and targeted automatically at low magnification, the method enables fully automated data collection. Furthermore, the particles on the tubes can be automatically identified and centered using 2D classification enabling particle picking without requiring prior information. Altogether, our approach that we call specimen preparation on a tube RASTR holds promise for overcoming air-water interface and preferred orientation challenges and offers the potential for fully automated cryo-EM data collection and structure determination.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11303004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-06eCollection Date: 2024-08-01DOI: 10.1093/pnasnexus/pgae260
Darren L C Y Li Shing Hiung, Jasmin M Schuster, Murray I Duncan, Nicholas L Payne, Brian Helmuth, Jackson W F Chu, Julia K Baum, Viviana Brambilla, John Bruno, Sarah W Davies, Maria Dornelas, Patrick Gagnon, Tamar Guy-Haim, Jennifer M Jackson, James J Leichter, Joshua S Madin, Zachary L Monteith, Ana M Queirós, Eric V C Schneider, Samuel Starko, Brendan S Talwar, Alex S J Wyatt, Hannah E Aichelman, Nathaniel Bensoussan, Carlo Caruso, Karl Castillo, Francis Choi, Yun-Wei Dong, Joaquim Garrabou, Dorian Guillemain, Nicholas Higgs, Yuwu Jiang, Diego K Kersting, David J Kushner, Guilherme O Longo, Christopher Neufeld, Marion Peirache, Tim Smyth, Joshua L Sprague, Gaëlle Urvoy, Frederic Zuberer, Amanda E Bates
As on land, oceans exhibit high temporal and spatial temperature variation. This "ocean weather" contributes to the physiological and ecological processes that ultimately determine the patterns of species distribution and abundance, yet is often unrecognized, especially in tropical oceans. Here, we tested the paradigm of temperature stability in shallow waters (<12.5 m) across different zones of latitude. We collated hundreds of in situ, high temporal-frequency ocean temperature time series globally to produce an intuitive measure of temperature variability, ranging in scale from quarter-diurnal to annual time spans. To estimate organismal sensitivity of ectotherms (i.e. microbes, algae, and animals whose body temperatures depend upon ocean temperature), we computed the corresponding range of biological rates (such as metabolic rate or photosynthesis) for each time span, assuming an exponential relationship. We found that subtropical regions had the broadest temperature ranges at time spans equal to or shorter than a month, while temperate and tropical systems both exhibited narrow (i.e. stable) short-term temperature range estimates. However, temperature-dependent biological rates in tropical regions displayed greater ranges than in temperate systems. Hence, our results suggest that tropical ectotherms may be relatively more sensitive to short-term thermal variability. We also highlight previously unexplained macroecological patterns that may be underpinned by short-term temperature variability.
{"title":"Ocean weather, biological rates, and unexplained global ecological patterns.","authors":"Darren L C Y Li Shing Hiung, Jasmin M Schuster, Murray I Duncan, Nicholas L Payne, Brian Helmuth, Jackson W F Chu, Julia K Baum, Viviana Brambilla, John Bruno, Sarah W Davies, Maria Dornelas, Patrick Gagnon, Tamar Guy-Haim, Jennifer M Jackson, James J Leichter, Joshua S Madin, Zachary L Monteith, Ana M Queirós, Eric V C Schneider, Samuel Starko, Brendan S Talwar, Alex S J Wyatt, Hannah E Aichelman, Nathaniel Bensoussan, Carlo Caruso, Karl Castillo, Francis Choi, Yun-Wei Dong, Joaquim Garrabou, Dorian Guillemain, Nicholas Higgs, Yuwu Jiang, Diego K Kersting, David J Kushner, Guilherme O Longo, Christopher Neufeld, Marion Peirache, Tim Smyth, Joshua L Sprague, Gaëlle Urvoy, Frederic Zuberer, Amanda E Bates","doi":"10.1093/pnasnexus/pgae260","DOIUrl":"10.1093/pnasnexus/pgae260","url":null,"abstract":"<p><p>As on land, oceans exhibit high temporal and spatial temperature variation. This \"ocean weather\" contributes to the physiological and ecological processes that ultimately determine the patterns of species distribution and abundance, yet is often unrecognized, especially in tropical oceans. Here, we tested the paradigm of temperature stability in shallow waters (<12.5 m) across different zones of latitude. We collated hundreds of in situ, high temporal-frequency ocean temperature time series globally to produce an intuitive measure of temperature variability, ranging in scale from quarter-diurnal to annual time spans. To estimate organismal sensitivity of ectotherms (i.e. microbes, algae, and animals whose body temperatures depend upon ocean temperature), we computed the corresponding range of biological rates (such as metabolic rate or photosynthesis) for each time span, assuming an exponential relationship. We found that subtropical regions had the broadest temperature ranges at time spans equal to or shorter than a month, while temperate and tropical systems both exhibited narrow (i.e. stable) short-term temperature range estimates. However, temperature-dependent biological rates in tropical regions displayed greater ranges than in temperate systems. Hence, our results suggest that tropical ectotherms may be relatively more sensitive to short-term thermal variability. We also highlight previously unexplained macroecological patterns that may be underpinned by short-term temperature variability.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11302846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899137","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}
Wound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that is related to commensal microbiota and skin fibrosis remains mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterizes microbial composition and divergence between the pathological and normal skin tissues. Moreover, the data show elevation of interleukin-8 (IL-8) in both the circulation and keloid tissue, which elicited the collagen accumulation and migratory program of dermal fibroblasts via CXCR1/2 receptor. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease.
{"title":"Commensal microbiome dysbiosis elicits interleukin-8 signaling to drive fibrotic skin disease.","authors":"Wenyu Zhang, Qili Peng, Xian Huang, Qing Huang, Zhiliang Zhang, Fuli Li, Naisheng Zheng, Binsheng Shi, Zhihong Fan, Tomasz Maj, Rui Chen","doi":"10.1093/pnasnexus/pgae273","DOIUrl":"10.1093/pnasnexus/pgae273","url":null,"abstract":"<p><p>Wound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that is related to commensal microbiota and skin fibrosis remains mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterizes microbial composition and divergence between the pathological and normal skin tissues. Moreover, the data show elevation of interleukin-8 (IL-8) in both the circulation and keloid tissue, which elicited the collagen accumulation and migratory program of dermal fibroblasts via CXCR1/2 receptor. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-30eCollection Date: 2024-07-01DOI: 10.1093/pnasnexus/pgae267
Feng Liu, Iliano V Coutinho-Abreu, Robyn Raban, Tam Thuy Dan Nguyen, Alejandra R Dimas, Joseph A Merriman, Omar S Akbari
The skin microbiome plays a pivotal role in the production of attractive cues detected by mosquitoes. Here, we leveraged recent advances in genetic engineering to significantly reduce the production of L-(+)-lactic acid as a strategy to reduce mosquito attraction to the highly prominent skin commensals Staphylococcus epidermidis and Corynebacterium amycolatum. Engraftment of these engineered bacteria onto the skin of mice reduced mosquito attraction and feeding for up to 11 uninterrupted days, which is considerably longer than the several hours of protection conferred by the leading chemical repellent N,N-diethyl-meta-toluamide. Taken together, our findings demonstrate engineering the skin microbiome to reduce attractive volatiles represents an innovative untapped strategy to reduce vector attraction, preventing bites, and pathogen transmission. These findings set the stage for new classes of long-lasting microbiome-based repellent products.
{"title":"Engineered skin microbiome reduces mosquito attraction to mice.","authors":"Feng Liu, Iliano V Coutinho-Abreu, Robyn Raban, Tam Thuy Dan Nguyen, Alejandra R Dimas, Joseph A Merriman, Omar S Akbari","doi":"10.1093/pnasnexus/pgae267","DOIUrl":"10.1093/pnasnexus/pgae267","url":null,"abstract":"<p><p>The skin microbiome plays a pivotal role in the production of attractive cues detected by mosquitoes. Here, we leveraged recent advances in genetic engineering to significantly reduce the production of L-(+)-lactic acid as a strategy to reduce mosquito attraction to the highly prominent skin commensals <i>Staphylococcus epidermidis</i> and <i>Corynebacterium amycolatum.</i> Engraftment of these engineered bacteria onto the skin of mice reduced mosquito attraction and feeding for up to 11 uninterrupted days, which is considerably longer than the several hours of protection conferred by the leading chemical repellent N,N-diethyl-meta-toluamide. Taken together, our findings demonstrate engineering the skin microbiome to reduce attractive volatiles represents an innovative untapped strategy to reduce vector attraction, preventing bites, and pathogen transmission. These findings set the stage for new classes of long-lasting microbiome-based repellent products.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-30eCollection Date: 2024-07-01DOI: 10.1093/pnasnexus/pgae252
Raymond Jimenez, Dominic Yurk, Steven Dell, Austin C Rutledge, Matt K Fu, William P Dempsey, Yaser Abu-Mostafa, Aditya Rajagopal, Alaina Brinley Rajagopal
Cardiovascular disease is the leading cause of death worldwide. Existing methods for continuous, noninvasive blood pressure (BP) monitoring suffer from poor accuracy, uncomfortable form factors, or a need for frequent calibration, limiting their adoption. We introduce a new framework for continuous BP measurement that is noninvasive and calibration-free called resonance sonomanometry. The method uses ultrasound imaging to measure both the arterial dimensions and artery wall resonances that are induced by acoustic stimulation, which offers a direct measure of BP by a fully determined physical model. The approach and model are validated in vitro using arterial mock-ups and then in multiple arteries in human subjects. This approach offers the promise of robust continuous BP measurements, providing significant benefits for early diagnosis and treatment of cardiovascular disease.
{"title":"Resonance sonomanometry for noninvasive, continuous monitoring of blood pressure.","authors":"Raymond Jimenez, Dominic Yurk, Steven Dell, Austin C Rutledge, Matt K Fu, William P Dempsey, Yaser Abu-Mostafa, Aditya Rajagopal, Alaina Brinley Rajagopal","doi":"10.1093/pnasnexus/pgae252","DOIUrl":"10.1093/pnasnexus/pgae252","url":null,"abstract":"<p><p>Cardiovascular disease is the leading cause of death worldwide. Existing methods for continuous, noninvasive blood pressure (BP) monitoring suffer from poor accuracy, uncomfortable form factors, or a need for frequent calibration, limiting their adoption. We introduce a new framework for continuous BP measurement that is noninvasive and calibration-free called resonance sonomanometry. The method uses ultrasound imaging to measure both the arterial dimensions and artery wall resonances that are induced by acoustic stimulation, which offers a direct measure of BP by a fully determined physical model. The approach and model are validated in vitro using arterial mock-ups and then in multiple arteries in human subjects. This approach offers the promise of robust continuous BP measurements, providing significant benefits for early diagnosis and treatment of cardiovascular disease.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287871/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-25DOI: 10.1093/pnasnexus/pgae290
Qiang Guo, Malcolm N Mistry, Xudong Zhou, Gang Zhao, Kanon Kino, Bo Wen, Kei Yoshimura, Yusuke Satoh, Ivana Cvijanovic, Yoonhee Kim, C. Ng, A. Vicedo-Cabrera, Ben Armstrong, A. Urban, K. Katsouyanni, P. Masselot, Shilu Tong, F. Sera, Veronika Huber, Michelle L. Bell, J. Kyselý, R. Abrutzky, Yuming Guo, Micheline de Sousa Zanotti Stagliorio Coêlho, Paulo Hilário Nascimento Saldiva, Eric Lavigne, N. V. Ortega, P. M. Correa, Haidong Kan, S. Osorio, Dominic Royé, Ene Indermitte, H. Orru, J. Jaakkola, N. Ryti, Mathilde Pascal, Alexandra Schneider, A. Analitis, A. Entezari, F. Mayvaneh, A. Zeka, P. Goodman, F. de’Donato, P. Michelozzi, B. Alahmad, César De la Cruz Valencia, Magali Hurtado Díaz, A. Overcenco, C. Ameling, D. Houthuijs, S. Rao, Gabriel Carrasco, X. Seposo, J. Madureira, Susana das Neves Pereira da Silva, I. Holobâcă, F. Acquaotta, N. Scovronick, Ho Kim, Whanhee Lee, Aurelio Tobias, Carmen Íñiguez, B. Forsberg, Martina S. Ragettli, Shih-chun Pan, Yue Leon Guo, Shanshan Li, Rochelle Schneider, V. Co
The rising humid heat is regarded as a severe threat to human survivability, but the proper integration of humid heat into heat-health alerts is still being explored. Using state-of-the-art epidemiological and climatological datasets, we examined the association between multiple heat stress indicators (HSIs) and daily human mortality in 739 cities worldwide. Notable differences were observed in the long-term trends and timing of heat events detected by HSIs. Air temperature (Tair) predicts heat-related mortality well in cities with a robust negative Tair-relative humidity correlation (CT-RH). However, in cities with near-zero or weak-positive CT-RH, HSIs considering humidity provide enhanced predictive power compared to Tair. Furthermore, the magnitude and timing of heat-related mortality measured by HSIs could differ largely from those associated with Tair in many cities. Our findings provide important insights into specific regions where humans are vulnerable to humid heat and can facilitate the further enhancement of heat-health alert systems.
{"title":"Regional variation in the role of humidity on city-level heat-related mortality","authors":"Qiang Guo, Malcolm N Mistry, Xudong Zhou, Gang Zhao, Kanon Kino, Bo Wen, Kei Yoshimura, Yusuke Satoh, Ivana Cvijanovic, Yoonhee Kim, C. Ng, A. Vicedo-Cabrera, Ben Armstrong, A. Urban, K. Katsouyanni, P. Masselot, Shilu Tong, F. Sera, Veronika Huber, Michelle L. Bell, J. Kyselý, R. Abrutzky, Yuming Guo, Micheline de Sousa Zanotti Stagliorio Coêlho, Paulo Hilário Nascimento Saldiva, Eric Lavigne, N. V. Ortega, P. M. Correa, Haidong Kan, S. Osorio, Dominic Royé, Ene Indermitte, H. Orru, J. Jaakkola, N. Ryti, Mathilde Pascal, Alexandra Schneider, A. Analitis, A. Entezari, F. Mayvaneh, A. Zeka, P. Goodman, F. de’Donato, P. Michelozzi, B. Alahmad, César De la Cruz Valencia, Magali Hurtado Díaz, A. Overcenco, C. Ameling, D. Houthuijs, S. Rao, Gabriel Carrasco, X. Seposo, J. Madureira, Susana das Neves Pereira da Silva, I. Holobâcă, F. Acquaotta, N. Scovronick, Ho Kim, Whanhee Lee, Aurelio Tobias, Carmen Íñiguez, B. Forsberg, Martina S. Ragettli, Shih-chun Pan, Yue Leon Guo, Shanshan Li, Rochelle Schneider, V. Co","doi":"10.1093/pnasnexus/pgae290","DOIUrl":"https://doi.org/10.1093/pnasnexus/pgae290","url":null,"abstract":"\u0000 The rising humid heat is regarded as a severe threat to human survivability, but the proper integration of humid heat into heat-health alerts is still being explored. Using state-of-the-art epidemiological and climatological datasets, we examined the association between multiple heat stress indicators (HSIs) and daily human mortality in 739 cities worldwide. Notable differences were observed in the long-term trends and timing of heat events detected by HSIs. Air temperature (Tair) predicts heat-related mortality well in cities with a robust negative Tair-relative humidity correlation (CT-RH). However, in cities with near-zero or weak-positive CT-RH, HSIs considering humidity provide enhanced predictive power compared to Tair. Furthermore, the magnitude and timing of heat-related mortality measured by HSIs could differ largely from those associated with Tair in many cities. Our findings provide important insights into specific regions where humans are vulnerable to humid heat and can facilitate the further enhancement of heat-health alert systems.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141803715","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}
Atmospheric sulfate aerosols contribute significantly to air pollution and climate change. Sulfate formation mechanisms during winter haze events in northern China have recently received considerable attention, with more than ten studies published in high-impact journals. However, the conclusions from in-field measurements, laboratory studies, and numerical simulations are inconsistent and even contradictory. Here, we propose a physically based yet simple method to clarify the debate on the dominant sulfate formation pathway. Based on the hazes evolving in the synoptic scale, first, a characteristic sulfate formation rate is derived using the Eulerian mass conservation equation constrained by in-situ observations. Then, this characteristic value is treated as a guideline to determine the dominant sulfate formation pathway with a zero-dimensional chemical box model. Our observation-derived results establish a linkage between studies from laboratory experiments and chemical transport model simulations. A convergent understanding could therefore be reached on sulfate formation mechanisms in China’s wintertime haze. The novel method is universal and can be applied to various haze conditions and different secondary products.
{"title":"Can we reach consensus on the dominant sulfate formation pathway in China’s haze?","authors":"Mingxu Liu, Yu Song, Tiantian Wang, Xinyi Dang, Fang Shang, Xipeng Jin, Mile Du, Weigang Wang, Yele Sun, Qiang Zhang, Ling Kang, Xuhui Cai, Hongsheng Zhang, T. Zhu","doi":"10.1093/pnasnexus/pgae291","DOIUrl":"https://doi.org/10.1093/pnasnexus/pgae291","url":null,"abstract":"\u0000 Atmospheric sulfate aerosols contribute significantly to air pollution and climate change. Sulfate formation mechanisms during winter haze events in northern China have recently received considerable attention, with more than ten studies published in high-impact journals. However, the conclusions from in-field measurements, laboratory studies, and numerical simulations are inconsistent and even contradictory. Here, we propose a physically based yet simple method to clarify the debate on the dominant sulfate formation pathway. Based on the hazes evolving in the synoptic scale, first, a characteristic sulfate formation rate is derived using the Eulerian mass conservation equation constrained by in-situ observations. Then, this characteristic value is treated as a guideline to determine the dominant sulfate formation pathway with a zero-dimensional chemical box model. Our observation-derived results establish a linkage between studies from laboratory experiments and chemical transport model simulations. A convergent understanding could therefore be reached on sulfate formation mechanisms in China’s wintertime haze. The novel method is universal and can be applied to various haze conditions and different secondary products.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141803868","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}
Volatile organic compounds (VOCs) are ubiquitous in vehicle cabin environments, which can significantly impact the health of drivers and passengers, whereas quick and intelligent prediction methods are lacking. In this study, we firstly analyzed the variations of environmental parameters, VOC levels and potential sources inside a new car during 7 summer workdays, indicating that formaldehyde had the highest concentration and about one third of the measurements exceeded the standard limit for in-cabin air quality. Feature importance analysis reveals that the most important factor affecting in-cabin VOC emission behaviors is the material surface temperature rather than the air temperature. By introducing the attention mechanism and ensemble strategy, we present an LSTM-A-E deep learning model to predict the concentrations of 12 observed typical VOCs, together with other five deep learning models for comparison. By comparing the prediction-observation discrepancies and five evaluation metrics, the LSTM-A-E model demonstrates better performance, which is more consistent with field measurements. Extension of the developed model for predicting the 10-day VOC concentrations in a realistic residence further illustrates its excellent environmental adaptation. This study probes the not-well-explored in-cabin VOC dynamics via observation and deep learning approaches, facilitating rapid prediction and exposure assessment of VOCs in the vehicle micro-environment.
{"title":"Cabin air dynamics: Unraveling the patterns and drivers of volatile organic compound distribution in vehicles.","authors":"Rui Zhang, Minglu Zhao, Hengwei Wang, Haimei Wang, Hui Kong, Keliang Wang, Petros Koutrakis, Shaodan Huang, Jianyin Xiong","doi":"10.1093/pnasnexus/pgae243","DOIUrl":"10.1093/pnasnexus/pgae243","url":null,"abstract":"<p><p>Volatile organic compounds (VOCs) are ubiquitous in vehicle cabin environments, which can significantly impact the health of drivers and passengers, whereas quick and intelligent prediction methods are lacking. In this study, we firstly analyzed the variations of environmental parameters, VOC levels and potential sources inside a new car during 7 summer workdays, indicating that formaldehyde had the highest concentration and about one third of the measurements exceeded the standard limit for in-cabin air quality. Feature importance analysis reveals that the most important factor affecting in-cabin VOC emission behaviors is the material surface temperature rather than the air temperature. By introducing the attention mechanism and ensemble strategy, we present an LSTM-A-E deep learning model to predict the concentrations of 12 observed typical VOCs, together with other five deep learning models for comparison. By comparing the prediction-observation discrepancies and five evaluation metrics, the LSTM-A-E model demonstrates better performance, which is more consistent with field measurements. Extension of the developed model for predicting the 10-day VOC concentrations in a realistic residence further illustrates its excellent environmental adaptation. This study probes the not-well-explored in-cabin VOC dynamics via observation and deep learning approaches, facilitating rapid prediction and exposure assessment of VOCs in the vehicle micro-environment.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11264407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-20eCollection Date: 2024-07-01DOI: 10.1093/pnasnexus/pgae275
Xuan Thang Pham, Yoshifumi Abe, Yasutaka Mukai, Daisuke Ono, Kenji F Tanaka, Yu Ohmura, Hiroaki Wake, Akihiro Yamanaka
Melanin-concentrating hormone-producing neurons (MCH neurons), found mainly in the lateral hypothalamus and surrounding areas, play essential roles in various brain functions, including sleep and wakefulness, reward, metabolism, learning, and memory. These neurons coexpress several neurotransmitters and act as glutamatergic neurons. The contribution of glutamate from MCH neurons to memory- and metabolism-related functions has not been fully investigated. In a mouse model, we conditionally knocked out Slc17a6 gene, which encodes for vesicular glutamate transporter 2 (vGlut2), in the MCH neurons exclusively by using two different methods: the Cre recombinase/loxP system and in vivo genome editing using CRISPR/Cas9. Then, we evaluated several aspects of memory and measured metabolic rates using indirect calorimetry. We found that mice with MCH neuron-exclusive vGlut2 ablation had higher discrimination ratios between novel and familiar stimuli for novel object recognition, object location, and three-chamber tests. In contrast, there was no significant change in body weight, food intake, oxygen consumption, respiratory quotient, or locomotor activity. These findings suggest that glutamatergic signaling from MCH neurons is required to regulate memory, but its role in regulating metabolic rate is negligible.
{"title":"Glutamatergic signaling from melanin-concentrating hormone-producing neurons: A requirement for memory regulation, but not for metabolism control.","authors":"Xuan Thang Pham, Yoshifumi Abe, Yasutaka Mukai, Daisuke Ono, Kenji F Tanaka, Yu Ohmura, Hiroaki Wake, Akihiro Yamanaka","doi":"10.1093/pnasnexus/pgae275","DOIUrl":"10.1093/pnasnexus/pgae275","url":null,"abstract":"<p><p>Melanin-concentrating hormone-producing neurons (MCH neurons), found mainly in the lateral hypothalamus and surrounding areas, play essential roles in various brain functions, including sleep and wakefulness, reward, metabolism, learning, and memory. These neurons coexpress several neurotransmitters and act as glutamatergic neurons. The contribution of glutamate from MCH neurons to memory- and metabolism-related functions has not been fully investigated. In a mouse model, we conditionally knocked out <i>Slc17a6</i> gene, which encodes for vesicular glutamate transporter 2 (vGlut2), in the MCH neurons exclusively by using two different methods: the Cre recombinase/loxP system and in vivo genome editing using CRISPR/Cas9. Then, we evaluated several aspects of memory and measured metabolic rates using indirect calorimetry. We found that mice with MCH neuron-exclusive vGlut2 ablation had higher discrimination ratios between novel and familiar stimuli for novel object recognition, object location, and three-chamber tests. In contrast, there was no significant change in body weight, food intake, oxygen consumption, respiratory quotient, or locomotor activity. These findings suggest that glutamatergic signaling from MCH neurons is required to regulate memory, but its role in regulating metabolic rate is negligible.</p>","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11259978/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-16DOI: 10.1093/pnasnexus/pgae283
M. D. Broda, Petra Borovska, D. Kollenda, Marcel Linka, Naomi de Haas, Samuel de Haas, Benjamin de Haas
The SARS-CoV-2 pandemic has highlighted the importance of contact tracing for epidemiological mitigation. Contact tracing interviews (CTIs) typically rely on episodic memory, which is prone to decline over time. Here, we provide a quantitative estimate of reporting decline for age- and gender-representative samples from the UK and Germany, emulating >15,000 CTIs. We find that the number of reported contacts declines as a power function of recall delay and is significantly higher for younger subjects and for those who used memory aids, such as a scheduler. We further find that these factors interact with delay: Older subjects and those who made no use of memory aids have steeper decline functions. These findings can inform epidemiological modelling and policies in the context of infectious diseases.
{"title":"Estimating the human bottleneck for contact tracing","authors":"M. D. Broda, Petra Borovska, D. Kollenda, Marcel Linka, Naomi de Haas, Samuel de Haas, Benjamin de Haas","doi":"10.1093/pnasnexus/pgae283","DOIUrl":"https://doi.org/10.1093/pnasnexus/pgae283","url":null,"abstract":"\u0000 The SARS-CoV-2 pandemic has highlighted the importance of contact tracing for epidemiological mitigation. Contact tracing interviews (CTIs) typically rely on episodic memory, which is prone to decline over time. Here, we provide a quantitative estimate of reporting decline for age- and gender-representative samples from the UK and Germany, emulating >15,000 CTIs. We find that the number of reported contacts declines as a power function of recall delay and is significantly higher for younger subjects and for those who used memory aids, such as a scheduler. We further find that these factors interact with delay: Older subjects and those who made no use of memory aids have steeper decline functions. These findings can inform epidemiological modelling and policies in the context of infectious diseases.","PeriodicalId":74468,"journal":{"name":"PNAS nexus","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141641710","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}