Benjamin Howes, Manuela González‐Suárez, H. Jensen, L. Anjos, P. Develey, J. Hatfield, J. C. Morante‐Filho, Alexandre Uezu, Cristina Banks‐Leite
{"title":"Deforestation alters species interactions","authors":"Benjamin Howes, Manuela González‐Suárez, H. Jensen, L. Anjos, P. Develey, J. Hatfield, J. C. Morante‐Filho, Alexandre Uezu, Cristina Banks‐Leite","doi":"10.1002/ntls.20220027","DOIUrl":"https://doi.org/10.1002/ntls.20220027","url":null,"abstract":"","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"83 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78108359","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}
Daniel Martín‐Yerga, M. Bahri, M. Curd, Xiangdong Xu, Weiqun Li, T. Burnett, P. Withers, B. Mehdi, N. Browning, P. Unwin
Silicon is a promising negative electrode material for high-energy-density Li-ion batteries (LiBs) but suffers from significant degradation due to the mechanical stress induced by lithiation. Volume expansion and lithiation in Si are strongly anisotropic but associated early interfacial transformations linked to these phenomena and their implications for electrode performance remain poorly understood. Here we develop a novel correlative electrochemical multi-microscopy approach to study local interfacial degradation at the early stages for three different surface orientations of Si single crystals: Si(100), Si(110) and Si(311), after Li-ion electrochemical cycling. The experimental strategy combines scanning electrochemical cell microscopy (SECCM) measurements with subsequently recorded scanning transmission electron microscopy images of high-quality cross sections of Si electrodes, extracted at selected SECCM regions, using a novel Xe + plasma-focused ion beam procedure. These studies reveal significant surface orientation–dependent nanoscale degradation mechanisms that strongly control electrode performance. Si(100) was immune to interfacial degradation showing the best lithiation reversibility, whereas local nanoscale delamination was observed in Si(110) leading to a lower Coulombic efficiency. Continuous electrochemical deactivation of Si(311) was associated with delamination across the whole interface, Li trapping and formation of thick (ca. 60 nm) SiO 2 structures. These results demonstrate surface crystallography to be a critical factor when designing Si-based
{"title":"Link between anisotropic electrochemistry and surface transformations at single‐crystal silicon electrodes: Implications for lithium‐ion batteries","authors":"Daniel Martín‐Yerga, M. Bahri, M. Curd, Xiangdong Xu, Weiqun Li, T. Burnett, P. Withers, B. Mehdi, N. Browning, P. Unwin","doi":"10.1002/ntls.20210607","DOIUrl":"https://doi.org/10.1002/ntls.20210607","url":null,"abstract":"Silicon is a promising negative electrode material for high-energy-density Li-ion batteries (LiBs) but suffers from significant degradation due to the mechanical stress induced by lithiation. Volume expansion and lithiation in Si are strongly anisotropic but associated early interfacial transformations linked to these phenomena and their implications for electrode performance remain poorly understood. Here we develop a novel correlative electrochemical multi-microscopy approach to study local interfacial degradation at the early stages for three different surface orientations of Si single crystals: Si(100), Si(110) and Si(311), after Li-ion electrochemical cycling. The experimental strategy combines scanning electrochemical cell microscopy (SECCM) measurements with subsequently recorded scanning transmission electron microscopy images of high-quality cross sections of Si electrodes, extracted at selected SECCM regions, using a novel Xe + plasma-focused ion beam procedure. These studies reveal significant surface orientation–dependent nanoscale degradation mechanisms that strongly control electrode performance. Si(100) was immune to interfacial degradation showing the best lithiation reversibility, whereas local nanoscale delamination was observed in Si(110) leading to a lower Coulombic efficiency. Continuous electrochemical deactivation of Si(311) was associated with delamination across the whole interface, Li trapping and formation of thick (ca. 60 nm) SiO 2 structures. These results demonstrate surface crystallography to be a critical factor when designing Si-based","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72663482","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}
Yann Delaunois, A. Tits, Q. Grossman, S. Smeets, C. Malherbe, G. Eppe, G. V. van Lenthe, D. Ruffoni, P. Compère
{"title":"Design strategies of the mantis shrimp spike: How the crustacean cuticle became a remarkable biological harpoon","authors":"Yann Delaunois, A. Tits, Q. Grossman, S. Smeets, C. Malherbe, G. Eppe, G. V. van Lenthe, D. Ruffoni, P. Compère","doi":"10.1002/ntls.20220060","DOIUrl":"https://doi.org/10.1002/ntls.20220060","url":null,"abstract":"","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"38 5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77864125","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}
Abstract It has long been known that exons can serve as cis‐ regulatory sequences, such as enhancers. However, the prevalence of such dual‐use of exons and how they evolve remain elusive. Based on our recently predicted, highly accurate large sets of cis ‐regulatory module candidates (CRMCs) and non‐CRMCs in the human genome, we find that exonic transcription factor binding sites (TFBSs) occupy at least a third of the total exon lengths, and 96.7% of genes have exonic TFBSs. Both A/T and C/G in exonic TFBSs are more likely under evolutionary constraints than those in non‐CRMC exons. Exonic TFBSs in codons tend to encode loops rather than more critical helices and strands in protein structures, while exonic TFBSs in untranslated regions (UTRs) tend to avoid positions where known UTR‐related functions are located. Moreover, active exonic TFBSs tend to be in close physical proximity to distal promoters whose genes have elevated transcription levels. These results suggest that exonic TFBSs might be more prevalent than originally thought and likely in dual‐use. We proposed a parsimonious model that well explains the observed evolutionary behaviors of exonic TFBS as well as how a stretch of codons evolve into a TFBS. Key points There are more exonic regulatory sequences in the human genome than originally thought. Exonic transcription factor binding sites are more likely under negative selection or positive selection than counterpart nonregulatory sequences. Exonic transcription factor binding sites tend to be located in genome sequences that encode less critical loops in protein structures, or in less critical parts in 5′ and 3′ untranslated regions.
{"title":"Prevalent use and evolution of exonic regulatory sequences in the human genome","authors":"Jing Chen, Pengyu Ni, Siwen Wu, Meng Niu, Jun‐tao Guo, Zhengsheng Su","doi":"10.1002/ntls.20220058","DOIUrl":"https://doi.org/10.1002/ntls.20220058","url":null,"abstract":"Abstract It has long been known that exons can serve as cis‐ regulatory sequences, such as enhancers. However, the prevalence of such dual‐use of exons and how they evolve remain elusive. Based on our recently predicted, highly accurate large sets of cis ‐regulatory module candidates (CRMCs) and non‐CRMCs in the human genome, we find that exonic transcription factor binding sites (TFBSs) occupy at least a third of the total exon lengths, and 96.7% of genes have exonic TFBSs. Both A/T and C/G in exonic TFBSs are more likely under evolutionary constraints than those in non‐CRMC exons. Exonic TFBSs in codons tend to encode loops rather than more critical helices and strands in protein structures, while exonic TFBSs in untranslated regions (UTRs) tend to avoid positions where known UTR‐related functions are located. Moreover, active exonic TFBSs tend to be in close physical proximity to distal promoters whose genes have elevated transcription levels. These results suggest that exonic TFBSs might be more prevalent than originally thought and likely in dual‐use. We proposed a parsimonious model that well explains the observed evolutionary behaviors of exonic TFBS as well as how a stretch of codons evolve into a TFBS. Key points There are more exonic regulatory sequences in the human genome than originally thought. Exonic transcription factor binding sites are more likely under negative selection or positive selection than counterpart nonregulatory sequences. Exonic transcription factor binding sites tend to be located in genome sequences that encode less critical loops in protein structures, or in less critical parts in 5′ and 3′ untranslated regions.","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135036386","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}
K. Hinrichs, Brianna Blevins, A. Furchner, N. S. Yadavalli, Sergiy Minko, R. Horvath, Markus Mangold
The mid-infrared (mid-IR) anisotropic optical response of a material probes vibrational fingerprints and absorption bands sensitive to order, structure and direction dependent stimuli. Such anisotropic properties play a fundamental role in catalysis, optoelectronic, photonic, polymer and biomedical research and applications. Infrared dual-comb polarimetry (IR-DCP) is introduced as a powerful new spectroscopic method for the analysis of complex dielectric functions and anisotropic samples in the mid-IR range. IR DCP enables novel hyperspectral and time-resolved applications far beyond the technical possibilities of classical Fourier-transform IR (FTIR) approaches. The method unravels structure–spectra relations at high spectral bandwidth (100 cm–1) and short integration times of 65 μ s, with previously unattainable time resolutions for spectral IR polarimetric measurements for potential studies of noncyclic and irreversible processes. The polarimetric capabilities of IR-DCP are demonstrated by investigating an anisotropic inhomogeneous free-standing nanofiber scaffold for neural tissue applications. Polarization sensitive multi-angle dual-comb transmission amplitude and absolute phase measurements (separately for ss-, pp-, ps-and sp-polarized light) allow the in-depth probing of the samples’ orientation dependent vibrational absorption properties. Mid-IR anisotropies can be quickly identified by cross-polarized IR-DCP polarimetry.
{"title":"Mid‐infrared dual‐comb polarimetry of anisotropic samples","authors":"K. Hinrichs, Brianna Blevins, A. Furchner, N. S. Yadavalli, Sergiy Minko, R. Horvath, Markus Mangold","doi":"10.1002/ntls.20220056","DOIUrl":"https://doi.org/10.1002/ntls.20220056","url":null,"abstract":"The mid-infrared (mid-IR) anisotropic optical response of a material probes vibrational fingerprints and absorption bands sensitive to order, structure and direction dependent stimuli. Such anisotropic properties play a fundamental role in catalysis, optoelectronic, photonic, polymer and biomedical research and applications. Infrared dual-comb polarimetry (IR-DCP) is introduced as a powerful new spectroscopic method for the analysis of complex dielectric functions and anisotropic samples in the mid-IR range. IR DCP enables novel hyperspectral and time-resolved applications far beyond the technical possibilities of classical Fourier-transform IR (FTIR) approaches. The method unravels structure–spectra relations at high spectral bandwidth (100 cm–1) and short integration times of 65 μ s, with previously unattainable time resolutions for spectral IR polarimetric measurements for potential studies of noncyclic and irreversible processes. The polarimetric capabilities of IR-DCP are demonstrated by investigating an anisotropic inhomogeneous free-standing nanofiber scaffold for neural tissue applications. Polarization sensitive multi-angle dual-comb transmission amplitude and absolute phase measurements (separately for ss-, pp-, ps-and sp-polarized light) allow the in-depth probing of the samples’ orientation dependent vibrational absorption properties. Mid-IR anisotropies can be quickly identified by cross-polarized IR-DCP polarimetry.","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79685042","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}
Christian T. Haakansson, Peter D. Watson, Timothy R. Corkish, H. T. Robinson, A. McKinley, D. Wild
{"title":"Noncovalent chalcogen and tetrel bonding interactions: Spectroscopic study of halide–carbonyl sulfide complexes","authors":"Christian T. Haakansson, Peter D. Watson, Timothy R. Corkish, H. T. Robinson, A. McKinley, D. Wild","doi":"10.1002/ntls.20220057","DOIUrl":"https://doi.org/10.1002/ntls.20220057","url":null,"abstract":"","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87260976","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}
Vishnu Shankar, Basil Michael, A. Celli, Zhenpeng Zhou, Melanie D. Ashland, R. Tibshirani, M. Snyder, R. Zare
End stage renal disease (ESRD), characterized by cessation in kidney function, has been linked to severe metabolic disturbances, caused by buildup of toxic solutes in blood. To remove these solutes, ESRD patients undergo dialysis. As a proof of concept, we tested whether ESRD-related metabolic signatures can be detected in perspiration samples using a combined methodology. Our rapid methodology involves swabbing a glass slide across the patient’s forehead, detecting the metabolites in the imprint using desorption electrospray ionization mass spectrometry, and identifying the key differences using machine learning methods. Based on collecting 42 healthy and 27 ESRD samples, we find saturated fatty acids are consistently suppressed in ESRD patients, with little change after dialysis. Also, our method enables the detection of uremic solutes, where we find elevated levels of uric acid (6.7 fold higher on average) that sharply decrease after dialysis. Beyond the study of individual metabolites, we find that a lasso model, which selects for 8 m/z fragments from 24,602 detected analytes, achieves area under the curve performance of 0.85 and 0.87 on training (n=52) and validation sets (n=17) respectively. Together, these results suggest that this methodology is promising for detecting signatures relevant for Precision Health. Hosted file VShankar_Sweat_Analysis_Paper_Final.docx available at https://authorea.com/users/509712/ articles/587032-identification-of-end-stage-renal-disease-metabolic-signatures-fromhuman-perspiration
{"title":"Identification of end‐stage renal disease metabolic signatures from human perspiration","authors":"Vishnu Shankar, Basil Michael, A. Celli, Zhenpeng Zhou, Melanie D. Ashland, R. Tibshirani, M. Snyder, R. Zare","doi":"10.1002/ntls.20220048","DOIUrl":"https://doi.org/10.1002/ntls.20220048","url":null,"abstract":"End stage renal disease (ESRD), characterized by cessation in kidney function, has been linked to severe metabolic disturbances, caused by buildup of toxic solutes in blood. To remove these solutes, ESRD patients undergo dialysis. As a proof of concept, we tested whether ESRD-related metabolic signatures can be detected in perspiration samples using a combined methodology. Our rapid methodology involves swabbing a glass slide across the patient’s forehead, detecting the metabolites in the imprint using desorption electrospray ionization mass spectrometry, and identifying the key differences using machine learning methods. Based on collecting 42 healthy and 27 ESRD samples, we find saturated fatty acids are consistently suppressed in ESRD patients, with little change after dialysis. Also, our method enables the detection of uremic solutes, where we find elevated levels of uric acid (6.7 fold higher on average) that sharply decrease after dialysis. Beyond the study of individual metabolites, we find that a lasso model, which selects for 8 m/z fragments from 24,602 detected analytes, achieves area under the curve performance of 0.85 and 0.87 on training (n=52) and validation sets (n=17) respectively. Together, these results suggest that this methodology is promising for detecting signatures relevant for Precision Health. Hosted file VShankar_Sweat_Analysis_Paper_Final.docx available at https://authorea.com/users/509712/ articles/587032-identification-of-end-stage-renal-disease-metabolic-signatures-fromhuman-perspiration","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91360630","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}
C. Schulz, Q. Lemaire, A. Berthier, Amandine Descat, M. Kouach, A. Vercoutter‐Edouart, Ikram El Yazidi‐Belkoura, Stéphan Hardivillé, J. Goossens, P. Lefebvre, T. Lefebvre
{"title":"Control of lipid metabolism by the dynamic and nutrient‐dependent post‐translational modification\u0000 O\u0000 ‐GlcNAcylation","authors":"C. Schulz, Q. Lemaire, A. Berthier, Amandine Descat, M. Kouach, A. Vercoutter‐Edouart, Ikram El Yazidi‐Belkoura, Stéphan Hardivillé, J. Goossens, P. Lefebvre, T. Lefebvre","doi":"10.1002/ntls.20220006","DOIUrl":"https://doi.org/10.1002/ntls.20220006","url":null,"abstract":"","PeriodicalId":74244,"journal":{"name":"Natural sciences (Weinheim, Germany)","volume":"48 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75571761","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}
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