Interface Focus最新文献

{"title":"The social lives of isolates (and small language families): the case of the Northwest Amazon.","authors":"Rik Van Gijn, Sietze Norder, Leonardo Arias, Nicholas Q Emlen, Matheus C B C Azevedo, Allison Caine, Saskia Dunn, Austin Howard, Nora Julmi, Olga Krasnoukhova, Mark Stoneking, Jurriaan Wiegertjes","doi":"10.1098/rsfs.2022.0054","DOIUrl":"10.1098/rsfs.2022.0054","url":null,"abstract":"<p><p>The Americas are home to patches of extraordinary linguistic (genealogical) diversity. These high-diversity areas are particularly unexpected given the recent population of the Americas. In this paper, we zoom in on one such area, the Northwest Amazon, and address the question of how the diversity in this area has persisted to the present. We contrast two hypotheses that claim opposite mechanisms for the maintenance of diversity: the isolation hypothesis suggests that isolation facilitates the preservation of diversity, while the integration hypothesis proposes that conscious identity preservation in combination with contact drives diversity maintenance. We test predictions for both hypotheses across four disciplines: biogeography, cultural anthropology, population genetics and linguistics. Our results show signs of both isolation and integration, but they mainly suggest considerable diversity in how groups of speakers have interacted with their surroundings.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 1","pages":"20220054"},"PeriodicalIF":3.6,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9732644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10551233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Untangling the evolution of body-part terminology in Pano: conservative versus innovative traits in body-part lexicalization.","authors":"Roberto Zariquiey,&nbsp;Javier Vera,&nbsp;Simon J Greenhill,&nbsp;Pilar Valenzuela,&nbsp;Russell J Gray,&nbsp;Johann-Mattis List","doi":"10.1098/rsfs.2022.0053","DOIUrl":"10.1098/rsfs.2022.0053","url":null,"abstract":"<p><p>Although language-family specific traits which do not find direct counterparts outside a given language family are usually ignored in quantitative phylogenetic studies, scholars have made ample use of them in qualitative investigations, revealing their potential for identifying language relationships. An example of such a family specific trait are body-part expressions in Pano languages, which are often lexicalized forms, composed of bound roots (also called body-part prefixes in the literature) and non-productive derivative morphemes (called here body-part formatives). We use various statistical methods to demonstrate that whereas body-part roots are generally conservative, body-part formatives exhibit diverse chronologies and are often the result of recent and parallel innovations. In line with this, the phylogenetic structure of body-part roots projects the major branches of the family, while formatives are highly non-tree-like. Beyond its contribution to the phylogenetic analysis of Pano languages, this study provides significative insights into the role of grammatical innovations for language classification, the origin of morphological complexity in the Amazon and the phylogenetic signal of specific grammatical traits in language families.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 1","pages":"20220053"},"PeriodicalIF":4.4,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9732641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9227689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan).","authors":"Leonardo Arias, Nicholas Q Emlen, Sietze Norder, Nora Julmi, Magdalena Lemus Serrano, Thiago Chacon, Jurriaan Wiegertjes, Austin Howard, Matheus C B C Azevedo, Allison Caine, Saskia Dunn, Mark Stoneking, Rik Van Gijn","doi":"10.1098/rsfs.2022.0056","DOIUrl":"10.1098/rsfs.2022.0056","url":null,"abstract":"<p><p>Northwestern Amazonia is home to a great degree of linguistic diversity, and the human societies in that region are part of complex networks of interaction that predate the arrival of Europeans. This study investigates the population and language contact dynamics between two languages found within this region, Yukuna and Tanimuka, which belong to the Arawakan and Tukanoan language families, respectively. We use evidence from linguistics, ethnohistory, ethnography and population genetics to provide new insights into the contact dynamics between these and other human groups in NWA. Our results show that the interaction between these groups intensified in the last 500 years, to the point that it is difficult to differentiate between them genetically. However, this close interaction has led to more substantial contact-induced language changes in Tanimuka than in Yukuna, consistent with a scenario of language shift and asymmetrical power relations.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 1","pages":"20220056"},"PeriodicalIF":4.4,"publicationDate":"2022-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9732642/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10551232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: <i>in vitro</i> and <i>in vivo</i>.","authors":"Sarah Lecinski, Jack W Shepherd, Kate Bunting, Lara Dresser, Steven D Quinn, Chris MacDonald, Mark C Leake","doi":"10.1098/rsfs.2022.0042","DOIUrl":"10.1098/rsfs.2022.0042","url":null,"abstract":"<p><p>In eukaryotes, intracellular physico-chemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion and protein folding. However, mapping crowding and viscoelasticity in living cells remains challenging. One approach uses passive rheology in which diffusion of exogenous fluorescent particles internalized in cells is tracked and physico-chemical properties inferred from derived mean square displacement relations. Recently, the crGE2.3 Förster resonance energy transfer biosensor was developed to quantify crowding in cells, though it is unclear how this readout depends on viscoelasticity and the molecular weight of the crowder. Here, we present correlative, multi-dimensional data to explore diffusion and molecular crowding characteristics of molecular crowding agents using super-resolved fluorescence microscopy and ensemble time-resolved spectroscopy. We firstly characterize <i>in vitro</i> and then apply these insights to live cells of budding yeast <i>Saccharomyces cerevisiae</i>. It is to our knowledge the first time this has been attempted. We demonstrate that these are usable both <i>in vitro</i> and in the case of endogenously expressed sensors in live cells. Finally, we present a method to internalize fluorescent beads as <i>in situ</i> viscoelasticity markers in the cytoplasm of live yeast cells and discuss limitations of this approach including impairment of cellular function.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"12 6","pages":"20220042"},"PeriodicalIF":3.6,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9560789/pdf/rsfs.2022.0042.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10589516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: theme issue on complex rheology in biological systems","authors":"C. Schaefer, G. McKinley, T. McLeish","doi":"10.1098/rsfs.2022.0058","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0058","url":null,"abstract":"Recent years have witnessed unprecedented growth in interdisciplinary engagement and collaboration of physical and life sciences, to which the very existence of the Royal Society Journal ‘Interface Focus’ testifies. The subject of rheology itself brings together physics, chemistry, chemical engineering, mathematics and computing. In the biological context, the interdisciplinarity becomes even richer. Cell biology in plants, animals and prokaryotes is usually described in terms of components, biochemical networks and signalling. Yet local flows, and deformations of the entire cell as well as its individual parts [1,2], are essential to function. Questions on such mechanical properties and phenomena are rarely addressed. At the tissue biology level, there are new challenges especially in the highly nonlinear range of deformations [3,4], coupling to smaller structures, and pathologies. Vascular biology (e.g. haematology) is clearly a field where rheology is vital [5], but other key rheological control problems emerge in digestive [6] and reproductive biology [7]. Other biological flows contain rheologically induced structural or phase transitions, and the understanding of how biological fluids and soft solids flow and deform is a key scientific area within this collaboration of physical and life sciences (blood [8], the cytosol, silk protein solutions [9], saliva, mucus [10], synovial fluid, biofilms [11–13], tissue buckling [14], bacterial rheotaxis [15] and E. coli bacteria swimming in media with liquid crystalline order [16] are just some examples [17]). This theme issue on ‘Complex rheology in biological systems’ brings together biorheological work across distinct disciplines in the physics and life sciences. Below,we summarize these contributions and extract common ideas andmethodologies. We hope this will promote their adoption across the field, and thereby accelerate the resolution of outstanding and unresolved problems in biorheology. Beyond that, this theme issue aims to raise awareness of new research questions that have not yet been fully formulated in some of the sub-fields, yet are key to awider understanding. As is generally true in the ‘physics of livingmatter’movement, the biological examples point to new physics and chemistry that is not evident in non-biological systems.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":" ","pages":""},"PeriodicalIF":4.4,"publicationDate":"2022-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46397082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical modelling of oxygen transport in a muscle-on-chip device.","authors":"David Hardman,&nbsp;Manh-Louis Nguyen,&nbsp;Stéphanie Descroix,&nbsp;Miguel O Bernabeu","doi":"10.1098/rsfs.2022.0020","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0020","url":null,"abstract":"<p><p>Muscle-on-chip devices aim to recapitulate the physiological characteristics of <i>in vivo</i> muscle tissue and so maintaining levels of oxygen transported to cells is essential for cell survival and for providing the normoxic conditions experienced <i>in vivo</i>. We use finite-element method numerical modelling to describe oxygen transport and reaction in a proposed three-dimensional muscle-on-chip bioreactor with embedded channels for muscle cells and growth medium. We determine the feasibility of ensuring adequate oxygen for muscle cell survival in a device sealed from external oxygen sources and perfused via medium channels. We investigate the effects of varying elements of the bioreactor design on oxygen transport to optimize muscle tissue yield and maintain normoxic conditions. Successful co-culturing of muscle cells with motor neurons can boost muscle tissue function and so we estimate the maximum density of seeded neurons supported by oxygen concentrations within the bioreactor. We show that an enclosed bioreactor can provide sufficient oxygen for muscle cell survival and growth. We define a more efficient arrangement of muscle and perfusion chambers that can sustain a predicted 50% increase in maximum muscle volume per perfusion vessel. A study of simulated bioreactors provides functions for predicting bioreactor designs with normoxic conditions for any size of perfusion vessel, muscle chamber and distance between chambers.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"12 5","pages":"20220020"},"PeriodicalIF":4.4,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9152064","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Current strategies with implementation of three-dimensional cell culture: the challenge of quantification.","authors":"Jonathan Temple,&nbsp;Eirini Velliou,&nbsp;Mona Shehata,&nbsp;Raphaël Lévy","doi":"10.1098/rsfs.2022.0019","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0019","url":null,"abstract":"<p><p>From growing cells in spheroids to arranging them on complex engineered scaffolds, three-dimensional cell culture protocols are rapidly expanding and diversifying. While these systems may often improve the physiological relevance of cell culture models, they come with technical challenges, as many of the analytical methods used to characterize traditional two-dimensional (2D) cells must be modified or replaced to be effective. Here we review the advantages and limitations of quantification methods based either on biochemical measurements or microscopy imaging. We focus on the most basic of parameters that one may want to measure, the number of cells. Precise determination of this number is essential for many analytical techniques where measured quantities are only meaningful when normalized to the number of cells (e.g. cytochrome p450 enzyme activity). Thus, accurate measurement of cell number is often a prerequisite to allowing comparisons across different conditions (culturing conditions or drug and treatment screening) or between cells in different spatial states. We note that this issue is often neglected in the literature with little or no information given regarding how normalization was performed, we highlight the pitfalls and complications of quantification and call for more accurate reporting to improve reproducibility.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"12 5","pages":"20220019"},"PeriodicalIF":4.4,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9205780","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential of stem cell seeded three-dimensional scaffold for regeneration of full-thickness skin wounds.","authors":"Irfan Khan,&nbsp;Marium Naz Siddiqui,&nbsp;Fatima Jameel,&nbsp;Rida-E-Maria Qazi,&nbsp;Asmat Salim,&nbsp;Shazmeen Aslam,&nbsp;Midhat Batool Zaidi","doi":"10.1098/rsfs.2022.0017","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0017","url":null,"abstract":"<p><p>Hypoxic wounds are tough to heal and are associated with chronicity, causing major healthcare burden. Available treatment options offer only limited success for accelerated and scarless healing. Traditional skin substitutes are widely used to improve wound healing, however, they lack proper vascularization. Mesenchymal stem cells (MSCs) offer improved wound healing; however, their poor retention, survival and adherence at the wound site negatively affect their therapeutic potential. The aim of this study is to enhance skin regeneration in a rat model of full-thickness dermal wound by transplanting genetically modified MSCs seeded on a three-dimensional collagen scaffold. Rat bone marrow MSCs were efficiently incorporated in the acellular collagen scaffold. Skin tissues with transplanted subcutaneous scaffolds were histologically analysed, while angiogenesis was assessed both at gene and protein levels. Our findings demonstrated that three-dimensional collagen scaffolds play a potential role in the survival and adherence of stem cells at the wound site, while modification of MSCs with jagged one gene provides a conducive environment for wound regeneration with improved proliferation, reduced inflammation and enhanced vasculogenesis. The results of this study represent an advanced targeted approach having the potential to be translated in clinical settings for targeted personalized therapy.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"12 5","pages":"20220017"},"PeriodicalIF":4.4,"publicationDate":"2022-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372646/pdf/rsfs.2022.0017.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9981139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An insight into the iPSCs-derived two-dimensional culture and three-dimensional organoid models for neurodegenerative disorders.","authors":"Anushka Bhargava, Ana M Sandoval Castellanos, Sonali Shah, Ke Ning","doi":"10.1098/rsfs.2022.0040","DOIUrl":"10.1098/rsfs.2022.0040","url":null,"abstract":"<p><p>The use of induced pluripotent stem cells (iPSCs) is a promising approach when used as models to study neurodegenerative disorders (NDDs) <i>in vitro</i>. iPSCs have been used in <i>in vitro</i> two-dimensional cultures; however, these two-dimensional cultures do not mimic the physiological three-dimensional cellular environment. The use of iPSCs-derived three-dimensional organoids has risen as a powerful alternative to using animal models to study NDDs. These iPSCs-derived three-dimensional organoids can resemble the complexity of the tissue of interest, making it an approachable, cost-effective technique, to study NDDs in an ethical manner. Furthermore, the use of iPSCs-derived organoids will be an important tool to develop new therapeutics and pharmaceutics to treat NDDs. Herein, we will highlight how iPSCs-derived two-dimensional cultures and three-dimensional organoids have been used to study NDDs, as well as the advantages and disadvantages of both techniques.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"12 5","pages":"20220040"},"PeriodicalIF":3.6,"publicationDate":"2022-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372641/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9152058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"'Cloudbuster': a Python-based open source application for three-dimensional reconstruction and quantification of stacked biological imaging samples.","authors":"A Rohwedder, S Knipp, F O Esteves, M Hale, S E Ketchen, D Treanor, A Brüning-Richardson","doi":"10.1098/rsfs.2022.0016","DOIUrl":"10.1098/rsfs.2022.0016","url":null,"abstract":"<p><p>Three-dimensional (3D) spheroid cultures are generating increasing interest in cancer research, e.g. for the evaluation of pharmacological effects of novel small molecule inhibitors. This is mainly due to the fact that such 3D structures reflect physiological characteristics of tumours and the cellular microenvironments they reside in more faithfully than two-dimensional (2D) cell cultures; in addition, they allow the reduction of animal experiments while providing significantly relevant human-based models. Quantification of such organoid structures as well as the mainly slice-based acquisition and thus forced 2D representation of 3D spheroids provide a challenge for the interpretation of the associated generated data. Here, we provide a novel open-source workflow to reconstruct a 3D entity from slice-recorded microscopical images with or without treatment with anti-migratory small molecule inhibitors. This reconstruction produces distinct point clouds as basis for subsequent comparison of basic readout parameters using average computer processor, memory and graphics resources within an acceptable time frame. We were able to validate the usefulness of this workflow using 3D data generated by various imaging techniques, including <i>z</i>-stacks from confocal microscopy and histochemically labelled spheroid sectioning, and demonstrate the possibility to accurately characterize inhibitor effects in great detail.</p>","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"12 5","pages":"20220016"},"PeriodicalIF":3.6,"publicationDate":"2022-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372645/pdf/rsfs.2022.0016.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9981138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}