Hfsp Journal最新文献_第6页

Delayed coupling theory of vertebrate segmentation. 脊椎动物分割的延迟耦合理论。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2008-12-10 DOI: 10.2976/1.3027088

Luis G Morelli, Saúl Ares, Leah Herrgen, Christian Schröter, Frank Jülicher, Andrew C Oates

{"title":"Delayed coupling theory of vertebrate segmentation.","authors":"Luis G Morelli, Saúl Ares, Leah Herrgen, Christian Schröter, Frank Jülicher, Andrew C Oates","doi":"10.2976/1.3027088","DOIUrl":"https://doi.org/10.2976/1.3027088","url":null,"abstract":"Rhythmic and sequential subdivision of the elongating vertebrate embryonic body axis into morphological somites is controlled by an oscillating multicellular genetic network termed the segmentation clock. This clock operates in the presomitic mesoderm (PSM), generating dynamic stripe patterns of oscillatory gene-expression across the field of PSM cells. How these spatial patterns, the clock's collective period, and the underlying cellular-level interactions are related is not understood. A theory encompassing temporal and spatial domains of local and collective aspects of the system is essential to tackle these questions. Our delayed coupling theory achieves this by representing the PSM as an array of phase oscillators, combining four key elements: a frequency profile of oscillators slowing across the PSM; coupling between neighboring oscillators; delay in coupling; and a moving boundary describing embryonic axis elongation. This theory predicts that the segmentation clock's collective period depends on delayed coupling. We derive an expression for pattern wavelength across the PSM and show how this can be used to fit dynamic wildtype gene-expression patterns, revealing the quantitative values of parameters controlling spatial and temporal organization of the oscillators in the system. Our theory can be used to analyze experimental perturbations, thereby identifying roles of genes involved in segmentation.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":"3 1","pages":"55-66"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.3027088","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28290649","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}

引用次数: 131

Highly thermosensitive Ca dynamics in a HeLa cell through IP(3) receptors. 通过IP(3)受体在HeLa细胞中的高度热敏钙动力学。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2009-03-04 DOI: 10.2976/1.3073779

Vadim Tseeb, Madoka Suzuki, Kotaro Oyama, Kaoru Iwai, Shin'ichi Ishiwata

引用次数: 52

Fluid dynamics in developmental biology: moving fluids that shape ontogeny. 发育生物学中的流体动力学：塑造个体发育的流动流体。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2008-12-30 DOI: 10.2976/1.3043738

Julyan H E Cartwright, Oreste Piro, Idan Tuval

引用次数: 68

How can mathematics help us explore vertebrate segmentation? 数学如何帮助我们探索脊椎动物的分割?

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2009-01-27 DOI: 10.2976/1.3072371

Ruth E Baker, Santiago Schnell

引用次数: 15

Analysis of the fitness effect of compensatory mutations. 补偿突变的适应效应分析。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2008-12-03 DOI: 10.2976/1.2990075

Liqing Zhang, Layne T Watson

{"title":"Analysis of the fitness effect of compensatory mutations.","authors":"Liqing Zhang, Layne T Watson","doi":"10.2976/1.2990075","DOIUrl":"10.2976/1.2990075","url":null,"abstract":"This paper extends previous work on the Darwinian evolutionary fitness effect of the fixation of deleterious mutations by incorporating compensatory mutations, which are mutations (deleterious by themselves) that ameliorate other deleterious mutations, thus reducing the genetic load of populations. Since having compensatory mutations essentially changes the distributional shapes of deleterious mutations, the effect of compensatory mutations is studied by comparing distributions of deleterious mutations without compensatory mutations to those with compensatory mutations. The effect of effective population size (N(e)), fitness distributional shape, and mutation rate on population fitness reduction is studied. Results indicate that, first, the smaller a population's N(e), the larger the effect of compensatory mutations on fitness recovery, and the compensatory effect increases sharply with decreasing N(e). Second, the larger the squared coefficient of variation in the fitness effect of deleterious mutations, the larger the effect of compensatory mutations. Third, for fixed N(e), the higher the rate of deleterious mutations, the more effective compensatory mutation is in fitness recovery, and this effect is more pronounced for smaller N(e).","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":" ","pages":"47-54"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689613/pdf/HJFOA5-000003-000047_1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40005335","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}

引用次数: 0

Spherical topology in cardiac simulations. 心脏模拟中的球面拓扑。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2009-03-04 DOI: 10.2976/1.3074105

Steffan Puwal, Bradley J Roth, David Garfinkle

引用次数: 0

Active gels as a description of the actin-myosin cytoskeleton. 活性凝胶描述肌动蛋白-肌球蛋白细胞骨架。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2009-01-06 DOI: 10.2976/1.3054712

Jean-François Joanny, Jacques Prost

引用次数: 167

Who moves whom during primitive streak formation in the chick embryo. 在鸡胚的原始条纹形成过程中，谁移动谁。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2009-03-31 DOI: 10.2976/1.3103933

Manli Chuai, Cornelis J Weijer

{"title":"Who moves whom during primitive streak formation in the chick embryo.","authors":"Manli Chuai, Cornelis J Weijer","doi":"10.2976/1.3103933","DOIUrl":"https://doi.org/10.2976/1.3103933","url":null,"abstract":"Gastrulation is a critical stage in the development of all vertebrates. During gastrulation mesendoderm cells move inside the embryo to form the gut, muscles, and skeleton. In amniotes the mesendoderm cells move inside the embryo through a structure known as the primitive streak, extending from the posterior pole anterior through the midline of the embryo. Primitive streak formation involves large scale cell flows of a layer of highly polarized epithelial epiblast cells. The epiblast is separated from a lower layer of hypoblast cells through a well developed basal lamina. Recent experiments in which in vivo extracellular matrix dynamics was followed via labeling with fibronectin specific fluorescent antibodies and time-lapse microscopy have suggested that extracellular matrix dynamics essentially coincides with the observed epiblast cell displacements (Zamir et al., 2008, PLoS Biol 6, e247). These observations raise the important question of who moves whom and where do cells derive traction. We discuss these matters and their implications for our understanding of the mechanisms underlying cell flows during primitive streak formation in the chick embryo.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":" ","pages":"71-6"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.3103933","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40049039","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}

引用次数: 25

Nucleocytoplasmic transport: a thermodynamic mechanism. 核细胞质运输:一种热力学机制。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2009-03-18 DOI: 10.2976/1.3080807

Ronen Benjamine Kopito, Michael Elbaum

{"title":"Nucleocytoplasmic transport: a thermodynamic mechanism.","authors":"Ronen Benjamine Kopito, Michael Elbaum","doi":"10.2976/1.3080807","DOIUrl":"https://doi.org/10.2976/1.3080807","url":null,"abstract":"The nuclear pore supports molecular communication between cytoplasm and nucleus in eukaryotic cells. Selective transport of proteins is mediated by soluble receptors, whose regulation by the small GTPase Ran leads to cargo accumulation in, or depletion from, the nucleus, i.e., nuclear import or nuclear export. We consider the operation of this transport system by a combined analytical and experimental approach. Provocative predictions of a simple model were tested using cell-free nuclei reconstituted in Xenopus egg extract, a system well suited to quantitative studies. We found that accumulation capacity is limited, so that introduction of one import cargo leads to egress of another. Clearly, the pore per se does not determine transport directionality. Moreover, different cargo reach a similar ratio of nuclear to cytoplasmic concentration in steady-state. The model shows that this ratio should in fact be independent of the receptor-cargo affinity, though kinetics may be strongly influenced. Numerical conservation of the system components highlights a conflict between the observations and the popular concept of transport cycles. We suggest that chemical partitioning provides a framework to understand the capacity to generate concentration gradients by equilibration of the receptor-cargo intermediary.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":" ","pages":"130-41"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.3080807","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40049037","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}

引用次数: 31

Throwing a glance at the neural code: rapid information transmission in the visual system. 看一眼神经编码:信息在视觉系统中的快速传递。

Hfsp Journal Pub Date : 2009-01-01 Epub Date: 2008-12-03 DOI: 10.2976/1.3027089

Tim Gollisch

{"title":"Throwing a glance at the neural code: rapid information transmission in the visual system.","authors":"Tim Gollisch","doi":"10.2976/1.3027089","DOIUrl":"https://doi.org/10.2976/1.3027089","url":null,"abstract":"Our visual system can operate at fascinating speeds. Psychophysical experiments teach us that the processing of complex natural images and visual object recognition require a mere split second. Even in everyday life, our gaze seldom rests for long on any particular spot of the visual scene before a sudden movement of the eyes or the head shifts it to a new location. These observations challenge our understanding of how neurons in the visual system of the brain represent, process, and transmit the relevant visual information quickly enough. This article argues that the speed of visual processing provides an adjuvant framework for studying the neural code in the visual system. In the retina, which constitutes the first stage of visual processing, recent experiments have highlighted response features that allow for particularly rapid information transmission. This sets the stage for discussing some of the fundamental questions in the research of neural coding. How do downstream brain regions read out signals from the retina and combine them with intrinsic signals that accompany eye movements? And, how do the neural response features ultimately affect perception and behavior?","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":" ","pages":"36-46"},"PeriodicalIF":0.0,"publicationDate":"2009-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.3027089","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40005334","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}

引用次数: 28