Hfsp Journal最新文献_第10页

Gene regulatory network inference using out of equilibrium statistical mechanics. 基于非平衡统计力学的基因调控网络推断。

Hfsp Journal Pub Date : 2008-08-01 Epub Date: 2008-07-23 DOI: 10.2976/1.2957743

Arndt Benecke

{"title":"Gene regulatory network inference using out of equilibrium statistical mechanics.","authors":"Arndt Benecke","doi":"10.2976/1.2957743","DOIUrl":"https://doi.org/10.2976/1.2957743","url":null,"abstract":"Spatiotemporal control of gene expression is fundamental to multicellular life. Despite prodigious efforts, the encoding of gene expression regulation in eukaryotes is not understood. Gene expression analyses nourish the hope to reverse engineer effector-target gene networks using inference techniques. Inference from noisy and circumstantial data relies on using robust models with few parameters for the underlying mechanisms. However, a systematic path to gene regulatory network reverse engineering from functional genomics data is still impeded by fundamental problems. Recently, Johannes Berg from the Theoretical Physics Institute of Cologne University has made two remarkable contributions that significantly advance the gene regulatory network inference problem. Berg, who uses gene expression data from yeast, has demonstrated a nonequilibrium regime for mRNA concentration dynamics and was able to map the gene regulatory process upon simple stochastic systems driven out of equilibrium. The impact of his demonstration is twofold, affecting both the understanding of the operational constraints under which transcription occurs and the capacity to extract relevant information from highly time-resolved expression data. Berg has used his observation to predict target genes of selected transcription factors, and thereby, in principle, demonstrated applicability of his out of equilibrium statistical mechanics approach to the gene network inference problem.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":"2 4","pages":"183-8"},"PeriodicalIF":0.0,"publicationDate":"2008-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.2957743","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28140587","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: 11

Molecular motors: a traffic cop within? 分子马达:里面有个交警?

Hfsp Journal Pub Date : 2008-08-01 Epub Date: 2008-07-09 DOI: 10.2976/1.2956447

M A Welte, S P Gross

引用次数: 29

Actomyosin purse strings: renewable resources that make morphogenesis robust and resilient. 肌动球蛋白:可再生资源，使形态发生强健和有弹性。

Hfsp Journal Pub Date : 2008-08-01 Epub Date: 2008-07-23 DOI: 10.2976/1.2955565

Alice Rodriguez-Diaz, Yusuke Toyama, Daniel L Abravanel, John M Wiemann, Adrienne R Wells, U Serdar Tulu, Glenn S Edwards, Daniel P Kiehart

{"title":"Actomyosin purse strings: renewable resources that make morphogenesis robust and resilient.","authors":"Alice Rodriguez-Diaz, Yusuke Toyama, Daniel L Abravanel, John M Wiemann, Adrienne R Wells, U Serdar Tulu, Glenn S Edwards, Daniel P Kiehart","doi":"10.2976/1.2955565","DOIUrl":"https://doi.org/10.2976/1.2955565","url":null,"abstract":"Dorsal closure in Drosophila is a model system for cell sheet morphogenesis and wound healing. During closure two sheets of lateral epidermis move dorsally to close over the amnioserosa and form a continuous epidermis. Forces from the amnioserosa and actomyosin-rich, supracellular purse strings at the leading edges of these lateral epidermal sheets drive closure. Purse strings generate the largest force for closure and occur during development and wound healing throughout phylogeny. We use laser microsurgery to remove some or all of the purse strings from developing embryos. Free edges produced by surgery undergo characteristic responses as follows. Intact cells in the free edges, which previously had no purse string, recoil away from the incision and rapidly assemble new, secondary purse strings. Next, recoil slows, then pauses at a turning point. Following a brief delay, closure resumes and is powered to completion by the secondary purse strings. We confirm that the assembly of the secondary purse strings requires RhoA. We show that alpha-actinin alternates with nonmuscle myosin II along purse strings and requires nonmuscle myosin II for its localization. Together our data demonstrate that purse strings are renewable resources that contribute to the robust and resilient nature of closure.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":"2 4","pages":"220-37"},"PeriodicalIF":0.0,"publicationDate":"2008-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.2955565","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28140590","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: 68

Optical microscopy beyond the diffraction limit. 超出衍射极限的光学显微镜。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-04-18 DOI: 10.2976/1.2912559

Igor I Smolyaninov

{"title":"Optical microscopy beyond the diffraction limit.","authors":"Igor I Smolyaninov","doi":"10.2976/1.2912559","DOIUrl":"https://doi.org/10.2976/1.2912559","url":null,"abstract":"Over the past century the resolution of far-field optical microscopes, which rely on propagating optical modes, was widely believed to be limited because of diffraction to a value on the order of a half-wavelength lambda2 of the light used. Although immersion microscopes had slightly improved resolution on the order of lambda2n, the increased resolution was limited by the small range of refractive indices, n, of available transparent materials. We are experiencing quick demolition of the diffraction limit in optical microscopy. Over the past few years numerous nonlinear optical microscopy techniques based on photoswitching and saturation of fluorescence demonstrated far-field resolution of 20 to 30 nm. The latest exciting example of these techniques has been demonstrated by Huang et al. [Science 319, 810-813 (2008)]. Moreover, recent progress in metamaterials indicates that artificial optical media can be created, which do not exhibit the diffraction limit. Resolution of linear \"immersion\" microscopes based on such metamaterials appears limited only by losses, which can be compensated by gain media. Thus, optical microscopy is quickly moving towards the 10 nm resolution scale, which should bring about numerous revolutionary advances in biomedical imaging.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":"2 3","pages":"129-31"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.2912559","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28215076","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: 15

Fixing the location and dimensions of functional neocortical columns. 确定功能新皮质柱的位置和尺寸。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-05-23 DOI: 10.2976/1.2919545

Henry Markram

{"title":"Fixing the location and dimensions of functional neocortical columns.","authors":"Henry Markram","doi":"10.2976/1.2919545","DOIUrl":"https://doi.org/10.2976/1.2919545","url":null,"abstract":"The quest to understand the way in which neurons interconnect to form circuits that function as a unit began when Ramon y Cajal concluded that axo‐dendritic apposition were too conspicuous to be incidental and proposed that two neurons must be communicating through these points of contact (see Shepherd and Erulkar, 1997, Trends Neurosci., 20, 385–392). Lorente de Nó was probably the first to predict that a defined group of vertically displaced neurons in the neocortex could form functional units (Lorente de Nó, 1938, Physiology of the Nervous System, 20, OUP: 291–330) for which Mountcastle found experimental evidence (see Mountcastle, 1997, Brain, 120, 701–722) and which was ultimately demonstrated by Hubel and Wiesel in their elegant discovery of the orientation selective columns (Hubel and Wiesel, 1959, J. Physiol., 148, 574–591). Until today, however, it is still not clear what shapes functional columns. Anatomical units, as in the barrel cortex, would make it easier to explain, but the neocortex is largely a continuous slab of closely packed neurons from which multiple modules emerge that can overlap partially or even completely on the same anatomical space. Are the columns in fixed anatomical locations or are they dynamically assigned and what anatomical and physiological properties are operating to shape their dimensions? A recent study explores how the geometry of single neurons places structural constraints on the dimensions of columns in the visual cortex (Stepanyants et al., 2008, Cereb Cortex, 18, 13–24).","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":"2 3","pages":"132-5"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.2919545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28215077","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: 21

Kinetic proofreading of gene activation by chromatin remodeling. 染色质重塑对基因活化的动力学校正。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-04-22 DOI: 10.2976/1.2909080

R Blossey, H Schiessel

引用次数: 33

Transistor analogs of emergent iono-neuronal dynamics. 涌现离子-神经元动力学的晶体管模拟。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-04-18 DOI: 10.2976/1.2905393

Guy Rachmuth, Chi-Sang Poon

{"title":"Transistor analogs of emergent iono-neuronal dynamics.","authors":"Guy Rachmuth, Chi-Sang Poon","doi":"10.2976/1.2905393","DOIUrl":"https://doi.org/10.2976/1.2905393","url":null,"abstract":"Neuromorphic analog metal-oxide-silicon (MOS) transistor circuits promise compact, low-power, and high-speed emulations of iono-neuronal dynamics orders-of-magnitude faster than digital simulation. However, their inherently limited input voltage dynamic range vs power consumption and silicon die area tradeoffs makes them highly sensitive to transistor mismatch due to fabrication inaccuracy, device noise, and other nonidealities. This limitation precludes robust analog very-large-scale-integration (aVLSI) circuits implementation of emergent iono-neuronal dynamics computations beyond simple spiking with limited ion channel dynamics. Here we present versatile neuromorphic analog building-block circuits that afford near-maximum voltage dynamic range operating within the low-power MOS transistor weak-inversion regime which is ideal for aVLSI implementation or implantable biomimetic device applications. The fabricated microchip allowed robust realization of dynamic iono-neuronal computations such as coincidence detection of presynaptic spikes or pre- and postsynaptic activities. As a critical performance benchmark, the high-speed and highly interactive iono-neuronal simulation capability on-chip enabled our prompt discovery of a minimal model of chaotic pacemaker bursting, an emergent iono-neuronal behavior of fundamental biological significance which has hitherto defied experimental testing or computational exploration via conventional digital or analog simulations. These compact and power-efficient transistor analogs of emergent iono-neuronal dynamics open new avenues for next-generation neuromorphic, neuroprosthetic, and brain-machine interface applications.","PeriodicalId":55056,"journal":{"name":"Hfsp Journal","volume":"2 3","pages":"156-66"},"PeriodicalIF":0.0,"publicationDate":"2008-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2976/1.2905393","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28217193","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: 47

Brain controlled robots. 大脑控制的机器人。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-05-23 DOI: 10.2976/1.2931144

Mitsuo Kawato

引用次数: 24

Fast fluorescence microscopy for imaging the dynamics of embryonic development. 胚胎发育动态成像的快速荧光显微镜。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-05-13 DOI: 10.2976/1.2907579

Julien Vermot, Scott E Fraser, Michael Liebling

引用次数: 74

The HFSP Journal one year on: moving forward with a new feature. 《HFSP杂志》一年来:以新特色向前迈进。

Hfsp Journal Pub Date : 2008-06-01 Epub Date: 2008-05-12 DOI: 10.1080/19552068.2008.9635743

Arturo Falaschi

引用次数: 0