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structural organization

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Articles
Emerg Top Life Sci (2019) 3 (5): 579–586.
Published: 10 September 2019
... biology succeeded in reconstructing complex synthetic in vitro metabolic networks (SIVMNs) from individual proteins in a defined fashion bottom-up. In this review, we will highlight some examples of SIVMNs and discuss how the further advancement of SIVMNs will require the structural organization...
Articles
Emerg Top Life Sci (2018) 2 (5): 677–680.
Published: 21 December 2018
...Armando del Río Hernández; Samuel F. H. Barnett; Pakorn Kanchanawong To understand how complex machines perform their functions, it is essential to map out the ‘blueprints’ of how their internal components are organized. Focal adhesions (FAs) are complex mechanobiological structures involved...
Images
Molecular <b>organization</b> and <b>structure</b> of proteins from the tubulin superfami...
Published: 14 December 2018
Figure 3. Molecular organization and structure of proteins from the tubulin superfamily. ( a ) Domain organization and comparison between the three principle families: tubulin, FtsZ and CetZ. The common colours represent approximate regions of the primary sequences that show high structural More
Images
Schematic representation of the chemotaxis system and its signaling cascade...
Published: 14 November 2018
complex, resulting in a change in the direction of rotation. In archaea, CheY requires the presence of CheF in order to bind to the archaellum. The exact composition and structural organization of the archaeal switch complex is yet not resolved. MCP, methyl-accepting chemotaxis protein; OM, outer membrane More
Articles
Emerg Top Life Sci (2018) 2 (4): 647–657.
Published: 14 December 2018
... of the distribution, sequence and structural organization points to a far more complex scenario in archaea. Recent studies revealed that the SmAP family plays a role in important biological processes. These activities go beyond the RNA chaperone function of the bacterial Sm-like protein variant Hfq, which was also...
Articles
Emerg Top Life Sci (2017) 1 (6): 675–683.
Published: 22 December 2017
... acid sequences of putative single-enzyme TPPs from >40 organisms were identified and clustered into three different groups based on obvious differences in structural topologies [ 30 ]. Although the three-dimensional crystal structures of several single-enzyme TPPs from Thermoplasma acidophilum...
Articles
Emerg Top Life Sci (2019) 3 (2): 233–243.
Published: 03 May 2019
... through changes in the elevation, slope and regularity of the size spectrum, exposing mechanistic questions about integrated ecosystem structure, as well as how organism physiology and ecological interactions respond to multiple climatic stressors. Despite its application by ecosystem modellers...
Images
Distribution of members of the archaeal Lsm protein family within the DPANN...
Published: 14 December 2018
of adjacent genes were adjusted to a uniform width. The distances between genes were maintained and the gene products can be inferred from the color code provided below. Organisms for which crystal structures of their SmAPs or Hfq-like-SmAPs exist are in bold letters. Note: although Sulfolobus solfataricus More
Articles
Emerg Top Life Sci (2020) 4 (6): 677–689.
Published: 24 November 2020
... banking. These unique MSC properties are attractive to provide effective new cell-based therapies for unmet medical needs. Currently, the infusion of suspended MSCs is accepted as a promising therapy to treat systemic inflammatory diseases. However, low cell engraftment/retention in target organs and off...
Articles
Emerg Top Life Sci (2020) 4 (2): 229–240.
Published: 04 September 2020
...? Ecological intensification harnesses ecological processes to increase food production per area through management processes that often diversify croplands to support beneficial organisms supplying these services. By adding more diverse vegetation back into landscapes, the agricultural matrix can also become...
Articles
Emerg Top Life Sci (2019) 3 (5): 615–622.
Published: 18 October 2019
... developed for several applications, including the controlled release of therapeutic agents and the repair of damaged organs. Current goals include the ability to manipulate synthetic tissues by remote signaling and the formation of hybrid structures with fabricated or natural living tissues...
Articles
Emerg Top Life Sci (2019) 3 (5): 477–482.
Published: 04 September 2019
... comprising many subunits, for structural and mechanistic studies. First introduced in 2004, MultiBac is now in use in many laboratories worldwide, accelerating research programmes in academia and industry. We have continuously optimized our MultiBac system, providing customized reagents and standard...
Articles
Emerg Top Life Sci (2019) 3 (5): 587–595.
Published: 28 August 2019
...Friedrich C. Simmel One approach towards the creation of bottom-up synthetic biological systems of higher complexity relies on the subcompartmentalization of synthetic cell structures using artificially generated organelles — roughly mimicking the architecture of eukaryotic cells. Organelles create...
Articles
Emerg Top Life Sci (2019) 3 (4): 357–369.
Published: 06 August 2019
...J. Harry Caufield; Peipei Ping Protein–protein interactions, or PPIs, constitute a basic unit of our understanding of protein function. Though substantial effort has been made to organize PPI knowledge into structured databases, maintenance of these resources requires careful manual curation. Even...
Articles
Emerg Top Life Sci (2018) 2 (4): 459–468.
Published: 22 November 2018
...Nicholas P. Robinson; Corinna Bang; Ruth A. Schmitz Archaea, the third domain of life containing unique membrane composition and highly diverse cell wall structures, were only recognized 40 years ago. Initially identified in extreme environments, they are currently recognized as organisms...
Articles
Emerg Top Life Sci (2018) 2 (2): 289–298.
Published: 29 June 2018
..., low-latitude glaciation, potential changes in the redox structure of the global ocean, and the origin and diversification of animal life. How these different events related to one another remains an active area of research, particularly how these environmental changes influenced, and were influenced...
Articles
Emerg Top Life Sci (2017) 1 (1): 23–30.
Published: 04 April 2017
...Daniel Walker; Paul Williams The ability of bacterial cells to synchronize their behaviour through quorum sensing (QS) regulatory networks enables bacterial populations to mount co-operative responses against competing micro-organisms and host immune defences and to adapt to environmental...
Images
<b>Organization</b> of some multidomain proteins involved in mechanotransduction. ...
Published: 21 December 2018
Figure 3. Organization of some multidomain proteins involved in mechanotransduction. ( A ) Schematics of several key proteins involved in the ECM–myosin pathway, all shown in their inhibited form. Intergrins form heterodimeric transmembrane complexes and link ECM to talin. Talin attaches between More
Images
Amino acid sequence conservation and three-dimensional fold of TPP enzymes ...
Published: 22 December 2017
Figure 1. Amino acid sequence conservation and three-dimensional fold of TPP enzymes from different domains of life (left) and different parasitic nematode species (right). ( A ) Multiple sequence alignments with ( B ) amino acid conservation mapped onto the TPP structures of T. acidophilum More
Articles
Emerg Top Life Sci (2019) 3 (5): 433–434.
Published: 11 November 2019
... ) 10.1042/ETLS20190103 18 Erb , T.J. ( 2019 ) Structural organization of biocatalytic systems: the next dimension of synthetic metabolism . Emerg. Top. Life Sci. 3 ( 5 ) 10.1042/ETLS20190015 19 Simmel , F.C. ( 2019 ) Synthetic organelles . Emerg. Top. Life Sci. 3 ( 5 ) 10.1042...
Images
Discoidal and filamentous <b>structures</b> offer a better scaling of surface area...
Published: 28 August 2019
Figure 2. Discoidal and filamentous structures offer a better scaling of surface area with volume than spheres. Graph showing the dependence of the surface-to-volume ratio on volume of spherical (black line) and cylindrical (yellow, cyan, green and orange lines) compartments. Arrows on the black More
Articles
Emerg Top Life Sci (2021) 5 (1): 89–101.
Published: 08 January 2021
... to be a powerful approach to monitor the structural organization and dynamics of proteins and membrane-mimetic systems. We have provided a review of recent literature on the applications of REES to get information on dynamic insights into protein structure. Furthermore, we have provided examples of studies using...
Articles
Emerg Top Life Sci (2018) 2 (4): 535–546.
Published: 14 November 2018
... complex, resulting in a change in the direction of rotation. In archaea, CheY requires the presence of CheF in order to bind to the archaellum. The exact composition and structural organization of the archaeal switch complex is yet not resolved. MCP, methyl-accepting chemotaxis protein; OM, outer membrane...
Images
Time chart highlighting the position of the rise of algae (dashed red line)...
Published: 29 June 2018
) the rise of algae, recording a long-term average increase by a factor of four [ 61 ]. ( d ) Relative abundances of the steranes cholestane (red), ergostane (blue) and stigmastane (green) through time [ 22 ]. ( e ) First appearances of fossils in the geological record and radiation of organism groups (data More
Images
MultiBac applications.  The MultiBac system is depicted schematically in th...
Published: 04 September 2019
structures of samples produced using MultiBac is shown on the left, marked by their Protein Data Bank identifier (PDB-ID). 6GEJ, SWR1-nucleosome complex [ 25 ]; 6F3T, human TFIID subcomplex TAF5–TAF6–TAF9 [ 35 ]; 6HLP, human neurokinin 1 receptor GPCR [ 36 ]; 6R8F, human BRISC–SHMT2 complex [ 37 ]; 6QJ4 More
Articles
Emerg Top Life Sci (2019) 3 (5): 567–571.
Published: 04 September 2019
... [ 8 ]. While liquid–liquid phase separation in cells, as observed in membrane-less organelles, is also rapidly gaining significance in extant biology [ 9 – 11 ], coacervates have primarily been utilised by the synthetic cell community for their structural features and ability to effectively sequester...
Articles
Emerg Top Life Sci (2018) 2 (2): 201–212.
Published: 09 August 2018
... are interpreted on the basis of morphology as early members of extant phyla rather than stem representatives of larger groups such as Deuterostomia, Protostomia, Bilateria or even Metazoa [ 3 ]. Most skeletons combine minerals with structural organic matter, where the physiological cost of producing...
Articles
Emerg Top Life Sci (2021) 5 (2): 203–220.
Published: 23 February 2021
.../j.molcel.2013.01.029 17 Rajabi , K. , Ashcroft , A.E. and Radford , S.E. ( 2015 ) Mass spectrometric methods to analyze the structural organization of macromolecular complexes . Methods 89 , 13 – 21 10.1016/j.ymeth.2015.03.004 18 Zhang , Y. , Fonslow , B.R. , Shan...
Articles
Emerg Top Life Sci (2020) 4 (3): 265–280.
Published: 16 June 2020
... 66 Souquere , S. , Beauclair , G. , Harper , F. , Fox , A. and Pierron , G. ( 2010 ) Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies . Mol. Biol. Cell 21 , 4020 – 4027 10.1091/mbc.e10-08-0690 67...
Articles
Emerg Top Life Sci (2020) 4 (2): 111–118.
Published: 24 August 2020
... , A. and Holcman , D. ( 2017 ) Polymer physics of nuclear organization and function . Phys. Rep. 678 , 1 – 83 10.1016/j.physrep.2017.02.002 26 Tjong , H. , Li , W. , Kalhor , R. , Dai , C. , Hao , S. , Gong , K. et al. ( 2016 ) Population- based 3D genome structure...
Articles
Emerg Top Life Sci (2021) ETLS20210231.
Published: 20 December 2021
... have been replaced with other organisms [ 2 ]. However, while the majority of these so called ‘regime’ or ‘phase’ shifts have reported changes from coral to algal dominance, other outcomes are possible including the dominance of a range of animal groups. While the shifts to algal dominance on coral...
Articles
Emerg Top Life Sci (2020) 4 (2): 119–127.
Published: 07 September 2020
... ]. The understanding of structural features of thermophilic enzymes has supported DEE to improve enzyme thermoresistance [ 37 ], activity at cold temperatures [ 38 , 39 ] and tolerance to higher organic solvent contents [ 40–42 ]. Two main structural features of thermoresistant enzymes (increased core packing...
Articles
Emerg Top Life Sci (2020) 4 (3): 247–261.
Published: 13 October 2020
... of condensation in cytoskeletal organization. In this review, we highlight how the interplay between polymerization and condensation leads to the formation of the cytoskeleton. Correspondence: Tina Wiegand ( wiegand@mpi-cbg.de ) The cellular cytoskeleton is a dynamic structure consisting of filaments...
Articles
Emerg Top Life Sci (2020) 4 (2): 191–206.
Published: 15 June 2020
..., or on, the developing mesentery ( Figure 4 ) [ 24 ]. This topographical relationship is of considerable importance and is retained into adulthood where the mesentery is the primary mechanism by which all abdominal digestive organs are centrally connected [ 29 ]. Whilst these organs developed in a midline structure (i.e...
Articles
Emerg Top Life Sci (2022) ETLS20210237.
Published: 12 January 2022
...Jeffrey S. Shima; Craig W. Osenberg; Suzanne H. Alonzo; Erik G. Noonburg; Stephen E. Swearer The lunar cycle drives variation in nocturnal brightness. For the epipelagic larvae of coral reef organisms, nocturnal illumination may have widespread and underappreciated consequences. At sea, the onset...
Articles
Emerg Top Life Sci (2021) 5 (2): 239–248.
Published: 04 March 2021
... image segmentation and machine learning at the agricultural, organ, and cellular scales in plants. We show how the methodologies for segmentation and classification differ due to the diversity of physical characteristics found at these different scales. We also discuss the hardware technologies most...
Articles
Emerg Top Life Sci (2018) 2 (4): 607–618.
Published: 22 November 2018
.... Deviations from the genetic code known in most organisms have been gathered under two different types termed ‘reassignment’ and ‘recoding’ [ 3 ]. In specialised niches, such as certain mitochondria [ 4 , 5 ], the meaning of particular codons is reassigned such that wherever that codon occurs it has the new...
Articles
Emerg Top Life Sci (2021) 5 (2): 231–237.
Published: 05 February 2021
...Joseph M. Jez; Christopher N. Topp; Megan L. Matthews; Amy Marshall-Colón Plants are complex organisms that adapt to changes in their environment using an array of regulatory mechanisms that span across multiple levels of biological organization. Due to this complexity, it is difficult to predict...
Articles
Emerg Top Life Sci (2021) 5 (3): 475–485.
Published: 19 April 2021
...), geophysical survey (e.g. ground-penetrating radar, GPR), the detection of volatile organic compounds produced by decomposition (either using instrumentation/mass spectrometry or cadaver dogs) and finally, observed changes in vegetation structure. To date, there have been very few detailed studies that have...
Articles
Emerg Top Life Sci (2018) 2 (4): 547–559.
Published: 14 December 2018
...Figure 3. Molecular organization and structure of proteins from the tubulin superfamily. ( a ) Domain organization and comparison between the three principle families: tubulin, FtsZ and CetZ. The common colours represent approximate regions of the primary sequences that show high structural...
Articles
Emerg Top Life Sci (2019) 3 (5): 551–558.
Published: 04 September 2019
... but an important task. In this short review, I discuss several approaches how to realize division of cell-like compartments, from simply relying on the physical principles of destabilization by growth, or applying external forces, to the design of self-assembling and self-organizing machineries that may...
Articles
Emerg Top Life Sci (2018) 2 (4): 453–458.
Published: 14 December 2018
... CRISPR evolution At the end of the 1960s, a (now-outdated) five-kingdom system was proposed to classify all forms of cellular life, dividing organisms into either the prokaryotic monera (the eubacteria, more commonly referred to as bacteria) or alternatively into the eukaryotic divisions...
Articles
Emerg Top Life Sci (2021) 5 (2): 337–347.
Published: 11 May 2021
... restores continuous vegetative cover without interfering with cash-crop productivity ( Figure 1C ). The PGC concept is potentially applicable to annual and perennial, organic and conventional, cash-crop production. Perennial groundcovers are already used in orchards[ 6 ], have been trialed in vegetable...
Articles
Emerg Top Life Sci (2018) 2 (4): 581–593.
Published: 22 November 2018
... made on the understanding of structure–function relationships in in vitro studies, in vivo studies are lacking and little is known about the exact mechanisms of action and the identity of substrates. To this end, basic tools are available for the genetic study of several archaeal model organisms...
Articles
Emerg Top Life Sci (2018) 2 (2): 173–180.
Published: 26 July 2018
..., and protection from viral attack do not explain both the materials used and the complexity of the forms built by organisms [ 44 ]. Thus, our current understanding of the purpose of biomineralized structures in modern clades indicates that protection from predation is a major factor in the evolution...
Articles
Emerg Top Life Sci (2018) 2 (1): 1–8.
Published: 06 February 2018
.... MicroED has been successful at determining structures of proteins, protein complexes, oligopeptides, drugs and small organic molecules as well as material science samples such as hydrated gold clusters. CMOS complementary metal–oxide–semiconductor cryoEM cryo-electron microscopy cryo...
Articles
Emerg Top Life Sci (2019) 3 (5): 573–578.
Published: 01 November 2019
... of these reactions is important to elucidate the phenomenon of life [ 1 , 2 ]. While performing experiments on cells, however, the simultaneous interaction of structural components, as well as various catalysts, has been an obstacle, which has led to artifacts or unknown protein activities that hinder clarification...
Articles
Emerg Top Life Sci (2019) 3 (5): 559–566.
Published: 20 August 2019
... millions of biomolecules self-organize to form autonomous self-sustaining systems. Systematically working on simplified minimal systems may help to disentangle some of the enormous complexity. In this perspective, we reflect on a possible route towards making synthetic cells, which we provisionally...
Articles
Emerg Top Life Sci (2020) 4 (6): 613–625.
Published: 17 November 2020
...Zi Hong Mok; Gordon Proctor; Maya Thanou The emergence of nanomaterials for dental treatments is encouraged by the nanotopography of the tooth structure, together with the promising benefits of nanomedicine. The use of nanoparticles in dentistry, also termed as ‘nanodentistry', has manifested...
Articles
Emerg Top Life Sci (2021) 5 (4): 507–517.
Published: 15 September 2021
.... ( 2017 ) Guided self-organization and cortical plate formation in human brain organoids . Nat. Biotechnol. 35 , 659 – 666 10.1038/nbt.3906 17 George , J. , Hsu , C.-C. , Nguyen , L.T.B. , Ye , H. and Cui , Z. ( 2020 ) Neural tissue engineering with structured...