scholarly journals Structural and Mechanistic Features of ClyA-Like α-Pore-Forming Toxins

Toxins ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 343 ◽  
Author(s):  
Bastian Bräuning ◽  
Michael Groll
Keyword(s):  
Crystal Structures ◽  
Functional Traits ◽  
Pore Formation ◽  
Research Topic ◽  
Protein Family ◽  
Complex Structures ◽  
Open Questions ◽  
Technological Advances ◽  
Broad Variety

Recent technological advances have seen increasing numbers of complex structures from diverse pore-forming toxins (PFT). The ClyA family of α-PFTs comprises a broad variety of assemblies including single-, two- and three-component toxin systems. With crystal structures available for soluble subunits of all major groups in this extended protein family, efforts now focus on obtaining molecular insights into physiological pore formation. This review provides an up-to-date discussion on common and divergent structural and functional traits that distinguish the various ClyA family PFTs. Open questions of this research topic are outlined and discussed.

scholarly journals Five-Card AND Computations in Committed Format Using Only Uniform Cyclic Shuffles

2021 ◽  
Author(s):  
Yuta Abe ◽  
Yu-ichi Hayashi ◽  
Takaaki Mizuki ◽  
Hideaki Sone
Keyword(s):  
State Of The Art ◽  
Research Topic ◽  
The State ◽  
Major Research ◽  
Open Questions

AbstractIn card-based cryptography, designing AND protocols in committed format is a major research topic. The state-of-the-art AND protocol proposed by Koch, Walzer, and Härtel in ASIACRYPT 2015 uses only four cards, which is the minimum permissible number. The minimality of their protocol relies on somewhat complicated shuffles having non-uniform probabilities of possible outcomes. Restricting the allowed shuffles to uniform closed ones entails that, to the best of our knowledge, six cards are sufficient: the six-card AND protocol proposed by Mizuki and Sone in 2009 utilizes the random bisection cut, which is a uniform and cyclic (and hence, closed) shuffle. Thus, a question has arisen: “Can we improve upon this six-card protocol using only uniform closed shuffles?” In other words, the existence or otherwise of a five-card AND protocol in committed format using only uniform closed shuffles has been one of the most important open questions in this field. In this paper, we answer the question affirmatively by designing five-card committed-format AND protocols using only uniform cyclic shuffles. The shuffles that our protocols use are the random cut and random bisection cut, both of which are uniform cyclic shuffles and can be easily implemented by humans.

scholarly journals Epigenomics and gene regulation in mammalian social systems

2020 ◽  
Vol 66 (3) ◽  
pp. 307-319 ◽  
Author(s):  
Tania P Guerrero ◽  
Jörns Fickel ◽  
Sarah Benhaiem ◽  
Alexandra Weyrich
Keyword(s):  
Gene Regulation ◽  
Social Systems ◽  
Metabolic Responses ◽  
Future Research ◽  
Epigenetic Mechanisms ◽  
Naturally Occurring ◽  
Open Questions ◽  
Technological Advances ◽  
Gene Environment ◽  
The Social

Abstract Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene–environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEIs, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.

Directed Growth of Branched Nanowire Structures

MRS Bulletin ◽  
2007 ◽  
Vol 32 (2) ◽  
pp. 127-133 ◽  
Author(s):  
Kimberly A. Dick ◽  
Knut Deppert ◽  
Lisa S. Karlsson ◽  
Magnus W. Larsson ◽  
Werner Seifert ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Metal Nanoparticles ◽  
Crystal Structures ◽  
Complex Structures ◽  
General Morphology ◽  
Zinc Blende ◽  
Directed Growth ◽  
Branched Structures ◽  
The Relationship ◽  
Hexagonal Wurtzite Crystal

AbstractWe describe the production of hierarchical branched nanowire structures by the sequential seeding of multiple wire generations with metal nanoparticles. Such complex structures represent the next step in the study of functional nanowires, as they increase the potential functionality of nanostructures produced in a self-assembled way. It is possible, for example, to fabricate a variety of active heterostructure segments with different compositions and diameters within a single connected structure. The focus of this work is on epitaxial III-V semiconductor branched nanowire structures, with the two materials GaP and In As used as typical examples of branched structures with cubic (zinc blende) and hexagonal (wurtzite) crystal structures. The general morphology of these structures will be described, as well as the relationship between morphology and crystal structure.

scholarly journals Anatomy of Hematopoiesis and Local Microenvironments in the Bone Marrow. Where to?

2021 ◽  
Vol 12 ◽  
Author(s):  
Qingqing Wu ◽  
Jizhou Zhang ◽  
Daniel Lucas
Keyword(s):  
Stem Cells ◽  
Bone Marrow ◽  
Blood Cell ◽  
Hematopoietic Stem Cells ◽  
Spatial Organization ◽  
Hematopoietic Stem ◽  
Daughter Cells ◽  
Open Questions ◽  
Complex Anatomy ◽  
Technological Advances

The shape and spatial organization -the anatomy- of a tissue profoundly influences its function. Knowledge of the anatomical relationships between parent and daughter cells is necessary to understand differentiation and how the crosstalk between the different cells in the tissue leads to physiological maintenance and pathological perturbations. Blood cell production takes place in the bone marrow through the progressive differentiation of stem cells and progenitors. These are maintained and regulated by a heterogeneous microenvironment composed of stromal and hematopoietic cells. While hematopoiesis has been studied in extraordinary detail through functional and multiomics approaches, much less is known about the spatial organization of blood production and how local cues from the microenvironment influence this anatomy. Here, we discuss some of the studies that revealed a complex anatomy of hematopoiesis where discrete local microenvironments spatially organize and regulate specific subsets of hematopoietic stem cells and/or progenitors. We focus on the open questions in the field and discuss how new tools and technological advances are poised to transform our understanding of the anatomy of hematopoiesis.

The crystal structure of [Fe2(PIMIC6)(AnthCO2)(CH3CN)]·[Fe2(PIMIC6)(AnthCO2)(CH3CN)0.9(CH2Cl2)0.1]·[Fe2(PIMIC6)(AnthCO2)(OH2)]·0.75CH3CN: a crystallographer's nightmare or a fascinating case of disorder?

2018 ◽  
Vol 74 (2) ◽  
pp. 122-131
Author(s):  
Sabine Becker
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Refinement ◽  
Complex Structures ◽  
Asymmetric Unit ◽  
Acid Anion ◽  
Large Crystal ◽  
Disordered Structure ◽  
Disordered Structures ◽  
Structural Database

Refinement of large crystal structures as well as that of disordered structures can be challenging. If both features come together, structure refinement has the potential of becoming a crystallographer's nightmare. Here, the refinement of the large and highly disordered structure of [Fe2(PIMIC6)(AnthCO2)(CH3CN)]·[Fe2(PIMIC6)(AnthCO2)(CH3CN)0.9(CH2Cl2)0.1]·[Fe2(PIMIC6)(AnthCO2)(OH2)]·0.75CH3CN [(1), PIMIC6 is a phenol–imine-based macrocycle, AnthCO2is an anthracene acid anion] is described and discussed. A total of 5311 parameters had to be refined to generate a model that allows for 14 400 possible arrangements of (1) in the asymmetric unit, making this structure one of the most complex structures in the Cambridge Structural Database to date. All disorders are exceptionally well resolved and exhaustive parameterizing affords a refinement model that is unique with respect to the detail of disorder refinement.

Cooperation and coercion

Linguistics ◽  
2016 ◽  
Vol 54 (4) ◽  
Author(s):  
Jenny Audring ◽  
Geert Booij
Keyword(s):  
Lexical Semantics ◽  
The Other ◽  
Complex Structures ◽  
Top Down ◽  
Broad Variety ◽  
The One ◽  
Semantic Flexibility

AbstractCoercion is a much-discussed topic in the linguistic literature. This article expands the usual range of cases at the most subtle and the extreme end: it demonstrates how coercion extends into semantic flexibility on the one hand and into idiomaticity on the other. After discussing a broad variety of coercion cases in syntax and morphology and briefly reviewing the equally diverse literature, we identify three mechanisms – selection, enrichment, and override – that have alternatively been proposed to account for coercion effects. We then present an approach that combines all three mechanisms, arguing that they can be unified along a single axis: the degree of top-down influence of complex structures on lexical semantics.

The application of phase relationships to complex structures. III. The optimum use of phase relationships

1971 ◽  
Vol 27 (4) ◽  
pp. 368-376 ◽  
Author(s):  
G. Germain ◽  
P. Main ◽  
M. M. Woolfson
Keyword(s):  
Computer Program ◽  
Crystal Structures ◽  
Figure Of Merit ◽  
Complex Structures ◽  
Fourfold Increase ◽  
Phase Relationships ◽  
Strong Relationships

An improvement is described in the automatic procedure for solving crystal structures incorporated in the computer program LSAM. The development of signs from an initial set containing symbols is carried only as far as is necessary to establish strong relationships between the symbols. The information so gained is used in a fresh beginning of the symbolic-addition process. Some failure of relationships between symbols is allowed to give a multisolution method. A phase-permutation computer program for non-centrosymmetric structures, MULTAN, incorporates a weighted tangent formula. This is of the form {\rm tan}\varphi_{\bf h} = {{\sum_{\bf h'}w_{\bf h'},w_{\bf h-h'}|E_{\bf h'}E_{\bf h-h'}| \sin (\varphi_{\bf h'} + \varphi_{\bf h-h'})}\over{\sum_{\bf h'}w_{\bf h'},w_{\bf h-h'}|E_{\bf h'}E_{\bf h-h'}| \cos (\varphi_{\bf h'} + \varphi_{\bf h-h'})}} = {{T_{\bf h}}\over{B_{\bf h}}} and w_{\bf h} = {\rm tanh}\{ \sigma_3\sigma_2^{-3/2}|E_{\bf h}|(T_{\bf h}^2 + B_{\bf h}^2)^{1/2}\}.All phases are accepted as soon as they are found with the associated weight. This gives a fourfold increase in speed in development of the complete phase set. An absolute figure of merit is described to indicate probably correct phase sets for multisolution methods.

Fungal functional ecology: Bringing a trait-based approach to plant-associated fungi

2019 ◽  
Author(s):  
Amy E. Zanne ◽  
Kessy Abarenkov ◽  
Michelle E. Afkhami ◽  
Carlos A. Aguilar-Trigueros ◽  
Scott Bates ◽  
...  
Keyword(s):  
Soil Water ◽  
Functional Diversity ◽  
Functional Traits ◽  
Quantitative Trait ◽  
Current Knowledge ◽  
Functional Ecology ◽  
Ecological Knowledge ◽  
Detection And Identification ◽  
Technological Advances ◽  
Identification Of Fungi

Fungi play many essential roles in ecosystems. They facilitate plant access to nutrients and water, serve as decay agents that cycle carbon and nutrients through the soil, water and atmosphere, and are major regulators of macro-organismal populations. Although technological advances are improving the detection and identification of fungi, there still exist key gaps in our ecological knowledge of this kingdom, especially related to function. Trait-based approaches have been instrumental in strengthening our understanding of plant functional ecology and, as such, provide excellent models for deepening our understanding of fungal functional ecology in ways that complement insights gained from traditional and -omics-based techniques. In this review, we synthesize current knowledge of fungal functional ecology, taxonomy and systematics and introduce a novel database of fungal functional traits (FunFun). FunFun is built to interface with other databases to explore and predict how fungal functional diversity varies by taxonomy, guild, and other evolutionary or ecological grouping variables. To highlight how a quantitative trait-based approach can provide new insights, we describe multiple targeted examples and end by suggesting next steps in the rapidly growing field of fungal functional ecology.

scholarly journals Not all mitochondrial carrier proteins support permeability transition pore formation: no involvement of uncoupling protein 1

2009 ◽  
Vol 30 (3) ◽  
pp. 187-192 ◽  
Author(s):  
Paul G. Crichton ◽  
Nadeene Parker ◽  
Antonio J. Vidal-Puig ◽  
Martin D. Brand
Keyword(s):  
Cyclosporin A ◽  
Pore Formation ◽  
Uncoupling Protein ◽  
Permeability Transition Pore ◽  
Permeability Transition ◽  
Protein Family ◽  
Carrier Protein ◽  
Uncoupling Protein 1 ◽  
Mitochondrial Carrier ◽  
Mitochondrial Carrier Protein

The mPTP (mitochondrial permeability transition pore) is a non-specific channel that is formed in the mitochondrial inner membrane in response to several stimuli, including elevated levels of matrix calcium. The pore is proposed to be composed of the ANT (adenine nucleotide translocase), voltage-dependent anion channel and cyclophilin D. Knockout studies, however, have demonstrated that ANT is not essential for permeability transition, which has led to the proposal that other members of the mitochondrial carrier protein family may be able to play a similar function to ANT in pore formation. To investigate this possibility, we have studied the permeability transition properties of BAT (brown adipose tissue) mitochondria in which levels of the mitochondrial carrier protein, UCP1 (uncoupling protein 1), can exceed those of ANT. Using an improved spectroscopic assay, we have quantified mPTP formation in de-energized mitochondria from wild-type and Ucp1KO (Ucp1-knockout) mice and assessed the dependence of pore formation on UCP1. When correctly normalized for differences in mitochondrial morphology, we find that calcium-induced mPTP activity is the same in both types of mitochondria, with similar sensitivity to GDP (~50% inhibited), although the portion sensitive to cyclosporin A is higher in mitochondria lacking UCP1 (~80% inhibited, compared with ~60% in mitochondria containing UCP1). We conclude that UCP1 is not a component of the cyclosporin A-sensitive mPTP in BAT and that playing a role in mPTP formation is not a general characteristic of the mitochondrial carrier protein family but is, more likely, restricted to specific members including ANT.

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