How to Measure Grana – Ultrastructural Features of Thylakoid Membranes of Plant Chloroplasts

Granum is a basic structural unit of the thylakoid membrane network of plant chloroplasts. It is composed of multiple flattened membranes forming a stacked arrangement of a cylindrical shape. Grana membranes are composed of lipids and tightly packed pigment-protein complexes whose primary role is the catalysis of photosynthetic light reactions. These membranes are highly dynamic structures capable of adapting to changing environmental conditions by fine-tuning photochemical efficiency, manifested by the structural reorganization of grana stacks. Due to a nanometer length scale of the structural granum features, the application of high-resolution electron microscopic techniques is essential for a detailed analysis of the granum architecture. This mini-review overviews recent approaches to quantitative grana structure analyses from electron microscopy data, highlighting the basic manual measurements and semi-automated workflows. We outline and define structural parameters used by different authors, for instance, granum height and diameter, thylakoid thickness, end-membrane length, Stacking Repeat Distance, and Granum Lateral Irregularity. This article also presents insights into efficient and effective measurements of grana stacks visualized on 2D micrographs. The information on how to correctly interpret obtained data, taking into account the 3D nature of grana stacks projected onto 2D space of electron micrograph, is also given. Grana ultrastructural observations reveal key features of this intriguing membrane arrangement, broadening our knowledge of the thylakoid network’s remarkable plasticity.

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Structure of contact sites between the outer and inner mitochondrial membranes investigated by HVEM tomography

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100167299 ◽

1996 ◽

Vol 54 ◽

pp. 966-967

Author(s):

C.A. Mannella ◽

K.F. Buttle ◽

K.A. O‘Farrell ◽

A. Leith ◽

M. Marko

Keyword(s):

Liver Mitochondrion ◽

Adenine Nucleotide ◽

Protein Complexes ◽

Mitochondrial Membranes ◽

Electron Microscopic ◽

Contact Sites ◽

Transmission Electron ◽

Precursor Proteins ◽

Membrane Contacts ◽

And Function

Early transmission electron microscopy of plastic-embedded, thin-sectioned mitochondria indicated that there are numerous junctions between the outer and inner membranes of this organelle. More recent studies have suggested that the mitochondrial membrane contacts may be the site of protein complexes engaged in specialized functions, e.g., import of mitochondrial precursor proteins, adenine nucleotide channeling, and even intermembrane signalling. It has been suggested that the intermembrane contacts may be sites of membrane fusion involving non-bilayer lipid domains in the two membranes. However, despite growing interest in the nature and function of intramitochondrial contact sites, little is known about their structure.We are using electron microscopic tomography with the Albany HVEM to determine the internal organization of mitochondria. We have reconstructed a 0.6-μm section through an isolated, plasticembedded rat-liver mitochondrion by combining 123 projections collected by tilting (+/- 70°) around two perpendicular tilt axes. The resulting 3-D image has confirmed the basic inner-membrane organization inferred from lower-resolution reconstructions obtained from single-axis tomography.

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Plasmonic hot-electron photodetection with quasi-bound states in the continuum and guided resonances

Nanophotonics ◽

10.1515/nanoph-2021-0069 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Wenhao Wang ◽

Lucas V. Besteiro ◽

Peng Yu ◽

Feng Lin ◽

Alexander O. Govorov ◽

...

Keyword(s):

Bound States ◽

Structural Parameters ◽

Hybrid Structure ◽

Fine Tuning ◽

Hot Electrons ◽

Hot Electron ◽

Perfect Absorption ◽

High Loss ◽

Guided Mode ◽

The Continuum

Abstract Hot electrons generated in metallic nanostructures have shown promising perspectives for photodetection. This has prompted efforts to enhance the absorption of photons by metals. However, most strategies require fine-tuning of the geometric parameters to achieve perfect absorption, accompanied by the demanding fabrications. Here, we theoretically propose a Ag grating/TiO2 cladding hybrid structure for hot electron photodetection (HEPD) by combining quasi-bound states in the continuum (BIC) and plasmonic hot electrons. Enabled by quasi-BIC, perfect absorption can be readily achieved and it is robust against the change of several structural parameters due to the topological nature of BIC. Also, we show that the guided mode can be folded into the light cone by introducing a disturbance to become a guided resonance, which then gives rise to a narrow-band HEPD that is difficult to be achieved in the high loss gold plasmonics. Combining the quasi-BIC and the guided resonance, we also realize a multiband HEPD with near-perfect absorption. Our work suggests new routes to enhance the light-harvesting in plasmonic nanosystems.

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Domains of the rat rDNA promoter must be aligned stereospecifically

Molecular and Cellular Biology ◽

10.1128/mcb.12.3.1266-1275.1992 ◽

1992 ◽

Vol 12 (3) ◽

pp. 1266-1275

Author(s):

W Q Xie ◽

L I Rothblum

Keyword(s):

Protein Complexes ◽

Point Mutations ◽

In Vitro Transcription ◽

Promoter Elements ◽

Repeat Distance ◽

Deletion Mutations ◽

The Core ◽

In Vivo Experiments

Efficient transcription from the rat rDNA promoter results from an undefined interaction between the core (CPE) and upstream (UPE) promoter elements or the protein complexes which form on them. These interactions were demonstrated by the behavior of promoters that contained either linker-scanning or deletion mutations of the UPE in combination with point mutations of the CPE (bidomain mutants). In vivo transcription experiments using point mutations within the CPE (G----A mutation at either -16 or -7) demonstrated that the CPE may in fact consist of two domains. Whereas both of these mutants were rescued by the addition of UBF to in vitro transcription reactions, the CPE mutant -7A/G was inactive in vivo. Experiments with these bidomain mutants demonstrated that the UPE was required for the rescue of the CPE mutants. We also examined the hypothesis that this interaction might require a stereospecific alignment of the promoter elements. Our results indicate that the promoter consists of several domains with differing responses to mutations that alter the distance between, or within, the promoter elements. For example, the insertion or deletion of half-multiples of the helical repeat distance between -167 and -147 had no significant effect on transcription. On the other hand, some sites were sensitive to deletions of any size but not to insertions of up to 20 bp. The analyses of two sites yielded results suggesting that they lay between domains of the promoter that must be on the same side of the DNA helix for promoter activity. The first of these sites mapped between -106 and -95.(ABSTRACT TRUNCATED AT 250 WORDS)

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Platelet adhesion: Structural and functional diversity of short dystrophin and utrophins in the formation of dystrophinassociated-protein complexes related to actin dynamics

Thrombosis and Haemostasis ◽

10.1160/th04-11-0765 ◽

2005 ◽

Vol 94 (12) ◽

pp. 1203-1212 ◽

Cited By ~ 18

Author(s):

Doris Cerecedo ◽

Dalila Martínez-Rojas ◽

Oscar Chávez ◽

Francisco Martínez-Pérez ◽

Francisco García-Sierra ◽

...

Keyword(s):

Actin Cytoskeleton ◽

Platelet Adhesion ◽

Protein Complexes ◽

Human Platelets ◽

Actin Dynamics ◽

Actin Binding ◽

Dynamic Cell ◽

Associated Proteins ◽

Coated Surfaces ◽

Dynamic Structures

SummaryPlatelets are dynamic cell fragments that modify their shape during activation. Utrophin and dystrophins are minor actin-binding proteins present in muscle and non-muscle cytoskeleton. In the present study, we characterised the pattern of Dp71 isoforms and utrophin gene products by immunoblot in human platelets. Two new dystrophin isoforms were found, Dp71f and Dp71d, as well as the Up71 isoform and the dystrophin-associated proteins, α and β-dystrobrevins. Distribution of Dp71d/Dp71Δ110 m, Up400/Up71 and dystrophin-associated proteins in relation to the actin cytoskeleton was evaluated by confocal microscopy in both resting and platelets adhered on glass. Formation of two dystrophin-associated protein complexes (Dp71d/Dp71Δ110 m ~DAPC and Up400/Up71~DAPC) was demonstrated by co-immunoprecipitation and their distribution in relation to the actin cytoskeleton was characterised during platelet adhesion. The Dp71d/Dp71Δ110 m ~DAPC is maintained mainly at the granulomere and is associated with dynamic structures during activation by adhesion to thrombin-coated surfaces. Participation of both Dp71d/Dp71Δ110 m ~DAPC and Up400/Up71~DAPC in the biological roles of the platelets is discussed.

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Chemical and Laser Ablation Synthesis of Monometallic and Bimetallic Ni-Based Nanoparticles

Catalysts ◽

10.3390/catal10121453 ◽

2020 ◽

Vol 10 (12) ◽

pp. 1453

Author(s):

Niusha Lasemi ◽

Günther Rupprechter

Keyword(s):

Laser Ablation ◽

Liquid Phase ◽

Surface Composition ◽

Structural Parameters ◽

Nanoparticle Synthesis ◽

Femtosecond Laser Ablation ◽

Laser Ablation In Liquid ◽

Electron Microscopic ◽

Wet Chemical Synthesis ◽

Bimetallic Nanoparticle

The catalytic properties of nanoparticles depend on their size, shape and surface/defect structure, with the entire catalyst performance being governed by the corresponding distributions. Herein, we present two routes of mono- and bimetallic nanoparticle synthesis that enable control of the structural parameters, i.e., wet-chemical synthesis and laser ablation in liquid-phase. The latter is particularly suited to create defect-rich nanoparticles. Impregnation routes were applied to prepare Ni and NiCu nanoparticles, whereas nano- and femtosecond laser ablation in liquid-phase were employed to prepare Ni and NiAu nanoparticles. The effects of the Ni:Cu ratio in impregnation and of laser fluence and liquid-medium on laser ablation are discussed. The atomic structure and (surface) composition of the nanoparticles were characterized by electron microscopic (BF-TEM, DF-TEM, HRTEM) and spectroscopic/diffraction techniques (EDX, SAED, XPS, IR), complemented by theory (DFT). The chemically synthesized bimetallic NiCu nanoparticles initially had Cu-rich surfaces, which changed to Ni-rich upon reaction. For laser ablation, depending on conditions (fluence, type of liquid), highly defective, ordered, or core/shell-like nanoparticles were produced. The case studies highlight the specific benefits of each preparation method for catalyst synthesis and discuss the potential of nanoparticles produced by pulsed laser ablation for catalytic applications.

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Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development

Journal of Experimental Botany ◽

10.1093/jxb/eraa348 ◽

2020 ◽

Vol 71 (20) ◽

pp. 6246-6261 ◽

Cited By ~ 2

Author(s):

Dawei Dai ◽

Lifang Jin ◽

Zhenzhen Huo ◽

Shumei Yan ◽

Zeyang Ma ◽

...

Keyword(s):

Rna Editing ◽

Protein Complexes ◽

Plant Mitochondria ◽

Mitochondrial Protein ◽

Electron Microscopic Examination ◽

Complex Iii ◽

Mitochondrial Rna ◽

Pentatricopeptide Repeat ◽

Electron Microscopic ◽

Ppr Protein

Abstract Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.

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Binding of a phosphoprotein to the 3' untranslated region of the mouse protamine 2 mRNA temporally represses its translation.

Molecular and Cellular Biology ◽

10.1128/mcb.13.10.6547 ◽

1993 ◽

Vol 13 (10) ◽

pp. 6547-6557 ◽

Cited By ~ 102

Author(s):

Y K Kwon ◽

N B Hecht

Keyword(s):

Rna Binding ◽

Protein Complexes ◽

Male Gamete ◽

Human Growth ◽

Primary Role ◽

Developmentally Regulated ◽

Reticulocyte Lysates ◽

Rna Protein Complexes ◽

Mammalian Spermatozoa ◽

Protamine 2

The synthesis of the protamines, the predominant nuclear proteins of mammalian spermatozoa, is regulated during germ cell development by mRNA storage for about 7 days in the cytoplasm of differentiating spermatids. Two highly conserved sequences, the Y and H elements present in the 3' untranslated regions (UTRs) of all known mammalian protamine mRNAs, form RNA-protein complexes and specifically bind a protein of 18 kDa. Here, we show that translation of fusion mRNAs was markedly repressed in reticulocyte lysates supplemented with a mouse testis extract enriched for the 18-kDa protein when the mRNAs contained the 3' UTR of mouse protamine 2 (mP2) or the Y and H elements of mP2. No significant decrease was seen when the fusion mRNAs contained the 3' UTR of human growth hormone. The 18-kDa protein is developmentally regulated in male germ cells, requires phosphorylation for RNA binding, and is found in the ribonucleoprotein particle fractions of a testicular postmitochondrial supernatant. We propose that a phosphorylated 18-kDa protein plays a primary role in repressing translation of mP2 mRNA by interaction with the highly conserved Y and H elements. At a later stage of male gamete differentiation, the 18-kDa protein no longer binds to the mRNA, likely as a result of dephosphorylation, enabling the protamine mRNA to be translated.

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ELLSTAT: shape modeling for solution small-angle scattering of proteins and protein complexes with automated statistical characterization

Journal of Applied Crystallography ◽

10.1107/s0021889806029591 ◽

2006 ◽

Vol 39 (5) ◽

pp. 671-675 ◽

Cited By ~ 16

Author(s):

William T. Heller

Keyword(s):

Small Angle ◽

Protein Complexes ◽

Structural Parameters ◽

Shape Modeling ◽

Scattering Data ◽

Model Parameters ◽

Data Sets ◽

Statistical Characterization ◽

X Ray ◽

Angle Scattering

A method is presented for constructing one- and two-ellipsoid, core-shell-ellipsoid, cylinder and ellipsoid-plus-cylinder models from small-angle X-ray and neutron scattering data that calculates statistics on the resulting structural parameters. The method, implemented in the softwareELLSTAT, is capable of simultaneously fitting against several data sets and calculates averages, standard deviations and coefficients of linear correlation between the structural parameters of the resulting models. In this way, an improved understanding of the extent of the variability in and the interdependency between the model parameters that fit the input scattering data is developed, thereby providing a measure of the uniqueness of the models.

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