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Crystallization of the malaria pigment hemozoin sequesters the toxic heme byproduct of hemoglobin digestion in Plasmodium -infected red blood cells (RBCs). Recently, we applied electron and X-ray imaging and diffraction methods to elucidate this process. We observed crystals oriented with their {100} faces at the inner membrane surface of the digestive vacuole (DV) of Plasmodium falciparum in parasitized RBCs. Modeling of the soft X-ray tomographic (SXT) images of a trophozoite-stage parasite indicated a 4-16 nm DV membrane thickness, suggesting a possible role for lipid multilayers. Here, we reanalyzed the trophozoite SXT images quantitatively via X-ray absorption to map the DV membrane thickness. Making use of the chemical structure and crystal density of the lipid, we found, predominantly, a bilayer 4.2 nm thick, and the remainder was interpreted as patches ∼8 nm thick. Image analysis of electron micrographs also yielded a 4-5 nm DV membrane thickness. The DV lipid membrane is thus mainly a bilayer, so induced hemozoin nucleation occurs primarily via the inner of the membrane's two leaflets. We argue that such a leaflet embodying mono- and di-acyl lipids with appropriate OH or NH bearing head groups may catalyse hemozoin nucleation by stereochemical and lattice match to the {100} crystal face, involving a two-dimensional nucleation aggregate of ∼100 molecules.

Molecular exchange between the cell nucleus and cytoplasm is one of the most fundamental features of eukaryotic cell biology. The nuclear pores act as a conduit of this transport, both for cargo that crosses the pore autonomously as well as that whose translocation requires an intermediary receptor. The major class of such receptors is regulated by the small GTPase Ran, via whose interaction the nucleo-cytoplasmic transport system functions as a selective molecular pump. We propose a simple analytical model for transport that includes both translocation and receptor binding kinetics. The model is suitable for steady-state kinetics such as fluorescence recovery after photobleaching. Time constants appear as a combination of parameters whose effects on measured kinetics are not separable. Competitive cargo binding to receptors and large cytoplasmic volume buffer the transport properties of any particular cargo. Specific limits to the solutions provide a qualitative insight and interpretation of nuclear transport in the cellular context. Most significantly, we find that under realistic conditions receptor binding, rather than permeability of the nuclear pores, may be rate-limiting for nucleo-cytoplasmic exchange.

VirE2 is a ssDNA binding protein essential for virulence in Agrobacterium tumefaciens. A tetracysteine mutant (VirE2-TC) was prepared for in vitro and in vivo fluorescence imaging based on the ReAsH reagent. VirE2-TC was found to be biochemically active as it binds both ssDNA and the acidic secretion chaperone VirE1. It was also biologically functional in complementing virE2 null strains transforming Arabidopsis thaliana roots and Nicotiana tabacum leaves. In vitro experiments demonstrated a two-color fluorescent complex using VirE2-TC/ReAsH and Alexa Fluor 488 labeled ssDNA. In vivo, fluorescent VirE2-TC/ReAsH was detected in bacteria and in plant cells at time frames relevant to transformation.

Heme detoxification is a critical step in the life cycle of malaria-causing parasites, achieved by crystallization into physiologically insoluble hemozoin. The mode of nucleation has profound implications for understanding the mechanism of action of antimalarial drugs that inhibit hemozoin growth. Several lines of evidence point to involvement of acylglycerol lipids in the nucleation process. Hemozoin crystals have been reported to form within lipid nanospheres; alternatively, it has been found in vitro that they are nucleated at an acylglycerol lipid–water interface. We have applied cryogenic soft X-ray tomography and three-dimensional electron microscopy to address the location and orientation of hemozoin crystals within the digestive vacuole (DV), as a signature of their nucleation and growth processes. Cryogenic soft X-ray tomography in the “water window” is particularly advantageous because contrast generation is based inherently on atomic absorption. We find that hemozoin nucleation occurs at the DV inner membrane, with crystallization occurring in the aqueous rather than lipid phase. The crystal morphology indicates a common {100} orientation facing the membrane as expected of templated nucleation. This is consistent with conclusions reached by X-ray fluorescence and diffraction in a companion work. Uniform dark spheres observed in the parasite were identified as hemoglobin transport vesicles. Their analysis supports a model of hemozoin nucleation primarily in the DV. Modeling of the contrast at the DV membrane indicates a 4-nm thickness with patches about three times thicker, possibly implicated in the nucleation.

The deadliest form of human malaria is caused by the protozoan parasite Plasmodium falciparum. The complex life cycle of this parasite is associated with tight transcriptional regulation of gene expression. Nuclear positioning and chromatin dynamics may play an important role in regulating P. falciparum virulence genes. We have applied an emerging technique of electron microscopy to construct a 3D model of the parasite nucleus at distinct stages of development within the infected red blood cell. We have followed the distribution of nuclear pores and chromatin throughout the intra-erythrocytic cycle, and have found a striking coupling between the distributions of nuclear pores and chromatin organization. Pore dynamics involve clustering, biogenesis, and division among daughter cells, while chromatin undergoes stage-dependent changes in packaging. Dramatic changes in heterochromatin distribution coincide with a previously identified transition in gene expression and nucleosome positioning during the mid-to-late schizont phase. We also found a correlation between euchromatin positioning at the nuclear envelope and the local distribution of nuclear pores, as well as a dynamic nuclear polarity during schizogony. These results suggest that cyclic patterns in gene expression during parasite development correlate with gross changes in cellular and nuclear architecture.

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.

Passage of polymers through pores narrower than the hydrodynamic diameter is impeded by an entropic penalty for their confinement. This might be balanced by an attractive interaction with the pore ...

Mammalian cytokinetic abscission is mediated by the ESCRT membrane fission machinery. While much has been clarified on the topology and kinetics of abscission through high-resolution microscopy, key questions regarding the mechanism of abscission remain open. Here we apply cryogenic soft-X-ray tomography to elucidate new ultrastructural details in the intercellular membrane bridge connecting cells undergoing abscission. In particular, we resolve defined ring-like structures inside the midbody dark zone that have been inaccessible to EM and identify membrane extrusions at the abscission sites. In cells at late stages of abscission we resolve a complex array of helical spirals, extending the structural information obtained by EM. Our results highlight the advantages of soft-X-ray tomography and emphasize the importance of using complementary approaches for characterizing cellular structures. Notably, by providing new structural data from intact cells we present a realistic view on the topology of abscission and suggest new mechanistic models for ESCRT mediated abscission.

Nucleocytoplasmic exchange of proteins and RNAs is mediated by receptors that usher their cargo through the nuclear pores. Peptide localization signals on each cargo determine the receptors with which it will interact. Those interactions are normally regulated by the small GTPase Ran. Hydrolysis of GTP provides the chemical energy required to create a bona fide thermodynamic pump that selectively and directionally accumulates its substrates across the nuclear envelope. A common perception is that cargo delivery is irreversible, e.g., a protein imported to the nucleus does not return to the cytoplasm except perhaps via a specific export receptor. Quantitative measurements using cell-free nuclei reconstituted in Xenopus egg extract show that nuclear accumulation follows first-order kinetics and reaches steady state at a level that follows a Michaelis–Menten function of the cytoplasmic cargo concentration. This saturation suggests that receptor-mediated translocation across the nuclear pore occurs bidirectionally. The reversibility of accumulation was demonstrated directly by exchange of the cytosolic medium and by fluorescence recovery after photobleaching. Based on our results, we offer a simple biophysical model that predicts the observed behavior. A far-reaching consequence is that the nuclear localization signal dictates the fate of a protein population rather than that of the individual molecules that bear it, which remain free to shuttle back and forth. This implies an open communication between the nucleus and cytoplasm and a ubiquitous mechanism for signaling in both directions.

Agrobacterium tumefaciens infects plant cells by the transfer of DNA. A key factor in this process is the bacterial virulence protein VirE2, which associates stoichiometrically with the transported single-stranded (ss) DNA molecule (T-strand). As observed in vitro by transmission electron microscopy, VirE2-ssDNA readily forms an extended helical complex with a structure well suited to the tasks of DNA protection and nuclear import. Here we have elucidated the role of the specific molecular chaperone VirE1 in regulating VireE2-VirE2 and VirE2-ssDNA interactions. VirE2 alone formed functional filamentous aggregates capable of ssDNA binding. In contrast, co-expression with VirE1 yielded monodisperse VirE1-VirE2 complexes. Cooperative binding of VirE2 to ssDNA released VirE1, resulting in a controlled formation mechanism for the helical complex that is further promoted by macromolecular crowding. Based on this in vitro evidence, we suggest that the constrained volume of the VirB channel provides a natural site for the exchange of VirE2 binding from VirE1 to the T-strand.

International audience; VirE2 is the major secreted protein of Agrobacterium tumefaciens in its genetic transformation of plant hosts. It is co-expressed with a small acidic chaperone VirE1, which prevents VirE2 oligomerization. After secretion into the host cell, VirE2 serves functions similar to a viral capsid in protecting the single-stranded transferred DNA en route to the nucleus. Binding of VirE2 to ssDNA is strongly cooperative and depends moreover on protein-protein interactions. In order to isolate the protein-DNA interactions , imaging surface plasmon resonance (SPRi) studies were conducted using surface-immobilized DNA substrates of length comparable to the protein-binding footprint. Binding curves revealed an important influence of substrate rigidity with a notable preference for poly-T sequences and absence of binding to both poly-A and double-stranded DNA fragments. Dissociation at high salt concentration confirmed the electrostatic nature of the interaction. VirE1-VirE2 heterodimers also bound to ssDNA, though by a different mechanism that was insensitive to high salt. Neither VirE2 nor VirE1-VirE2 followed the Lang-muir isotherm expected for reversible monomeric binding. The differences reflect the cooperative self-interactions of VirE2 that are suppressed by VirE1.

In nucleated cells, proteins designed for nuclear import form complexes with soluble nuclear transport receptors prior to translocation across the nuclear envelope. The directionality of transport is due to the asymmetric distribution of the protein Ran, which dissociates import cargo complexes only in its nuclear RanGTP form. Using fluorescence correlation spectroscopy, we have studied the stability of cargo complexes in solution in the presence and in the absence of RanGTP. We find that RanGTP has a higher affinity for the major import receptor, the importin α/β heterodimer, when importin α does not carry a cargo, suggesting that some nuclear transport targets might be preferentially released. To cite this article: C. Fradin et al., C. R. Biologies 328 (2005).

Type IV secretion systems (T4SSs) are used by various bacteria to deliver protein and DNA molecules to a wide range of target cells. These include systems that are directly involved in pathogenesis, such as the secretion of pertussis toxin by Bordetella pertussis into human cells and the delivery of single-stranded DNA (ssDNA) into plants by Agrobacterium. These complex systems are composed of proteins that span the bacterial cytoplasm. The Agrobacterium T4SS is composed of 12 virulence proteins and delivers its transferred ssDNA and several virulence protein substrates to a variety of eukaryotic cells. Recent studies on the Agrobacterium T4SS have revealed new information on the localization and structure of its proteins in the bacteria, the biochemical properties of its transport signal, the route of a DNA substrate through the secretion system, and the initial point of contact of the system with its host. These findings have expanded our knowledge and understanding of the still mostly obscure structure and function of the T4SSs.

Assembly of a eukaryotic nucleus involves three distinct events: membrane recruitment, fusion to form a double nuclear membrane, and nuclear pore complex (NPC) assembly. We report that importin beta negatively regulates two of these events, membrane fusion and NPC assembly. When excess importin beta is added to a full Xenopus nuclear reconstitution reaction, vesicles are recruited to chromatin but their fusion is blocked. The importin beta down-regulation of membrane fusion is Ran-GTP reversible. Indeed, excess RanGTP (RanQ69L) alone stimulates excessive membrane fusion, leading to intranuclear membrane tubules and cytoplasmic annulate lamellae-like structures. We propose that a precise balance of importin beta to Ran is required to create a correct double nuclear membrane and simultaneously to repress undesirable fusion events. Interestingly, truncated importin beta 45-462 allows membrane fusion but produces nuclei lacking any NPCs. This reveals distinct importin beta-regulation of NPC assembly. Excess full-length importin beta and beta 45-462 act similarly when added to prefused nuclear intermediates, i.e., both block NPC assembly. The importin beta NPC block, which maps downstream of GTPgammaS and BAPTA-sensitive steps in NPC assembly, is reversible by cytosol. Remarkably, it is not reversible by 25 microM RanGTP, a concentration that easily reverses fusion inhibition. This report, using a full reconstitution system and natural chromatin substrates, significantly expands the repertoire of importin beta. Its roles now encompass negative regulation of two of the major events of nuclear assembly: membrane fusion and NPC assembly.

Several million macromolecules are exchanged each minute between the nucleus and cytoplasm by receptor-mediated transport. Most of this traffic is controlled by the small GTPase Ran, which regulates assembly and disassembly of the receptor-cargo complexes in the appropriate cellular compartment. Here we applied dynamic force spectroscopy to study the interaction of Ran with the nuclear import receptor importin beta1 (impbeta) at the single-molecule level. We found that the complex alternates between two distinct conformational states of different adhesion strength. The application of an external mechanical force shifts equilibrium toward one of these states by decreasing the height of the interstate activation energy barrier. The other state can be stabilized by a functional Ran mutant that increases this barrier. These results support a model whereby functional control of Ran-impbeta is achieved by a population shift between pre-existing alternative conformations.

A new method of laser-induced lithography for direct writing of carbon on a glass surface is described, in which deposition occurs from a transparent precursor solution. At the glass–solution interface where the laser spot is focused, a micro-explosion process takes place, leading to the deposition of pure carbon on the glass surface. Transmission electron microscopy (TEM) analysis shows two distinct co-existing phases. The dominant one shows a mottled morphology with diffraction typical of cubic (sp3) diamond. The other region shows an ordered array of graphene sheets with diffraction pattern typical of sp2-bonded carbon. The sp3 crystallites range in size from 9 to 30 A and are scattered randomly throughout the sample. A UV Raman spectrum shows a broad band at the location of the expected diamond peak, together with a peak corresponding to the graphite region. We conclude that the patterned carbon is composed of a mixture of nanocrystalline sp3 and sp2 carbon forms.

The vertebrate nuclear pore complex, 30 times the size of a ribosome, assembles from a library of soluble subunits and two membrane proteins. Using immunodepletion of Xenopus nuclear reconstitution extracts, it has previously been possible to assemble nuclei lacking pore subunits tied to protein import, export, or mRNA export. However, these altered pores all still possessed the bulk of pore structure. Here, we immunodeplete a single subunit, the Nup107-160 complex, using antibodies to Nup85 and Nup133, two of its components. The resulting reconstituted nuclei are severely defective for NLS import and DNA replication. Strikingly, they show a profound defect for every tested nucleoporin. Even the integral membrane proteins POM121 and gp210 are absent or unorganized. Scanning electron microscopy reveals pore-free nuclei, while addback of the Nup107-160 complex restores functional pores. We conclude that the Nup107-160 complex is a pivotal determinant for vertebrate nuclear pore complex assembly.

Compartmentalization of the cytoplasm by membranes should have a strong influence on the diffusion of macromolecules inside a cell, and we have studied how this could be reflected in fluorescence correlation spectroscopy (FCS) experiments. We derived the autocorrelation function measured by FCS for fluorescent particles diffusing close to a soft membrane, and show it to be the sum of two contributions: short timescale correlations come from the diffusion of the particles (differing from free diffusion because of the presence of an obstacle), whereas long timescale correlations arise from fluctuations of the membrane itself (which create intensity fluctuations by modulating the number of detected particles). In the case of thermal fluctuations this second type of correlation depends on the elasticity of the membrane. To illustrate this calculation, we report the results of FCS experiments carried out close to a vesicle membrane. The measured autocorrelation functions display very distinctly the two expected contributions, and allow both to recover the diffusion coefficient of the fluorophore and to characterize the membrane fluctuations in term of a bending rigidity. Our results show that FCS measurements inside cells can lead to erroneous values of the diffusion coefficient if the influence of membranes is not recognized.

The most resilient remains of plants in most archaeological sites are the siliceous phytoliths—special cells that are partially or completely silicified during the plant's life. These cells have characteristic morphologies, and thus the phytoliths can often be used to identify the taxonomic affinities of plants brought to an archaeological site. In order to determine what they were used for, other means of analysis are needed. We present here a method to distinguish burnt from unburnt phytolith assemblages. The method is based on measuring the refractive index (RI) of individual phytoliths. The phytoliths even from a single plant have a range of RI values. Burning a phytolith sample causes a shift to higher RI. Comparing burnt and unburnt samples we demonstrate that it is possible to differentiate between them based on the fraction of phytoliths with RI higher than 1·440. This serves as a basis for a simplified mode of measurement that requires only the use of a petrographic light microscope and a mineral oil of RI 1·440. We apply the simplified method to two Natufian samples from Hayonim cave (Western Galilee, Israel).

Self-healing, where a modification in some parameter is reversed with time without any external intervention, is one of the particularly interesting properties of halide perovskites. While there are a number of studies showing such self-healing in perovskites, they all are carried out on thin films, where the interface between the perovskite and another phase (including the ambient) is often a dominating and interfering factor in the process. Here, self-healing in perovskite (methylammonium, formamidinium, and cesium lead bromide (MAPbBr3 , FAPbBr3 , and CsPbBr3 )) single crystals is reported, using two-photon microscopy to create damage (photobleaching) ≈110 µm inside the crystals and to monitor the recovery of photoluminescence after the damage. Self-healing occurs in all three perovskites with FAPbBr3 the fastest (≈1 h) and CsPbBr3 the slowest (tens of hours) to recover. This behavior, different from surface-dominated stability trends, is typical of the bulk and is strongly dependent on the localization of degradation products not far from the site of the damage. The mechanism of self-healing is discussed with the possible participation of polybromide species. It provides a closed chemical cycle and does not necessarily involve defect or ion migration phenomena that are often proposed to explain reversible phenomena in halide perovskites.

Bacterial cells often contain dense granules. Among these, polyphosphate bodies (PPBs) store inorganic phosphate for a variety of essential functions. Identification of PPBs has until now been accomplished by analytical methods that required drying or chemically fixing the cells. These methods entail large electron doses that are incompatible with low-dose imaging of cryogenic specimens. We show here that Scanning Transmission Electron Microscopy (STEM) of fully hydrated, intact, vitrified bacteria provides a simple means for mapping of phosphorus-containing dense granules based on quantitative sensitivity of the electron scattering to atomic number. A coarse resolution of the scattering angles distinguishes phosphorus from the abundant lighter atoms: carbon, nitrogen and oxygen. The theoretical basis is similar to Z contrast of materials science. EDX provides a positive identification of phosphorus, but importantly, the method need not involve a more severe electron dose than that required for imaging. The approach should prove useful in general for mapping of heavy elements in cryopreserved specimens when the element identity is known from the biological context.

We report an experimental study of the dynamics of particles driven along biopolymer tracks by active protein motors. We use extracts of Xenopus laevis eggs, which support the formation of cytoskeletal networks (microtubules and actin filaments) in vitro and provide all the biochemical factors needed for particle motion. 3 μm polystyrene beads adsorb motor proteins non-specifically and serve as the transport substrate. We observe an enhanced diffusive motion with time scaling of the mean squared displacement as t3/2. At the shortest times, the data indicate a crossover to a subdiffusive or saturated regime, due to intermittent adhesion of the motor proteins to the microtubules. The time interval over which this behavior was observed varied widely. On inhibiting one or the other family of the microtubule-associated motor proteins, the interval on which such saturation was observed increased, yet the t3/2 behavior at longer times was unaffected.

International audience; Shigella enters epithlial cells via internalization into a vacuole. Subsequent vacuolar membrane rupture allows bacterial escape into the cytosol for replication and cell-to-cell spread. Bacterial effectors such as IpgD, a PI(4,5)P2 phosphatase that generates PI(5)P and alters host actin, facilitate this internalization. Here, we identify host proteins involved in Shigella uptake and vacuolar membrane rupture by high-content siRNA screening and subsequently focus on Rab11, a constituent of the recycling compartment. Rab11-positive vesicles are recruited to the invasion site before vacuolar rupture, and Rab11 knockdown dramatically decreases vacuolar membrane rupture. Additionally, Rab11 recruitment is absent and vacuolar rupture is delayed in the ipgD mutant that does not dephosphorylate PI(4,5)P₂ into PI(5)P. Ultrastructural analyses of Rab11-positive vesicles further reveal that ipgD mutant-containing vacuoles become confined in actin structures that likely contribute to delayed vacular rupture. These findings provide insight into the underlying molecular mechanism of vacuole progression and rupture during Shigella invasion.

We evaluate the temporal relation between protein expression by cationic lipid-mediated transfection and cell division using time lapse fluorescence microscopy. Detailed image analysis provides new insights on the single cell level while simultaneously achieving appropriate statistics. Earlier evidence by less direct methods such as flow cytometry indicates a primary route for transfection involving nuclear envelope breakdown, but also suggests the existence of a pathway independent of mitosis. We confirm and quantify both mechanisms. We found the timing for successful transfection to be unexpectedly flexible, contrary to assertions of a narrow time window. Specifically, cells dividing more than 24h after exposure to the transfection medium express the probed protein at a comparable level to cells in a mitotic state during or shortly after transfection. This finding can have a profound impact on the guidance and development of non-viral gene delivery materials.

Centripetal motion of surface-adherent particles is a classic experimental system for studying surface dynamics on a eukaryotic cell. To investigate bead migration over the entire cell surface, we have developed an experimental assay using multinuclear giant fibroblasts, which provide expanded length scales and an unambiguous frame of reference. Beads coated by adhesion ligands concanavalin A or fibronectin are placed in specific locations on the cell using optical tweezers, and their subsequent motion is tracked over time. The adhesion, as well as velocity and directionality of their movement, expose distinct regions of the cytoplasm and membrane. Beads placed on the peripheral lamella initiate centripetal motion, whereas beads placed on the central part of the cell attach to a stationary cortex and do not move. Careful examination by complementary three-dimensional methods shows that the motion of a bead placed on the cell periphery takes place after engulfment into the cytoplasm, whereas stationary beads, placed near the cell center, are not engulfed. These results demonstrate that centripetal motion of adhering particles may occur inside as well as outside the cell. Inhibition of actomyosin activity is used to explore requirements for engulfment and aspects of the bead movement. Centripetal movement of adherent particles seems to depend on mechanisms distinct from those driving overall cell contractility.

The nuclear pore complex sits as the gateway between the genomic, nuclear environment and the primarily enzymatic realm of the cytoplasm. Large channels traversing the two membranes of the nuclear envelope, the nuclear pores govern the passage of specific molecules between these two major compartments of the cell. Its ability to limit passage to specific molecules, and furthermore to pump them against a gradient in concentration, raises intriguing physical questions. This article reviews basic aspects of the structure and operation of this biochemical pump, whose thermodynamic cycle differs from that of conventional machines.

A method for creating microscale-patterned surfaces by direct-write lithography is described. A tightly focused, low-power infrared laser beam is applied to a homogeneous precursor solution containing soluble reagents. When the laser is focused directly at a glass–solution interface, it initiates the local precipitation of a solid product that attaches firmly to the substrate. Operating the laser momentarily forms isolated spots, whereas moving the microscope stage or the laser spot draws continuous lines. The method has been demonstrated for metallic silver and gold, for oxidized copper, and for molybdenum disulfide, suggesting a broad range of suitable materials. Silver patterns were further modified by chemical reactions. Their morphology and physical properties can be altered during deposition by the use of capping agents, which may provide an onset for further functionalization.

We show that within a living eukaryotic cell, mean square displacement of an engulfed microsphere shows enhanced diffusion scaling as t(3/2) at short times, with a clear crossover to subdiffusive or ordinary diffusion scaling at longer times. The motion, observed nearby the nucleus, is due to interactions with microtubule-associated motor proteins rather than thermal Brownian motion. We propose that time-dependent friction introduced by the intracellular polymer networks leads to sub-ballistic motion, analogous to subdiffusion observed in passive networks of semiflexible biopolymers.

X-linked lissencephaly is a severe brain malformation affecting males. Recently it has been demonstrated that the doublecortin gene is implicated in this disorder. In order to study the function of Doublecortin, we analyzed the protein upon transfection of COS cells. Doublecortin was found to bind to the microtubule cytoskeleton. In vitro assays (using biochemical methods, DIC microscopy and electron microscopy) demonstrate that Doublecortin binds microtubules directly, stabilizes them and causes bundling. In vivo assays also show that Doublecortin stabilizes microtubules and causes bundling. Doublecortin is a basic protein with an iso-electric point of 10, typical of microtubule-binding proteins. However, its sequence contains no known microtubule-binding domain(s). The results obtained in this study with Doublecortin and our previous work on another lissencephaly gene ( LIS1 ) emphasize the central role of regulation of microtubule dynamics and stability during neuronal morphogenesis.

Metal ions play essential roles in many aspects of biological chemistry, including oxygen transport, enzyme catalysis, and maintenance of biopolymer integrity. Cryo-electron microscopy is in principle sensitive to metal ions due to the stronger Coulomb potential relative to surrounding light elements, but conventional defocus phase contrast may not be the ideal approach to visualization. In tomography even small gold nanoparticles (

The dynamics of a polymer network are studied by direct view observation of the motion of a single point within a single polymer. Taking advantage of rather rigid biological microtubules as a case study, we expand the space and time scales of the system to those accessible by optical microscopy and standard video tools. Tracking is achieved by chemically attaching an optically resolved microsphere to a single point on the filament. We study the time dynamics of this point, without spatial averaging inherent in scattering methods. It is shown that the mean square displacement of the individual point is sensitive to local filament and network properties. [S0031-9007(97)05158-2] PACS numbers: 83.10.Nn An essential physical question in the study of polymer dynamics is how to relate the bulk rheological response of a network to the molecular-scale motions executed by an individual monomer. The latter are driven by random thermal collisions with the surrounding solvent molecules, and constrained at two levels: the embedding of the monomer within the polymer and the entanglement of the polymer within the network. In conventional chemical polymers the relevant length scales are on the order of 1 nm, far too small to be resolved by direct imaging techniques. Typical methods of study include light and neutron scattering, which are sensitive to local fluctuations in the density of the bulk sample. Light scattering can provide superb time resolution, while the few-angstrom wavelength of neutrons offers much improved spatial sensitivity. Nonetheless, these methods make a spatial averaging of the fluctuations taking place in a large volume of the sample. Attention is typically focused on the time domain, with use of fluctuation-dissipation arguments to relate modes of response to the thermally generated fluctuations. Recently, there have been a number of attempts to investigate local dynamics by direct imaging methods. The main trend has been to exploit biological polymers for their relative stiffness compared to simple synthetic ones, and also for their intrinsic biophysical interest. One approach has been to fluorescently label an entire polymer and watch its motion using video microscopy. The polymer is analyzed by measuring the wave vector [1] or the cosine correlation function [2]. In these methods the dynamics of a monomer is studied implicitly by measuring the dynamics of the entire polymer. Another method has been to implant a large bead in a network and investigate its restricted diffusion due to collisions with the surrounding filaments [3]. In this method, interpretation in terms of single filament dynamics must involve some a priori assumption. The approach described here is to prepare a system in which it is possible to image monomer motion directly, and to study the polymer network via the dynamics of a single monomer [4]. To this end, we expand the size and time scales of the system by exploiting biological polymers known as microtubules. These self-assembling filaments are stiff enough to maintain an average direction from end to end, yet sufficiently flexible to display thermally driven undulations. We “tag” a single monomer by attaching to it an optically resolvable bead (Fig. 1) and trace the bead’s position by video analysis. The motion of the bead displays the thermally driven motion of the microtubule itself. Using the clock provided by the video frame rate, we measure the mean square displacement (MSD) vs time interval of the bead. Classical random walk diffusion predicts that the MSD grows linearly in time, and our results lie in the deviations from this familiar situation. We interpret the data to probe the internal state of the network, e.g., to detect entanglement or quenched stress. Background for this experiment is set by considering a bead attached to a single microtubule whose dynamics are governed by thermally driven bending fluctuations. The important parameters governing the MSD at a point

Cryo-transmission electron tomography (CET) has emerged as a vital tool for structural biology studies of cells and viruses. Direct imaging of fully hydrated, vitrified material represents the state of the art for preservation of biological samples. Lacking heavy metal stains, CET relies on phase contrast typically obtained by defocusing the sample. The dependence on phase coherence, as well as cumulative radiation damage on frozen hydrated specimens, impose an inherent upper limit on sample thickness and usable tilt range. Even with energy filtration to remove the contribution of inelastic scattering, CET suffers from "missing wedge" effects and low signal-to-noise ratio. Scanning transmission electron microscopy (STEM) circumvents the need for phase contrast with incoherent detection, and has recently been extended to biological tomography. However the weak electron scattering by light elements was thought to preclude its application to unstained cryogenic specimens. We show this not to be the case. To the contrary, we find that raster scanning permits a higher total dose than conventional wide-field imaging, and the independent STEM detection in bright and dark field detectors provides sufficient contrast to show detailed cellular architecture similar to that provided by wide-field tomography. An important difference is that the specimen remains dynamically in focus even at high very tilts up to 70°. This significantly improves the depth resolution in reconstructions. Sample thickness limitations are also relaxed. We demonstrate the cryo-STEM tomography (CSTET) method using unstained, vitrified bacteria and human epithelial cells.

Genetically encoded supramolecular protein assemblies (SMPAs) are induced to form in living cells by combination of distinct self-assembly properties. A single fusion construct contains genes encoding the heavy chain (H) of human ferritin and the citrine fluorescent protein, the latter exposing a weak dimerization interface, as well as a nuclear localization signal. Upon expression in HeLa cells, in vivo confocal fluorescence and differential interference contrast imaging revealed extended SMPA structures exclusively in the nuclei. Assemblies were typically round and took alveolar, shell-like, or hybrid structure. Transmission electron microscopy revealed a crystalline packing. Site-specific mutagenesis of the citrine dimerization interface clarified the mechanism of SMPA formation. The constituent proteins retained their activity in iron binding and fluorescence emission, thus suggesting a general strategy for formation of synthetic cellular bodies with specific biochemical function.

Summary In Plasmodium falciparum , the deadliest form of human malaria, the nuclear periphery has drawn much attention due to its role as a sub-nuclear compartment involved in virulence gene expression. Recent data have implicated components of the nuclear envelope in regulating gene expression in several eukaryotes. Special attention has been given to nucleoporins that compose the nuclear pore complex (NPC). However, very little is known about components of the nuclear envelope in Plasmodium parasites. Here we characterize PfSec13, an unusual nucleoporin of P. falciparum , which shows unique structural similarities suggesting that it is a fusion between Sec13 and Nup145C of yeast. Using super resolution fluorescence microscopy (3D-SIM) and in vivo imaging, we show that the dynamic localization of PfSec13 during parasites9 intra-erythrocytic development corresponds with that of the NPCs and that these dynamics are associated with microtubules rather than with F-actin. In addition, PfSec13 does not co-localize with the heterochormatin markers HP1 and H3K9me3, suggesting euchromatic location of the NPCs. The proteins associated with PfSec13 indicate that this unusual Nup is involved in several cellular processes. Indeed, ultrastructural and chromatin immunoprecipitation analyses revealed that, in addition to the NPCs, PfSec13 is found in the nucleoplasm where it is associated with chromatin. Finally, we used peptide nucleic acids (PNA) to downregulate PfSec13 and show that it is essential for parasite proliferation in human erythrocytes.

Microtubules are ordered polymers of the protein tubulin that are part of the flexible, plastic, and even self-effacing skeleton of eukaryotic cells [1,2]. They are hollow cylinders, 25 nm in diameter and tens of microns long [3]. Microtubules have large bending rigidity, with a persistence length of the order of millimeters [4]. The elastic properties of microtubules and their interaction with the cell membrane are essential in defining cell morphology. This Letter is concerned with microtubules within artificial phospholipid vesicles, their shapes, and the shape transformations induced by membrane tension. A single microtubule deforms a vesicle into an oval. Under tension, the microtubule buckles and the vesicle recovers a spherical shape. This allows a measurement of the microtubule bending rigidity. A large number of microtubules organize inside a vesicle into a linear bundle which protrudes without piercing the membrane. The vesicle contains the bundle by extending a pair of narrow tubes about the microtubule extremities while maintaining

Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.

A volatile liquid wetting a substrate forms a thick, uniform film in equilibrium with a saturated vapor phase. We show that under evaporating conditions such a liquid is effectively non-wetting, i.e. stable as a droplet on top of a thin film. This is in agreement with recent observations. Here we calculate the contact angle of the droplet as a function of the liquid-vapor surface tension and the partial pressure. This effect will be useful as a means of probing the microscopic interfacial forces involved in wetting via macroscopic measurements.

SummaryAgrobacterium is known for gene transfer to plants. In addition to a linear ssDNA oligonucleotide, Agrobacterium tumefaciens secretes an abundant ssDNA-binding effector, VirE2. In many ways VirE2 adapts the conjugation mechanism to transform the eukaryotic host. The crystal structure of VirE2 shows two compact domains joined by a flexible linker. Bound to ssDNA, VirE2 forms an ordered solenoidal shell, or capsid known as the T-complex. Here, we present a three-dimensional reconstruction of the VirE2-ssDNA complex using cryo-electron microscopy and iterative helical real-space reconstruction. High-resolution refinement was not possible due to inherent heterogeneity in the protein structure. By a combination of computational modeling, chemical modifications, mass spectroscopy, and electron paramagnetic resonance, we found that the N-terminal domain is tightly constrained by both tangential and longitudinal links, while the C terminus is weakly constrained. The quaternary structure is thus rigidly assembled while remaining locally flexible. This flexibility may be important in accommodating substrates without sequence specificity.

Equilibrium crystal shapes are defined uniquely by the Wulff construction. The classical kinematic theory of crystal growth, due mainly to Frank and Chernov, provides a mathematically equivalent prescription for the limiting growth shape. To connect these two well studied states, we derive a local geometric growth model and examine the transient shape evolution of an equilibrium form containing both facets and rough regions. Our model is appropriate to the weakly driven growth of a two-dimensional single crystal with n-gonal symmetry and arbitrary closed initial shape. The model links disparate kinetic processes determined by the local interfacial structure to the isotropic growth drive, and reproduces the experimentally observed transition from a partly rounded equilibrium shape to a highly faceted crystal which we term 'global kinetic faceting'. We solve for the transient shape dynamics globally, and locally, and in the latter case present a curvature evolution equation valid for any local growth law. Both approaches show that, during kinetic faceting, rough orientations grow out of existence with decreasing curvature.

Soft X-ray cryo-microscopy (cryo-XT) offers an ideal complement to electron cryo-microscopy (cryo-EM). Cryo-XT is applicable to samples more than an order of magnitude thicker than cryo-EM, albeit at a more modest resolution of tens of nanometers. Furthermore, the natural contrast obtained in the “water-window” by differential absorption by organic matter vs water yields detailed images of organelles, membranes, protein complexes, and other cellular components. Cryo-XT is thus ideally suited for tomography of eukaryotic cells. The increase in sample thickness places more stringent demands on sample preparation, however. The standard method for cryo-EM, i.e., plunging to a cryogenic fluid such as liquid ethane, is no longer ideally suited to obtain vitrification of thick samples for cryo-XT. High pressure freezing is an alternative approach, most closely associated with freeze-substitution and embedding, or with electron cryo-microscopy of vitreous sections (CEMOVIS). We show here that high pressure freezing can be adapted to soft X-ray tomography of whole vitrified samples, yielding a highly reliable method that avoids crystallization artifacts and potentially offers improved imaging conditions in samples not amenable to plunge-freezing.

The deadliest form of human malaria is caused by the protozoan parasite Plasmodium falciparum. The complex life cycle of this parasite is associated with tight transcriptional regulation of gene expression. Nuclear positioning and chromatin dynamics may play an important role in regulating P. falciparum virulence genes. We have applied an emerging technique of electron microscopy to construct a 3D model of the parasite nucleus at distinct stages of development within the infected red blood cell. We have followed the distribution of nuclear pores and chromatin throughout the intra-erythrocytic cycle, and have found a striking coupling between the distributions of nuclear pores and chromatin organization. Pore dynamics involve clustering, biogenesis, and division among daughter cells, while chromatin undergoes stage-dependent changes in packaging. Dramatic changes in heterochromatin distribution coincide with a previously identified transition in gene expression and nucleosome positioning during the mid-to-late schizont phase. We also found a correlation between euchromatin positioning at the nuclear envelope and the local distribution of nuclear pores, as well as a dynamic nuclear polarity during schizogony. These results suggest that cyclic patterns in gene expression during parasite development correlate with gross changes in cellular and nuclear architecture.

Delivery of DNA to the cell nucleus is an essential step in many types of viral infection, transfection, gene transfer by the plant pathogen Agrobacterium tumefaciens and in strategies for gene therapy. Thus, the mechanism by which DNA crosses the nuclear pore complex (NPC) is of great interest. Using nuclei reconstituted in vitro in Xenopus egg extracts, we previously studied DNA passage through the nuclear pores using a single-molecule approach based on optical tweezers. Fluorescently labeled DNA molecules were also seen to accumulate within nuclei. Here we find that this import of DNA relies on a soluble protein receptor of the importin family. To identify this receptor, we used different pathway-specific cargoes in competition studies as well as pathway-specific dominant negative inhibitors derived from the nucleoporin Nup153. We found that inhibition of the receptor transportin suppresses DNA import. In contrast, inhibition of importin beta has little effect on the nuclear accumulation of DNA. The dependence on transportin was fully confirmed in assays using permeabilized HeLa cells and a mammalian cell extract. We conclude that the nuclear import of DNA observed in these different vertebrate systems is largely mediated by the receptor transportin. We further report that histones, a known cargo of transportin, can act as an adaptor for the binding of transportin to DNA.

Single crystals of ice are grown from vapor, and viewed by means of an interference microscope. The basal facet persists until melting, but the prism facet disappears above about -2 \ifmmode^\circ\else\textdegree\fi{}C, the surface taking a dome shape. With the temperature dropping from near 0 \ifmmode^\circ\else\textdegree\fi{}C, a facet reappears at -1.35 \ifmmode^\circ\else\textdegree\fi{}C. The measured curvature just above the transition is consistent with the prediction of a ``universal curvature jump'' by Jayaprakash, Saam, and Teitel. The surface curvature near the facet edge is also measured.

Abnormal neuronal migration is manifested in brain malformations such as lissencephaly. The impairment in coordinated cell motility likely reflects a faulty mechanism of cell polarization or coupling between polarization and movement. Here we report on the relationship between the polarity kinase MARK2/Par-1 and its substrate, the well-known lissencephaly-associated gene doublecortin (DCX), during cortical radial migration. We have previously shown usingin uteroelectroporation that reduced MARK2 levels resulted in multipolar neurons stalled at the intermediate zone border, similar to the phenotype observed in the case of DCX silencing. However, whereas reduced MARK2 stabilized microtubules, we show here that knock-down of DCX increased microtubule dynamics. This led to the hypothesis that simultaneous reduction may alleviate the phenotype. Coreduction of MARK2 and DCX resulted in a partial restoration of the normal neuronal migration phenotypein vivo. The kinetic behavior of the centrosomes reflected the different molecular mechanisms activated when either protein was reduced. In the case of reducing MARK2 processive motility of the centrosome was hindered, whereas when DCX was reduced, centrosomes moved quickly but bidirectionally. Our results stress the necessity for successful coupling between the polarity pathway and cytoplasmic dynein-dependent activities for proper neuronal migration.