Envelope Dynamics Research Articles

Single Molecule Imaging of HIV-1 Envelope Dynamics and Gag Lattice Association Exposes Determinants Responsible for Virus Incorporation

Single Molecule Imaging of HIV-1 Envelope Dynamics and Gag Lattice Association Exposes Determinants Responsible for Virus Incorporation

Envelope dynamics and stability with non-linear space-charge forces

We developed a model to calculate the stability of Gaussian beam distributions with non-linear space-charge forces in the presence of random and skew-quadrupole errors. The effect of the space-charge force on the beam matrix is calculated analytically including full cross-plane coupling in 4D phase space, which allows us to perform fast parameter studies. For stability analysis, we find the fixed points of the beam including the space-charge forces and construct a Jacobi-matrix by slightly perturbing the periodic solution. The stability of envelope oscillations is inferred by eigenvalue analysis. Furthermore, we employ envelope tracking as a complementary method and compare the results of the eigenvalue analysis with FFT data from the tracked envelope. The non-linearity of the space-charge force in combination with lattice errors and beam coupling opens up for envelope-lattice resonances and envelope coupling resonances. Hitting these resonances leads to envelope blow-up, causing an effective beam mismatch. Therefore, we finally examine the effect of beam mismatch on the envelope tune-shift and its stability.

Nuclear envelope dynamics during mammalian spermatogenesis: new insights on male fertility.

The production of highly specialized spermatozoa from undifferentiated spermatogonia is a strictly organized and programmed process requiring extensive restructuring of the entire cell. One of the most remarkable cellular transformations accompanying the various phases of spermatogenesis is the profound remodelling of the nuclear architecture, in which the nuclear envelope (NE) seems to be crucially involved. In recent years, several proteins from the distinct layers forming the NE (i.e. the inner and outer nuclear membranes as well as the nuclear lamina) have been associated with meiosis and/or spermiogenesis in different mammalian species. Among these are A- and B-type lamins, Dpy-19-like protein 2 (DPY19L2), lamin B receptor (LBR), lamina-associated polypeptide 1 (LAP1), LAP2/emerin/MAN1 (LEM) domain-containing proteins, spermatogenesis-associated 46 (SPATA46) and diverse elements of the linker of nucleoskeleton and cytoskeleton (LINC) complex, namely Sad-1/UNC-84 homology (SUN) and Klarsicht/ANC-1/Syne-1 homology (KASH) domain-containing proteins. Herein, we summarize the current state of the art on the cellular and subcellular distribution of NE proteins expressed during mammalian spermatogenesis, and discuss the latest research developments regarding their testis-specific functions. This review provides a comprehensive and innovative overview of the NE network as a regulatory platform and as an essential determinant of efficient meiotic chromosome recombination as well as spermiogenesis-associated nuclear remodelling and differentiation in mammalian male germline cells. Thus, this review provides important novel insights on the biological relevance of NE proteins for male fertility.

Mining Within-Trial Oscillatory Brain Dynamics to Address the Variability of Optimized Spatial Filters.

Data-driven spatial filtering algorithms optimize scores, such as the contrast between two conditions to extract oscillatory brain signal components. Most machine learning approaches for the filter estimation, however, disregard within-trial temporal dynamics and are extremely sensitive to changes in training data and involved hyperparameters. This leads to highly variable solutions and impedes the selection of a suitable candidate for, e.g., neurotechnological applications. Fostering component introspection, we propose to embrace this variability by condensing the functional signatures of a large set of oscillatory components into homogeneous clusters, each representing specific within-trial envelope dynamics. The proposed method is exemplified by and evaluated on a complex hand force task with a rich within-trial structure. Based on electroencephalography data of 18 healthy subjects, we found that the components' distinct temporal envelope dynamics are highly subject-specific. On average, we obtained seven clusters per subject, which were strictly confined regarding their underlying frequency bands. As the analysis method is not limited to a specific spatial filtering algorithm, it could be utilized for a wide range of neurotechnological applications, e.g., to select and monitor functionally relevant features for brain-computer interface protocols in stroke rehabilitation.

Nuclear envelope organization in Dictyostelium discoideum.

The nuclear envelope consists of the outer and the inner nuclear membrane, the nuclear lamina and the nuclear pore complexes, which regulate nuclear import and export. The major constituent of the nuclear lamina of Dictyostelium is the lamin NE81. It can form filaments like B-type lamins and it interacts with Sun1, as well as with the LEM/HeH-family protein Src1. Sun1 and Src1 are nuclear envelope transmembrane proteins involved in the centrosome-nucleus connection and nuclear envelope stability at the nucleolar regions, respectively. In conjunction with a KASH-domain protein, Sun1 usually forms a so-called LINC complex. Two proteins with functions reminiscent of KASH-domain proteins at the outer nuclear membrane of Dictyostelium are known; interaptin which serves as an actin connector and the kinesin Kif9 which plays a role in the microtubule-centrosome connector. However, both of these lack the conserved KASH-domain. The link of the centrosome to the nuclear envelope is essential for the insertion of the centrosome into the nuclear envelope and the appropriate spindle formation. Moreover, centrosome insertion is involved in permeabilization of the mitotic nucleus, which ensures access of tubulin dimers and spindle assembly factors. Our recent progress in identifying key molecular players at the nuclear envelope of Dictyostelium promises further insights into the mechanisms of nuclear envelope dynamics.

Acute Modulation of Mycobacterial Cell Envelope Biogenesis by Front‐Line Tuberculosis Drugs

AbstractFront‐line tuberculosis (TB) drugs have been characterized extensively in vitro and in vivo with respect to gene expression and cell viability. However, little work has been devoted to understanding their effects on the physiology of the cell envelope, one of the main targets of this clinical regimen. Herein, we use metabolic labeling methods to visualize the effects of TB drugs on cell envelope dynamics in mycobacterial species. We developed a new fluorophore–trehalose conjugate to visualize trehalose monomycolates of the mycomembrane using super‐resolution microscopy. We also probed the relationship between mycomembrane and peptidoglycan dynamics using a dual metabolic labeling strategy. Finally, we found that metabolic labeling of both cell envelope structures reports on drug effects on cell physiology in two hours, far faster than a genetic sensor of cell envelope stress. Our work provides insight into acute drug effects on cell envelope biogenesis in live mycobacteria.

Acute Modulation of Mycobacterial Cell Envelope Biogenesis by Front-Line Tuberculosis Drugs.

Front-line tuberculosis (TB) drugs have been characterized extensively in vitro and in vivo with respect to gene expression and cell viability. However, little work has been devoted to understanding their effects on the physiology of the cell envelope, one of the main targets of this clinical regimen. Herein, we use metabolic labeling methods to visualize the effects of TB drugs on cell envelope dynamics in mycobacterial species. We developed a new fluorophore-trehalose conjugate to visualize trehalose monomycolates of the mycomembrane using super-resolution microscopy. We also probed the relationship between mycomembrane and peptidoglycan dynamics using a dual metabolic labeling strategy. Finally, we found that metabolic labeling of both cell envelope structures reports on drug effects on cell physiology in two hours, far faster than a genetic sensor of cell envelope stress. Our work provides insight into acute drug effects on cell envelope biogenesis in live mycobacteria.

Improving nuclear envelope dynamics by EBV BFRF1 facilitates intranuclear component clearance through autophagy.

Although a vesicular nucleocytoplasmic transport system is believed to exist in eukaryotic cells, the features of this pathway are mostly unknown. Here, we report that the BFRF1 protein of the Epstein-Barr virus improves vesicular transport of nuclear envelope (NE) to facilitate the translocation and clearance of nuclear components. BFRF1 expression induces vesicles that selectively transport nuclear components to the cytoplasm. With the use of aggregation-prone proteins as tools, we found that aggregated nuclear proteins are dispersed when these BFRF1-induced vesicles are formed. BFRF1-containing vesicles engulf the NE-associated aggregates, exit through from the NE, and putatively fuse with autophagic vacuoles. Chemical treatment and genetic ablation of autophagy-related factors indicate that autophagosome formation and autophagy-linked FYVE protein-mediated autophagic proteolysis are involved in this selective clearance of nuclear proteins. Remarkably, vesicular transport, elicited by BFRF1, also attenuated nuclear aggregates accumulated in neuroblastoma cells. Accordingly, induction of NE-derived vesicles by BFRF1 facilitates nuclear protein translocation and clearance, suggesting that autophagy-coupled transport of nucleus-derived vesicles can be elicited for nuclear component catabolism in mammalian cells.-Liu, G.-T., Kung, H.-N., Chen, C.-K., Huang, C., Wang, Y.-L., Yu, C.-P., Lee, C.-P. Improving nuclear envelope dynamics by EBV BFRF1 facilitates intranuclear component clearance through autophagy.

Generalized parametrization methods for centroid and envelope dynamics of charged particle beams in coupled lattices

For almost 60 years, the well-known Courant-Snyder (CS) theory has been employed as the standard method to describe the uncoupled dynamics of charged particle beams in electromagnetic focusing lattices. Meanwhile, the generalization of the CS theory to coupled dynamics with two or more degrees of freedom has been attempted in numerous directions. The parametrization method developed by Qin and Davidson is particularly noteworthy, because their method enables the treatment of complicated coupled beam dynamics using a remarkably similar mathematical structure to that of the original CS theory. In this paper, we revisit the Qin-Davidson parametrization method and extend it to include beam centroid motions. The linear terms in the quadratic Hamiltonian for the coupled dynamics are handled by introducing a special time-dependent canonical transformation. In this manner, we show that the centroid dynamics is decoupled from the envelope dynamics, even for the cases of coupled lattice, and all formulations of the Qin-Davidson method can be applied in a straightforward manner.

Chaotic bursting in semiconductor lasers.

We investigate the dynamic mechanisms for low frequency fluctuations in semiconductor lasers subjected to delayed optical feedback, using the Lang-Kobayashi model. This system of delay differential equations displays pronounced envelope dynamics, ranging from erratic, so called low frequency fluctuations to regular pulse packages, if the time scales of fast oscillations and envelope dynamics are well separated. We investigate the parameter regions where low frequency fluctuations occur and compute their Lyapunov spectra. Using the geometric singular perturbation theory, we study this intermittent chaotic behavior and characterize these solutions as bursting slow-fast oscillations.

Nonlinear equations of the ion vibration envelope in quadrupole mass filters with cylindrical rods

This paper develops the method of envelope equations to describe the oscillatory motion of ions in quadrupole mass analysers with round rods. Nonlinear equations for the description of the envelope dynamics are obtained taking into account the dodecapole (twelve-pole), the icosapole (twenty-pole) and octopole field distortions. It is shown that the effective potential which determines the ion vibration envelope has a quadratic part, with a magnitude and sign that depend on the location of the ion working point. It also contains a nonlinear part, which does not depend on the ion working point location near the tip of the first stability zone. The motion of ions in quadrupole mass filters with cylindrical rods has a nonlinear character at a theoretical mass resolving power over 1000. In the linear approach, nonlinear effects of the ion motion occur in a narrow zone near the boundaries of the first stability region. This explains low sensitivity of mass analysis within stability islands, which is a direct result of the quadrupole excitations at a frequency different from the main excitation frequency. Thus, the boundaries do not depend on nonlinear field distortions. The results of this theoretical approach are illustrated using the transmission peak shape modelling for mass analysers with different values of the rod radius r relative to the inscribed radius r0.It is shown, that the 6th and 10th order field distortions never compensate each other. However, the octopole field suppresses them completely in the range 1.115<r/r0<1.135, which is considered as an optimum. It is also shown that very substantial improvements in a peak shape can be achieved by adding minor (less than 1%) octopole distortions.

Molecular outflow launched beyond the disk edge

One of the long-standing problems of star formation is the excess of angular momentum of the parent molecular cloud. In the classical picture, a fraction of angular momentum of the circumstellar material is removed by the magneto-centrifugally driven disk wind that is launched from a wide region throughout the disk. In this work, we investigate the kinematics in the envelope-disk transition zone of the Class I object BHB07-11, in the B59 core. For this purpose, we used the Atacama Large Millimeter/submillimeter Array in extended configuration to observe the thermal dust continuum emission ($\lambda_0 \sim$ 1.3 mm) and molecular lines (CO, C$^{18}$O and H$_2$CO), which are suitable tracers of disk, envelope, and outflow dynamics at a spatial resolution of $\sim 30$ AU. We report a bipolar outflow that was launched at symmetric positions with respect to the disk ($\sim$80~AU in radius), but was concentrated at a distance of 90--130~AU from the disk center. The two outflow lobes had a conical shape and the gas inside was accelerating. The large offset of the launching position coincided with the landing site of the infall material from the extended spiral structure (seen in dust) onto the disk. This indicates that bipolar outflows are efficiently launched within a narrow region outside the disk edge. We also identify a sharp transition in the gas kinematics across the tip of the spiral structure, which pinpoints the location of the so-called centrifugal barrier.

Mass Transport from the Envelope to the Disk of V346 Nor: A Case Study for the Luminosity Problem in an FUor-type Young Eruptive Star

Abstract A long-standing open issue of the paradigm of low-mass star formation is the luminosity problem: most protostars are less luminous than theoretically predicted. One possible solution is that the accretion process is episodic. FU Ori-type stars (FUors) are thought to be the visible examples for objects in the high accretion state. FUors are often surrounded by massive envelopes, which replenish the disk material and enable the disk to produce accretion outbursts. However, we have insufficient information on the envelope dynamics in FUors, about where and how mass transfer from the envelope to the disk happens. Here we present ALMA observations of the FUor-type star V346 Nor at 1.3 mm continuum and in different CO rotational lines. We mapped the density and velocity structure of its envelope and analyze the results using channel maps, position–velocity diagrams, and spectro-astrometric methods. We found that V346 Nor is surrounded by gaseous material on a 10,000 au scale in which a prominent outflow cavity is carved. Within the central ∼700 au, the circumstellar matter forms a flattened pseudo-disk where material is infalling with conserved angular momentum. Within ∼350 au, the velocity profile is more consistent with a disk in Keplerian rotation around a central star of . We determined an infall rate from the envelope onto the disk of yr−1, a factor of a few higher than the quiescent accretion rate from the disk onto the star, hinting at a mismatch between the infall and accretion rates as the cause of the eruption.

Single or multiple frequency generators in on-going brain activity: A mechanistic whole-brain model of empirical MEG data

During rest, envelopes of band-limited on-going MEG signals co-vary across the brain in consistent patterns, which have been related to resting-state networks measured with fMRI. To investigate the genesis of such envelope correlations, we consider a whole-brain network model assuming two distinct fundamental scenarios: one where each brain area generates oscillations in a single frequency, and a novel one where each brain area can generate oscillations in multiple frequency bands. The models share, as a common generator of damped oscillations, the normal form of a supercritical Hopf bifurcation operating at the critical border between the steady state and the oscillatory regime. The envelopes of the simulated signals are compared with empirical MEG data using new methods to analyse the envelope dynamics in terms of their phase coherence and stability across the spectrum of carrier frequencies.Considering the whole-brain model with a single frequency generator in each brain area, we obtain the best fit with the empirical MEG data when the fundamental frequency is tuned at 12Hz. However, when multiple frequency generators are placed at each local brain area, we obtain an improved fit of the spatio-temporal structure of on-going MEG data across all frequency bands. Our results indicate that the brain is likely to operate on multiple frequency channels during rest, introducing a novel dimension for future models of large-scale brain activity.

Visualization of mycobacterial membrane dynamics in live cells.

Mycobacteria are endowed with a highly impermeable mycomembrane that confers intrinsic resistance to many antibiotics. Several unique mycomembrane glycolipids have been isolated and structurally characterized, but the underlying organization and dynamics of glycolipids within the cell envelope remain poorly understood. We report here a study of mycomembrane dynamics that was enabled by trehalose–fluorophore conjugates capable of labeling trehalose glycolipids in live actinomycetes. We identified fluorescein–trehalose analogues that are metabolically incorporated into the trehalose mycolates of representative Mycobacterium, Corynebacterium, Nocardia, and Rhodococcus species. Using these probes, we studied the mobilities of labeled glycolipids by time-lapse microscopy and fluorescence recovery after photobleaching experiments and found that mycomembrane fluidity varies widely across species and correlates with mycolic acid structure. Finally, we discovered that treatment of mycobacteria with ethambutol, a front-line tuberculosis (TB) drug, significantly increases mycomembrane fluidity. These findings enhance our understanding of mycobacterial cell envelope structure and dynamics and have implications for development of TB drug cocktails.

Dynamics and Structure-Function Relationships of the Lamin B Receptor (LBR).

The lamin B receptor (LBR) is a multi-spanning membrane protein of the inner nuclear membrane that is often employed as a “reporter” of nuclear envelope dynamics. We show here that the diffusional mobility of full-length LBR exhibits significant regional variation along the nuclear envelope, consistent with the existence of discrete LBR microdomains and the occurrence of multiple, asymmetrically-spaced anastomoses along the nuclear envelope-endoplasmic reticulum interface. Interestingly, a commonly used fusion protein that contains the amino-terminal region and the first transmembrane domain of LBR exhibits reduced mobility at the nuclear envelope, but behaves similarly to full-length LBR in the endoplasmic reticulum. On the other hand, carboxy-terminally truncated mutants that retain the first four transmembrane domains and a part or the whole of the amino-terminal region of LBR are generally hyper-mobile. These results suggest that LBR dynamics is structure and compartment specific. They also indicate that native LBR is probably “configured” by long-range interactions that involve the loops between adjacent transmembrane domains and parts of the amino-terminal region.

Vesicular PtdIns(3,4,5)P3 and Rab7 are key effectors of sea urchin zygote nuclear membrane fusion.

Regulation of nuclear envelope dynamics is an important example of the universal phenomena of membrane fusion. The signalling molecules involved in nuclear membrane fusion might also be conserved during the formation of both pronuclear and zygote nuclear envelopes in the fertilised egg. Here, we determine that class-I phosphoinositide 3-kinases (PI3Ks) are needed for in vitro nuclear envelope formation. We show that, in vivo, PtdIns(3,4,5)P3 is transiently located in vesicles around the male pronucleus at the time of nuclear envelope formation, and around male and female pronuclei before membrane fusion. We illustrate that class-I PI3K activity is also necessary for fusion of the female and male pronuclear membranes. We demonstrate, using coincidence amplified Förster resonance energy transfer (FRET) monitored using fluorescence lifetime imaging microscopy (FLIM), a protein-lipid interaction of Rab7 GTPase and PtdIns(3,4,5)P3 that occurs during pronuclear membrane fusion to create the zygote nuclear envelope. We present a working model, which includes several molecular steps in the pathways controlling fusion of nuclear envelope membranes.

SIRT2 regulates nuclear envelope reassembly through ANKLE2 deacetylation.

ABSTRACTSirtuin 2 (SIRT2) is an NAD-dependent deacetylase known to regulate microtubule dynamics and cell cycle progression. SIRT2 has also been implicated in the pathology of cancer, neurodegenerative diseases and progeria. Here, we show that SIRT2 depletion or overexpression causes nuclear envelope reassembly defects. We link this phenotype to the recently identified regulator of nuclear envelope reassembly ANKLE2. ANKLE2 acetylation at K302 and phosphorylation at S662 are dynamically regulated throughout the cell cycle by SIRT2 and are essential for normal nuclear envelope reassembly. The function of SIRT2 therefore extends beyond the regulation of microtubules to include the regulation of nuclear envelope dynamics.

Flexibility Envelopes for Power System Operational Planning

Modern power systems are undergoing a transitional phase, increasingly incorporating renewable energy sources (RES) to harness their economic and environmental benefits. The main challenge with this transitional phase is the management of the increased variability and uncertainty in the power balance. Legacy operation and planning practices are gradually seen as becoming inadequate or ill-adapted in addressing this challenge. One particular gap in the state of the art, which is of great importance, is estimating the operational flexibility potential of individual power system assets and their aggregation at the system level. System operators need to evaluate and plan ahead flexibility adequacy for their power systems in order to ensure feasible and economical operation under high RES penetration. Likewise, asset owners need to integrate the notion of asset flexibility as part of their investment and operations decisions. To this end, we propose the concept of the flexibility envelope to describe the flexibility potential dynamics of a power system and its individual resources in the operational planning time-frame. We demonstrate that the resulting envelope dynamics can be a starting point for flexibility adequacy planning in systems with highly variable generation.

The Torsin Activator LULL1 Is Required for Efficient Growth of Herpes Simplex Virus 1.

TorsinA is a membrane-tethered AAA+ ATPase implicated in nuclear envelope dynamics as well as the nuclear egress of herpes simplex virus 1 (HSV-1). The activity of TorsinA and the related ATPase TorsinB strictly depends on LAP1 and LULL1, type II transmembrane proteins that are integral parts of the Torsin/cofactor AAA ring, forming a composite, membrane-spanning assembly. Here, we use CRISPR/Cas9-mediated genome engineering to create single- and double knockout (KO) cell lines of TorA and TorB as well as their activators, LAP1 and LULL1, to investigate the effect on HSV-1 production. Consistent with LULL1 being the more potent Torsin activator, a LULL1 KO reduces HSV-1 growth by one order of magnitude, while the deletion of other components of the Torsin system in combination causes subtle defects. Notably, LULL1 deficiency leads to a 10-fold decrease in the number of viral genomes per host cell without affecting viral protein production, allowing us to tentatively assign LULL1 to an unexpected role that precedes HSV-1 nuclear egress. In this study, we conduct the first comprehensive genetic and phenotypic analysis of the Torsin/cofactor system in the context of HSV-1 infection, establishing LULL1 as the most important component of the Torsin system with respect to viral production.