Search

In the late stages of the HIV-1 life cycle, membrane localization and self-assembly of Gag polyproteins induce membrane deformation and budding. Release of the virion requires direct interaction between immature Gag lattice and upstream ESCRT machinery at the viral budding site, followed by assembly of downstream ESCRT-III factors, culminating in membrane scission. However, molecular details of upstream ESCRT assembly dynamics at the viral budding site remain unclear. In this work, using coarse-grained (CG) molecular dynamics (MD) simulations, we investigated the interactions between Gag, ESCRT-I, ESCRT-II, and membrane to delineate the dynamical mechanisms by which upstream ESCRTs assemble templated by late-stage immature Gag lattice. We first systematically derived "bottom-up" CG molecular models and interactions of upstream ESCRT proteins from experimental structural data and extensive all-atom MD simulations. Using these molecular models, we performed CG MD simulations of ESCRT-I oligomerization and ESCRT-I/II supercomplex formation at the neck of the budding virion. Our simulations demonstrate that ESCRT-I can effectively oligomerize to higher-order complexes templated by the immature Gag lattice both in the absence of ESCRT-II and when multiple copies of ESCRT-II are localized at the bud neck. The ESCRT-I/II supercomplexes formed in our simulations exhibit predominantly columnar structures, which has important implications for the nucleation pathway of downstream ESCRT-III polymers. Importantly, ESCRT-I/II supercomplexes bound to Gag initiate membrane neck constriction by pulling the inner edge of the bud neck closer to the ESCRT-I headpiece ring. Our findings serve to elucidate a network of interactions between upstream ESCRT machinery, immature Gag lattice, and membrane neck that regulate protein assembly dynamics at the HIV-1 budding site.

Bibenzyl derivatives comprising two benzene rings are secondary plant metabolites with significant therapeutic value. To date, bibenzyl derivatives in the Plant kingdom have been primarily identified in bryophytes, orchids, and Cannabis sativa. The metabolic cost investment by plant species for the synthesis of these bioactive secondary metabolites is rationalized as a mechanism of plant defense in response to oxidative stress induced by biotic/abiotic factors. Bibenzyl derivatives are synthesized from core phenylpropanoid biosynthetic pathway offshoots in plant species. Mangrove and mangrove associate species thrive under extreme ecological niches such as a hypersaline intertidal environment through unique adaptive and acclimative characteristics, primarily involving osmotic adjustments followed by oxidative stress abatement. Several primary/secondary bioactive metabolites in mangrove species have been identified as components of salinity stress adaptation/acclimation/mitigation; however, the existence of a bibenzyl scaffold in mangrove species functioning in this context remains unknown. We here report the confirmed detection of a core bibenzyl scaffold from extensive gas chromatography-mass spectrometry and gas chromatography-flame ionization detection analyses of 28 mangrove and mangrove associate species from the Indian Sundarbans. We speculate that the common presence of this bibenzyl core molecule in 28 mangrove and associate species may be related to its synthesis via branches of the phenylpropanoid biosynthetic pathway induced under high salinity, which functions to detoxify reactive oxygen species as a protection for the maintenance of plant metabolic processes. This finding reveals a new eco-physiological functional role of bibenzyls in unique mangrove ecosystem.

The ESCRT complexes drive membrane scission in HIV-1 release, autophagosome closure, multivesicular body biogenesis, cytokinesis, and other cell processes. ESCRT-I is the most upstream complex and bridges the system to HIV-1 Gag in virus release. The crystal structure of the headpiece of human ESCRT-I comprising TSG101-VPS28-VPS37B-MVB12A was determined, revealing an ESCRT-I helical assembly with a 12-molecule repeat. Electron microscopy confirmed that ESCRT-I subcomplexes form helical filaments in solution. Mutation of VPS28 helical interface residues blocks filament formation in vitro and autophagosome closure and HIV-1 release in human cells. Coarse-grained (CG) simulations of ESCRT assembly at HIV-1 budding sites suggest that formation of a 12-membered ring of ESCRT-I molecules is a geometry-dependent checkpoint during late stages of Gag assembly and HIV-1 budding and templates ESCRT-III assembly for membrane scission. These data show that ESCRT-I is not merely a bridging adaptor; it has an essential scaffolding and mechanical role in its own right.

The appearance of ice I in the smallest possible clusters and the nature of its phase coexistence with liquid water could not thus far be unraveled. The experimental and theoretical infrared spectroscopic and free-energy results of this work show the emergence of the characteristic hydrogen-bonding pattern of ice I in clusters containing only around 90 water molecules. The onset of crystallization is accompanied by an increase of surface oscillator intensity with decreasing surface-to-volume ratio, a spectral indicator of nanoscale crystallinity of water. In the size range from 90 to 150 water molecules, we observe mixtures of largely crystalline and purely amorphous clusters. Our analysis suggests that the liquid-ice I transition in clusters loses its sharp 1st-order character at the end of the crystalline-size regime and occurs over a range of temperatures through heterophasic oscillations in time, a process without analog in bulk water.

Host proteins CPSF6, NUP153, and SEC24C are vital for HIV-1 infection. They bind to the viral capsid protein and contribute to shuttling of virions through the cytoplasm (SEC24C), import into the nucleus (NUP153 and CPSF6) and subsequent trafficking to preferred integration sites (CPSF6). Here, Wei et al. combine structural, biochemical and virological assays to emphasize the importance of prion-like low complexity domains surrounding short phenylalanine-glycine regions in binding and increasing the avidity when interacting with viral capsid.

Tensile-strained germanium (ε-Ge) has attracted significant interest due to its unique properties in emerging optoelectronic devices. High tensile-strained Ge materials with superior quality are still being investigated due to the intrinsic instability of ε-Ge against the formation of stacking faults (SFs). This work seeks to improve the understanding of these limits by closely examining, experimentally, the mechanisms by which tensile strain is relaxed in Ge. Here, ε-Ge layers were grown on highly mismatched In0.53Ga0.47As and In0.51Al0.49As virtual substrates (f = 3.4%), formed as quantum dots (QDs) by molecular beam epitaxy, and their strain relaxation mechanism was analyzed. Both In0.51Al0.49As and In0.53Ga0.47As growth templates were created using an Al0.49In0.51x(Ga0.51)1−xAs linearly graded metamorphic buffer on GaAs(001)/2° and InP(001)/0.5° substrates, respectively. Fully 3D growth (Volmer–Weber growth mode) due to high tensile strain resulted in Ge QDs with an average diameter and height of ∼50 nm and ∼20 nm, respectively, and a uniform density of ∼320 μm−2. Analysis of the interfacial electronic structure using high-resolution transmission electron microscopy collected from the Ge QDs indicated that minimal tensile strain was retained in Ge due to SF formation, corroborated via the Raman results. All Ge QDs contain multiple SFs of the close-packed {111} planes nucleated by Shockley partial dislocations with Burger vectors b = 〈112〉. The presence of additional misfit dislocations at the Ge/In0.51Al0.49As or Ge/In0.53Ga0.47As heterointerface, not associated with SFs, indicates further relaxation by perfect dislocations with Burger vectors b = ½〈110〉. The tensile misfit of 3.4% in Ge revealed instability against SF formation, and the availability of a defect type must have the effect of lowering the critical layer thickness for ε-Ge layers. Thus, the above results suggest that a maximum tensile strain amount >3.4% is not achievable in Ge without the formation of Shockley partial dislocations. [ABSTRACT FROM AUTHOR]

Crop acreage analysis and yield estimation are of prime importance in field-level agricultural monitoring and management. This enables prudent decision making during any crop failure event and for ensuing crop insurance. The free availability of the high resolution Sentinel-2 satellite datasets has created new possibilities for mapping and monitoring agricultural lands in this regard. In the present study conducted on the Tamluk Subdivision of the Purba Medinipur District of West Bengal, the heterogeneous crop area was mapped according to the respective crop type, using Sentinel-2 multi-spectral images and two machine learning algorithms- K Nearest Neighbour (KNN) and Random Forest (RF). Plot-level field information was collected from different cropland types to frame the training and validation datasets (comprising 70% and 30% of the total dataset, respectively) for cropland classification and accuracy assessment. Through this, the major summer crop acreage was identified (Boro rice, vegetables and betel vine- the three main crops in the study area). The extracted maps had an overall accuracy of 97.16% and 97.22%, respectively, in the KNN and RF classifications, with respective Kappa index values of 95.99% and 96.08%, and the RF method proved to be more accurate. This study was particularly useful in mapping the betel leaf acreage herein since scant information exists for this crop and it is cultivated by many smallholder farmers in the region. The methods used in this paper can be readily applied elsewhere for accurately enumerating the respective crop acreages.

Antifreeze proteins (AFPs) inhibit ice growth in organisms living in cold environments. Hyperactive insect AFPs are particularly effective, binding ice through "anchored clathrate" motifs. It has been hypothesized that the binding of hyperactive AFPs to ice is facilitated by preordering of water at the ice-binding site (IBS) of the protein in solution. The antifreeze protein TmAFP displays the best matching of its binding site to ice, making it the optimal candidate to develop ice-like order in solution. Here we use multiresolution simulations to unravel the mechanism by which TmAFP recognizes and binds ice. We find that water at the IBS of the antifreeze protein in solution does not acquire ice-like or anchored clathrate-like order. Ice recognition occurs by slow diffusion of the protein to achieve the proper orientation with respect to the ice surface, followed by fast collective organization of the hydration water at the IBS to form an anchored clathrate motif that latches the protein to the ice surface. The simulations suggest that anchored clathrate order could develop on the large ice-binding surfaces of aggregates of ice-nucleating proteins (INP). We compute the infrared and Raman spectra of water in the anchored clathrate motif. The signatures of the OH stretch of water in the anchored clathrate motif can be distinguished from those of bulk liquid in the Raman spectra, but not in the infrared spectra. We thus suggest that Raman spectroscopy may be used to probe the anchored clathrate order at the ice-binding surface of INP aggregates.

This article provides a concise overview of the synthesis and significance of modified C-nucleosides in medicinal chemistry. C-nucleosides, which are more resistant to hydrolysis than N-nucleosides, have various applications in drug design and chemical biology. The article discusses the development of synthetic methodologies for C-nucleoside analogues and their role as inhibitors of purine nucleoside phosphorylase or IMP dehydrogenase. It also highlights the use of nucleoside analogues in chemotherapy, gene expression inhibition, and other therapeutic strategies. The article concludes with a discussion of different synthetic strategies and the importance of C-nucleoside scaffolds in biology and medicine. The text explores various methods for the synthesis of C-nucleoside analogues, including the use of carbon nucleophiles and intermolecular cyclization. Specific compounds, such as showdomycin and pseudouridimycin, are mentioned for their potential applications in medicinal chemistry and chemical biology. The development of efficient and selective techniques for C-glycosidation processes is still ongoing, but these methods show promise for the synthesis of new molecules and the discovery of new properties and modes of action. [Extracted from the article]

A novel, tunnel field-effect transistor (TFET)-based adiabatic logic (TBAL) circuit topology has been proposed, evaluated and benchmarked with several device architectures (planar MOSFET, FinFET, and TFET) and AL implementations (efficient charge recovery logic, 2N-2N2P, positive feedback adiabatic logic) operating in the ultra-low voltage (0.3 V ≥ VDD ≤ 0.6 V) regime. By incorporating adiabatic logic functionality into standard combinational logic, an 80% reduction in energy/cycle was achieved. A further 80% reduction in energy/cycle was demonstrated by utilizing near broken-gap TFET devices and simultaneous scaling of supply voltage to 0.3 V, resulting in a 96% reduction in energy/cycle as compared to conventional Si CMOS. Extension of operating frequency beyond 10 MHz, coupled with sub-threshold circuit operation, shows the feasibility of TBAL for energy-efficient Internet of Things applications.

Relaxed, high-quality, compositionally step-graded InAsyP1-y layers with an As composition of y=0.4, corresponding to a lattice mismatch of similar to1.3% were grown on InP substrates using solid-source molecular-beam epitaxy. Each layer was found to be nearly fully relaxed observed by triple axis x-ray diffraction, and plan-view transmission electron microscopy revealed an average threading dislocations of 4x10(6) cm(-2) within the InAs0.4P0.6 cap layer. Extremely ordered crosshatch morphology was observed with very low surface roughness (3.16 nm) compared to cation-based In0.7Al0.3As/InxAl1-xAs/InP graded buffers (10.53 nm) with similar mismatch and span of lattice constants on InP. The results show that InAsyP1-y graded buffers on InP are promising candidates as virtual substrates for infrared and high-speed metamorphic III-V devices. (C) 2003 American Institute of Physics.

In this paper, for the first time, the performance analysis of short channel In0.53Ga0.47As quantum well (QW) 3-D tri-gate technology with advanced high-κ gate dielectric, TaSiOx is presented. We benchmark the projected performance of sub-10 nm In0.53Ga0.47As transistor technology as a function of fin width, fin aspect ratio, and gate length scaling based on present-day lithographic advancement aiding InGaAs QW tri-gate technology as a replacement to Si for sub-10 nm transistor technology. The highly scaled oxide (EOT ~ 12Å) while retaining superior interfacial properties (Dit ~ 4 × 1011 cm-2eV-1) provides higher ON current for given idle performance. Furthermore, the simulated In0.53Ga0.47As tri-gate transistor exhibits superior gate electrostatic control with low OFF-state current (IOFF) ~ 24.5 nA/μm, peak transconductance (gm) ~ 2 mS/ μm and high ION/IOFF ratio~ 2.3 × 103, aiding the case of alternate channel transistors for high-speed and low-power CMOS logic.