Lessons from a Minimal Genome: What Are the Essential Organizing Principles of a Cell Built from Scratch?

One of the primary challenges facing synthetic biology is reconstituting a living system from its component parts. A particularly difficult landmark is reconstituting a self-organizing system that can undergo autonomous chromosome compaction, segregation, and cell division. Here, we discuss how the syn3.0 minimal genome can inform us of the core self-organizing principles of a living cell and how these self-organizing processes can be built from the bottom up. The review underscores the importance of fundamental biology in rebuilding life from its molecular constituents.     

RLPAS: Reinforcement Learning-based Proactive Auto-Scaler for Resource Provisioning in Cloud Environment

Mobile Networks and Applications - Public cloud system offers Infrastructure-as-a-Service (IaaS) to deliver the computational resources on demand. Resource requirements of a cloud environment are...     

A Generalized Cubemap for Encoding 360° VR Videos using Polynomial Approximation

360^° VR videos provide users with an immersive visual experience. To encode 360^° VR videos, spherical pixels must be mapped onto a two‐dimensional domain to take advantage of the existing video encoding and storage standards. In VR industry, standard cubemap projection is the most widely used projection method for encoding 360^° VR videos. However, it exhibits pixel density variation at different regions due to projection distortion. We present a generalized algorithm to improve the efficiency of cubemap projection using polynomial approximation. In our algorithm, standard cubemap projection can be regarded as a special form with 1st‐order polynomial. Our experiments show that the generalized cubemap projection can significantly reduce the projection distortion using higher order polynomials. As a result, pixel distribution can be well balanced in the resulting 360^° VR videos. We use PSNR, S‐PSNR and CPP‐PSNR to evaluate the visual quality and the experimental results demonstrate promising performance improvement against standard cubemap projection and Google's equi‐angular cubemap.     

Small-Molecule Inhibitors of the Proteasome's Regulatory Particle

Cells need to synthesize and degrade proteins consistently. Maintaining a balanced level of protein in the cell requires a carefully controlled system and significant energy. Degradation of unwanted or damaged proteins into smaller peptide units can be accomplished by the proteasome. The proteasome is composed of two main subunits. The first is the core particle (20S CP), and within this core particle are three types of threonine proteases. The second is the regulatory complex (19S RP), which has a myriad of activities including recognizing proteins marked for degradation and shuttling the protein into the 20S CP to be degraded. Small-molecule inhibitors of the 20S CP have been developed and are exceptional treatments for multiple myeloma (MM). 20S CP inhibitors disrupt the protein balance, leading to cellular stress and eventually to cell death. Unfortunately, the 20S CP inhibitors currently available have dose-limiting off-target effects and resistance can be acquired rapidly. Herein, we discuss small molecules that have been discovered to interact with the 19S RP subunit or with a protein closely associated with 19S RP activity. These molecules still elicit their toxicity by preventing the proteasome from degrading proteins, but do so through different mechanisms of action.     

Special issue on exploring new Natural User Experiences

Universal Access in the Information Society -     

The three Rs of river ecosystem resilience: Resources,recruitment, and refugia

Resilience in river ecosystems requires that organisms must persist in the face of highly dynamic hydrological and geomorphological variations. Disturbance events such as floods and droughts are postulated to shape life history traits that support resilience, but river management and conservation would benefit from greater understanding of the emergent effects in communities of river organisms. We unify current knowledge of taxonomic‐, phylogenetic‐, and trait‐based aspects of river communities that might aid the identification and quantification of resilience mechanisms. Temporal variations in river productivity, physical connectivity, and environmental heterogeneity resulting from floods and droughts are highlighted as key characteristics that promote resilience in these dynamic ecosystems. Three community‐wide mechanisms that underlie resilience are (a) partitioning (competition/facilitation) of dynamically varying resources, (b) dispersal, recolonization, and recruitment promoted by connectivity, and (c) functional redundancy in communities promoted by resource heterogeneity and refugia. Along with taxonomic and phylogenetic identity, biological traits related to feeding specialization, dispersal ability, and habitat specialization mediate organism responses to disturbance. Measures of these factors might also enable assessment of the relative contributions of different mechanisms to community resilience. Interactions between abiotic drivers and biotic aspects of resource use, dispersal, and persistence have clear implications for river conservation and management. To support these management needs, we propose a set of taxonomic, phylogenetic, and life‐history trait metrics that might be used to measure resilience mechanisms. By identifying such indicators, our proposed framework can enable targeted management strategies to adapt river ecosystems to global change.     

Combining 1,3-Ditriazolylbenzene and Quinoline to Discover a New G-Quadruplex-Interactive Small Molecule Active against Cancer Stem-Like Cells

Quadruplex nucleic acids are promising targets for cancer therapy. In this study we used a fragment-based approach to create new flexible G-quadruplex (G4) DNA-interactive small molecules with good calculated oral drug-like properties, based on quinoline and triazole heterocycles. G4 melting temperature and polymerase chain reaction (PCR)-stop assays showed that two of these compounds are selective G4 ligands, as they were able to induce and stabilize G4s in a dose- and DNA sequence-dependent manner. Molecular docking studies have suggested plausible quadruplex binding to both the G-quartet and groove, with the quinoline module playing the major role. Compounds were screened for cytotoxicity against four cancer cell lines, where 4,4′-(4,4′-(1,3-phenylene)bis(1H-1,2,3-triazole-4,1-diyl))bis(1-methylquinolin-1-ium) ( 1 d ) showed the greater activity. Importantly, dose–response curves show that 1 d is cytotoxic in the human colon cancer HT-29 cell line enriched in cancer stem-like cells, a subpopulation of cells implicated in chemoresistance. Overall, this study identified a new small molecule as a promising lead for the development of drugs targeting G4 in cancer stem cells.     

The influence of cap rock composition on hydrocarbon seep type in the Zagros oil fields,a study using Advanced Spaceborne Thermal Emission and Reflection Radiometer mineral map

The persistent natural hydrocarbon seepage in onshore basins challenges observation and exploration technologies, which are required to document and assess these valuable indications of the presence of oil and gas in the subsurface. This paper aims at demonstrating the relationship between the compositional variation of an evaporite cap rock and the types of seeps occurring at the surface. For this purpose, the multispectral Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) data was utilized for mapping mineral variations of a petroleum system in the Zagros oil fields. Relative absorption-band depth (RBD), band rationing and the boosted regression trees (BRT) were applied to enhance and classify the mineral composition of evaporite, sandstone, and marly limestone formations. The gas seeps were associated with the areas of gypsum-bearing evaporite cap rock while oil seeps were mostly associated with calcite and clay zones within the cap rock, which was more prone to fracturing during the tectonic activities of the basin. It is suggested that the application of remote sensing in the oil and gas industry could be widened by detection of sleep-induced alteration to assess the efficiency of cap rock and to evaluate the productivity of reservoirs at a regional scale.