Phenomenon of Quantum Entanglement in a System Composed of Two Minimal Protocells

The quantum mechanical self-assembly of two separate photoactive supramolecular systems with different photosynthetic centers was investigated by means of density functional theory methods. Quantum entangled energy transitions from one subsystem to the other and the assembly of logically controlled artificial minimal protocells were modeled. The systems studied were based on different photoactive sensitizer molecules covalently bonded to a non-canonical oxo-guanine::cytosine supramolecule with the precursor of a fatty acid (pFA) molecule attached via Van der Waals forces, all surrounded by water molecules. The electron correlation interactions responsible for the weak hydrogen and Van der Waals chemical bonds increased due to the addition of polar water solvent molecules. The distances between the separated sensitizer, nucleotide, pFA, and water molecules are comparable to Van der Waals and hydrogen bonding radii. As a result, the overall system becomes compressed, resulting in photo-excited electron tunneling from the sensitizer (bis(4-diphenylamine-2-phenyl)-squarine or 1,4-bis(N,N-dimethylamino)naphthalene) to the pFA molecules. Absorption spectra as well as electron transfer trajectories associated with the different excited states were calculated using time dependent density functional theory methods. The results allow separation of the quantum entangled photosynthetic transitions within the same minimal protocell and with the neighboring minimal protocell. The transferred electron is used to cleave a “waste” organic molecule resulting in the formation of the desired product. A two variable, quantum entangled AND logic gate was proposed, consisting of two input photoactive sensitizer molecules and one output (pFA molecule). It is proposed that a similar process might be applied for the destruction of tumor cancer cells or to yield building blocks in artificial cells.     

Question 9: Quantum Self-Assembly and Photoinduced Electron Tunneling in Photosynthetic Systems of Artificial Minimal Living Cells

Natural and artificial living cells and their substructures are self-assembling, due to electron correlation interactions among biological and water molecules, which lead to attractive dispersion forces and hydrogen bonds. Dispersion forces are weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen bond is a special type of quantum attractive interaction that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom; and this hydrogen atom exist in two quantum states. The best method to simulate these dispersion forces and hydrogen bonds is to perform quantum mechanical non-local density functional potential calculations of artificial minimal living cells consisting of around 1,000 atoms. The cell systems studied are based on peptide nucleic acid and are 3.0–4.2 nm in diameter. The electron tunneling and associated light absorption of the most intense transitions, as calculated by the time dependent density functional theory method, differs from spectroscopic experiments by only 0.2–0.3 nm, which is within the value of experiment errors. This agreement implies that the quantum mechanically self-assembled structures of artificial minimal living cells very closely approximate realistic ones.     

Prebiotic Methylation and the Evolution of Methyl Transfer Reactions in Living Cells

An hypothesis is presented for theprebiotic origin of methyl groups and the evolution ofmethyl transfer reactions in living cells. This hypothesis,described in terms of prebiotic and early biotic chemicalevolution, is based on experimental observations in our laband in those of others, and on the mechanisms of enzymaticmethyl transfer reactions that occur in living cells. Ofparticular interest is our demonstration of the reductivemethylation of ethanolamine and glycine in aqueous solutionby excess formaldehyde. These reactions, involving prebioticcompounds and conditions, are mechanistically analogous tothe de novo origin of methyl groups in modern cellsby reduction of methylene tetrahydrofolate. Furthermore,modern cellular methyl transfers from S-adenosylmethionineto amine nitrogen may involve formaldehyde as anintermediate and subsequent reductive methylation, analogousto the prebiotic chemistry observed herein.     

Possibility of high performance quantum computation by superluminal evanescent photons in living systems

Penrose and Hameroff have suggested that microtubules in living systems function as quantum computers by utilizing evanescent photons. On the basis of the theorem that the evanescent photon is a superluminal particle, the possibility of high performance computation in living systems has been studied. From the theoretical analysis, it is shown that the biological brain can achieve large quantum bits computation compared with the conventional processors at room temperature.     

Nanofabrication of Gate-defined GaAs/AlGaAs Lateral Quantum Dots

A quantum computer is a computer composed of quantum bits (qubits) that takes advantage of quantum effects, such as superposition of states and entanglement, to solve certain problems exponentially faster than with the best known algorithms on a classical computer. Gate-defined lateral quantum dots on GaAs/AlGaAs are one of many avenues explored for the implementation of a qubit. When properly fabricated, such a device is able to trap a small number of electrons in a certain region of space. The spin states of these electrons can then be used to implement the logical 0 and 1 of the quantum bit. Given the nanometer scale of these quantum dots, cleanroom facilities offering specialized equipment- such as scanning electron microscopes and e-beam evaporators- are required for their fabrication. Great care must be taken throughout the fabrication process to maintain cleanliness of the sample surface and to avoid damaging the fragile gates of the structure. This paper presents the detailed fabrication protocol of gate-defined lateral quantum dots from the wafer to a working device. Characterization methods and representative results are also briefly discussed. Although this paper concentrates on double quantum dots, the fabrication process remains the same for single or triple dots or even arrays of quantum dots. Moreover, the protocol can be adapted to fabricate lateral quantum dots on other substrates, such as Si/SiGe.     

A single aromatic core mutation converts a designed “primitive” protein from halophile to mesophile folding

The halophile environment has a number of compelling aspects with regard to the origin of structured polypeptides (i.e., proteogenesis) and, instead of a curious niche that living systems adapted into, the halophile environment is emerging as a candidate “cradle” for proteogenesis. In this viewpoint, a subsequent halophile‐to‐mesophile transition was a key step in early evolution. Several lines of evidence indicate that aromatic amino acids were a late addition to the codon table and not part of the original “prebiotic” set comprising the earliest polypeptides. We test the hypothesis that the availability of aromatic amino acids could facilitate a halophile‐to‐mesophile transition by hydrophobic core‐packing enhancement. The effects of aromatic amino acid substitutions were evaluated in the core of a “primitive” designed protein enriched for the 10 prebiotic amino acids (A,D,E,G,I,L,P,S,T,V)—having an exclusively prebiotic core and requiring halophilic conditions for folding. The results indicate that a single aromatic amino acid substitution is capable of eliminating the requirement of halophile conditions for folding of a “primitive” polypeptide. Thus, the availability of aromatic amino acids could have facilitated a critical halophile‐to‐mesophile protein folding adaptation—identifying a selective advantage for the incorporation of aromatic amino acids into the codon table.     

Stereoselective decarboxylation of amino acids in the solid state,with special reference to chiral discrimination in prebiotic evolution

Summary The decarboxylations of sublimated solidd- andl-leucine by nonpolarized -rays give quite different quantum yields, indicating significant selection. The G(CO₂) value for thed-isomer is higher than that for thel-isomer by a factor of 2 within a dose range of 10³–10⁵ rads. The G value for thedl-racemate is close to that of thed-isomer. The effect vanishes if instead of sublimation, crystallization from aqueous solution is the last preparation step. Our results on sublimated leucine agree well with those reported for -induced decarboxylation of solid -phenylalanine prepared similarly by sublimation. The asymmetry increases with longer cooling periods after irradiation. An intrinsic energy difference due to parity nonconservation between enantiomers is discussed as a possible stereoselective mechanism, with special reference to the prebiotic origin of asymmetry in living matter. Other possible sources of the observed effects are also discussed.     

金属还原菌希瓦氏菌厌氧呼吸能力及其在环境修复中的研究进展

Shewanella oneidensis MR-1是一种模式金属还原菌,它能够在厌氧条件下,将多种金属化合物和人工合成染料等作为电子受体还原代谢。因此,该菌常常被用于生态修复等研究。厌氧条件下,S.oneidensis MR-1能够将细胞质内或细胞内膜产生的电子通过定位于细胞内膜、细胞膜周质和细胞外膜上的c-血红色素蛋白或还原酶所组成的具有多样性的电子传递系统,最终传递到存在于细菌细胞外环境中的电子受体。通过对多种电子传递过程的介绍,进一步阐明其对污染物修复和纳米材料合成的机理,从而为未来对该类微生物的利用和开发提供更为充分的理论依据。     

Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side.     

rgf1, a mutation reducing grain filling in maize through effects on basal endosperm and pedicel development

The maize cob presents an excellent opportunity to screen visually for mutations affecting assimilate partitioning in the developing kernel. We have identified a defective kernel mutant termed rgf1, reduced grain filling, with a final grain weight 30% of the wild type. In contrast with most defective endosperm mutants, rgf1 shows gene dosage-dependent expression in the endosperm. rgf1 kernels possess a small endosperm incompletely filling the papery pericarp, but embryo development is unaffected and the seeds are viable. The mutation conditions defective pedicel development and greatly reduces expression of endosperm transfer layer-specific markers. rgf1 exhibits striking morphological similarities to the mn1 mutant, but maps to a locus approximately 4 cM away from mn1 on chromosome 2 of maize. Despite reduced starch accumulation in the mutant, no obvious lesion in starch biosynthesis has been detected. Free sugar levels are unaltered in rgf1 endosperm. Rates of sugar uptake, measured over short (8 h) periods in cultured kernels, are increased in rgf1 compared to the wild type. rgf1 and wild-type kernels, excised at 5 DAP and cultured in vitro also develop differently in response to variations in sugar regime: glucose concentrations above 1% arrest placentochalazal development of rgf1 kernels, but have no effect on cultured wild-type kernels. These findings suggest that either uptake or perception of sugar(s) in endosperm cells at 5-10 DAP determines the rgf1 kernel phenotype.     

A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels

High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.     

A computational study of liposome logic: towards cellular computing from the bottom up

In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This “liposome logic” approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in “top-down” synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of “bottom-up” liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie’s stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up.     

Gastroprotective effect of apricot kernel oil in ethanol-induced gastric mucosal injury in rats

We investigated the gastroprotective effect of apricot kernel oil on ethanol induced gastric ulcer in rats. Male Wistar albino rats were divided into control, ethanol and apricot kernel oil + ethanol groups. The fatty acid composition of apricot kernel oil was determined using GC-MS. A gastric ulcer index was defined as the area percentage of the gastric mucosa consisting of ulcerated tissue. Gastric tissue was investigated by TUNEL staining for apoptosis, immunohistochemical iNOS staining, measurement of gastric IL-10 and IL-6 expression by ELISA and assays of catalase, malondialdehyde and superoxide dismutase. The ethanol group exhibited a higher gastric ulcer score, increased IL-6 level, increased number of inducible nitric oxide synthase-positive and TUNEL positive cells, and a higher MDA level compared to the control group. The apricot kernel oil + ethanol group exhibited significantly fewer gastric lesions compared to the ethanol group. Apricot kernel oil protects rat gastric mucosa against ethanol induced injury by its anti-inflammatory, anti-oxidative and anti-apoptotic effects, and might be useful for reducing the severity of gastric ulcers.     

Toward the assembly of a minimal divisome

The construction of an irreducible minimal cell having all essential attributes of a living system is one of the biggest challenges facing synthetic biology. One ubiquitous task accomplished by any living systems is the division of the cell envelope. Hence, the assembly of an elementary, albeit sufficient, molecular machinery that supports compartment division, is a crucial step towards the realization of self-reproducing artificial cells. Looking backward to the molecular nature of possible ancestral, supposedly more rudimentary, cell division systems may help to identify a minimal divisome. In light of a possible evolutionary pathway of division mechanisms from simple lipid vesicles toward modern life, we define two approaches for recapitulating division in primitive cells: the membrane deforming protein route and the lipid biosynthesis route. Having identified possible proteins and working mechanisms participating in membrane shape alteration, we then discuss how they could be integrated into the construction framework of a programmable minimal cell relying on gene expression inside liposomes. The protein synthesis using recombinant elements (PURE) system, a reconstituted minimal gene expression system, is conceivably the most versatile synthesis platform. As a first step towards the de novo synthesis of a divisome, we showed that the N-BAR domain protein produced from its gene could assemble onto the outer surface of liposomes and sculpt the membrane into tubular structures. We finally discuss the remaining challenges for building up a self-reproducing minimal cell, in particular the coupling of the division machinery with volume expansion and genome replication.     

珠江口伶仃洋中华白海豚栖息地利用对海岸线等变迁的响应

沿岸鲸豚类栖息地易受人类活动的干扰，导致其分布和核心栖息地发生变化。珠江口-漠阳江口中华白海豚种群是目前所知全球范围内最大的种群，其中伶仃洋水域是其重要的栖息地。近年来，珠江口伶仃洋周边城市发展带来的人类活动增加，白海豚的生存压力日益增大，分析伶仃洋中华白海豚对栖息地环境变化的响应，研究对应的保护策略显得非常迫切。以多源陆地资源卫星Landsat为数据源，通过影像分析近43年珠江口伶仃洋围填海造成的海域流失，结合近20年来采用截线抽样法收集的海豚观测数据，运用含障碍核插值（Kernel interpolation with barriers）方法，分析白海豚的分布及核心栖息地的变化。结果显示：1986-2015年期间，研究区域内流失的海域面积为344.08km²；目击分布离人工海岸线的平均距离大于自然海岸线的平均距离，目击分布到自然海岸线和人工海岸线的平均距离均在减小，表明过去20年白海豚的栖息地使用选择发生了一些变化，被迫适应人类活动的干扰；1997-2016年白海豚的分布范围呈现先增加后减小，白海豚栖息地使用的重心偏向伶仃洋东部水域，核心栖息地趋向主航道和无人海岛附近水域萎缩，可能是海豚因海域食物资源减少而迫不得已的选择。不同时期，珠江口中华白海豚国家级自然保护区所覆盖的核心栖息地比例呈递减趋势，占比由79.9%下降到49.4%，当前有必要对保护区范围和功能区作出一些优化调整，以适应栖息地使用的变化格局。     

Detection of single quantum dots in model organisms with sheet illumination microscopy

Single-molecule detection and tracking is important for observing biomolecule interactions in the microenvironment. Here we report selective plane illumination microscopy (SPIM) with single-molecule detection in living organisms, which enables fast imaging and single-molecule tracking and optical penetration beyond 300 μm. We detected single nanocrystals in Drosophila larvae and zebrafish embryo. We also report our first tracking of single quantum dots during zebrafish development, which displays a transition from flow to confined motion prior to the blastula stage. The new SPIM setup represents a new technique, which enables fast single-molecule imaging and tracking in living systems.     

Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells

Yeast is a model eukaryote with a variety of biological resources. Here we developed a method to track a quantum dot (QD)-conjugated protein in the budding yeast Saccharomyces cerevisiae. We chemically conjugated QDs with the yeast prion Sup35, incorporated them into yeast spheroplasts, and tracked the motions by conventional two-dimensional or three-dimensional tracking microscopy. The method paves the way toward the individual tracking of proteins of interest inside living yeast cells.