Nanomodification of living organisms by biomimetic mineralization

In nature, a few living organisms such as diatoms, magnetotactic bacteria, and eggs have developed specific mineral structures, which can provide extensive protection or unique functions. However, most organisms do not have such structured materials due to their lack of biomineralization ability. The artificial introduction of biomimetic-constructed nanominerals is challenging but holds great promise. In this overview, we highlight two typical types of mineral-living complex systems. One involves biological surface-induced nanomaterials, which produces artificial living-mineral core-shell structures such as the mineralencapsulated yeast, cyanobacteria, bacteria and viruses. The other involves internal nanominerals that could endow organisms with unique structures and properties. The applications of these biomimetic generated nanominerals are further discussed, mainly in four potential areas: storage, protection, “stealth” and delivery. Since biomineralization combines chemical, nano and biological technologies, we suggest that nanobiomimetic mineralization may open up another window for interdisciplinary research. Specifically, this is a novel material-based biological regulation strategy and the integration of living organisms with functional nanomaterials can create “super” or intelligent nanoscale living complexes for biotechnological practices.      

Quantum mechanical modeling of self-assembly and photoinduced electron transfer in PNA-based artificial living organisms

In order to support the creation of both artificial living organisms in the USA LANL "Protocell Assembly" project and programmable nano-biorobots in the EU "Programmable Artificial Cell Evolution" project, we used quantum mechanical (QM), density functional theory (DFT), the semiempirical PM3 method, and molecular mechanics (MM) software to investigate various complex photosynthetic systems based on peptide nucleic acid (PNA) in a water environment. Quantum mechanical DFT PBEPBE simulations, including electron correlations, confirm that water molecules that surround all the photosynthetic complex of the LANL protoorganism are main constructing factors and stabilize this system consisting of: PNA fragment attached by covalent bond sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule, lipid precursor molecule and fragment of lipid molecules mono layer. The absorption spectrum shift to the red wavelengths in the complex artificial protocell photosynthetic center might be used as the measure of the complexity of this system. The electron pi-pi* transitions in the first and third excited states are from HOMO and HOMO-1 located on the conjugated water molecules and sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO of the lipid precursor molecule as calculated using the time dependent (TD) PBEPBE/6-31G model. Electron charge tunneling in the first and third excited states should induce metabolic photodissociation of the lipid precursor molecule because of localization of the transferred electron cloud on the head (waste) of the lipid precursor molecule. TD electron correlation PBEPBE/6-31G calculations show that in the different energies of excitation, the charge transfer tunneling is from sensitizer to lipid precursor and cytosine molecules. One should note that in a water solvent, the electron charge transfer pi-pi* transition in the fifth and sixth excited state is from the HOMO and HOMO-1 located on the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the LUMO+2 located on the cytosine-PNA fragment molecule. Investigation results indicate that strong back electron tunneling from the sensitizer 1,4-bis(N,N-dimethylamino)naphthalene molecule to the cytosine molecule in the LANL artificial photosynthetic system exists.     

Photon statistics and correlation analysis of ultraweak light originating from living organisms for extraction of biological information

Ultraweak photon emission phenomena in the visible to near-IR region, originating from biological organisms, are known. This biophoton emission is generated during metabolic processes and constitutes physiological information. We investigated a technique for characterizing the optical radiation field based on photon statistics and correlation analysis to extract information on regulation processes in biochemical reactions and their interactions. We developed the system based on the time-interval measurement of photoelectrons in a photon-counting region and employed data processing with a nonstationary optical field with correction for the correlative properties of the photomultiplier dark current. We analyzed biophoton emission from cellular slime mold (Dictyosterium discoideum) and observed the characteristic variation of this organism's super-Poisson statistics during the developmental process.     

Capillary-based static self-assembly in higher organisms

Organized structures produced by dynamic self-assembly are often observed in animal groups. Static self-assembly, however, has to date only been observed at the cellular and sub-cellular levels. The aim of this study was to analyse organized structures in immobile whirligig beetle groups on the water surface. We used theoretical and computational approaches to model the meniscus around whirligig beetles and to calculate the surface energy for configurations involving two beetles. Theoretical predictions were then tested using live insects and resin casts. Observations were also made for three and more casts. The meniscus of whirligig beetles had a bipolar shape with two concave parts. For two beetles, predicted configurations based on energy minima corresponded to beetles in contact by their extremities, forming lines and arrows, and agreed well with observations. Experimental results for three and more beetle casts revealed new geometrical arrangements similar to those obtained with colloids at interfaces. This study provides the first example of static self-assembly at the inter-organism level and shows the importance of capillary interactions in such formations. We identify the ecological context in which our findings are of relevance.     

Molecular circuits for associative learning in single-celled organisms

We demonstrate how a single-celled organism could undertake associative learning. Although to date only one previous study has found experimental evidence for such learning, there is no reason in principle why it should not occur. We propose a gene regulatory network that is capable of associative learning between any pre-specified set of chemical signals, in a Hebbian manner, within a single cell. A mathematical model is developed, and simulations show a clear learned response. A preliminary design for implementing this model using plasmids within Escherichia coli is presented, along with an alternative approach, based on double-phosphorylated protein kinases.     

Mortality differences among organisms causing septicemia in hemodialysis patients

Septicemia is a serious problem in hemodialysis patients because it can lead to life-threatening complications and a persistently elevated risk of death. Most analyses have not examined whether there are differences in mortality risk among the organisms that cause these episodes of septicemia. This study was a retrospective cohort analysis of first septicemia hospitalizations during the first year of hemodialysis. Time to death (both in-hospital and within 12 weeks post-discharge) was compared among the different septicemia-causing organisms based on discharge diagnoses in Medicare billing data from 1996 to 2001. The effect of various complications on mortality risk was also evaluated. There were 22,130 septicemia hospitalizations identified. The most common organism identified was Staphylococcus aureus (27%), with no other organism having an incidence >10%. The overall unadjusted death rate from admission through 12 weeks of follow-up was 34%. During the first hospitalization, the death rate was 14%, and during the 12-week period after the hospitalization it was 20%. In adjusted analyses, S. aureus was associated with a 20% higher risk of death both during the in-hospital period and the 12-week post-discharge period, when compared with all other specified organisms. Hospitalizations complicated by meningitis, stroke, or endocarditis were also associated with increased risk of mortality, independent of the organism causing septicemia. Septicemia hospitalizations are associated with a high mortality rate--both during the initial hospitalization and after discharge. Meningitis, stroke, and endocarditis represent particularly serious complications. Overall, septicemia hospitalizations (especially for S. aureus) are serious events, and patients would benefit from better treatment and prevention.     

Photocontrolled living polymerizations

Living polymerizations involve the creation of polymer chains without significant irreversible chain transfer or chain termination. Such processes are widely used to access well-defined macromolecular materials with controlled architectures, such as block and star polymers. Although this concept was first realized for anionic polymerizations in the 1950s, many key recent advances have been made, most notably in the area of radical polymerization. Here, we report a living photopolymerization that involves photoexcited monomers. Exposure of metal-containing ferrocenophane monomers to Pyrex-filtered light from a mercury lamp (lambda>310 nm) or to bright sunlight in the presence of an anionic initiator leads to living polymerizations, in which the conversion and molecular weight of the resulting polymer can be controlled by the irradiation time. Photoirradiation selectively weakens the iron-cyclopentadienyl bond in the monomer, allowing the use of moderately basic and highly functional-group-tolerant initiators. The polymerization proceeds through attack of the initiator and propagating anion on the iron atom of the photoexcited monomer and, remarkably, the polymerization rate decreases with increasing temperature. Block copolymer formation is possible when the light source is alternately switched on and off in between sequential addition of different monomers, providing unprecedented, photocontrolled access to new types of functional polymers.     

Strategic environmental assessments for genetically modified organisms

Genetically modified crops appear to provide a promising option in finding sustainable solutions to end global hunger and poverty, but strategic decisions need to be made on how to spend limited agricultural research funds. Potentially, strategic environmental assessment (SEA) may be used as part of an environmental management system to introduce mainstreaming of environmental considerations in the policy research and priority-setting process of development organizations to help achieve international development goals. This paper sets out a possible biotechnology SEA process that integrates qualitative and quantitative assessments with a focus on risk assessment and management within the SEA and policy environmental assessment frameworks. It uses the International Association for Impact Assessment six performance criteria for SEAs: integration; sustainability; focus; accountability; participation; and iteration.     

Single particle tracking of fluorescent nanodiamonds in cells and organisms

Ever since the discovery of fullerenes in 1985, nanocarbon has demonstrated a wide range of applications in various areas of science and engineering. Compared with metal, oxide, and semiconductor nanoparticles, the carbon-based nanomaterials have distinct advantages in both biotechnological and biomedical applications due to their inherent biocompatibility. Fluorescent nanodiamond (FND) joined the nanocarbon family in 2005. It was initially developed as a contrast agent for bioimaging because it can emit bright red photoluminescence from negatively charged nitrogen-vacancy centers built in the diamond matrix. A notable application of this technology is to study the cytoplasmic dynamics of living cells by tracking single bioconjugated FNDs in intracellular medium. This article provides a critical review on recent advances and developments of such single particle tracking (SPT) research. It summarizes SPT and related studies of FNDs in cells (such as cancer cell lines) and organisms (including zebrafish embryos, fruit fly embryos, whole nematodes, and mice) using assorted imaging techniques.     

共生生物搜索算法在水声信道均衡中的应用

由于多径效应和频散效应导致水声信道中声信号衰减和失真严重,传统均衡技术不能满足在水声信道中应用的要求,近年来神经网络在均衡技术方面的突出表现受到广泛关注,因此,本文提出一种高效的神经网络训练算法,即基于非线性自回归神经网络的改进共生生物搜索算法(简称NARX-nSOS算法)实现水声信道均衡。该算法在非线性自回归神经网络(Nonlinear Autoregressive Neural Network with Exogenous Inputs, NARX)均衡器的基础上,用共生生物搜索算法(Symbiotic Organisms Search, SOS)来进行优化,并结合反向学习算法(Opposition-Based Learning, OBL)来提高该算法的收敛能力,利用计算机对NARX-nSOS算法的有效性进行了仿真验证,结果证明NARXnSOS算法加快了收敛速度,通信质量得到了显著提高。     

Magnetometric diagnostics of ferritin in living matter

Investigations in a broad sample set of living matter, including plants and silty soil fractions from various climate and soil zones, microorganisms, and muscle tissues of birds and mammals (a total of about 200 samples) show that iron in native substances occurs in the form of nanodimensional particles of hydroxide (ferrihydrite). Based on the data of Mössbauer spectroscopy and magnetic measurements, these nanoparticles can be identified as nuclei of the globular protein ferritin. Most measurements were performed at 290 K (i.e., without using cryogenic techniques).     

Probing single molecules in single living cells

Single-molecule detection in single living cells has been achieved by using confocal fluorescence microscopy and externally tagged probe molecules. The intracellular background fluorescence is substantially higher than that in aqueous buffer, but this background is continuous and stable and does not significantly interfere with the measurement of single-molecule photon bursts. As a result, single-molecule data have been obtained on three types of fluorescent probes at spatially resolved locations (e.g., cytoplasm and nucleus) inside human HeLa cells. First, the iron transport protein transferrin labeled with tetramethylrhodamine undergoes rapid receptor-mediated endocytosis, and single transferrin molecules are detected inside living cells. Second, the cationic dye rhodamine 6G (R6G) enters cultured cells by a potential-driven process, and single R6G molecules are observed as intense photon bursts when they move in and out of the intracellular laser beam. Third, we report results on synthetic oligonucleotides that are tagged with a fluorescent dye and are taken up by living cells via a passive, nonendocytic pathway.