Approximate analytical solution of fractional order biochemical reaction model and its stability analysis

Approximate analytical solution of the system of coupled nonlinear Ordinary Differential Equations (ODEs) of a biochemical reaction model is much relevant due to its practical significance to biochemists.In this paper,an effective and powerful mathematical technique,viz.fractional homotopy analysis transform method (FHATM),is employed to get the numerical solutions of biochemical reaction model with time fractional derivatives.The adopted scheme is the beautiful copulation of homotopy analysis technique and Laplace transform algorithm.This paper shows that the adopted scheme is quite easy as well as computationally attractive in the context of a solution procedure.The Caputo-type fractional derivatives are considered in the present paper.Approximate results of the probability density functions of the time fractional biochemical reaction model are computed for miscellaneous fractional Brownian motions as well as for classical motion and are presented graphically.The time fractional biochemical reaction model with respect to stability analysis for various values of fractional order q is also analyzed.In the context of stability discussion,we have used the fractional Routh-Hurwitz stability criterion to establish the local stability of the biochemical reaction model of fractional order.     

Yield-related QTLs and Their Applications in Rice Genetic Improvement

Grain yield is one of the most important indexes in rice breeding,which is governed by quantitative trait loci (QTLs).Different map-ping populations have been used to explore the QTLs controlling yield related traits.Primary populations such as F 2 and recombi-nant inbred line populations have been widely used to discover QTLs in rice genome-wide,with hundreds of yield-related QTLs detected.Advanced populations such as near isogenic lines (NILs) are efficient to further fine-map and clone target QTLs.NILs for primarily identified QTLs have been proposed and confirmed to be the ideal population for map-based cloning.To date,20 QTLs directly affecting rice grain yield and its components have been cloned with NIL-F 2 populations,and 14 new grain yield QTLs have been validated in the NILs.The molecular mechanisms of a continuously increasing number of genes are being unveiled,which aids in the understanding of the formation of grain yield.Favorable alleles for rice breeding have been ’mined’ from natural cultivars and wild rice by association analysis of known functional genes with target trait performance.Reasonable combination of favorable alleles has the potential to increase grain yield via use of functional marker assisted selection.     

Three-dimensional biomagnetic Maxwell fluid flow over a stretching surface in presence of heat source/sink

The present paper deals with the study of three-dimensional boundary layer flow of biomagnetic Maxwell fluid over a plane horizontal surface stretched linearly along two mutually perpendicular directions. Basic principles of magnetohydrodynamics (MHD) and ferro-hydrodynamics (FHD) have been employed. The effect of heat generation/absorption has been taken into consideration. The study is theoretical and is conducted by using a combination of approximate and numerical techniques. By using the method of similarity transformation, the governing nonlinear partial differential equations are converted into a set of coupled ordinary differential equations. In the sequel, a suitable numerical method has been developed to solve the coupled differential equations. The accuracy of the numerical method has been checked by comparing the numerical results with those of an earlier study reported in available literatures. Effects of various parameters involved in the study, viz. the magnetohydrodynamic and ferromagnetic parameters, Deborah number, stretching ratio and heat generation on the fluid flow profiles are investigated and the results have been presented graphically. Variations of the skin friction, heat transfer rate and relative wall pressure with change in hydrodynamic and ferromagnetic parameters have also been illustrated. It is found that due to the influence of the Kelvin force, the velocity component in xx-direction is greater than the corresponding one in the hydrodynamic case, but the opposite is true for the velocity component in the yy-direction. We also found that the temperature of the fluid for hydrodynamic flow is greater than that for MHD or FHD flow. It is even greater for BFD flows. The numerical results of the study reveal that the characteristics of blood flow are significantly affected by the presence of a magnetic field.     

Genotoxicity biomarkers in aquatic bioindicators

Pollution of the aquatic environment is an ever-growing problem, as waters are the ultimate sink for the large number of xenobiotics from multiple sources. DNA damaging agents have a significant ecological relevance since they are implicated in many pathological processes and exert effects beyond that of individual being active through following generations. A large number of methods have been applied to evaluate genotoxic damage in different aquatic species. Comet assay, as method for de- tecting DNA alterations, and micronucleus test, as an index of chromosomal damage are the most widely applied and validated methods in field studies. These methods were applied in different vertebrate and invertebrate aquatic species, but only mollusk and fish species have been employed in routine biomonitoring programs. Mussels, due to their widely geographical distribution and the suitability for caging represent the bioindicator of choice in field studies. Mytilus species is the most used marine mussel. The use of fish is limited to specific geographic areas. The present review mainly focuses on the application of comet assay and micronucleus test in mussels. A number of biomonitoring studies in mussels, using comet assay or micronucleus test, revealed exposure to different classes of genotoxic compounds with a good discrimination power. The different evidence from the two as- says, reflects different biological mechanisms for the two genetic endpoints, DNA damage and chromosomal damage, suggesting their combined application in the field. Different endogenous and exogenous factors have been shown to modulate the genotoxic responses in mussels, acting as confounding factors in environmental monitoring. The use of standardized protocol for caging, sampling and genotoxity evaluation is critical in biomonitoring studies. The use of a multimarker approach coupling genotoxicity biomarkers with physiological and biochemical factors allows to have a complete picture of the environmental pollution [Current Zoology 60 （2）： 273-284, 2014].     

Feruloylation in Grasses： Current and Future Perspectives

In the cell walls of forage grasses, ferulic acid is esterified to arabinoxylans and participates with lignin monomers in oxidative coupling pathways to generate ferulate-polysaccharide-lignin complexes that cross-link the cell wall. The accumulation of ferulates and the cross-linking of arabinoxylans via diferulate esters are hypothesized to function in various processes in plants. The specific roles of arabinoxylan feruloylation as well as the nature, cellular localization, and substrate for arabinoxylans feruloylation of cell walls are reviewed. The various approaches that have been used for assessing the specific roles of feruloylation are described and assessed. I argue that, until recently, the specific role of feruloylation in these various processes has been established largely by indirect experiments and, although these studies reached similar conclusions about the potential importance of wall feruloylation, they suffer from a common problem： namely they depend on correlations between two processes and do not stem from a detailed understanding of the mechanisms of feruloylation. I also argue that the nature of arabinoxylan feruloylation remains uncertain.     

Control of stem cell fate by engineering their micro and nanoenvironment

Stem cells are capable of long-term self-renewal and differentiation into specialised cell types, making them an ideal candidate for a cell source for regenerative medicine. The control of stem cell fate has become a major area of interest in the field of regenerative medicine and therapeutic intervention. Conventional methods of chemically inducing stem cells into specific lineages is being challenged by the advances in biomaterial technology, with evidence highlighting that material properties are capable of driving stem cell fate. Materials are being designed to mimic the clues stem cells receive in their in vivo stem cell niche including topographical and chemical instructions. Nanotopographical clues that mimic the extracellular matrix(ECM) in vivo have shown to regulate stem cell differentiation. The delivery of ECM components on biomaterials in the form of short peptides sequences has also proved successful in directing stem cell lineage. Growth factors responsible for controlling stem cell fate in vivo have also been delivered via biomaterials to provide clues to determine stem cell differentiation. An alternative approach to guide stem cells fate is to provide genetic clues including delivering DNA plasmids and small interfering RNAs via scaffolds. This review, aims to provide an overview of the topographical, chemical and molecular clues that biomaterials can provide to guide stem cell fate. The promising features and challenges of such approaches will be highlighted, to provide directions for future advancements in this exciting area of stem cell translation for regenerative medicine.     

Salivary IgA enhancement strategy for development of a nasal-spray anti-caries mucosal vaccine

Dental caries remains one of the most common global chronic diseases caused by Streptococcus mutans,which is prevalent all over the world.The caries prevalence of children aged between 5-6 years old in China is still in very high rate.A potent and effective anti-caries vaccine has long been expected for caries prevention but no vaccines have been brought to market till now mainly due to the low ability to induce and maintain protective antibody in oral fluids.This review will give a brief historical retrospect on study of dental caries and pathogenesis,effective targets for anti-caries vaccines,oral immune system and immunization against dental caries.Then,salivary IgA antibodies and the protective responses are discussed in the context of the ontogeny of mucosal immunity to indigenous oral streptococcal.The methods and advancement for induction of specific anticaries salivary sIgA antibodies and enhancement of specific anti-caries salivary sIgA antibodies by intranasal immunization with a safe effective mucosal adjuvant are described.The progress in the enhancement of salivary sIgA antibodies and anticaries protection by intranasal immunization with flagellin-PAc fusion protein will be highlighted.Finally,some of the main strategies that have been used for successful mucosal vaccination of caries vaccine are reviewed,followed by discussion of the mucosal adjuvant choice for achieving protective immunity at oral mucosal membranes for development of a nasal-spray or nasal-drop anti-caries vaccine for human.     

What have we learned about the kallikrein-kinin and renin-angiotensin systems in neurological disorders?

The kallikrein-kinin system(KKS) is an intricate endogenous pathway involved in several physiological and pathological cascades in the brain. Due to the pathological effects of kinins in blood vessels and tissues, their formation and degradation are tightly controlled. Their components have been related to several central nervous system diseases such as stroke, Alzheimer's disease, Parkinson's disease, multiple sclerosis, epilepsy and others. Bradykinin and its receptors(B1R and B2R) may have a role in the pathophysiology of certain central nervous system diseases. It has been suggested that kinin B1R is up-regulated in pathological conditions and has a neurodegenerative pattern, while kinin B2R is constitutive and can act as a neuroprotective factor in many neurological conditions. The renin angiotensin system(RAS) is an important blood pressure regulator and controls both sodium and water intake. AngⅡ is a potent vasoconstrictor molecule and angiotensin converting enzyme is the major enzyme responsible for its release. AngⅡ acts mainly on the AT1 receptor, with involvement in several systemic and neurological disorders. Brain RAS has been associated with physiological pathways, but is also associated with brain disorders. This review describes topics relating to the involvement of both systems in several forms of brain dysfunction and indicates components of the KKS and RAS that have been used as targets in several pharmacological approaches.     

Anterograde and Retrograde Regulation of Nuclear Genes Encoding Mitochondrial Proteins during Growth,Development, and Stress

Mitochondrial biogenesis and function in plants require the expression of over 1000 nuclear genes encoding mitochondrial proteins （NGEMPs）. The expression of these genes is regulated by tissue-specific, developmental, internal, and external stimuli that result in a dynamic organelle involved in both metabolic and a variety of signaling processes. Although the metabolic and biosynthetic machinery of mitochondria is relatively well understood, the factors that regu- late these processes and the various signaling pathways involved are only beginning to be identified at a molecular level. The molecular components of anterograde （nuclear to mitochondrial） and retrograde （mitochondrial to nuclear） signaling pathways that regulate the expression of NGEMPs interact with chloroplast-, growth-, and stress-signaling pathways in the cell at a variety of levels, with common components involved in transmission and execution of these signals. This positions mitochondria as important hubs for signaling in the cell, not only in direct signaling of mitochondrial function per se, but also in sensing and/or integrating a variety of other internal and external signals. This integrates and optimizes growth with energy metabolism and stress responses, which is required in both photosynthetic and non-photosynthetic cells.     

Conceptual comparison of metabolic pathways with electronic circuits

1 Introduction Based on the review of the previous work on genecircuits [1–7] , this paper discusses an electronic circuitwhich has been designed to mimic glycolysis, the CitricAcid (TCA) cycle and the electron transport chain. En-zymes play a vital role in metabolic pathways. Thespecificity of enzymic action is explained in terms of theprecise fitting of enzyme and substrate [8–9] . Enzymes areusually very specific…     

Directly Writing Resistor,Inductor and Capacitor to Composite Functional Circuits: A Super-Simple Way for Alternative Electronics

Background

The current strategies for making electronic devices are generally time, water, material and energy consuming. Here, the direct writing of composite functional circuits through comprehensive use of GaIn₁₀-based liquid metal inks and matching material is proposed and investigated, which is a rather easy going and cost effective electronics fabrication way compared with the conventional approaches.

Methods

Owing to its excellent adhesion and electrical properties, the liquid metal ink was demonstrated as a generalist in directly making various basic electronic components such as planar resistor, inductor and capacitor or their combination and thus composing circuits with expected electrical functions. For a precise control of the geometric sizes of the writing, a mask with a designed pattern was employed and demonstrated. Mechanisms for justifying the chemical components of the inks and the magnitudes of the target electronic elements so as to compose various practical circuits were disclosed.

Results

Fundamental tests on the electrical components including capacitor and inductor directly written on paper with working time up to 48 h and elevated temperature demonstrated their good stability and potential widespread adaptability especially when used in some high frequency circuits. As the first proof-of-concept experiment, a typical functional oscillating circuit including an integrated chip of 74HC04 with a supply voltage of 5 V, a capacitor of 10 nF and two resistors of 5 kΩ and 1 kΩ respectively was directly composed on paper through integrating specific electrical elements together, which presented an oscillation frequency of 8.8 kHz.

Conclusions

The present method significantly extends the roles of the metal ink in recent works serving as only a single electrical conductor or interconnecting wires. It opens the way for directly writing out complex functional circuits or devices on different substrates. Such circuit composition strategy has generalized purpose and can be extended to more areas, even daily pervasive electronics.     

Living electronics: A catalogue of engineered living electronic components

Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.     

Computational studies and peptidomimetic design for the human p53-MDM2 complex

The interaction between human p53 and MDM2 is a key event in controlling cell growth. Many studies have suggested that a p53 mimic would be sufficient to inhibit MDM2 to reduce cell growth in cancerous tissue. In order to design a potent p53 mimic, molecular dynamics (MD) simulations were used to examine the binding interface and the effect of mutating key residues in the human p53-MDM2 complex. The Generalized Born surface area (GBSA) method was used to estimate free energies of binding, and a computational alanine-scanning approach was used to calculate the relative effects in the free energy of binding for key mutations. Our calculations determine the free energy of binding for a model p53-MDM2 complex to be -7.4 kcal/mol, which is in very good agreement with the experimentally determined values (-6.6--8.8 kcal/mol). The alanine-scanning results are in good agreement with experimental data and calculations by other groups. We have used the information from our studies of human p53-MDM2 to design a beta-peptide mimic of p53. MD simulations of the mimic bound to MDM2 estimate a free energy of binding of -8.8 kcal/mol. We have also applied alanine scanning to the mimic-MDM2 complex and reveal which mutations are most likely to alter the binding affinity, possibly giving rise to escape mutants. The mimic was compared to nutlins, a new class of inhibitors that block the formation of the p53-MDM2 complex. There are interesting similarities between the nutlins and our mimic, and the differences point to ways that both inhibitors may be improved. Finally, an additional hydrophobic pocket is noted in the interior of MDM2. It may be possible to design new inhibitors to take advantage of that pocket.     

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine. Notwithstanding, a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies for circuit design. Thus, future success of these devices depends on obtaining circuits with scalable complexity and reusable parts. Here we show how to build complex computational devices using multicellular consortia and space as key computational elements. This spatial modular design grants scalability since its general architecture is independent of the circuit’s complexity, minimizes wiring requirements and allows component reusability with minimal genetic engineering. The potential use of this approach is demonstrated by implementation of complex logical functions with up to six inputs, thus demonstrating the scalability and flexibility of this method. The potential implications of our results are outlined.     

Synthetic genetic circuits for programmable biological functionalities

Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.     

Ultrafast light harvesting dynamics in the cryptophyte phycocyanin 645.

Steady-state and femtosecond time-resolved optical methods have been used to study spectroscopic features and energy transfer dynamics in the soluble antenna protein phycocyanin 645 (PC645), isolated from a unicellular cryptophyte Chroomonas CCMP270. Absorption, emission and polarization measurements as well as one-colour pump-probe traces are reported in combination with complementary quantum chemical calculations of electronic transitions of the bilins. Estimation of bilin spectral positions and energy transfer rates aids in the development of a model for light harvesting by PC645. At higher photon energies light is absorbed by the centrally located dimer (DBV, beta50/beta61) and the excitation is subsequently funneled through a complex interference of pathways to four peripheral pigments (MBV alpha19, PCB beta158). Those chromophores transfer the excitation energy to the red-most bilins (PCB beta82). We suggest that the final resonance energy transfer step occurs between the PCB 82 bilins on a timescale estimated to be approximately 15 ps. Such a rapid final energy transfer step cannot be rationalized by calculations that combine experimental parameters and quantum chemical calculations, which predict the energy transfer time to be 40 ps.     

Design of enhanced agonists through the use of a new virtual screening method: application to peptides that bind class I major histocompatibility complex (MHC) molecules

A new screening procedure is described that uses docking calculations to design enhanced agonist peptides that bind to major histocompatibility complex (MHC) class I receptors. The screening process proceeds via single mutations of one amino acid at the positions that directly interact with the MHC receptor. The energetic and structural effects of these mutations have been studied using fragments of the original ligand that vary in length. The results of these docking studies indicate that the mutant affinity ranking of long peptides can be practically reproduced with a screening approach performed using fragments of six residues. Fragments of four and five residues could mimic, in some cases, the structural arrangement of the side chains of the full-length peptide. We have compared the structural and energetic results of the docking calculations with experimental data using three unrelated ligand peptides that differ greatly in their affinity for the MHC complex. Analysis of the affinity of the fragments led to the identification of three important parameters in the construction of fragments that mimic the structural and energetic properties of the full-length ligand: the length of the fragment; its intermolecular energy; and the number and localization, internal or terminal, of the anchor residues. The results of this new peptide-design methodology have been applied to suggest new peptides derived from the MUC1-8 peptide that could be used as murine vaccines that trigger the immune response through the MHC class I protein H-2K(b).     

Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway

Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production.