Role of RNA polymerase IV in plant small RNA metabolism.

In addition to the three RNA polymerases (RNAP I-III) shared by all eukaryotic organisms, plant genomes encode a fourth RNAP (RNAP IV) that appears to be specialized in the production of siRNAs. Available data support a model in which dsRNAs are generated by RNAP IV and RNA-dependent RNAP 2 (RDR2) and processed by DICER (DCL) enzymes into 21- to 24-nt siRNAs, which are associated with different ARGONAUTE (AGO) proteins for transcriptional or posttranscriptional gene silencing. However, it is not yet clear what fraction of genomic siRNA production is RNAP IV-dependent, and to what extent these siRNAs are preferentially processed by certain DCL(s) or associated with specific AGOs for distinct downstream functions. To address these questions on a genome-wide scale, we sequenced approximately 335,000 siRNAs from wild-type and RNAP IV mutant Arabidopsis plants by using 454 technology. The results show that RNAP IV is required for the production of >90% of all siRNAs, which are faithfully produced from a discrete set of genomic loci. Comparisons of these siRNAs with those accumulated in rdr2 and dcl2 dcl3 dcl4 and those associated with AGO1 and AGO4 provide important information regarding the processing, channeling, and functions of plant siRNAs. We also describe a class of RNAP IV-independent siRNAs produced from endogenous single-stranded hairpin RNA precursors.

An allelic series reveals essential roles for FY in plant development in addition to flowering-time control

The autonomous pathway functions to promote flowering in Arabidopsis by limiting the accumulation of the floral repressor FLOWERING LOCUS C (FLC). Within this pathway FCA is a plant-specific, nuclear RNA-binding protein, which interacts with FY, a highly conserved eukaryotic polyadenylation factor. FCA and FY function to control polyadenylation site choice during processing of the FCA transcript. Null mutations in the yeast FY homologue Pfs2p are lethal. This raises the question as to whether these essential RNA processing functions are conserved in plants. Characterisation of an allelic series of fy mutations reveals that null alleles are embryo lethal. Furthermore, silencing of FY, but not FCA, is deleterious to growth in Nicotiana. The late-flowering fy alleles are hypomorphic and indicate a requirement for both intact FY WD repeats and the C-terminal domain in repression of FLC. The FY C-terminal domain binds FCA and in vitro assays demonstrate a requirement for both C-terminal FY-PPLPP repeats during this interaction. The expression domain of FY supports its roles in essential and flowering-time functions. Hence, FY may mediate both regulated and constitutive RNA 3'-end processing.

Optimisation of fuel usage and steam availability in the power and steam plant of a paper mill

This paper presents the results of a project aimed at minimising fuel usage while maximising steam availability in the power and steam plant of a large newsprint mill. The approach taken was to utilise the better regulation and plant wide optimisation capabilities of Advanced Process Control, especially Model Predictive Control (MPC) techniques. These have recently made their appearance in the pulp and paper industry but are better known in the oil and petrochemical industry where they have been used for nearly 30 years. The issue in the power and steam plant is to ensure that sufficient steam is available when the paper machines require it and yet not to have to waste too much steam when one or more of the machines suffers an outage. This is a problem for which MPC is well suited. It allows variables to be kept within declared constraint ranges, a feature which has been used, effectively, to increase the steam storage capacity of the existing plant. This has resulted in less steam being condensed when it is not required and in significant reductions in the need for supplementary firing. The incidence of steam being dump-condensed while also supplementary firing the Combined Heat & Power (CHP) plant has been reduced by 95% and the overall use of supplementary firing is less than 30% of what it was. In addition the plant runs more smoothly and requires less operator time. The yearly benefit provided by the control system is greater than £200,000, measured in terms of 2005 gas prices.

Control of meiotic recombination frequency in plant genomes.

Sexual eukaryotes reproduce via the meiotic cell division, where ploidy is halved and homologous chromosomes undergo reciprocal genetic exchange, termed crossover (CO). CO frequency has a profound effect on patterns of genetic variation and species evolution. Relative CO rates vary extensively both within and between plant genomes. Plant genome size varies by over 1000-fold, largely due to differential expansion of repetitive sequences, and increased genome size is associated with reduced CO frequency. Gene versus repeat sequences associate with distinct chromatin modifications, and evidence from plant genomes indicates that this epigenetic information influences CO patterns. This is consistent with data from diverse eukaryotes that demonstrate the importance of chromatin structure for control of meiotic recombination. In this review I will discuss CO frequency patterns in plant genomes and recent advances in understanding recombination distributions.

Long term peripheral nerve regeneration using a novel PCL nerve conduit.

The gold standard in surgical management of a peripheral nerve gap is currently autologous nerve grafting. This confers patient morbidity and increases surgical time therefore innovative experimental strategies towards engineering a synthetic nerve conduit are welcome. We have developed a novel synthetic conduit made of poly ε-caprolactone (PCL) that has demonstrated promising peripheral nerve regeneration in short-term studies. This material has been engineered to permit translation into clinical practice and here we demonstrate that histological outcomes in a long-term in vivo experiment are comparable with that of autologous nerve grafting. A 1cm nerve gap in a rat sciatic nerve injury model was repaired with a PCL nerve conduit or an autologous nerve graft. At 18 weeks post surgical repair, there was a similar volume of regenerating axons within the nerve autograft and PCL conduit repair groups, and similar numbers of myelinated axons in the distal stump of both groups. Furthermore, there was evidence of comparable re-innervation of end organ muscle and skin with the only significant difference the lower wet weight of the muscle from the PCL conduit nerve repair group. This study stimulates further work on the potential use of this synthetic biodegradable PCL nerve conduit in a clinical setting.

Design trade-offs for energy regeneration and control in vehicle suspensions

This paper investigates the fundamental trade-offs involved in designing energy-regenerative suspensions, in particular, focusing on efficiency of power extraction and its effect on vehicle dynamics and control. It is shown that typical regenerative devices making use of linear-to-rotational elements can be modelled as a parallel arrangement of an inerter and a dissipative admittance. Taking account of typical adjustable parameters of the generator, it is shown, for a given suspension damping coefficient, that the power efficiency ratio scales with inertance. For a typical passenger vehicle, it is shown that there is a feasible compromise, namely that good efficiency is achievable with an inertance value that is not detrimental to vehicle performance. A prototype is designed and tested with a resistive termination and experimental results show good agreement between ideal and experimental admittances. The possibility to use dynamic (rather than purely resistive) loads to improve vehicle control without limiting the energy recovery is discussed. © 2013 Copyright Taylor and Francis Group, LLC.

Bioelectronics meets nanomedicine for cardiovascular implants: PEDOT-based nanocoatings for tissue regeneration.

BACKGROUND: An exciting direction in nanomedicine would be to analyze how living cells respond to conducting polymers. Their application for tissue regeneration may advance the performance of drug eluting stents by addressing the delayed stent re-endothelialization and late stent thrombosis. METHODS: The suitability of poly (3, 4-ethylenedioxythiophene) (PEDOT) thin films for stents to promote cell adhesion and proliferation is tested in correlation with doping and physicochemical properties. PEDOT doped either with poly (styrenesulfonate) (PSS) or tosylate anion (TOS) was used for films' fabrication by spin coating and vapor phase polymerization respectively. PEGylation of PEDOT: TOS for reduced immunogenicity and biofunctionalization of PEDOT: PSS with RGD peptides for induced cell proliferation was further applied. Atomic Force Microscopy and Spectroscopic Ellipsometry were implemented for nanotopographical, structural, optical and conductivity measurements in parallel with wettability and protein adsorption studies. Direct and extract testing of cell viability and proliferation of L929 fibroblasts on PEDOT samples by MTT assay in line with SEM studies follow. RESULTS: All PEDOT thin films are cytocompatible and promote human serum albumin adsorption. PEDOT:TOS films were found superior regarding cell adhesion as compared to controls. Their nanotopography and hydrophilicity are significant factors that influence cytocompatibility. PEGylation of PEDOT:TOS increases their conductivity and hydrophilicity with similar results on cell viability with bare PEDOT:TOS. The biofunctionalized PEDOT:PSS thin films show enhanced cell proliferation. CONCLUSIONS: The application of PEDOT polymers has evolved as a new perspective to advance stents. GENERAL SIGNIFICANCE: In this work, nanomedicine involving nanotools and novel nanomaterials merges with bioelectronics to stimulate tissue regeneration for cardiovascular implants. This article is part of a Special Issue entitled Organic Bioelectronics - Novel Applications in Biomedicine.

Dependence of dye regeneration and charge collection on the pore-filling fraction in solid-state dye-sensitized solar cells

Solid-state dye-sensitized solar cells rely on effective infiltration of a solid-state hole-transporting material into the pores of a nanoporous TiO 2 network to allow for dye regeneration and hole extraction. Using microsecond transient absorption spectroscopy and femtosecond photoluminescence upconversion spectroscopy, the hole-transfer yield from the dye to the hole-transporting material 2,2′,7,7′-tetrakis(N,N-di-p- methoxyphenylamine)-9,9'-spirobifluorene (spiro-OMeTAD) is shown to rise rapidly with higher pore-filling fractions as the dye-coated pore surface is increasingly covered with hole-transporting material. Once a pore-filling fraction of ≈30% is reached, further increases do not significantly change the hole-transfer yield. Using simple models of infiltration of spiro-OMeTAD into the TiO2 porous network, it is shown that this pore-filling fraction is less than the amount required to cover the dye surface with at least a single layer of hole-transporting material, suggesting that charge diffusion through the dye monolayer network precedes transfer to the hole-transporting material. Comparison of these results with device parameters shows that improvements of the power-conversion efficiency beyond ≈30% pore filling are not caused by a higher hole-transfer yield, but by a higher charge-collection efficiency, which is found to occur in steps. The observed sharp onsets in photocurrent and power-conversion efficiencies with increasing pore-filling fraction correlate well with percolation theory, predicting the points of cohesive pathway formation in successive spiro-OMeTAD layers adhered to the pore walls. From percolation theory it is predicted that, for standard mesoporous TiO2 with 20 nm pore size, the photocurrent should show no further improvement beyond an ≈83% pore-filling fraction. Solid-state dye-sensitized solar cells capable of complete hole transfer with pore-filling fractions as low as ∼30% are demonstrated. Improvements of device efficiencies beyond ∼30% are explained by a stepwise increase in charge-collection efficiency in agreement with percolation theory. Furthermore, it is predicted that, for a 20 nm pore size, the photocurrent reaches a maximum at ∼83% pore-filling fraction. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.