Orientation of Non-Native 2-Monosubstituted and 2,3-Disubstituted 1,4-Naphthoquinones in the A1 binding site of PSI and the effect on the rate of electron transfer : an electron paramagnetic resonance spectroscopy study

The proce-ss ofoxygenic photosynthesis is vital to life on Earth. the central event in photosynthesis is light induced electron transfer that converts light into energy for growth. Ofparticular significance is the membrane bound multisubunit protein known as Photosystem I (PSI). PSI is a reaction centre that is responsible for the transfer of electrons across the membrane to reduce NADP+ to NADPH. The recent publication ofa high resolution X-ray structure of PSI has shown new information about the structure, in particular the electron transfer cofactors, which allows us to study it in more detail. In PSI, the secondary acceptor is crucial for forward electron transfer. In this thesis, the effect of removing the native acceptor phylloquinone and replacing it with a series of structurally related quinones was investigated via transient electron paramagnetic resonance (EPR) experiments. The orientation of non native quinones in the binding site and their ability to function in the electron transfer process was determined. It was found that PSI will readily accept alkyl naphthoquinones and anthraquinone. Q band EPR experiments revealed that the non-native quinones are incorporated into the binding site with the same orientation of the headgroup as in the native system. X band EPR spectra and deuteration experiments indicate that monosubstituted naphthoquinones are bound to the Al site with their side group in the position occupied by the methyl group in native PSI (meta to the hydrogen bonded carbonyl oxygen). X band EPR experiments show that 2, 3- disubstituted methyl naphthoquinones are also incorporated into the Al site in the same orientation as phylloquinone, even with the presence of a halogen- or sulfur-containing side chain in the position normally occupied by the phytyl tail ofphylloquinone. The exception to this is 2-bromo-3-methyl --.- _. -. - -- - - 4 _._ _ _ - _ _ naphthoquinone which has a poorly resolved spectrum, making determination of the orientation difficuh. All of the non-native quinones studied act as efficient electron acceptors. However, forward electron transfer past the quinone could only be demonstrated for anthraquinone, which has a more negative midpoint potential than phylloquinone. In the case of anthraquinone, an increased rate of forward electron transfer compared to native PSI was found. From these results we can conclude that the rate ofelectron transfer from Al to Fx in native PSI lies in the normal region ofthe Marcus Curve.

Optimizing Computational Frameworks to Study the Influence of the Protein Environment on the Individual Site Energies of Chromophores in Photosystem II of Photosynthesis

Photosynthesis is a process in which electromagnetic radiation is converted into chemical energy. Photosystems capture photons with chromophores and transfer their energy to reaction centers using chromophores as a medium. In the reaction center, the excitation energy is used to perform chemical reactions. Knowledge of chromophore site energies is crucial to the understanding of excitation energy transfer pathways in photosystems and the ability to compute the site energies in a fast and accurate manner is mandatory for investigating how protein dynamics ef-fect the site energies and ultimately energy pathways with time. In this work we developed two software frameworks designed to optimize the calculations of chro-mophore site energies within a protein environment. The first is for performing quantum mechanical energy optimizations on molecules and the second is for com-puting site energies of chromophores in a fast and accurate manner using the polar-izability embedding method. The two frameworks allow for the fast and accurate calculation of chromophore site energies within proteins, ultimately allowing for the effect of protein dynamics on energy pathways to be studied. We use these frame-works to compute the site energies of the eight chromophores in the reaction center of photosystem II (PSII) using a 1.9 Å resolution x-ray structure of photosystem II. We compare our results to conflicting experimental data obtained from both isolat-ed intact PSII core preparations and the minimal reaction center preparation of PSII, and find our work more supportive of the former.

The Ligand and Membrane-binding Behaviour of the Phosphatidylinositol Transfer Proteins (PITPa & PITPb)

Human Class I phosphatidylinositol transfer proteins (PITPs) exists in two forms: PITPα and PITPβ. PITPs are believed to be lipid transfer proteins based on their capacity to transfer either phosphatidylinositol (PI) or phosphatidylcholine (PC) between membrane compartments in vitro. In Drosophila, the PITP domain is found to be part of a multi-domain protein named retinal degeneration B (RdgBα). The PITP domain of RdgBα shares 40 % sequence identity with PITPα and has been shown to possess PI and PC binding and transfer activity. The detailed molecular mechanism of ligand transfer by the human PITPs and the Drosophila PITP domain remains to be fully established. Here, we investigated the membrane interactions of these proteins using dual polarization interferometry (DPI). DPI is a technique that measures protein binding affinity to a flat immobilized lipid bilayer. In addition, we also measured how quickly these proteins transfer their ligands to lipid vesicles using a fluorescence resonance energy transfer (FRET)-based assay. DPI investigations suggest that PITPβ had a two-fold higher affinity for membranes compared to PITPα. This was reflected by a four-fold faster ligand transfer rate for PITPβ in comparison to PITPα as determined by the FRET assay. Interestingly, DPI analysis also demonstrated that PI-bound human PITPs have lower membrane affinity compared to PC-bound PITPs. In addition, the FRET studies demonstrated the significance of membrane curvature in the ligand transfer rate of PITPs. The ligand transfer rate was higher when the accepting vesicles were highly curved. Furthermore, when the accepting vesicles contained phosphatidic acid (PA) which have smaller head groups, the transfer rate increased. In contrast, when the accepting vesicles contained phosphoinositides which have larger head groups, the transfer rate was diminished. However, PI, the favorite ligand of PITPs, or the presence of anionic lipids did not appear to influence the ligand transfer rate of PITPs. Both DPI and FRET examinations revealed that the PITP domain of RdgBα was able to bind to membranes. However, the RdgBα PITP domain appears to be a poor binder and transporter of PC.

Expression of steroidogenic proteins and genes in bovine placenta from conventional and somatic cell nuclear transfer (SCNT) gestations

Pendant la grossesse, les hormones stéroïdes jouent un rôle indispensable dans la régulation des principales manifestations physiologiques telles que la reconnaissance maternelle de la gestation, la réceptivité de l'endomètre, le début du développement embryonnaire ainsi que le maintien de la gestation. Cependant, on sait très peu sur la production de ces hormones et les principaux facteurs des voies intracellulaires impliqués dans le processus de stéroïdogenèse dans le placenta bovin pendant les stades initiaux et plus avancés de la gestation. Par ailleurs, certaines anomalies du placenta chez les bovins suite à une mauvaise production de stéroïdes n'ont pas encore été démontrées. Les objectifs de cette thèse étaient donc de : 1) déterminer la présence et la localisation des principales protéines stéroïdiennes dans le placenta de bovins provenant de gestations de 50 à 120 jours, 2) comparer l'expression placentaire d'une série de gènes et de protéines stéroïdiennes entre une gestation impliquant un transfert de noyaux de cellules somatiques (SCNT) et une gestation non-clonale; 3) étudier l'impact des hormones trophiques et des seconds messagers sur la stéroïdogenèse dans le placenta bovin à 140 +10 jours de gestation. L’utilisation de techniques d’immunohistochimie, d’immunobuvardage et de PCR quantitatif nous a permis d’évaluer la présence d'un large éventail de gènes stéroïdiens (STAR, CYP11A1, HSD3B1, CYP17A1 et SCARB1) qui participent au transport du cholestérol et dans la production de différents types de stéroïdes. Dans cette thèse, nous avons démontré la capacité du placenta bovin d’initier la stéroïdogenèse au début de la gestation et nous avons également déterminé les principales cellules impliquées dans ce processus. Nous avons constaté que les tissus maternels expriment les principaux marqueurs de stéroïdogenèse suggérant une plus grande capacité stéroïdogénique que les tissus fœtaux. En outre, un modèle d'expression des protéines complémentaires stéroïdogéniques entre la caroncule et le cotylédon a été observé, indiquant que la stéroïdogenèse placentaire exige une communication cellule à cellule entre les cellules de la mère et du fœtus. Après avoir démontré les principales cellules impliquées dans la synthèse des hormones stéroïdiennes dans le placenta bovin en début de gestation, nous avons ensuite étudié les modifications possibles de la stéroïdogenèse dans les tissus SCNT cotylédonaires à 40 jours de gestation. Nous avons identifié d'importantes modifications dans l'expression des gènes STAR, CYP11A1, HSD3B1, CYP17A1, et SULT1E1. Conséquemment, nous postulons que l'expression réduite des gènes stéroïdiens peut provoquer une insuffisance de la biosynthèse des hormones stéroïdiennes, ce qui pourrait contribuer à un développement anormal du placenta et du fœtus dans les gestations SCNT à court ou long terme. Finalement, nous avons développé un modèle efficace de culture d’explants de placentome qui nous a permis d'explorer les mécanismes sous-jacents spécifiques à la stéroïdogenèse placentaire. Nous avons exploré l'effet stimulant des hormones trophiques et différents messagers secondaires sur l'expression de différentes protéines stéroïdogéniques ainsi que le taux de progestérone (P4) dans les explants de placentome. En utilisant les techniques de RIA et de PCR quantitatif, nous avons constaté que même si les analogues de l'hormone lutéinisante (hCG) ont un effet stimulant sur plusieurs gènes stéroïdiens, le calcium ionophore est le principal modulateur dans la synthèse de la P4. Ces résultats suggèrent que dans le placenta bovin, la synthèse de la P4 est modulée principalement par l'afflux de calcium intracellulaire, et apparemment les nucléotides cycliques ne semblent pas contrôler ce processus. En conclusion, cette étude contribue de manière significative à une meilleure compréhension des mécanismes d'entraînement de la synthèse des stéroïdes placentaires au début de la gestation et permet aussi d’apporter de nouveaux éclairages sur l'importance des stéroïdes placentaires dans la régulation du développement du placenta et du fœtus.

Morphological and functional characterization of placenta during gestation in bovine clones derived by somatic nuclear transfer

La technique de clonage par transfert nucléaire de cellules somatiques (SCNT) présente une page importante dans les annales scientifiques, mais son application pratique demeure incertaine dû à son faible taux de succès. Les anomalies placentaires et de développement fœtal se traduisent par des pertes importantes de gestation et des mortalités néonatales. Dans un premier temps, la présente étude a caractérisé les changements morphologiques des membranes fœtales durant la gestation clonée en les comparant à des gestations contrôles obtenues à partir de l’insémination artificielle. Les différentes anomalies morphologiques des placentomes telles que l’œdème chorioallantoique, la présence de zones hyperéchoiques et irrégulières dans la membrane amniotique et la présence de cellules inflammatoires dégénérées compromettent le développement fœtal normal de la gestation clonée. L’examen ultrasonographique représente une technique diagnostique importante pour faire le suivi d’une gestation et de caractériser les changements placentaires dans le cadre d’évaluation globale du bien-être fœtal. Le profil hormonal de trois stéroïdes (progestérone (P4), estrone sulfate (E1S), et œstradiol (E2)) et de la protéine B spécifique de gestation (PSPB) dans le sérum des vaches porteuses de clones SCNT a été déterminé et associé aux anomalies de gestations clonées. Une diminution de la P4 sérique au jour 80, une élévation du niveau de la concentration de la PSPB au jour 150, et une augmentation de la concentration d’E2 sérique durant le deuxième et troisième tiers de la gestation clonée coïncident avec les anomalies de gestation déjà reportées. Ces changements du profil hormonal associés aux anomalies phénotypiques du placenta compromettent le déroulement normal de la gestation clonée et gênent le développement et le bien-être fœtal. Sur la base des observations faites sur le placenta de gestation clonée, le mécanisme moléculaire pouvant expliquer la disparition de l’épithélium du placenta (l’interface entre le tissue maternel et le placenta) a été étudié. L’étude a identifié des changements dans l’expression de deux protéines d’adhérence (E-cadhérin et β-catenin) de cellules épithéliales pouvant être associées aux anomalies du placenta chez les gestations clonées. Le tissu de cotylédons provenant de gestations clonées et contrôles a été analysé par Western blot, RT-PCR quantitatif, et par immunohistochimie. Les résultats présentaient une diminution significative (p<0.05) de l’expression des dites protéines dans les cellules trophoblastiques chez les gestations clonées. Le RT-PCR quantitatif démontrait que les gènes CCND1, CLDN1 et MSX1 ciblés par la voie de signalisation de la Wnt/β-catenin étaient significativement sous exprimés. La diminution de l’expression des protéines E-cadherin et β-catenin avec une réduction de l’activation de la protéine β-catenin durant le période d’attachement de l’embryon peut potentiellement expliquer l’absence totale ou partielle de l’attachement des membranes fœtales au tissu maternel et éventuellement, l’insuffisance placentaire caractéristique des gestations clonées chez la vache. La caractérisation morphologique et fonctionnelle du placenta durant les gestations clonées à haut risque est essentielle pour évaluer le statut de la gestation. Les résultats de la présente étude permettront de prédire le développement et le bien-être fœtal de façon critique à travers un protocole standardisé et permettre des interventions médicales pour améliorer le taux de succès des gestations clonées chez les bovins.

Technology transfer in the fish curing industry in india

Curing is the oldest and cheapest method of preservation of fish allover the world. Fish curing industry has not shown much improverrent from its primitive nature because this industry is mainly handled by illiterate and less educated fishermen/fisherwomen. They do not know much about,the importance of scientific methods of fish curing. The cured fish produced by them is unhygienic and poor in quality. Because of the negligenence and ignorance of the fish curers, a considerable quanti ty of this protein rich food is spoiled and lost every year. Research has been conducted extensively in the Cen tral and State sectors and various remedial measures have been suggested :to improve the fish curing industry in India. Inspi te of the preJudioa against cured fish because of their existing low quality, research work in recent years have indicated that their quality can be greaUy improved and shelf-life prolonged if the me thods are standardised. To achieve this aim, Cen tral and s tate Departments have already made considerable efforts to transfer the improved methods ~ the fish curing industry by way of traininq courses, demonstrations, Lab, to Land Prograrrmesi film shows, exhibitions, personal discussion etc. As the result of this, fish curers have started adopting the improved practices in fish curing. Still there seems to be a considerable qap between the techmology available and the technology adopted in this field. A comprehensive study on the extent of adoption of improved practices in fish curing and the factors involved in low or non-adoption of certain aspects is lackin~ at present. This gap has to be filled up. The possihle methods for the effective transfer of technology for the production and distribution of high quali ty cured fish products and improvement of soclo-economic condition of fishermen engaqed in fish curing have to be identified.

Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.

Adeno-associated virus-8-Mediated intravenous transfer of myostatin propeptide leads to systemic functional improvements of slow but not fast muscle

Myostatin is a member of the transformating growth factor-_ (TGF-_) superfamily of proteins and is produced almost exclusively in skeletal muscle tissue, where it is secreted and circulates as a serum protein. Myostatin acts as a negative regulator of muscle mass through the canonical SMAD2/3/4 signaling pathway. Naturally occurring myostatin mutants exhibit a ‘double muscling’ phenotype in which muscle mass is dramatically increased as a result of both hypertrophy and hyperplasia. Myostatin is naturally inhibited by its own propeptide; therefore, we assessed the impact of adeno associated virus-8 (AAV8) myostatin propeptide vectors when systemically introduced in MF-1 mice. We noted a significant systemic increase in muscle mass in both slow and fast muscle phenotypes, with no evidence of hyperplasia; however, the nuclei-to- cytoplasm ratio in all myofiber types was significantly reduced. An increase in muscle mass in slow (soleus) muscle led to an increase in force output; however, an increase in fast (extensor digitorum longus [EDL]) muscle mass did not increase force output. These results suggest that the use of gene therapeutic regimens of myostatin inhibition for age-related or disease-related muscle loss may have muscle-specific effects.

Grid computing solutions for distributed repositories of protein folding and unfolding simulations

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data and a data warehouse. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular we look at two aspects, first how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories --- this is an important and challenging aspect of P-found because the data volumes involved are too large to be centralised. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling new scientific discoveries.

P-found: grid-enabling distributed repositories of protein folding and unfolding simulations for data mining

The P-found protein folding and unfolding simulation repository is designed to allow scientists to perform data mining and other analyses across large, distributed simulation data sets. There are two storage components in P-found: a primary repository of simulation data that is used to populate the second component, and a data warehouse that contains important molecular properties. These properties may be used for data mining studies. Here we demonstrate how grid technologies can support multiple, distributed P-found installations. In particular, we look at two aspects: firstly, how grid data management technologies can be used to access the distributed data warehouses; and secondly, how the grid can be used to transfer analysis programs to the primary repositories — this is an important and challenging aspect of P-found, due to the large data volumes involved and the desire of scientists to maintain control of their own data. The grid technologies we are developing with the P-found system will allow new large data sets of protein folding simulations to be accessed and analysed in novel ways, with significant potential for enabling scientific discovery.

Liquid AP-UV-MALDI enables stable ion yields of multiply charged peptide and protein ions for sensitive analysis by mass spectrometry

In biological mass spectrometry (MS), two ionization techniques are predominantly employed for the analysis of larger biomolecules, such as polypeptides. These are nano-electrospray ionization [1, 2] (nanoESI) and matrix-assisted laser desorption/ionization [3, 4] (MALDI). Both techniques are considered to be “soft”, allowing the desorption and ionization of intact molecular analyte species and thus their successful mass-spectrometric analysis. One of the main differences between these two ionization techniques lies in their ability to produce multiply charged ions. MALDI typically generates singly charged peptide ions whereas nanoESI easily provides multiply charged ions, even for peptides as low as 1000 Da in mass. The production of highly charged ions is desirable as this allows the use of mass analyzers, such as ion traps (including orbitraps) and hybrid quadrupole instruments, which typically offer only a limited m/z range (< 2000–4000). It also enables more informative fragmentation spectra using techniques such as collisioninduced dissociation (CID) and electron capture/transfer dissociation (ECD/ETD) in combination with tandem MS (MS/MS). [5, 6] Thus, there is a clear advantage of using ESI in research areas where peptide sequencing, or in general, the structural elucidation of biomolecules by MS/MS is required. Nonetheless, MALDI with its higher tolerance to contaminants and additives, ease-of-operation, potential for highspeed and automated sample preparation and analysis as well as its MS imaging capabilities makes it an ionization technique that can cover bioanalytical areas for which ESI is less suitable. [7, 8] If these strengths could be combined with the analytical power of multiply charged ions, new instrumental configurations and large-scale proteomic analyses based on MALDI MS(/MS) would become feasible.

File Transfer Protocol

The discourse surrounding the virtual has moved away from the utopian thinking accompanying the rise of the Internet in the 1990s. The Cyber-gurus of the last decades promised a technotopia removed from materiality and the confines of the flesh and the built environment, a liberation from old institutions and power structures. But since then, the virtual has grown into a distinct yet related sphere of cultural and political production that both parallels and occasionally flows over into the old world of material objects. The strict dichotomy of matter and digital purity has been replaced more recently with a more complex model where both the world of stuff and the world of knowledge support, resist and at the same time contain each other. Online social networks amplify and extend existing ones; other cultural interfaces like youtube have not replaced the communal experience of watching moving images in a semi-public space (the cinema) or the semi-private space (the family living room). Rather the experience of viewing is very much about sharing and communicating, offering interpretations and comments. Many of the web’s strongest entities (Amazon, eBay, Gumtree etc.) sit exactly at this juncture of applying tools taken from the knowledge management industry to organize the chaos of the material world along (post-)Fordist rationality. Since the early 1990s there have been many artistic and curatorial attempts to use the Internet as a platform of producing and exhibiting art, but a lot of these were reluctant to let go of the fantasy of digital freedom. Storage Room collapses the binary opposition of real and virtual space by using online data storage as a conduit for IRL art production. The artworks here will not be available for viewing online in a 'screen' environment but only as part of a downloadable package with the intention that the exhibition could be displayed (in a physical space) by any interested party and realised as ambitiously or minimally as the downloader wishes, based on their means. The artists will therefore also supply a set of instructions for the physical installation of the work alongside the digital files. In response to this curatorial initiative, File Transfer Protocol invites seven UK based artists to produce digital art for a physical environment, addressing the intersection between the virtual and the material. The files range from sound, video, digital prints and net art, blueprints for an action to take place, something to be made, a conceptual text piece, etc. About the works and artists: Polly Fibre is the pseudonym of London-based artist Christine Ellison. Ellison creates live music using domestic devices such as sewing machines, irons and slide projectors. Her costumes and stage sets propose a physical manifestation of the virtual space that is created inside software like Photoshop. For this exhibition, Polly Fibre invites the audience to create a musical composition using a pair of amplified scissors and a turntable. http://www.pollyfibre.com John Russell, a founding member of 1990s art group Bank, is an artist, curator and writer who explores in his work the contemporary political conditions of the work of art. In his digital print, Russell collages together visual representations of abstract philosophical ideas and transforms them into a post apocalyptic landscape that is complex and banal at the same time. www.john-russell.org The work of Bristol based artist Jem Nobel opens up a dialogue between the contemporary and the legacy of 20th century conceptual art around questions of collectivism and participation, authorship and individualism. His print SPACE concretizes the representation of the most common piece of Unicode: the vacant space between words. In this way, the gap itself turns from invisible cipher to sign. www.jemnoble.com Annabel Frearson is rewriting Mary Shelley's Frankenstein using all and only the words from the original text. Frankenstein 2, or the Monster of Main Stream, is read in parts by different performers, embodying the psychotic character of the protagonist, a mongrel hybrid of used language. www.annabelfrearson.com Darren Banks uses fragments of effect laden Holywood films to create an impossible space. The fictitious parts don't add up to a convincing material reality, leaving the viewer with a failed amalgamation of simulations of sophisticated technologies. www.darrenbanks.co.uk FIELDCLUB is collaboration between artist Paul Chaney and researcher Kenna Hernly. Chaney and Hernly developed together a project that critically examines various proposals for the management of sustainable ecological systems. Their FIELDMACHINE invites the public to design an ideal agricultural field. By playing with different types of crops that are found in the south west of England, it is possible for the user, for example, to create a balanced, but protein poor, diet or to simply decide to 'get rid' of half the population. The meeting point of the Platonic field and it physical consequences, generates a geometric abstraction that investigates the relationship between modernist utopianism and contemporary actuality. www.fieldclub.co.uk Pil and Galia Kollectiv, who have also curated the exhibition are London-based artists and run the xero, kline & coma gallery. Here they present a dialogue between two computers. The conversation opens with a simple text book problem in business studies. But gradually the language, mimicking the application of game theory in the business sector, becomes more abstract. The two interlocutors become adversaries trapped forever in a competition without winners. www.kollectiv.co.uk

Maternally expressed gene1 is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression

Growth of the maize (Zea mays) endosperm is tightly regulated by maternal zygotic and sporophytic genes, some of which are subject to a parent-of-origin effect. We report here a novel gene, maternally expressed gene1 (meg1), which shows a maternal parent-of-origin expression pattern during early stages of endosperm development but biallelic expression at later stages. Interestingly, a stable reporter fusion containing the meg1 promoter exhibits a similar pattern of expression. meg1 is exclusively expressed in the basal transfer region of the endosperm. Further, we show that the putatively processed MEG1 protein is glycosylated and subsequently localized to the labyrinthine ingrowths of the transfer cell walls. Hence, the discovery of a parent-of-origin gene expressed solely in the basal transfer region opens the door to epigenetic mechanisms operating in the endosperm to regulate certain aspects of nutrient trafficking from the maternal tissue into the developing seed.

Codon and mRNA sequence optimization of microdystrophin transgenes improves expression and physiological outcome in dystrophic mdx mice following AAV2/8 gene transfer

Duchenne muscular dystrophy is a fatal muscle-wasting disorder. Lack of dystrophin compromises the integrity of the sarcolemma and results in myofibers that are highly prone to contraction-induced injury. Recombinant adenoassociated virus (rAAV)-mediated dystrophin gene transfer strategies to muscle for the treatment of Duchenne muscular dystrophy (DMD) have been limited by the small cloning capacity of rAAV vectors and high titers necessary to achieve efficient systemic gene transfer. In this study, we assess the impact of codon optimization on microdystrophin (ΔAB/R3-R18/ΔCT) expression and function in the mdx mouse and compare the function of two different configurations of codon-optimized microdystrophin genes (ΔAB/R3-R18/ΔCT and ΔR4-R23/ΔCT) under the control of a muscle-restrictive promoter (Spc5-12). Codon optimization of microdystrophin significantly increases levels of microdystrophin mRNA and protein after intramuscular and systemic administration of plasmid DNA or rAAV2/8. Physiological assessment demonstrates that codon optimization of ΔAB/R3-R18/ΔCT results in significant improvement in specific force, but does not improve resistance to eccentric contractions compared with noncodon-optimized ΔAB/ R3-R18/ΔCT. However, codon-optimized microdystrophin ΔR4-R23/ΔCT completely restored specific force generation and provided substantial protection from contraction-induced injury. These results demonstrate that codon optimization of microdystrophin under the control of a muscle-specific promoter can significantly improve expression levels such that reduced titers of rAAV vectors will be required for efficient systemic administration.

Recovery and upgrading bovine rumen protein by extrusion: Effect of lipid content on protein disulphide cross-linking, solubility and molecular weight

Bovine rumen protein with two levels of residual lipids (1.9% or 3.8%) was subjected to thermoplastic extrusion under different temperatures and moisture contents. Protein Solubility in different buffers, disulphide cross-linking and molecular weight distribution were determined on the extrudates. After extrusion, samples with 1.9% residual lipids content had a higher concentration of protein insoluble by undetermined forces, irrespective of feed moisture and processing temperature used. Lipid content of 3.8% in the feed material resulted in more protein participating in the extrudate network through non-covalent interactions (hydrophobic and electrostatic) and disulphide bonds. A small dependency of the extrusion process on moisture and temperature and a marked dependency on lipid content, especially phospholipid, was observed, Electrophoresis under non-reducing conditions showed that protein extrusion with low feed moisture promoted high molecular breakdown inside the barrel, probably due to intense shear force, and further protein aggregation at the die end. (C) 2009 Elsevier Ltd. All rights reserved.