Variation in the organization and subunit composition of the mammalian pyruvate dehydrogenase complex E2/E3BP core assembly

The final version of this article is available at the link below.Crucial to glucose homoeostasis in humans, the hPDC (human pyruvate dehydrogenase complex) is a massive molecular machine comprising multiple copies of three distinct enzymes (E1–E3) and an accessory subunit, E3BP (E3-binding protein). Its icosahedral E2/E3BP 60-meric ‘core’ provides the central structural and mechanistic framework ensuring favourable E1 and E3 positioning and enzyme co-operativity. Current core models indicate either a 48E2+12E3BP or a 40E2+20E3BP subunit composition. In the present study, we demonstrate clear differences in subunit content and organization between the recombinant hPDC core (rhPDC; 40E2+20E3BP), generated under defined conditions where E3BP is produced in excess, and its native bovine (48E2+12E3BP) counterpart. The results of the present study provide a rational basis for resolving apparent differences between previous models, both obtained using rhE2/E3BP core assemblies where no account was taken of relative E2 and E3BP expression levels. Mathematical modelling predicts that an ‘average’ 48E2+12E3BP core arrangement allows maximum flexibility in assembly, while providing the appropriate balance of bound E1 and E3 enzymes for optimal catalytic efficiency and regulatory fine-tuning. We also show that the rhE2/E3BP and bovine E2/E3BP cores bind E3s with a 2:1 stoichiometry, and propose that mammalian PDC comprises a heterogeneous population of assemblies incorporating a network of E3 (and possibly E1) cross-bridges above the core surface.This work was partly supported by EPSRC (under grants GR/R99393/01 and EP/C015452/1)

Symmetry and quantum query-to-communication simulation

Buhrman, Cleve and Wigderson (STOC'98) showed that for every Boolean function f : {-1,1}^n to {-1,1} and G in {AND_2, XOR_2}, the bounded-error quantum communication complexity of the composed function f o G equals O(Q(f) log n), where Q(f) denotes the bounded-error quantum query complexity of f. This is in contrast with the classical setting, where it is easy to show that R^{cc}(f o G) We show that the log n overhead is not required when f is symmetric, generalizing a result of Aaronson and Ambainis for the Set-Disjointness function (Theory of Computing'05). This upper bound assumes a shared entangled state, though for most symmetric functions the assumed number of entangled qubits is less than the communication and hence could be part of the communication. To prove this, we design an efficient distributed version of noisy amplitude amplification that allows us to prove the result when f is the OR function. In view of our first result, one may ask whether the log n overhead in the BCW simulation can be avoided even when f is transitive. We give a strong negative answer by showing that the log n overhead is still necessary for some transitive functions even when we allow the quantum communication protocol an error probability that can be arbitrarily close to 1/2. We also give, among other things, a general recipe to construct functions for which the log n overhead is required in the BCW simulation in the bounded-error communication model, even if the parties are allowed to share an arbitrary prior entangled state for free.</p

Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data

Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions. It may be reasonable to assume, proteins being the dominant macromolecules that carry out routine cellular functions, that understanding the dynamics of protein∶protein interactions might yield useful insights into the cellular responses. The large-scale protein interaction data sets are, however, unable to capture the changes in the profile of protein∶protein interactions. In order to understand how these interactions change dynamically, we have constructed conditional protein linkages for Escherichia coli by integrating functional linkages and gene expression information. As a case study, we have chosen to analyze UV exposure in wild-type and SOS deficient E. coli at 20 minutes post irradiation. The conditional networks exhibit similar topological properties. Although the global topological properties of the networks are similar, many subtle local changes are observed, which are suggestive of the cellular response to the perturbations. Some such changes correspond to differences in the path lengths among the nodes of carbohydrate metabolism correlating with its loss in efficiency in the UV treated cells. Similarly, expression of hubs under unique conditions reflects the importance of these genes. Various centrality measures applied to the networks indicate increased importance for replication, repair, and other stress proteins for the cells under UV treatment, as anticipated. We thus propose a novel approach for studying an organism at the systems level by integrating genome-wide functional linkages and the gene expression data

Understanding Communication Signals during Mycobacterial Latency through Predicted Genome-Wide Protein Interactions and Boolean Modeling

About 90% of the people infected with Mycobacterium tuberculosis carry latent bacteria that are believed to get activated upon immune suppression. One of the fundamental challenges in the control of tuberculosis is therefore to understand molecular mechanisms involved in the onset of latency and/or reactivation. We have attempted to address this problem at the systems level by a combination of predicted functional protein∶protein interactions, integration of functional interactions with large scale gene expression studies, predicted transcription regulatory network and finally simulations with a Boolean model of the network. Initially a prediction for genome-wide protein functional linkages was obtained based on genome-context methods using a Support Vector Machine. This set of protein functional linkages along with gene expression data of the available models of latency was employed to identify proteins involved in mediating switch signals during dormancy. We show that genes that are up and down regulated during dormancy are not only coordinately regulated under dormancy-like conditions but also under a variety of other experimental conditions. Their synchronized regulation indicates that they form a tightly regulated gene cluster and might form a latency-regulon. Conservation of these genes across bacterial species suggests a unique evolutionary history that might be associated with M. tuberculosis dormancy. Finally, simulations with a Boolean model based on the regulatory network with logical relationships derived from gene expression data reveals a bistable switch suggesting alternating latent and actively growing states. Our analysis based on the interaction network therefore reveals a potential model of M. tuberculosis latency

Identification of the onchocerciasis vector in the Kakoi-Koda focus of the Democratic Republic of Congo

Background: The objective of this study was to characterise the vector in a small hyper-endemic focus of onchocerciasis (the Kakoi-Koda focus) which has recently been discovered on the western slopes of the rift valley above Lake Albert. Methodology/Principal Findings: Aquatic stages of blackflies were collected by hand from streams and rivers, and anthropophilic adult females were collected by human landing catches. Using a combination of morphotaxonomy and DNA barcoding, the blackflies collected biting humans within the focus were identified as Simulium dentulosum and Simulium vorax, which were also found breeding in local streams and rivers. Simulium damnosum s.l., Simulium neavei and Simulium albivirgulatum were not found (except for a single site in 2009 where crabs were carrying S. neavei). Anthropophilic specimens from the focus were screened for Onchocerca DNA using discriminant qualitative real-time triplex PCR. One specimen of S. vorax was positive for Onchocerca volvulus in the body, and out of 155 S. dentulosum, 30% and 11% were infected and infective (respectively). Conclusions/Significance: Simulium dentulosum currently appears to be the main vector of human onchocerciasis within the Kakoi-Koda focus, and S. vorax may be a secondary vector. It remains possible that S. neavei was the main (or only) vector in the past having now become rare as a result of the removal of tree-cover and land-use changes. Simulium vorax has previously been shown to support the development of O. volvulus in the laboratory, but this is the first time that S. dentulosum has been implicated as a probable vector of onchocerciasis, and this raises the possibility that other blackfly species which are not generally considered to be anthropophilic vectors might become vectors under suitable conditions. Because S. dentulosum is not a vector in endemic areas surrounding the Kakoi-Koda focus, it is probable that the Kakoi-Koda focus is significantly isolated

Kajian potensi ekstrak bilberi sebagai penunjuk pH untuk memantau kesegaran makanan secara kromametri

Penunjuk pH sebagai suatu pendekatan untuk memantau kualiti atau kesegaran makanan semasa telah mendapat perhatian industri pembungkusan makanan. Penggunaan sumber semula jadi pigmen tumbuhan terutamanya daripada buah-buahan dan sayur-sayuran menjadi pilihan para pengguna untuk menggantikan pewarna sintetik dalam memastikan keselamatan makanan yang diambil setiap hari. Dalam kajian ini, ekstrak daripada bilberi telah digunakan sebagai pewarna sensitif pH. Perubahan warna sampel dikaji secara terperinci melalui kaedah kromametri dan juga kaedah spektrofotometri ultra-lembayung nampak. Warna merah terang terhasil dalam pH berasid, merah pudar pada neutral dan magenta ke kuning dalam pH beralkali. Keputusan kajian kromametri menunjukkan bahawa ekstrak bilberi berupaya mempamerkan perubahan warna yang jelas terhadap perubahan pH, iaitu terdapat perubahan nilai warna a* yang menyumbang kepada perubahan yang bererti dalam perbezaan warna keseluruhan (ΔE*). Nilai ΔE* juga ditentukan wujud hubungan linear dan kuantitatif terhadap julat pH tertentu. Oleh yang demikian, ekstrak bilberi didapati berpotensi sebagai bahan sensor untuk pH dalam membangunkan satu sensor pH bagi memantau kesegaran makanan terutamanya hasilan laut berbungkus memandangkan tahap kerosakan produk tersebut berkait rapat dengan perubahan pH ke arah alkali

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass

Left ventricular mass (LVM) and cardiac gene expression are complex traits regulated by factors both intrinsic and extrinsic to the heart. To dissect the major determinants of LVM, we combined expression quantitative trait locus1 and quantitative trait transcript (QTT) analyses of the cardiac transcriptome in the rat. Using these methods and in vitro functional assays, we identified osteoglycin (Ogn) as a major candidate regulator of rat LVM, with increased Ogn protein expression associated with elevated LVM. We also applied genome-wide QTT analysis to the human heart and observed that, out of 22,000 transcripts, OGN transcript abundance had the highest correlation with LVM. We further confirmed a role for Ogn in the in vivo regulation of LVM in Ogn knockout mice. Taken together, these data implicate Ogn as a key regulator of LVM in rats, mice and humans, and suggest that Ogn modifies the hypertrophic response to extrinsic factors such as hypertension and aortic stenosi