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Strong Eukaryotic IRESs Have Weak Secondary Structure  [PDF]
Xuhua Xia, Martin Holcik
PLOS ONE , 2009, DOI: 10.1371/journal.pone.0004136
Abstract: Background The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES) lack secondary structure and to examine the generality of the hypothesis. Methodology/Principal Findings IRESs of the yeast and the fruit fly are located in the 5′UTR immediately upstream of the initiation codon. The minimum folding energy (MFE) of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. Conclusions We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5′-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.
A structure filter for the Eukaryotic Linear Motif Resource
Allegra Via, Cathryn M Gould, Christine Gemünd, Toby J Gibson, Manuela Helmer-Citterich
BMC Bioinformatics , 2009, DOI: 10.1186/1471-2105-10-351
Abstract: Current methods assessing motif accessibility do not consider much of the information available, either predicting accessibility from primary sequence or regarding any motif occurring in a globular region as low confidence. We present a method considering accessibility and secondary structural context derived from experimentally solved protein structures to rectify this situation. Putatively functional motif occurrences are mapped onto a representative domain, given that a high quality reference SCOP domain structure is available for the protein itself or a close relative. Candidate motifs can then be scored for solvent-accessibility and secondary structure context. The scores are calibrated on a benchmark set of experimentally verified motif instances compared with a set of random matches. A combined score yields 3-fold enrichment for functional motifs assigned to high confidence classifications and 2.5-fold enrichment for random motifs assigned to low confidence classifications. The structure filter is implemented as a pipeline with both a graphical interface via the ELM resource http://elm.eu.org/ webcite and through a Web Service protocol.New occurrences of known linear motifs require experimental validation as the bioinformatics tools currently have limited reliability. The ELM structure filter will aid users assessing candidate motifs presenting in globular structural regions. Most importantly, it will help users to decide whether to expend their valuable time and resources on experimental testing of interesting motif candidates.In recent years it has become clear that proteins with highly modular architectures possess numerous short peptide motifs that are essential to their function [1-5]. Such peptides are termed Linear Motifs (LM) as, in contrast to the globular domains, their function is independent of tertiary structure and encoded solely by the amino acid sequence. They are found in a diverse range of proteins, such as membrane receptors, adaptors, scaf
Solution Structure of an Archaeal DNA Binding Protein with an Eukaryotic Zinc Finger Fold  [PDF]
Florence Guillière, Chloé Danioux, Carole Jaubert, Nicole Desnoues, Muriel Delepierre, David Prangishvili, Guennadi Sezonov, J. I?aki Guijarro
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0052908
Abstract: While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.
Longer First Introns Are a General Property of Eukaryotic Gene Structure  [PDF]
Keith R. Bradnam, Ian Korf
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003093
Abstract: While many properties of eukaryotic gene structure are well characterized, differences in the form and function of introns that occur at different positions within a transcript are less well understood. In particular, the dynamics of intron length variation with respect to intron position has received relatively little attention. This study analyzes all available data on intron lengths in GenBank and finds a significant trend of increased length in first introns throughout a wide range of species. This trend was found to be even stronger when using high-confidence gene annotation data for three model organisms (Arabidopsis thaliana, Caenorhabditis elegans, and Drosophila melanogaster) which show that the first intron in the 5′ UTR is - on average - significantly longer than all downstream introns within a gene. A partial explanation for increased first intron length in A. thaliana is suggested by the increased frequency of certain motifs that are present in first introns. The phenomenon of longer first introns can potentially be used to improve gene prediction software and also to detect errors in existing gene annotations.
Surprising Prokaryotic and Eukaryotic Diversity, Community Structure and Biogeography of Ethiopian Soda Lakes  [PDF]
Anders Lanzén, Addis Simachew, Amare Gessesse, Dominika Chmolowska, Inge Jonassen, Lise ?vre?s
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0072577
Abstract: Soda lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. This makes them valuable model systems for studying the connection between community structure and abiotic parameters such as pH and salinity. For the first time, we apply high-throughput sequencing to accurately estimate phylogenetic richness and composition in five soda lakes, located in the Ethiopian Rift Valley. The lakes were selected for their contrasting pH, salinities and stratification and several depths or spatial positions were covered in each lake. DNA was extracted and analyzed from all lakes at various depths and RNA extracted from two of the lakes, analyzed using both amplicon- and shotgun sequencing. We reveal a surprisingly high biodiversity in all of the studied lakes, similar to that of freshwater lakes. Interestingly, diversity appeared uncorrelated or positively correlated to pH and salinity, with the most “extreme” lakes showing the highest richness. Together, pH, dissolved oxygen, sodium- and potassium concentration explained approximately 30% of the compositional variation between samples. A diversity of prokaryotic and eukaryotic taxa could be identified, including several putatively involved in carbon-, sulfur- or nitrogen cycling. Key processes like methane oxidation, ammonia oxidation and ‘nitrifier denitrification’ were also confirmed by mRNA transcript analyses.
The crystal structure of the catalytic domain of a eukaryotic guanylate cyclase
Jonathan A Winger, Emily R Derbyshire, Meindert H Lamers, Michael A Marletta, John Kuriyan
BMC Structural Biology , 2008, DOI: 10.1186/1472-6807-8-42
Abstract: We have determined the crystal structure of the catalytic domain of a soluble guanylate cyclase from the green algae Chlamydomonas reinhardtii at 2.55 ? resolution, and show that it is a dimeric molecule.Comparison of the structure of the guanylate cyclase domain with the known structures of adenylate cyclases confirms the close similarity in architecture between these two enzymes, as expected from their sequence similarity. The comparison also suggests that the crystallized guanylate cyclase is in an inactive conformation, and the structure provides indications as to how activation might occur. We demonstrate that the two active sites in the dimer exhibit positive cooperativity, with a Hill coefficient of ~1.5. Positive cooperativity has also been observed in the homodimeric mammalian membrane-bound guanylate cyclases. The structure described here provides a reliable model for functional analysis of mammalian guanylate cyclases, which are closely related in sequence.The second messenger 3',5'-cyclic guanosine monophosphate (cGMP) is central to many signal transduction pathways, primarily eliciting effects by modulating the activities of phosphodiesterases, protein kinases, and ion channels [1-3]. In mammals, cGMP is synthesized by two distinct classes of guanylate cyclases, which are either cytoplasmic or membrane-bound [4]. Both classes of guanylate cyclase share a catalytic module that is closely related in sequence to that of mammalian adenylate cyclases. The catalytic domain is a class III nucleotide cyclase domain [5], which is distributed widely from bacteria to humans. The class III nucleotide cyclase domain is often found fused to diverse regulatory domains, but is also found as an isolated protein [6-8]. The mammalian membrane-bound guanylate cyclases, which respond to extracellular peptide binding or to the levels of intracellular Ca2+, function in maintenance of fluid homeostasis, inhibition of myocyte hypertrophy, skeletal development, and visual and ol
Optimal Encryption of Quantum Bits  [PDF]
P. Oscar Boykin,Vwani Roychowdhury
Physics , 2000, DOI: 10.1103/PhysRevA.67.042317
Abstract: We characterize the complete set of protocols that may be used to securely encrypt n quantum bits using secret and random classical bits. In addition to the application of such quantum encryption protocols to quantum data security, our framework allows for generalizations of many classical cryptographic protocols to quantum data. We show that the encrypted state gives no information without the secret classical data, and that 2n random classical bits are the minimum necessary for informationally secure quantum encryption. Moreover, the quantum operations are shown to have a surprising structure in a canonical inner product space. This quantum encryption protocol is a generalization of the classical one time pad concept. A connection is made between quantum encryption and quantum teleportation, and this allows for a new proof of optimality of teleportation.
Conjugate Gradient Method to Solve Fluid Structure Interaction Problem  [PDF]
Mamadou Diop, Ibrahima Mbaye
Applied Mathematics (AM) , 2017, DOI: 10.4236/am.2017.84036
Abstract: In this paper, we propose a method to solve coupled problem. Our computational method is mainly based on conjugate gradient algorithm. We use finite difference method for the structure and finite element method for the fluid. Conjugate gradient method gives suitable numerical results according to some papers.
To parallelize or not to parallelize, bugs issue  [PDF]
Alaa I. El-Nashar,Nakamura Masaki
Computer Science , 2013,
Abstract: Program correctness is one of the most difficult challenges in parallel programming. Message Passing Interface MPI is widely used in writing parallel applications. Since MPI is not a compiled language, the programmer will be enfaced with several programming bugs.This paper presents the most common programming bugs arise in MPI programs to help the programmer to compromise between the advantage of parallelism and the extra effort needed to detect and fix such bugs. An algebraic specification of an MPI-like programming language, called Simple MPI (SMPI), to be used in writing MPI programs specification has also been proposed. In addition, both nondeterminacy and deadlocks arise in SMPI programs have been verified using Maud system.
yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes
Matthew D Wilkerson, Shannon D Schlueter, Volker Brendel
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-7-r58
Abstract: Complete and accurate gene structure annotation is a prerequisite for the success of many types of genomic projects. For example, gene expression studies based on gene probes would be misleading unless the gene probes uniquely labelled distinct genes. Identification of potential transcription signals relies on correct determination of transcriptional start and termination sites. Characterization of orthologs or paralogs and other studies of molecular phylogeny are also compromised by incomplete or inaccurate gene structure annotation.Gene structure determination is particularly difficult for eukaryotic genomes. Here, we focus on protein-coding genes. In higher eukaryotes, most of these genes contain introns, and a large fraction of the genes appear to permit alternative splicing [1-3]. High-throughput computational gene structure annotation has been highly successful in providing a first glimpse of the gene content of a genome, but current methods fall short of the goal of complete and accurate gene structure annotation (for example, [4-6]). Recent research has focused on improving prediction sensitivity and specificity by combining multiple sources of evidence [7-9]. However, complexities of transcription and pre-mRNA processing, such as introns in non-coding regions, non-canonical splice sites, and utilization of alternative splice sites, still pose formidable challenges for merely computational methods. Re-annotation efforts for most eukaryotic model genomes have, therefore, relied in large part on manual inspection of gene structure evidence [5,10,11]. However, manual annotation also has shortcomings, such as being typically time-consuming, having exclusive participation, and providing annotations only intermittently [4,10,12].A policy of 'open annotation', using the internet as the forum for annotation, and bringing annotation into the mainstream has been suggested as a means to eliminate the restraints of manual annotation and to develop high quality gene anno
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