Unique Extension Research Articles

Unique Extension of Peritonsillar Abscess to the Masticator Space Encountered in the Early Phase of Antiviral Therapy for Hepatitis C

Background: To describe a unique case of peritonsillar abscess showing peculiar extension to the masticator space, encountered in the early phase of telaprevir therapy in combination with peginterferonalfa-2b and ribavirin for hepatitis C virus (HCV) infection. Methods: Review of clinical case records, including computed tomography and surgical approaches. Results: A 64-year-old woman was taking medications for HCV, including telaprevir therapy in combination with peginterferonalfa-2b and ribavirin every one week. She was also receiving medical treatment for diabetes mellitus. Her symptoms started 3 days after the commencement of antiviral therapy. She underwent surgery for drainage of the abscess, including endoscopy-assisted intraoral drainage and quinsy tonsillectomy. Conclusions: It is important to bear in mind that a patient suffering from multiple systemic diseases may display unique clinical presentations with head and neck infections. Endoscopy-assisted intraoral drainageof the lateral masticator space was less invasive than other approaches, obviating the need for identifying the facial nerve.

Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

BackgroundGroup II introns are widespread genetic elements endowed with a dual functionality. They are catalytic RNAs (ribozymes) that are able of self-splicing and they are also mobile retroelements that can invade genomic DNA. The group II intron RNA secondary structure is typically made up of six domains. However, a number of unusual group II introns carrying a unique extension of 53-56 nucleotides at the 3' end have been identified previously in bacteria of the Bacillus cereus group.MethodsIn the present study, we conducted combined sequence comparisons and phylogenetic analyses of introns, host gene, plasmid and chromosome of host strains in order to gain insights into mobility, dispersal, and evolution of the unusual introns and their extension. We also performed in vitro mutational and kinetic experiments to investigate possible functional features related to the extension.ResultsWe report the identification of novel copies of group II introns carrying a 3' extension including the first two copies in bacteria not belonging to the B. cereus group, Bacillus pseudofirmus OF4 and Bacillus sp. 2_A_57_CT2, an uncharacterized species phylogenetically close to B. firmus. Interestingly, the B. pseudofirmus intron has a longer extension of 70 bases. From sequence comparisons and phylogenetic analyses, several possible separate events of mobility involving the atypical introns could be identified, including both retrohoming and retrotransposition events. In addition, identical extensions were found in introns that otherwise exhibit little sequence conservation in the rest of their structures, with the exception of the conserved and catalytically critical domains V and VI, suggesting either separate acquisition of the extra segment by different group II introns or a strong selection pressure acting on the extension. Furthermore, we show by in vitro splicing experiments that the 3' extension affects the splicing properties differently in introns belonging to separate evolutionary branches.ConclusionsAltogether this study provides additional insights into the structural and functional evolution of unusual introns harboring a 3' extension and lends further evidence that these introns are mobile with their extension.

The RNA helicase Dhh1p cooperates with Rbp1p to promote porin mRNA decay via its non-conserved C-terminal domain

The yeast RNA helicase Dhh1p has been shown to associate with components of mRNA decay and is involved in mRNA decapping and degradation. An RNA-binding protein, Rbp1p, is known to bind to the 3′-UTR of porin (POR1) mRNA, and induces mRNA decay by an uncharacterized mechanism. Here, we show that Dhh1p can associate with POR1 mRNA and specifically promote POR1 mRNA decay via its interaction with Rbp1p. As compared to its mammalian homolog RCK/p54/DDX6, Dhh1p has a unique and long extension at its C-terminus. Interestingly, this non-conserved C-terminal region of Dhh1p is required for interaction with Rbp1p and modulating Rbp1p-mediated POR1 mRNA decay. Notably, expression of a C-terminal 81-residue deleted Dhh1p can fully complement the growth defect of a dhh1Δ strain and retains its function in regulating the mRNA level of an RNA-binding protein Edc1p. Moreover, mammalian DDX6 became capable of interacting with Rbp1p and could confer Rbp1p-mediated POR1 mRNA decay in the dhh1Δ strain upon fusion to the C-terminal unique region of Dhh1p. Thus, we propose that the non-conserved C-terminus of Dhh1p plays a role in defining specific interactions with mRNA regulatory factors that promote distinct mRNA decay.

Markov uniqueness of degenerate elliptic operators

Let be an open subset of R d and H = − P d=1 @icij@j a secondorder partial differential operator on L2() with domain C 1 c () where the coefficientscij 2 W 1,1 () are real symmetric and C = (cij) is a strictly positive-definite matrix over . In particular, H is locally strongly elliptic. We analyze the submarkovian extensions of H, i.e. the selfadjoint extensions which generate submarkovian semigroups. Our main result establishes that H is Markov unique, i.e. it has a unique submarkovian extension, if and only if cap(@) = 0 where cap(@) is the capacity of the boundary of measured with respect to H. The second main result establishes that Markov uniqueness of H is equivalent to the semigroup generated by the Friedrichs extension of H being conservative.

A Membrane-Bound Vertebrate Globin

The family of vertebrate globins includes hemoglobin, myoglobin, and other O2-binding proteins of yet unclear functions. Among these, globin X is restricted to fish and amphibians. Zebrafish (Danio rerio) globin X is expressed at low levels in neurons of the central nervous system and appears to be associated with the sensory system. The protein harbors a unique N-terminal extension with putative N-myristoylation and S-palmitoylation sites, suggesting membrane-association. Intracellular localization and transport of globin X was studied in 3T3 cells employing green fluorescence protein fusion constructs. Both myristoylation and palmitoylation sites are required for correct targeting and membrane localization of globin X. To the best of our knowledge, this is the first time that a vertebrate globin has been identified as component of the cell membrane. Globin X has a hexacoordinate binding scheme and displays cooperative O2 binding with a variable affinity (P 50∼1.3–12.5 torr), depending on buffer conditions. A respiratory function of globin X is unlikely, but analogous to some prokaryotic membrane-globins it may either protect the lipids in cell membrane from oxidation or may act as a redox-sensing or signaling protein.

The role of Bacillus anthracis RecD2 helicase in DNA mismatch repair

DNA mismatch repair (MMR) systems can be classified as either MutH-dependent or MutH-independent. In bacteria, extensive studies have been conducted with the MutH-dependent MMR in Escherichia coli and its close relatives. The picture of MutH-independent MMR in other bacteria is less clear, as MMR components other than MutS and MutL have not been identified in the majority of bacteria. Bacillus anthracis is one of the MutH-less Gram + bacteria in the phylum of Firmicutes. We used papillation as a tool to search for B. anthracis new mutator strains and identified a spontaneous mutator that carries a minitransposon insertion in the BAS4289 locus. The mutational frequency and specificity exhibited in this mutant were comparable to that of MMR-deficient strains with knockouts of mutL or mutS. It retained a similar UV sensitivity profile as that of the wild type. BAS4289 encodes a putative DNA helicase RecD2 that shares 30% sequence identity with Deinococcus radiodurans RecD2, a well characterized superfamily 1B helicase whose homologs are widely present in Firmicutes complete genomes. We demonstrated that the N-terminal region of RecD2, a unique sequence extension used to distinguish RecD2 from RecD1, was important for B. anthracis RecD2, as mutations in the N-terminal conserved motifs affected its DNA repair function. This is the first report of a RecD2 helicase being associated with MMR. RecD2 and our recently described YycJ protein are likely to be two additional components in the B. anthracis MutH-independent MMR system.

Distribution and Biochemical Properties of an M1-family Aminopeptidase in Plasmodium falciparum Indicate a Role in Vacuolar Hemoglobin Catabolism

Aminopeptidases catalyze N-terminal peptide bond hydrolysis and occupy many diverse roles across all domains of life. Here we present evidence that an M1-family aminopeptidase, PfA-M1, has been recruited to specialized roles in the human malaria parasite Plasmodium falciparum. PfA-M1 is abundant in two subcellular compartments in asexual intraerythrocytic parasites; that is, the food vacuole, where the catabolism of host hemoglobin takes place, and the nucleus. A unique N-terminal extension contributes to the observed dual targeting by providing a signal peptide and putative alternate translation initiation sites. PfA-M1 exists as two major isoforms, a nuclear 120-kDa species and a processed species consisting of a complex of 68- and 35-kDa fragments. PfA-M1 is both stable and active at the acidic pH of the food vacuole lumen. Determination of steady-state kinetic parameters for both aminoacyl-β-naphthylamide and unmodified dipeptide substrates over the pH range 5.0-8.5 reveals that k(cat) is relatively insensitive to pH, whereas K(m) increases at pH values below 6.5. At the pH of the food vacuole lumen (5.0-5.5), the catalytic efficiency of PfA-M1 remains high. Consistent with the kinetic data, the affinity of peptidic competitive inhibitors is diminished at acidic pH. Together, these results support a catalytic role for PfA-M1 in the food vacuole and indicate the importance of evaluating the potency of peptidic inhibitors at physiologically relevant pH values. They also suggest a second, distinct function for this enzyme in the parasite nucleus.

SO(3) homology of graphs and links

The SO(3) Kauffman polynomial and the chromatic polynomial of planar graphs are categorified by a unique extension of the Khovanov homology framework. Many structural observations and computations of homologies of knots and spin networks are included.

Independent natural extension

There is no unique extension of the standard notion of probabilistic independence to the case where probabilities are indeterminate or imprecisely specified. Epistemic independence is an extension that formalises the intuitive idea of mutual irrelevance between different sources of information. This gives epistemic independence very wide scope as well as appeal: this interpretation of independence is often taken as natural also in precise-probabilistic contexts. Nevertheless, epistemic independence has received little attention so far. This paper develops the foundations of this notion for variables assuming values in finite spaces. We define (epistemically) independent products of marginals (or possibly conditionals) and show that there always is a unique least-committal such independent product, which we call the independent natural extension. We supply an explicit formula for it, and study some of its properties, such as associativity, marginalisation and external additivity, which are basic tools to work with the independent natural extension. Additionally, we consider a number of ways in which the standard factorisation formula for independence can be generalised to an imprecise-probabilistic context. We show, under some mild conditions, that when the focus is on least-committal models, using the independent natural extension is equivalent to imposing a so-called strong factorisation property. This is an important outcome for applications as it gives a simple tool to make sure that inferences are consistent with epistemic independence judgements. We discuss the potential of our results for applications in Artificial Intelligence by recalling recent work by some of us, where the independent natural extension was applied to graphical models. It has allowed, for the first time, the development of an exact linear-time algorithm for the imprecise probability updating of credal trees.

Calcium and copper transport ATPases: analogies and diversities in transduction and signaling mechanisms

The calcium transport ATPase and the copper transport ATPase are members of the P-ATPase family and retain an analogous catalytic mechanism for ATP utilization, including intermediate phosphoryl transfer to a conserved aspartyl residue, vectorial displacement of bound cation, and final hydrolytic cleavage of Pi. Both ATPases undergo protein conformational changes concomitant with catalytic events. Yet, the two ATPases are prototypes of different features with regard to transduction and signaling mechanisms. The calcium ATPase resides stably on membranes delimiting cellular compartments, acquires free Ca2+ with high affinity on one side of the membrane, and releases the bound Ca2+ on the other side of the membrane to yield a high free Ca2+ gradient. These features are a basic requirement for cellular Ca2+ signaling mechanisms. On the other hand, the copper ATPase acquires copper through exchange with donor proteins, and undergoes intracellular trafficking to deliver copper to acceptor proteins. In addition to the cation transport site and the conserved aspartate undergoing catalytic phosphorylation, the copper ATPase has copper binding regulatory sites on a unique N-terminal protein extension, and has also serine residues undergoing kinase assisted phosphorylation. These additional features are involved in the mechanism of copper ATPase intracellular trafficking which is required to deliver copper to plasma membranes for extrusion, and to the trans-Golgi network for incorporation into metalloproteins. Isoform specific glyocosylation contributes to stabilization of ATP7A copper ATPase in plasma membranes.

Another Uniqueness Proof of the Dickson Simple Group G2(3)

In this article, we give a self-contained uniqueness proof for the Dickson simple group G=G2(3) using the first author's uniqueness criterion. The uniqueness proof for G2(3) was first given by Janko. His proof depends on Thompson's deep and technical characterization of G2(3). Let H′ be the amalgamated central product of SL 2(3) with itself. Then there is a unique extension H of H′ by a cyclic group of order 2 such that H has a center of order 2 and both factors SL 2(3) are normal in H. We prove that any simple group G having a 2-central involution z with centralizer CG(z)≅ H is isomorphic to G2(3).

A distributed energy-efficient clustering algorithm with improved coverage in wireless sensor networks

Coverage preservation, unique ID assignment and extension of network lifetime are important features for wireless sensor networks. Grouping sensor nodes into clusters is an effective way to improve the network performance. By analyzing communication energy consumption of the clusters and the impact of node failures on coverage with different densities, we propose a DEECIC (Distributed Energy-Efficient Clustering with Improved Coverage) algorithm. DEECIC aims at clustering with the least number of cluster heads to cover the whole network and assigning a unique ID to each node based on local information. In addition, DEECIC periodically updates cluster heads according to the joint information of nodes’ residual energy and distribution. The algorithm requires neither time synchronization nor knowledge of a node’s geographic location. Simulation results show that the proposed algorithm can prolong the network lifetime and improve network coverage effectively.

Central extensions of smooth 2–groups and a finite-dimensional string 2–group

We provide a model of the String group as a central extension of finite-dimensional 2-groups in the bicategory of Lie groupoids, left-principal bibundles, and bibundle maps. This bicategory is a geometric incarnation of the bicategory of smooth stacks and generalizes the more na\"ive 2-category of Lie groupoids, smooth functors, and smooth natural transformations. In particular this notion of smooth 2-group subsumes the notion of Lie 2-group introduced by Baez-Lauda. More precisely we classify a large family of these central extensions in terms of the topological group cohomology introduced by G. Segal, and our String 2-group is a special case of such extensions. There is a nerve construction which can be applied to these 2-groups to obtain a simplicial manifold, allowing comparison with with the model of A. Henriques. The geometric realization is an $A_\infty$-space, and in the case of our model, has the correct homotopy type of String(n). Unlike all previous models our construction takes place entirely within the framework of finite dimensional manifolds and Lie groupoids. Moreover within this context our model is characterized by a strong uniqueness result. It is a unique central extension of Spin(n).

Molecular Recognition of the Tes LIM2–3 Domains by the Actin-related Protein Arp7A

Actin-related proteins (Arps) are a highly conserved family of proteins that have extensive sequence and structural similarity to actin. All characterized Arps are components of large multimeric complexes associated with chromatin or the cytoskeleton. In addition, the human genome encodes five conserved but largely uncharacterized “orphan” Arps, which appear to be mostly testis-specific. Here we show that Arp7A, which has 43% sequence identity with β-actin, forms a complex with the cytoskeletal proteins Tes and Mena in the subacrosomal layer of round spermatids. The N-terminal 65-residue extension to the actin-like fold of Arp7A interacts directly with Tes. The crystal structure of the 1–65Arp7A·LIM2–3Tes·EVH1Mena complex reveals that residues 28–49 of Arp7A contact the LIM2–3 domains of Tes. Two alanine residues from Arp7A that occupy equivalent apolar pockets in both LIM domains as well as an intervening GPAK linker that binds the LIM2–3 junction are critical for the Arp7A-Tes interaction. Equivalent occupied apolar pockets are also seen in the tandem LIM domain structures of LMO4 and Lhx3 bound to unrelated ligands. Our results indicate that apolar pocket interactions are a common feature of tandem LIM domain interactions, but ligand specificity is principally determined by the linker sequence.

The influence of single elements on nested community structure

Summary 1. Asking whether or not an ecological community displays the structural property of nestedness is becoming increasingly common in ecological research. We note, however, a currently limited understanding of how individual matrix components (e.g. species as rows and sites as columns) and elements (e.g. a species’ occurrence at a site) contribute to overall community structure. 2. Here, we investigate the influence of single elements in a community matrix on overall community nestedness. We derive a unique extension to the popular nestedness algorithm NODF that is necessary for this analysis. 3. For 210 empirical communities, we show that elements, on average, determine a little less than 50% of a community’s nestedness value, with components determining the remainder. Looking at just matrix elements we find, on average, that 10% of elements determine 25% of a community’s nested structure. Further, we find statistical conclusions change for more than 20% of the empirical communities with the addition or removal of a single element. 4. Generally, the search for ecological pattern occurs by calculating a single metric designed to quantify the structure of an entire community. By showing the sensitivity of a metric to changes in a single element, our results cast doubt on the usefulness of this approach. That said, the extension to NODF that we present should allow researchers to better understand how individual elements in a community influence patterns of nestedness.

Minimal Extension Covers

Let A and B be finite groups and let S be the set of all extensions of A by B. A group G is called an extension cover of (A, B), if G contains all extensions in S as subgroups of G. A group G is called a minimal extension cover if G is an extension cover of minimal order. Let be the prime factorization of the odd number n and define . The group D n 1 ×…×D n k × Z 2 is the unique minimal extension cover of (Z n , Z 2). This article also constructs a minimal extension cover of (Z 2 n , Z 2). Some conjectures about minimal extension covers are examined as well.

The Cauchy–Kovalevskaya extension theorem in Hermitian Clifford analysis

Hermitian Clifford analysis is a higher dimensional function theory centered around the simultaneous null solutions, called Hermitian monogenic functions, of two Hermitian conjugate complex Dirac operators. As an essential step towards the construction of an orthogonal basis of Hermitian monogenic polynomials, in this paper a Cauchy–Kovalevskaya extension theorem is established for such polynomials. The minimal number of initial polynomials needed to obtain a unique Hermitian monogenic extension is determined, along with the compatibility conditions they have to satisfy. The Cauchy–Kovalevskaya extension principle then allows for a dimensional analysis of the spaces of spherical Hermitian monogenics, i.e. homogeneous Hermitian monogenic polynomials. A version of this extension theorem for specific real-analytic functions is also obtained.

On definability of types of finite Cantor-Bendixson rank

We prove that every type of finite Cantor-Bendixson rank over a model of a first-order theory without the strict order property is definable and has a unique nonforking extension to a global type. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Homogeneous Schrödinger Operators on Half-Line

The differential expression \({L_m=-\partial_x^2+(m^2-1/4)x^{-2}}\) defines a self-adjoint operator H m on L 2(0, ∞) in a natural way when m 2 ≥ 1. We study the dependence of H m on the parameter m show that it has a unique holomorphic extension to the half-plane Re m > −1, and analyze spectral and scattering properties of this family of operators.

Can I Breathe Yet? Reflections on My First Year in Extension

Gain insight into the rewards and challenges of Extension through the eyes of a novice 4-H agent. Exhilarating yet exhausting, a whirlwind of opportunities, issues, and adjustments confront new Extension personnel as they acclimate to the unique Extension environment and lifestyle. There are lessons discussed here that will advise both new personnel and their supervisors about life in our world of Extension from the novice perspective.