Homology Modules Research Articles

The finiteness of coassociated primes of generalized local homology modules

We present some finiteness results for co-associated primes of generalized local homology modules. Let M be a finitely generated R-module and N a linearly compact R-module. If N and HiI (N) satisfy the finiteness condition for co-associated primes for all i < k, then CoassR(HkI (M,N)) is a finite set. On the other hand, if HiI (N) = 0 for all i < t and TorjR (M,Hti (N)) = 0 for all j < h, then TorhR (M,HtI (N)) ≅ Hh+tI(M,N). Moreover, Coass(Hh+tI(M,N)) is also a finite set providedN satisfies the finiteness condition for co-associated primes. Finally, N is a semi-discrete linearly compact R-module such that 0:NI ≠ 0. Let t=WidthI (N) and h = tor_(M,HtI (N)); it follows that WidthI+Ann(M)(N) = t + h and Coass(Hh+tI(M,N)) is a finite set.

Research on Building Customized Furniture Product Model and Assembly Sequence

With the improvement of people’s living standard, mass customization production model has been the trend of the furniture industry. A model of furniture product design and assembly for customization is proposed. It can decompose customers’ needs and transform them into homologous modules set in the structure tree. Then through the assembly relationship graph and matrix of these product parts, an assembly sequence which can guide the assembly of products will be built by a genetic algorithm. This process will not only save manpower and resources, but also improve enterprise efficiency. In this article, an instance was given in order to verify the correctness of product design and assembly processes based on product family of mass customization.

Module organization and variance in protein-protein interaction networks.

A module is a group of closely related proteins that act in concert to perform specific biological functions through protein–protein interactions (PPIs) that occur in time and space. However, the underlying module organization and variance remain unclear. In this study, we collected module templates to infer respective module families, including 58,041 homologous modules in 1,678 species, and PPI families using searches of complete genomic database. We then derived PPI evolution scores and interface evolution scores to describe the module elements, including core and ring components. Functions of core components were highly correlated with those of essential genes. In comparison with ring components, core proteins/PPIs were conserved across multiple species. Subsequently, protein/module variance of PPI networks confirmed that core components form dynamic network hubs and play key roles in various biological functions. Based on the analyses of gene essentiality, module variance, and gene co-expression, we summarize the observations of module organization and variance as follows: 1) a module consists of core and ring components; 2) core components perform major biological functions and collaborate with ring components to execute certain functions in some cases; 3) core components are more conserved and essential during organizational changes in different biological states or conditions.

A cis-regulatory module activating transcription in the suspensor contains five cis-regulatory elements.

Little is known about the molecular mechanisms by which the embryo proper and suspensor of plant embryos activate specific gene sets shortly after fertilization. We analyzed the upstream region of the Scarlet Runner Bean (Phaseolus coccineus) G564 gene in order to understand how genes are activated specifically in the suspensor during early embryo development. Previously, we showed that a 54-bp fragment of the G564 upstream region is sufficient for suspensor transcription and contains at least three required cis-regulatory sequences, including the 10-bp motif (5′-GAAAAGCGAA-3′), the 10 bp-like motif (5′-GAAAAACGAA-3′), and Region 2 motif (partial sequence 5′-TTGGT-3′). Here, we use site-directed mutagenesis experiments in transgenic tobacco globular-stage embryos to identify two additional cis-regulatory elements within the 54-bp cis-regulatory module that are required for G564 suspensor transcription: the Fifth motif (5′-GAGTTA-3′) and a third 10-bp-related sequence (5′-GAAAACCACA-3′). Further deletion of the 54-bp fragment revealed that a 47-bp fragment containing the five motifs (the 10-bp, 10-bp-like, 10-bp-related, Region 2 and Fifth motifs) is sufficient for suspensor transcription, and represents a cis-regulatory module. A consensus sequence for each type of motif was determined by comparing motif sequences shown to activate suspensor transcription. Phylogenetic analyses suggest that the regulation of G564 is evolutionarily conserved. A homologous cis-regulatory module was found upstream of the G564 ortholog in the Common Bean (Phaseolus vulgaris), indicating that the regulation of G564 is evolutionarily conserved in closely related bean species.Electronic supplementary materialThe online version of this article (doi:10.1007/s11103-015-0308-z) contains supplementary material, which is available to authorized users.

Some Homology Representations for Grassmannians in Cross-Characteristics

Let F* be the finite field of q elements and let P(n,q) be the projective space of dimension n-1 over F*. We construct a family H^{n}_{k,i} of combinatorial homology modules associated to P(n,q) over a coefficient field F field of characteristic p_{0}>0 co-prime to q. As FGL(n,q)-representations the modules are obtained from the permutation action of GL(n,q) on the subspaces of F*^n. We prove a branching rule for H^{n}_{k,i} and use this rule to determine these homology representations completely. The main results are a duality theorem and the complete characterisation of H^{n}_{k,i} in terms of the standard irreducibles of GL(n,q) over F.

Functional characterization of c-Mpl ectodomain mutations that underlie congenital amegakaryocytic thrombocytopenia

Activation of the cell surface receptor, c-Mpl, by the cytokine, thrombopoietin (TPO), underpins megakaryocyte and platelet production in mammals. In humans, mutations in c-Mpl have been identified as the molecular basis of Congenital Amegakaryocytic Thrombocytopenia (CAMT). Here, we show that CAMT-associated mutations in c-Mpl principally lead to defective receptor presentation on the cell surface. In contrast, one CAMT mutant c-Mpl, F104S, was expressed on the cell surface, but showed defective TPO binding and receptor activation. Using mutational analyses, we examined which residues adjacent to F104 within the membrane-distal cytokine receptor homology module (CRM) of c-Mpl comprise the TPO-binding epitope, revealing residues within the predicted Domain 1 E-F and A-B loops and Domain 2 F′-G′ loop as key TPO-binding determinants. These studies underscore the importance of the c-Mpl membrane-distal CRM to TPO-binding and suggest that mutations within this CRM that perturb TPO binding could give rise to CAMT.

Thiol-dependent antioxidant activity of interphotoreceptor retinoid-binding protein

Interphotoreceptor retinoid-binding protein (IRBP), which is critical to photoreceptor survival and function, is comprised of homologous tandem modules each ∼300 amino acids, and contains 10 cysteines, possibly 8 as free thiols. Purification of IRBP has historically been difficult due to aggregation, denaturation and precipitation. Our observation that reducing agent 1,4-dithiothreitol dramatically prevents aggregation prompted investigation of possible functions for IRBP's free thiols. Bovine IRBP (bIRBP) was purified from retina saline washes by a combination of concanavalin A, ion exchange and size exclusion chromatography. Antioxidant activity of the purified protein was measured by its ability to inhibit oxidation of 2,2′-azinobis [3-ethylbenzothiazoline-6-sulfonate] by metmyoglobin. Homology modeling predicted the relationship of the retinoid binding sites to cysteine residues. As a free radical scavenger, bIRBP was more active than ovalbumin, thioredoxin, and vitamin E analog Trolox. Alkylation of free cysteines by N-ethylmaleimide inhibited bIRBP's antioxidant activity, but not its ability to bind all-trans retinol. Structural modeling predicted that Cys 1051 is at the mouth of the module 4 hydrophobic ligand-binding site. Its free radical scavenging activity points to a new function for IRBP in defining the redox environment in the subretinal space.

SOME PROPERTIES OF GENERALIZED LOCAL HOMOLOGY AND COHOMOLOGY MODULES

We study some properties of representable generalized local homology modules. By duality, we get some properties of good generalized local cohomology modules.

Dualizing complexes and homomorphisms vanishing in Koszul homology

Abstract Let C be a semidualizing complex over a noetherian local ring A. If there exists a local homomorphism A → B ${A \rightarrow B}$ vanishing at the level of the first Koszul homology modules (e.g. the Frobenius endomorphism in positive characteristic, or any homomorphism factorizing through a regular local ring) and of finite Gorenstein dimension relative to C, then C is dualizing.

A 2-ADIC CONTROL THEOREM FOR MODULAR CURVES

We study the behavior of ordinary parts of the homology modules of modular curves, associated to a decreasing sequence of congruence subgroups Γ1(N2r) for r ≥ 2, and prove a control theorem for these homology modules.

Structural and Functional Evolution of Positively Selected Sites in Pine Glutathione S-Transferase Enzyme Family*

Phylogenetic analyses have identified positive selection as an important driver of protein evolution, both structural and functional. However, the lack of appropriate combined functional and structural assays has generally hindered attempts to elucidate patterns of positively selected sites and their effects on enzyme activity and substrate specificity. In this study we investigated the evolutionary divergence of the glutathione S-transferase (GST) family in Pinus tabuliformis, a pine that is widely distributed from northern to central China, including cold temperate and drought-stressed regions. GSTs play important roles in plant stress tolerance and detoxification. We cloned 44 GST genes from P. tabuliformis and found that 26 of the 44 belong to the largest (Tau) class of GSTs and are differentially expressed across tissues and developmental stages. Substitution models identified five positively selected sites in the Tau GSTs. To examine the functional significance of these positively selected sites, we applied protein structural modeling and site-directed mutagenesis. We found that four of the five positively selected sites significantly affect the enzyme activity and specificity; thus their variation broadens the GST family substrate spectrum. In addition, positive selection has mainly acted on secondary substrate binding sites or sites close to (but not directly at) the primary substrate binding site; thus their variation enables the acquisition of new catalytic functions without compromising the protein primary biochemical properties. Our study sheds light on selective aspects of the functional and structural divergence of the GST family in pine and other organisms.

Molecular modeling and docking characterization of CzR1, a CC-NBS-LRR R-gene from Curcuma zedoaria Loeb. that confers resistance to Pythium aphanidermatum

Plant NBS-LRR R-genes recognizes several pathogen associated molecular patterns (PAMPs) and limit pathogen infection through a multifaceted defense response. CzR1, a coiled-coil-nucleotide-binding-site-leucine-rich repeat R-gene isolated from Curcuma zedoaria L exhibit constitutive resistance to different strains of P. aphanidermatum. Majority of the necrotrophic oomycetes are characterized by the presence of carbohydrate PAMPs β-glucans in their cell walls which intercat with R-genes. In the present study, we predicted the 3D (three dimensional) structure of CzR1 based on homology modeling using the homology module of Prime through the Maestro interface of Schrodinger package ver 2.5. The docking investigation of CzR1 with β-glucan using the Glide software suggests that six amino acid residues, Ser186, Glu187, Ser263, Asp264, Asp355 and Tyr425 act as catalytic residues and are involved in hydrogen bonding with ligand β-(1,3)-D-Glucan. The calculated distance between the carboxylic oxygen atoms of Glu187–Asp355 pair is well within the distance of 5Å suggesting a positive glucanase activity of CzR1. Elucidation of these molecular characteristics will help in in silico screening and understanding the structural basis of ligand binding to CzR1 protein and pave new ways towards a broad spectrum rhizome rot resistance development in the cultivated turmeric.

Optimization criteria and biological process enrichment in homologous multiprotein modules

Biological process enrichment is a widely used metric for evaluating the quality of multiprotein modules. In this study, we examine possible optimization criteria for detecting homologous multiprotein modules and quantify their effects on biological process enrichment. We find that modularity, linear density, and module size are the most important criteria considered, complementary to each other, and that graph theoretical attributes account for 36% of the variance in biological process enrichment. Variations in protein interaction similarity within module pairs have only minor effects on biological process enrichment. As random modules increase in size, both biological process enrichment and modularity tend to improve, although modularity does not show this upward trend in modules with size at most 50 proteins. To adjust for these trends, we recommend a size correction based on random sampling of modules when using biological process enrichment or other attributes to evaluate module boundaries. Characteristics of homologous multiprotein modules optimized for each of the optimization criteria are examined.

The Derived Category Analogue of the Hartshorne-Lichtenbaum Vanishing Theorem

Let $\mathfrak{a}$ be an ideal of a local ring $(R,\mathfrak{m})$ and $X$ a $d$-dimensional homologically bounded complex of $R$-modules whose all homology modules are finitely generated. We show that $H^d_{\mathfrak{a}}(X)=0$ if and only if $\dim \widehat{R}/\mathfrak{a} \widehat{R}+\mathfrak{p}>0$ for all prime ideals $\mathfrak{p}$ of $\hat{R}$ such that $\dim \hat{R}/\mathfrak{p}-\inf (X\otimes_R\hat{R})_{\mathfrak{p}}=d$.

MICAL, the Flavoenzyme Participating in Cytoskeleton Dynamics

MICAL (from the Molecule Interacting with CasL) indicates a family of recently discovered cytosolic, multidomain proteins, which uniquely couple an N-terminal FAD-containing monooxygenase-like domain to typical calponine homology, LIM and coiled-coil protein-interaction modules. Genetic and cell biology approaches have demonstrated an essential role of the catalytic activity of the monooxygenase-like domain in transducing the signal initiated by semaphorins interaction with their plexin receptors, which results in local actin cytoskeleton disassembly as part of fundamental processes that include differentiation, migration and cell-cell contacts in neuronal and non-neuronal cell types. This review focuses on the structure-function relations of the MICAL monooxygenase-like domain as they are emerging from the available in vitro studies on mouse, human and Drosophila MICAL forms that demonstrated a NADPH-dependent actin depolymerizing activity of MICAL. With Drosophila MICAL forms, actin depolymerization was demonstrated to be associated to conversion of Met44 to methionine sulfone through a postulated hydroxylating reaction. Arguments supporting the concept that MICAL effect on F-actin may be reversible will be discussed.

Some properties of local homology and local cohomology modules

We study some properties of representable or I-stable local homology modules HiI (M) where M is a linearly compact module. By duality, we get some properties of good or at local cohomology modules HIi (M) of A. Grothendieck.

ON THE VANISHING OF LOCAL HOMOLOGY MODULES

AbstractLet R be a commutative Noetherian ring, is an ideal of R and M is an R-module. We intend to establish the dual of Grothendieck's Vanishing Theorem for local homology modules. We conjecture that =0 for all i&gt;magRM. We prove this in several cases.

A Snapshot of the Physical and Functional Wiring of the Eps15 Homology Domain Network in the Nematode

Protein interaction modules coordinate the connections within and the activity of intracellular signaling networks. The Eps15 Homology (EH) module, a protein-protein interaction domain that is a key feature of the EH-network, was originally identified in a few proteins involved in endocytosis and vesicle trafficking, and has subsequently also been implicated in actin reorganization, nuclear shuttling, and DNA repair. Here we report an extensive characterization of the physical connections and of the functional wirings of the EH-network in the nematode. Our data show that one of the major physiological roles of the EH-network is in neurotransmission. In addition, we found that the proteins of the network intersect, and possibly coordinate, a number of “territories” of cellular activity including endocytosis/recycling/vesicle transport, actin dynamics, general metabolism and signal transduction, ubiquitination/degradation of proteins, DNA replication/repair, and miRNA biogenesis and processing.

Some results on local homology and local cohomology modules

In this paper, we obtain some results about the local homology modules of Artinian modules, and by Matlis duality we obtain some results about the local cohomology modules of finitely generated modules.

Generalized Local Homology for Artinian Modules

We introduce generalized local homology which is in some sense dual to generalized local cohomology, and study some properties of generalized local homology modules for artinian modules, such as the artinianness, noetherianness and the characterization of Width I(M) by generalized local homology. By using duality, we get back some properties of generalized local cohomology.