Spatial Processing in Cloud-Based Architectures

With spatial data, traditionally associated with on-premises GIS solutions, takes part in organization-wide digital transformation architectures, the resulting cloud-native data pipelines will become a reference architecture as workflows begin to extend further out to the edge, fog and individual units as distributed computing environments. This work explores the current landscape of that progression, affected industries and most impacted markets

DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking

<p>Abstract</p> <p>Background</p> <p>Protein-RNA interactions play fundamental roles in many biological processes. Understanding the molecular mechanism of protein-RNA recognition and formation of protein-RNA complexes is a major challenge in structural biology. Unfortunately, the experimental determination of protein-RNA complexes is tedious and difficult, both by X-ray crystallography and NMR. For many interacting proteins and RNAs the individual structures are available, enabling computational prediction of complex structures by computational docking. However, methods for protein-RNA docking remain scarce, in particular in comparison to the numerous methods for protein-protein docking.</p> <p>Results</p> <p>We developed two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking: the quasi-chemical potential (QUASI-RNP) and the Decoys As the Reference State potential (DARS-RNP). Both potentials use a coarse-grained representation for both RNA and protein molecules and are capable of dealing with RNA structures with posttranscriptionally modified residues. We compared the discriminative power of DARS-RNP and QUASI-RNP for selecting rigid-body docking poses with the potentials previously developed by the Varani and Fernandez groups.</p> <p>Conclusions</p> <p>In both bound and unbound docking tests, DARS-RNP showed the highest ability to identify native-like structures. Python implementations of DARS-RNP and QUASI-RNP are freely available for download at <url>http://iimcb.genesilico.pl/RNP/</url></p

The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein

Type-I DNA restriction–modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M2S1 methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years

Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life

Methyltransferases (MTases) form a major class of tRNA-modifying enzymes needed for the proper functioning of tRNA. Recently, RNA MTases from the TrmN/Trm14 family that are present in Archaea, Bacteria and Eukaryota have been shown to specifically modify tRNAPhe at guanosine 6 in the tRNA acceptor stem. Here, we report the first X-ray crystal structures of the tRNA m2G6 (N2-methylguanosine) MTase TTCTrmN from Thermus thermophilus and its ortholog PfTrm14 from Pyrococcus furiosus. Structures of PfTrm14 were solved in complex with the methyl donor S-adenosyl-l-methionine (SAM or AdoMet), as well as the reaction product S-adenosyl-homocysteine (SAH or AdoHcy) and the inhibitor sinefungin. TTCTrmN and PfTrm14 consist of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase (RFM) domain. These results represent the first crystallographic structure analysis of proteins containing both THUMP and RFM domain, and hence provide further insight in the contribution of the THUMP domain in tRNA recognition and catalysis. Electrostatics and conservation calculations suggest a main tRNA binding surface in a groove between the THUMP domain and the MTase domain. This is further supported by a docking model of TrmN in complex with tRNAPhe of T. thermophilus and via site-directed mutagenesis

SPOT-Seq-RNA: Predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction

RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/

THUMP from archaeal tRNA:m(2)(2)G10 methyltransferase, a genuine autonomously folding domain

The tRNA:m(2)(2)G10 methyltransferase of Pyrococus abyssi (PAB1283, a member of COG1041) catalyzes the N(2),N(2)-dimethylation of guanosine at position 10 in tRNA. Boundaries of its THUMP (THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases)—containing N-terminal domain [1–152] and C-terminal catalytic domain [157–329] were assessed by trypsin limited proteolysis. An inter-domain flexible region of at least six residues was revealed. The N-terminal domain was then produced as a standalone protein (THUMPα) and further characterized. This autonomously folded unit exhibits very low affinity for tRNA. Using protein fold-recognition (FR) methods, we identified the similarity between THUMPα and a putative RNA-recognition module observed in the crystal structure of another THUMP-containing protein (ThiI thiolase of Bacillus anthracis). A comparative model of THUMPα structure was generated, which fulfills experimentally defined restraints, i.e. chemical modification of surface exposed residues assessed by mass spectrometry, and identification of an intramolecular disulfide bridge. A model of the whole PAB1283 enzyme docked onto its tRNA(Asp) substrate suggests that the THUMP module specifically takes support on the co-axially stacked helices of T-arm and acceptor stem of tRNA and, together with the catalytic domain, screw-clamp structured tRNA. We propose that this mode of interactions may be common to other THUMP-containing enzymes that specifically modify nucleotides in the 3D-core of tRNA

Strangers from within, strangers from without: negotiations and uses of space in African American and immigrant literatures and cultures, 1900s-1950s

On June 24, 1916, the New Republic published an editorial that began: "The average Pole or Italian arriving at Ellis Island does not realize that he is the deadly foe of the native Negro . . . It is a silent conflict on a gigantic scale." While this statement illustrates only a limited view of the cross-cultural encounters that it describes, it is based on historical facts that anchor my dissertation which explores the relationship between cultural constructions of space and literary visions of ethnicity and Americanness in fiction. My parallel readings of African American and immigrant novels show that the disciplinary boundaries which are often drawn between African American literature and white ethnic literatures can be imaginatively negotiated by examining the construction of space and place in black and white-ethnic writing. I argue that both black and immigrant literature of the time casts the relationship between ethnic/racial subjects and spaces as a challenge to the contemporary definition of American identity. My dissertation offers an approach to ethnic literatures that seeks parallels and dialogues among ethnic groups and their literary representations, while simultaneously acknowledging the historically nonnegotiable differences. I turn to geocriticism as my analytical tool, thus focusing on literary spatiality as the key to these cross-ethnic negotiations.

Zastosowanie farmakologiczne i terapeutyczne Asparagus racemosus Willd

Phenolic compounds form one of the main classes of secondary metabolites. They display a large range of structures and are responsible for the major organoleptic characteristics of plant-derived foods and beverages, particularly color and taste properties. They also contribute to the nutritional qualities of fruits and vegetables. Among these compounds, flavonoids constitute one of the most prevailing groups among plant phenolics. Owing to their importance in food organoleptic properties and human health, a better understanding of their structures and biological activities indicates their potentials as therapeutic agents and also for predicting and controlling food quality. Due to the variety of pharmacological activities in the mammalian body, flavonoids are more correctly referred as “nutraceuticals”.Związki fenolowe są jedną z głównych grup metabolitów wtórnych. Mogą mieć bardzo różną strukturę i są odpowiedzialne za większość cech organoleptycznych żywności pochodzenia roślinnego i napojów, szczególnie za ich właściwości kolorystyczne i smakowe. Podwyższają także wartości odżywcze owoców i warzyw. Flawonoidy są jedną z największych grup fenoli roślinnych. Lepsze zrozumienie budowy i właściwości biologicznych tych związków może wykazać ich potencjał jako związków leczniczych, a także mających znaczenie w jakości żywności. Ze względu na różnorodność działań farmakologicznych w organizmach ssaków, flawonoidy powinno się nazywać „nutraceutykami”

The forms of address in contemporary Polish

In this paper we will attempt to describe the forms of address in present-day Polish and the patterning of their usage. Having no access to sources which could verify our hypotheses, we have thus based our judgments on intuition and experience alone. Therefore, our description will by no means be complete and well-documented.Taking into consideration the political status quo of Poland one could naively expect the address forms to be fairly homogeneous, with a solidarity pronoun being extensively used. In an allegedly unstratified society, the dominance of the deferential forms of address over solidarity pronouns would seem surprising to the early Marxist-Leninist ideologist. Moreover, some instances of nonreciprocal forms of address are encountered. It is our desire to show that the Polish system of address employs an extreme variety of forms and their usage is ruled by quite a complicated "code" (or set of rules). Furthermore, we wish to cast some light on the interdependence of the Polish system of address and the socio-political pattern. The observed phenomena will entitle us to put forward a hypothesis that politically induced changes do not necessarily affect social attitudes (as expressed in language).Ye